diff --git a/HTAN.dependencies.csv b/HTAN.dependencies.csv index f1eeb2cc..718716c5 100644 --- a/HTAN.dependencies.csv +++ b/HTAN.dependencies.csv @@ -1,1693 +1,1692 @@ -,Attribute,Label,Description,Required,Cond_Req,Valid Values,Conditional Requirements,Component +Unnamed: 0,Attribute,Label,Description,Required,Cond_Req,Valid Values,Conditional Requirements,Component HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Patient Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Patient -Ethnicity,Ethnicity,Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.",True,,"['hispanic or latino', 'not hispanic or latino', 'unknown', 'Not Reported', 'not allowed to collect']",,Demographics -Country of Residence,Country of Residence,CountryofResidence,Country of Residence at enrollment,False,,"['Benin', 'Tonga', 'Guam', 'Vanuatu', 'Libya', 'Norway', 'Bolivia', 'Mozambique', 'South Korea', 'Guadeloupe', 'Laos', 'Georgia', 'Madagascar', 'Algeria', 'Ecuador', 'Paraguay', 'Rwanda', 'Equatorial Guinea', 'Lesotho', 'Tunisia', 'Comoros', 'Kosovo', 'Tanzania', 'Denmark', 'Haiti', 'Italy', 'Cuba', 'Afghanistan', 'Malaysia', 'Sierra Leone', 'Taiwan', 'Western Sahara', 'Wallis and Futuna', 'North Macedonia', 'Samoa', 'Estonia', 'Yemen', 'Ethiopia', 'Mexico', 'Chile', 'Kiribati', 'Cayman Islands', 'Northern Mariana Islands', 'Germany', 'Jordan', 'Central African Republic', 'Macau', 'Syria', 'Bangladesh', 'India', 'Timor-Leste', 'Virgin Islands British', 'Turkey', 'France', 'Papua New Guinea', 'Netherlands', 'Djibouti', 'Guatemala', 'Indonesia', 'Nepal', 'Peru', 'Singapore', 'Andorra', 'Malta', 'San Marino', 'Liberia', 'United Arab Emirates', 'Gambia', 'Bermuda', 'Jersey', 'Nicaragua', 'French Guiana', 'Iran', 'Svalbard & Jan Mayen Islands', 'Argentina', 'Zambia', 'North Korea', 'Austria', 'Holy See', 'Philippines', 'Senegal', 'Tokelau', 'Croatia', 'Egypt', 'Slovakia', 'Suriname', 'Monaco', 'Sri Lanka', 'Tuvalu', 'Somalia', 'Grenada', 'Aruba', 'Morocco', 'Cambodia', 'Bahamas', 'Mayotte', 'South Sudan', 'State of Palestine', 'Tajikistan', 'Togo', 'Ghana', 'Burundi', 'Guernsey', 'Finland', 'Saint Kitts and Nevis', 'Cameroon', 'Greenland', 'Switzerland', 'Puerto Rico', 'Azerbaijan', 'Qatar', 'Uruguay', 'Uzbekistan', 'Honduras', 'Namibia', 'Curacao', 'United Kingdom', 'Panama', 'Reunion', 'Iraq', 'Cyprus', 'Sao Tome and Principe', 'Costa Rica', 'Montenegro', 'Angola', 'Mongolia', 'Myanmar', 'Czech Republic (Czechia)', 'Brunei', 'Moldova', 'Dominican Republic', 'New Caledonia', 'Liechtenstein', 'Portugal', 'Romania', 'United States', 'Israel', 'Democratic Republic of the Congo', 'Chad', 'Barbados', 'Gibraltar', 'Saint Pierre and Miquelon', 'Guyana', 'Sudan', 'Belize', 'Poland', 'Belgium', 'New Zealand', 'El Salvador', 'Saint Lucia', 'Lebanon', 'Eswatini', 'Nigeria', 'Saint Helena Ascension and Tristan da Cunha', 'Jamaica', 'Mauritius', 'Kuwait', 'Bhutan', 'Malawi', 'Botswana', 'Serbia', 'Slovenia', 'Thailand', 'Saudi Arabia', 'Russia', 'Kenya', 'Latvia', 'Venezuela', 'Bosnia and Herzegovina', 'Anguilla', 'Mauritania', 'Virgin Islands U.S.', 'Lithuania', 'Ukraine', 'Martinique', 'Nauru', 'Niue', 'Ireland', 'Belarus', 'Hong Kong', 'Uganda', 'Zimbabwe', 'Trinidad and Tobago', 'Faroe Islands', 'Federated States of Micronesia', 'Dominica', 'Bulgaria', 'Fiji', 'Kyrgyzstan', 'Albania', 'Niger', 'Saint Vincent and the Grenadines', 'Brazil', 'Iceland', 'Spain', 'Cook Islands', 'South Africa', 'Eritrea', 'Canada', 'Maldives', 'Sweden', 'Gabon', 'Solomon Islands', 'Turkmenistan', 'Luxembourg', 'Falkland Islands (Malvinas)', 'Guinea-Bissau', 'Montserrat', 'Seychelles', 'Marshall Islands', 'Hungary', 'Kazakhstan', 'Antigua and Barbuda', 'Bahrain', 'Armenia', 'Greece', 'Pakistan', 'Vietnam', 'Oman', ""Cote d'Ivoire"", 'Congo', 'Burkina Faso', 'Guinea', 'Mali', 'Palau', 'Isle of Man', 'Japan', 'Colombia', 'Australia', 'French Polynesia', 'China', 'Cape Verde', '']",,Demographics -Gender,Gender,Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]",True,,"['unknown', 'Unspecified', 'Not Reported', 'Female', 'Male']",,Demographics -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Demographics -Weeks Gestation at Birth,Weeks Gestation at Birth,WeeksGestationatBirth,Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.,False,,,,Demographics -Premature At Birth,Premature At Birth,PrematureAtBirth,The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,Demographics -Days to Birth,Days to Birth,DaystoBirth,Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable',False,,,,Demographics -Race,Race,Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.",True,,"['Other', 'white', 'asian', 'american indian or alaska native', 'unknown', 'black or african american', 'Not Reported', 'not allowed to collect', 'native hawaiian or other pacific islander']",,Demographics +Vital Status,Vital Status,VitalStatus,The survival state of the person registered on the protocol.,True,,"['Dead', 'Not Reported', 'Alive', 'unknown']",,Demographics +Race,Race,Race,"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation withina a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution.",True,,"['not allowed to collect', 'american indian or alaska native', 'black or african american', 'native hawaiian or other pacific islander', 'white', 'unknown', 'Other', 'asian', 'Not Reported']",,Demographics Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Demographics -Vital Status,Vital Status,VitalStatus,The survival state of the person registered on the protocol.,True,,"['Not Reported', 'Dead', 'unknown', 'Alive']",,Demographics -Age Is Obfuscated,Age Is Obfuscated,AgeIsObfuscated,The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.,False,,"['true', 'false', '']",,Demographics Occupation Duration Years,Occupation Duration Years,OccupationDurationYears,The number of years a patient worked in a specific occupation.,False,,,,Demographics +Weeks Gestation at Birth,Weeks Gestation at Birth,WeeksGestationatBirth,Numeric value used to describe the number of weeks starting from the approximate date of the biological mother's last menstrual period and ending with the birth of the patient.,False,,,,Demographics +Gender,Gender,Gender,"Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.]",True,,"['Female', 'Unspecified', 'unknown', 'Male', 'Not Reported']",,Demographics +Age Is Obfuscated,Age Is Obfuscated,AgeIsObfuscated,The age of the patient has been modified for compliance reasons. The actual age differs from what is reported. Other date intervals for this patient may also be modified.,False,,"['false', 'true', '']",,Demographics +Country of Residence,Country of Residence,CountryofResidence,Country of Residence at enrollment,False,,"['Saudi Arabia', 'Tunisia', 'Israel', 'Indonesia', 'Lesotho', 'Malta', 'India', 'Puerto Rico', 'Ethiopia', 'Guam', 'Serbia', 'Bosnia and Herzegovina', 'Lithuania', 'Ukraine', 'Burkina Faso', 'Guatemala', 'Yemen', 'Dominican Republic', 'Cambodia', 'State of Palestine', 'Cayman Islands', 'Maldives', 'Taiwan', 'Iraq', 'Saint Vincent and the Grenadines', 'Benin', 'Chad', 'Virgin Islands U.S.', 'Liechtenstein', 'Palau', 'Solomon Islands', 'Azerbaijan', 'Saint Kitts and Nevis', 'Mayotte', 'Aruba', 'Federated States of Micronesia', 'Brazil', 'Western Sahara', 'Ghana', 'Thailand', 'Sao Tome and Principe', 'Virgin Islands British', 'Panama', 'Bangladesh', 'Armenia', 'Saint Pierre and Miquelon', 'Libya', 'Holy See', 'Qatar', 'Turkey', 'Bermuda', 'Antigua and Barbuda', 'Germany', 'Isle of Man', 'Vietnam', 'Hong Kong', 'Trinidad and Tobago', 'Saint Lucia', 'Poland', 'Gabon', 'Nepal', 'Vanuatu', 'El Salvador', 'Portugal', 'Sri Lanka', 'Botswana', 'Mauritius', 'Timor-Leste', 'Peru', 'Argentina', 'Czech Republic (Czechia)', 'Northern Mariana Islands', 'Namibia', 'Uganda', 'Venezuela', 'Chile', 'Tajikistan', 'Svalbard & Jan Mayen Islands', 'Martinique', 'Papua New Guinea', 'Malaysia', 'Russia', 'United Arab Emirates', 'Senegal', 'Comoros', 'Anguilla', 'Finland', 'Moldova', 'Iceland', 'Gambia', 'Seychelles', 'Iran', 'Cameroon', 'Somalia', 'Italy', 'Belgium', 'Kuwait', 'Mozambique', 'Grenada', 'Bahamas', 'Guinea', 'Paraguay', 'Tuvalu', 'Suriname', 'Bahrain', 'Cook Islands', 'South Sudan', 'Burundi', 'Montenegro', 'Denmark', 'Singapore', 'Djibouti', 'Myanmar', 'Zimbabwe', 'Costa Rica', 'Barbados', 'United Kingdom', 'Bulgaria', 'Japan', 'Lebanon', 'Mongolia', 'French Guiana', 'Montserrat', 'Guyana', 'Oman', 'Georgia', 'Nauru', 'North Macedonia', 'Laos', 'Jamaica', 'South Korea', 'United States', 'Bhutan', 'San Marino', 'Hungary', 'Madagascar', 'Curacao', 'Latvia', 'Jordan', 'Ireland', 'Syria', 'Uruguay', 'Cuba', 'Mauritania', 'Mexico', 'Rwanda', 'Sierra Leone', 'North Korea', 'France', 'Tanzania', 'Saint Helena Ascension and Tristan da Cunha', 'Jersey', 'Mali', ""Cote d'Ivoire"", 'Nigeria', 'Slovenia', 'Equatorial Guinea', 'Nicaragua', 'Niue', 'Sweden', 'Belarus', 'Haiti', 'Eritrea', 'Zambia', 'Algeria', 'Congo', 'Uzbekistan', 'Democratic Republic of the Congo', 'Cyprus', 'Greece', 'Liberia', 'Kosovo', 'China', 'Reunion', 'Spain', 'Gibraltar', 'Honduras', 'Malawi', 'Netherlands', 'Kenya', 'Macau', 'Niger', 'Estonia', 'Australia', 'Dominica', 'French Polynesia', 'Guadeloupe', 'South Africa', 'Central African Republic', 'Canada', 'Kiribati', 'Romania', 'Greenland', 'Morocco', 'Switzerland', 'Tonga', 'Sudan', 'Monaco', 'Egypt', 'Afghanistan', 'Austria', 'Belize', 'Guernsey', 'New Zealand', 'New Caledonia', 'Angola', 'Albania', 'Ecuador', 'Wallis and Futuna', 'Colombia', 'Philippines', 'Andorra', 'Kyrgyzstan', 'Brunei', 'Faroe Islands', 'Falkland Islands (Malvinas)', 'Fiji', 'Kazakhstan', 'Tokelau', 'Turkmenistan', 'Eswatini', 'Luxembourg', 'Croatia', 'Norway', 'Pakistan', 'Cape Verde', 'Marshall Islands', 'Slovakia', 'Bolivia', 'Samoa', 'Guinea-Bissau', 'Togo', '']",,Demographics Year Of Birth,Year Of Birth,YearOfBirth,Numeric value to represent the calendar year in which an individual was born.,False,,,,Demographics -Year of Death,Year of Death,YearofDeath,Numeric value to represent the year of the death of an individual.,False,True,,"['Vital Status is ""Dead""']",Demographics +Ethnicity,Ethnicity,Ethnicity,"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau.",True,,"['not allowed to collect', 'hispanic or latino', 'unknown', 'not hispanic or latino', 'Not Reported']",,Demographics +Days to Birth,Days to Birth,DaystoBirth,Number of days between the date used for index and the date from a person's date of birth represented as a calculated negative number of days. If not applicable please enter 'Not Applicable',False,,,,Demographics +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Demographics +Premature At Birth,Premature At Birth,PrematureAtBirth,The yes/no/unknown indicator used to describe whether the patient was premature (less than 37 weeks gestation) at birth.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Demographics Days to Death,Days to Death,DaystoDeath,Number of days between the date used for index and the date from a person's date of death represented as a calculated number of days. If not applicable please enter 'Not Applicable',False,True,,"['Vital Status is ""Dead""']",Demographics -Cause of Death,Cause of Death,CauseofDeath,The cause of death,False,True,"['Spinal Muscular Atrophy', 'Toxicity', 'Surgical Complications', 'End-stage Renal Disease', 'Not Applicable', 'Renal Disorder NOS', 'Cardiovascular Disorder NOS', 'unknown', 'Infection', 'Not Reported', 'Cancer Related', 'Not Cancer Related', '']","['Vital Status is ""Dead""']",Demographics -Cause of Death Source,Cause of Death Source,CauseofDeathSource,The text term used to describe the source used to determine the patient's cause of death.,False,True,"['Obituary', 'Autopsy', 'unknown', 'Death Certificate', 'Social Security Death Index', 'Not Reported', 'Medical Record', '']","['Vital Status is ""Dead""']",Demographics +Cause of Death Source,Cause of Death Source,CauseofDeathSource,The text term used to describe the source used to determine the patient's cause of death.,False,True,"['Social Security Death Index', 'Death Certificate', 'Obituary', 'unknown', 'Autopsy', 'Medical Record', 'Not Reported', '']","['Vital Status is ""Dead""']",Demographics +Year of Death,Year of Death,YearofDeath,Numeric value to represent the year of the death of an individual.,False,True,,"['Vital Status is ""Dead""']",Demographics +Cause of Death,Cause of Death,CauseofDeath,The cause of death,False,True,"['Spinal Muscular Atrophy', 'Cancer Related', 'Surgical Complications', 'Infection', 'unknown', 'Not Cancer Related', 'Toxicity', 'Cardiovascular Disorder NOS', 'Not Applicable', 'Not Reported', 'Renal Disorder NOS', 'End-stage Renal Disease', '']","['Vital Status is ""Dead""']",Demographics Days to Vital Status Reference,Days to Vital Status Reference,DaystoVitalStatusReference,Number of days between the date used for index and the reference date for designation of vital status,False,True,,"['Vital Status is ""Alive""']",Demographics HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,FamilyHistory -Relative with Cancer History,Relative with Cancer History,RelativewithCancerHistory,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,False,,"['Not Reported', 'None', 'unknown', 'Yes - Cancer History Relative', '']",,FamilyHistory +Relative with Cancer History,Relative with Cancer History,RelativewithCancerHistory,The yes/no/unknown indicator used to describe whether any of the patient's relatives have a history of cancer.,False,,"['Yes - Cancer History Relative', 'Not Reported', 'None', 'unknown', '']",,FamilyHistory Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,FamilyHistory -Relationship Type,Relationship Type,RelationshipType,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,False,True,"['Foster Brother', 'Foster Son', 'Paternal Uncle', 'Niece Second Degree Relative', 'Daughter-in-law', 'Female Cousin', 'Grandmother', 'Sister', 'Natural Grandparent', 'Identical Twin Brother', 'Natural Sister', 'Stepfather', 'Wife', 'Paternal Great Aunt', 'Identical Twin Sibling', 'Maternal Great Aunt', 'Unrelated', 'Paternal Half Brother', 'Son', 'Legal Guardian', 'Refused', 'Adopted Daughter', 'Foster Daughter', 'Foster Father', 'Grandson', 'Brother-in-law', 'Son-in-law', 'Father-in-law', 'Step Sibling', 'Paternal Half Sibling', 'Stepson', 'Natural Child', 'Maternal Great Grandparent', 'Fraternal Twin Sibling', 'Male Cousin', 'Maternal Grandfather', 'Maternal Grandmother', 'unknown', 'Stepbrother', 'Fraternal Twin Brother', 'Aunt', 'Cousin', 'Half Brother', 'Natural Grandmother', 'Paternal Grandfather', 'Maternal Half Sister', 'Paternal Grandparent', 'Spouse', 'Nephew', 'Mother', 'Great Grandchild', 'Adoptive Mother', 'Domestic Partner', 'Paternal Aunt', 'Paternal Great Grandparent', 'Ward', 'Sibling', 'Paternal First Cousin Once Removed', 'Natural Father', 'Natural Grandchild', 'Adopted Son', 'Natural Mother', 'Father', 'Stepdaughter', 'Paternal Great Uncle', 'Natural Grandfather', 'Adoptive Father', 'Paternal First Cousin', 'Maternal Grandparent', 'Grandparent', 'Foster Mother', 'Natural Son', 'Stepmother', 'Full Brother', 'Daughter', 'Identical Twin Sister', 'Maternal First Cousin Once Removed', 'Maternal Half Sibling', 'Adoptive Sister', 'Maternal First Cousin', 'Brother', 'Not Reported', 'Natural Daughter', 'Full Sister', 'Maternal Half Brother', 'Maternal Uncle', 'Paternal Half Sister', 'Other', 'Step Child', 'Uncle', 'Child', 'Grandchild', 'Half Sibling', 'Mother-in-law', 'Husband', 'Stepsister', 'Maternal Aunt', 'Natural Sibling', 'Sister-in-law', 'Niece', 'First Cousin Once Removed', 'Paternal Grandmother', 'Adoptive Brother', 'First Cousin', 'Half Sister', 'Natural Parent', 'Granddaughter', 'Parent', 'Fraternal Twin Sister', 'Twin Sibling', 'Grandfather', 'Foster Sister', 'Grand Niece', 'Natural Brother', 'Maternal Great Uncle', 'Grand Nephew', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory -Relationship Primary Diagnosis,Relationship Primary Diagnosis,RelationshipPrimaryDiagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,False,True,"['Gynecologic Cancer', 'Pancreas Cancer', 'Rectal Cancer', 'Ewing Sarcoma', 'Lymphoma', 'Sarcoma', 'Uterine Cancer', 'Adrenal Gland Cancer', 'Bile Duct Cancer', 'CNS Cancer', 'Thyroid Cancer', 'Leukemia', 'Multiple Myeloma', 'Gallbladder Cancer', 'Basal Cell Cancer', 'Prostate Cancer', 'Breast Cancer', 'unknown', 'Osteosarcoma', 'Brain Cancer', 'Kidney Cancer', 'Colorectal Cancer', 'Hematologic Cancer', 'Neuroblastoma', 'Blood Cancer', 'Mesothelioma', 'Spleen Cancer', 'Skin Cancer', 'Head and Neck Cancer', 'Wilms Tumor', 'Esophageal Cancer', 'Liver Cancer', 'Cervical Cancer', 'Cancer', 'Lung Cancer', 'Rhabdomyosarcoma', 'Gastric Cancer', 'Melanoma', 'Glioblastoma', 'Kaposi Sarcoma', 'Throat Cancer', 'Testicular Cancer', 'Chondrosarcoma', 'Laryngeal Cancer', 'Ovarian Cancer', 'Tonsillar Cancer', 'Lymph Node Cancer', 'Bone Cancer', 'Not Reported', 'Tongue Cancer', 'Bladder Cancer', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory -Relationship Gender,Relationship Gender,RelationshipGender,The text term used to describe the gender of the patient's relative with a history of cancer.,False,True,"['unknown', 'Unspecified', 'Not Reported', 'Female', 'Male', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory -Relationship Age at Diagnosis,Relationship Age at Diagnosis,RelationshipAgeatDiagnosis,The age (in years) when the patient's relative was first diagnosed.,False,True,,"['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory Relatives with Cancer History Count,Relatives with Cancer History Count,RelativeswithCancerHistoryCount,The number of relatives the patient has with a known history of cancer.,False,True,,"['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory -Environmental Tobacco Smoke Exposure,Environmental Tobacco Smoke Exposure,EnvironmentalTobaccoSmokeExposure,"The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.",False,,"['no', 'yes', 'unknown', '']",,Exposure -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Exposure -Alcohol Exposure,Alcohol Exposure,AlcoholExposure,Indicate if individual has alcohol exposure,True,,"['Not Reported', 'No - Alcohol Exposure', 'Yes - Alcohol Exposure']",,Exposure +Relationship Type,Relationship Type,RelationshipType,The subgroup that describes the state of connectedness between members of the unit of society organized around kinship ties.,False,True,"['Brother-in-law', 'Foster Son', 'Paternal Grandparent', 'Stepfather', 'Niece Second Degree Relative', 'Paternal Great Grandparent', 'Adoptive Father', 'Natural Grandchild', 'Paternal Half Sibling', 'Unrelated', 'Half Sibling', 'Brother', 'Natural Parent', 'Maternal Half Brother', 'Legal Guardian', 'Mother-in-law', 'Natural Daughter', 'Maternal First Cousin', 'Grandchild', 'Twin Sibling', 'Grand Nephew', 'Parent', 'Paternal First Cousin', 'Spouse', 'Granddaughter', 'Maternal Half Sibling', 'Paternal Uncle', 'Natural Grandparent', 'Father-in-law', 'Grandson', 'Refused', 'Stepson', 'Adopted Daughter', 'Maternal Grandfather', 'Foster Brother', 'Father', 'Daughter-in-law', 'Stepdaughter', 'Adoptive Sister', 'Adopted Son', 'Maternal Great Aunt', 'Uncle', 'Domestic Partner', 'Paternal Half Sister', 'Sister-in-law', 'Female Cousin', 'Paternal Great Uncle', 'Wife', 'Natural Grandfather', 'Step Sibling', 'Stepbrother', 'Maternal Great Grandparent', 'Not Reported', 'Grandmother', 'Great Grandchild', 'Paternal Grandfather', 'First Cousin Once Removed', 'Half Brother', 'Grandparent', 'Half Sister', 'Son-in-law', 'Grandfather', 'Male Cousin', 'Fraternal Twin Sister', 'Maternal Grandparent', 'Cousin', 'Full Brother', 'Natural Child', 'Fraternal Twin Sibling', 'Sibling', 'Niece', 'Step Child', 'Natural Son', 'Nephew', 'Paternal Half Brother', 'Adoptive Mother', 'Identical Twin Sibling', 'Maternal Half Sister', 'Natural Brother', 'unknown', 'Sister', 'Stepmother', 'Stepsister', 'Full Sister', 'Mother', 'Foster Sister', 'Child', 'Fraternal Twin Brother', 'Adoptive Brother', 'Identical Twin Brother', 'Maternal Aunt', 'Maternal Uncle', 'Natural Mother', 'Husband', 'Paternal Great Aunt', 'Paternal Aunt', 'Maternal First Cousin Once Removed', 'Aunt', 'Daughter', 'Foster Daughter', 'Paternal First Cousin Once Removed', 'Natural Sibling', 'Natural Father', 'Ward', 'Other', 'Natural Sister', 'First Cousin', 'Grand Niece', 'Maternal Great Uncle', 'Paternal Grandmother', 'Identical Twin Sister', 'Son', 'Foster Father', 'Natural Grandmother', 'Maternal Grandmother', 'Foster Mother', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory +Relationship Primary Diagnosis,Relationship Primary Diagnosis,RelationshipPrimaryDiagnosis,The text term used to describe the malignant diagnosis of the patient's relative with a history of cancer.,False,True,"['Throat Cancer', 'Gastric Cancer', 'Osteosarcoma', 'Colorectal Cancer', 'Pancreas Cancer', 'Lymph Node Cancer', 'Wilms Tumor', 'Basal Cell Cancer', 'Gallbladder Cancer', 'Breast Cancer', 'Rectal Cancer', 'Rhabdomyosarcoma', 'Hematologic Cancer', 'Uterine Cancer', 'CNS Cancer', 'Multiple Myeloma', 'Kidney Cancer', 'Ewing Sarcoma', 'Neuroblastoma', 'Bile Duct Cancer', 'Sarcoma', 'Spleen Cancer', 'Esophageal Cancer', 'Tonsillar Cancer', 'Gynecologic Cancer', 'Thyroid Cancer', 'Bone Cancer', 'Brain Cancer', 'Lung Cancer', 'Liver Cancer', 'Blood Cancer', 'Prostate Cancer', 'Kaposi Sarcoma', 'Melanoma', 'Leukemia', 'Cancer', 'unknown', 'Mesothelioma', 'Tongue Cancer', 'Glioblastoma', 'Chondrosarcoma', 'Head and Neck Cancer', 'Not Reported', 'Skin Cancer', 'Testicular Cancer', 'Lymphoma', 'Laryngeal Cancer', 'Ovarian Cancer', 'Bladder Cancer', 'Cervical Cancer', 'Adrenal Gland Cancer', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory +Relationship Gender,Relationship Gender,RelationshipGender,The text term used to describe the gender of the patient's relative with a history of cancer.,False,True,"['Female', 'Unspecified', 'unknown', 'Male', 'Not Reported', '']","['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory +Relationship Age at Diagnosis,Relationship Age at Diagnosis,RelationshipAgeatDiagnosis,The age (in years) when the patient's relative was first diagnosed.,False,True,,"['Relative with Cancer History is ""Yes - Cancer History Relative""']",FamilyHistory +Alcohol Exposure,Alcohol Exposure,AlcoholExposure,Indicate if individual has alcohol exposure,True,,"['Not Reported', 'Yes - Alcohol Exposure', 'No - Alcohol Exposure']",,Exposure +Asbestos Exposure,Asbestos Exposure,AsbestosExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Exposure +Respirable Crystalline Silica Exposure,Respirable Crystalline Silica Exposure,RespirableCrystallineSilicaExposure,"The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.",False,,"['yes', 'no', 'unknown', '']",,Exposure Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Exposure -Smoking Exposure,Smoking Exposure,SmokingExposure,Indicate if individual has smoking exposure,True,,"['Not Reported', 'No - Smoking Exposure', 'Yes - Smoking Exposure']",,Exposure -Asbestos Exposure,Asbestos Exposure,AsbestosExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to asbestos.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,Exposure +Coal Dust Exposure,Coal Dust Exposure,CoalDustExposure,The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.,False,,"['yes', 'no', 'unknown', '']",,Exposure +Smoking Exposure,Smoking Exposure,SmokingExposure,Indicate if individual has smoking exposure,True,,"['No - Smoking Exposure', 'Not Reported', 'Yes - Smoking Exposure']",,Exposure +Radon Exposure,Radon Exposure,RadonExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to radon.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Exposure Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,Exposure -Respirable Crystalline Silica Exposure,Respirable Crystalline Silica Exposure,RespirableCrystallineSilicaExposure,"The yes/no/unknown indicator used to describe whether a patient was exposured to respirable crystalline silica, a widespread, naturally occurring, crystalline metal oxide that consists of different forms including quartz, cristobalite, tridymite, tripoli, ganister, chert and novaculite.",False,,"['no', 'yes', 'unknown', '']",,Exposure -Radon Exposure,Radon Exposure,RadonExposure,The yes/no/unknown indicator used to describe whether the patient was exposed to radon.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,Exposure -Coal Dust Exposure,Coal Dust Exposure,CoalDustExposure,The yes/no/unknown indicator used to describe whether a patient was exposed to fine powder derived by the crushing of coal.,False,,"['no', 'yes', 'unknown', '']",,Exposure -Alcohol Intensity,Alcohol Intensity,AlcoholIntensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,False,True,"['Heavy Drinker', 'Lifelong Non-Drinker', 'unknown', 'Non-Drinker', 'Occasional Drinker', 'Not Reported', 'Drinker', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure -Alcohol Type,Alcohol Type,AlcoholType,Type of alcohol use,False,True,"['Other', 'Liquor', 'unknown', 'Wine', 'Beer', 'Not Reported', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure -Alcohol History,Alcohol History,AlcoholHistory,A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.,False,True,"['Not Reported', 'no', 'yes', 'unknown', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Exposure +Environmental Tobacco Smoke Exposure,Environmental Tobacco Smoke Exposure,EnvironmentalTobaccoSmokeExposure,"The yes/no/unknown indicator used to describe whether a patient was exposed to smoke that is emitted from burning tobacco, including cigarettes, pipes, and cigars. This includes tobacco smoke exhaled by smokers.",False,,"['yes', 'no', 'unknown', '']",,Exposure Alcohol Drinks Per Day,Alcohol Drinks Per Day,AlcoholDrinksPerDay,Numeric value used to describe the average number of alcoholic beverages a person consumes per day.,False,True,,"['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure Alcohol Days Per Week,Alcohol Days Per Week,AlcoholDaysPerWeek,Numeric value used to describe the average number of days each week that a person consumes an alcoholic beverage.,False,True,,"['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure +Alcohol History,Alcohol History,AlcoholHistory,A response to a question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime.,False,True,"['Not Reported', 'yes', 'no', 'unknown', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure +Alcohol Type,Alcohol Type,AlcoholType,Type of alcohol use,False,True,"['Wine', 'unknown', 'Liquor', 'Other', 'Beer', 'Not Reported', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure +Alcohol Intensity,Alcohol Intensity,AlcoholIntensity,Category to describe the patient's current level of alcohol use as self-reported by the patient.,False,True,"['Non-Drinker', 'Lifelong Non-Drinker', 'Heavy Drinker', 'unknown', 'Drinker', 'Occasional Drinker', 'Not Reported', '']","['Alcohol Exposure is ""Yes - Alcohol Exposure""']",Exposure +Secondhand Smoke as Child,Secondhand Smoke as Child,SecondhandSmokeasChild,The text term used to indicate whether the patient was exposed to secondhand smoke as a child.,False,True,"['Not Reported', 'yes', 'no', 'unknown', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure Smoke Exposure Duration,Smoke Exposure Duration,SmokeExposureDuration,Text term used to describe the length of time the patient was exposed to an environmental factor.,False,True,"['Not Reported', 'Six Weeks or More', 'unknown', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Time between Waking and First Smoke,Time between Waking and First Smoke,TimebetweenWakingandFirstSmoke,The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.,False,True,"['Within 5 Minutes', 'After 60 Minutes', 'unknown', '31-60 Minutes', '6-30 Minutes', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Tobacco Smoking Status,Tobacco Smoking Status,TobaccoSmokingStatus,Category describing current smoking status and smoking history as self-reported by a patient,False,True,"['Current Reformed Smoker for < or = 15 yrs', 'unknown', 'Duration Not Specified', 'Smoking history not documented', 'Lifelong Non-Smoker', 'Not Reported', 'Current Reformed Smoker for > 15 yrs', 'Current Smoker', 'Current Reformed Smoker', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Pack Years Smoked,Pack Years Smoked,PackYearsSmoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Tobacco Use per Day,Tobacco Use per Day,TobaccoUseperDay,Numeric value that represents the number of times the patient uses tobacco each day.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Type of Smoke Exposure,Type of Smoke Exposure,TypeofSmokeExposure,The text term used to describe the patient's specific type of smoke exposure.,False,True,"['Factory smokestack smoke', 'Hashish smoke', 'Workrelated smoke military', 'Electrical fire smoke', 'Fire smoke NOS', 'Indoor coal burning stove or fireplace smoke', 'Accidental vehicle fire smoke', 'Accidental fire smoke NOS', 'Furnace or boiler smoke', 'Workrelated smoke generators', 'Indoor stove or fireplace smoke NOS', 'Workrelated smoke fire fighting', 'Machine smoke', 'Waste burning smoke', 'Workrelated smoke artificial smoke machines', 'Grease fire smoke', 'Smoke exposure NOS', 'Gas burning smoke propane', 'Accidental forest fire smoke', 'unknown', 'Electronic cigarette smoke NOS', 'Volcanic smoke', 'Oil burning smoke Kerosene', 'Tobacco smoke pipe', 'Environmental tobacco smoke', 'Coal smoke NOS', 'Aircraft smoke', 'Marijuana smoke', 'Grilling smoke', 'Oil burning smoke NOS', 'Wood burning smoke NOS', 'Smokehouse smoke', 'Workrelated smoke paint baking', 'Wood burning smoke factory', 'Accidental building fire smoke', 'Workrelated smoke NOS', 'Accidental grass fire smoke', 'Indoor wood burning stove or fireplace smoke', 'No Smoke Exposure', 'Field burning smoke', 'Tobacco smoke cigar', 'Tobacco smoke cigarettes', 'Workrelated smoke foundry', 'Workrelated smoke plastics factory', 'Burning tree smoke', 'Workrelated smoke plumbing', 'Recreational fire smoke', 'Cooking related smoke NOS', 'Workrelated smoke soldering/welding', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Secondhand Smoke as Child,Secondhand Smoke as Child,SecondhandSmokeasChild,The text term used to indicate whether the patient was exposed to secondhand smoke as a child.,False,True,"['Not Reported', 'no', 'yes', 'unknown', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Type of Smoke Exposure,Type of Smoke Exposure,TypeofSmokeExposure,The text term used to describe the patient's specific type of smoke exposure.,False,True,"['Workrelated smoke fire fighting', 'Furnace or boiler smoke', 'Workrelated smoke plumbing', 'No Smoke Exposure', 'Oil burning smoke NOS', 'Accidental vehicle fire smoke', 'Gas burning smoke propane', 'Tobacco smoke pipe', 'Tobacco smoke cigarettes', 'Environmental tobacco smoke', 'Workrelated smoke NOS', 'Electrical fire smoke', 'Workrelated smoke artificial smoke machines', 'Workrelated smoke foundry', 'Accidental forest fire smoke', 'Electronic cigarette smoke NOS', 'Wood burning smoke factory', 'Tobacco smoke cigar', 'Smoke exposure NOS', 'Factory smokestack smoke', 'Grease fire smoke', 'Coal smoke NOS', 'Machine smoke', 'Accidental grass fire smoke', 'Accidental building fire smoke', 'Workrelated smoke plastics factory', 'Workrelated smoke generators', 'Field burning smoke', 'Indoor wood burning stove or fireplace smoke', 'Workrelated smoke military', 'Indoor coal burning stove or fireplace smoke', 'Cooking related smoke NOS', 'Fire smoke NOS', 'Hashish smoke', 'unknown', 'Marijuana smoke', 'Workrelated smoke paint baking', 'Aircraft smoke', 'Indoor stove or fireplace smoke NOS', 'Recreational fire smoke', 'Smokehouse smoke', 'Waste burning smoke', 'Accidental fire smoke NOS', 'Wood burning smoke NOS', 'Workrelated smoke soldering/welding', 'Grilling smoke', 'Burning tree smoke', 'Volcanic smoke', 'Oil burning smoke Kerosene', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure Smokeless Tobacco Quit Age,Smokeless Tobacco Quit Age,SmokelessTobaccoQuitAge,Smokeless tobacco quit age,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Smoking Frequency,Smoking Frequency,SmokingFrequency,The text term used to generally decribe how often the patient smokes.,False,True,"['Every day', 'Some days', 'unknown', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Cigarettes per Day,Cigarettes per Day,CigarettesperDay,The average number of cigarettes smoked per day.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Pack Years Smoked,Pack Years Smoked,PackYearsSmoked,Numeric computed value to represent lifetime tobacco exposure defined as number of cigarettes smoked per day x number of years smoked divided by 20.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Tobacco Smoking Status,Tobacco Smoking Status,TobaccoSmokingStatus,Category describing current smoking status and smoking history as self-reported by a patient,False,True,"['Smoking history not documented', 'Current Reformed Smoker for < or = 15 yrs', 'Duration Not Specified', 'unknown', 'Current Reformed Smoker for > 15 yrs', 'Current Smoker', 'Not Reported', 'Lifelong Non-Smoker', 'Current Reformed Smoker', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Type of Tobacco Used,Type of Tobacco Used,TypeofTobaccoUsed,The text term used to describe the specific type of tobacco used by the patient.,False,True,"['Marijuana', 'Smokeless Tobacco', 'Pipe', 'Electronic Cigarette', 'unknown', 'Other', 'Not Reported', 'Cigarettes', 'Cigar', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure Tobacco Smoking Quit Year,Tobacco Smoking Quit Year,TobaccoSmokingQuitYear,The year in which the participant quit smoking.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Years Smoked,Years Smoked,YearsSmoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure Tobacco Smoking Onset Year,Tobacco Smoking Onset Year,TobaccoSmokingOnsetYear,The year in which the participant began smoking.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure -Type of Tobacco Used,Type of Tobacco Used,TypeofTobaccoUsed,The text term used to describe the specific type of tobacco used by the patient.,False,True,"['Other', 'Smokeless Tobacco', 'Cigar', 'unknown', 'Cigarettes', 'Marijuana', 'Electronic Cigarette', 'Not Reported', 'Pipe', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Smoking Frequency,Smoking Frequency,SmokingFrequency,The text term used to generally decribe how often the patient smokes.,False,True,"['Some days', 'Every day', 'unknown', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Cigarettes per Day,Cigarettes per Day,CigarettesperDay,The average number of cigarettes smoked per day.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Tobacco Use per Day,Tobacco Use per Day,TobaccoUseperDay,Numeric value that represents the number of times the patient uses tobacco each day.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Time between Waking and First Smoke,Time between Waking and First Smoke,TimebetweenWakingandFirstSmoke,The text term used to describe the approximate amount of time elapsed between the time the patient wakes up in the morning to the time they smoke their first cigarette.,False,True,"['Within 5 Minutes', '31-60 Minutes', 'unknown', 'After 60 Minutes', '6-30 Minutes', '']","['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure +Years Smoked,Years Smoked,YearsSmoked,Numeric value (or unknown) to represent the number of years a person has been smoking.,False,True,,"['Smoking Exposure is ""Yes - Smoking Exposure""']",Exposure Marijuana Use Per Week,Marijuana Use Per Week,MarijuanaUsePerWeek,Numeric value that represents the number of times the patient uses marijuana each day.,False,True,,"['Type is ""Marijuana smoke""']",Exposure -Diabetes Treatment Type,Diabetes Treatment Type,DiabetesTreatmentType,Text term used to describe the types of treatment used to manage diabetes.,False,,"['Other', 'Thiazolidinedione', 'Oral Hypoglycemic', 'Alpha-Glucosidase Inhibitor', 'Diet', 'unknown', 'Biguanide', 'Insulin', 'Sulfonylurea', 'Injected Insulin', 'Not Reported', '']",,FollowUp -Hormonal Contraceptive Use,Hormonal Contraceptive Use,HormonalContraceptiveUse,The text term used to indicate whether the patient used hormonal contraceptives.,False,,"['Current User', 'Former User', 'unknown', 'Not Reported', 'Never Used', '']",,FollowUp -Adverse Event,Adverse Event,AdverseEvent,Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.,False,,"['Laryngeal Stenosis', 'Facial Nerve Disorder', 'Stoma Site Infection', 'Intracranial Hemorrhage', 'Pancreatic Fistula', 'Soft Tissue Necrosis Lower Limb', 'Lymph Leakage', 'Urethral Anastomotic Leak', 'Lymphocyte Count Decreased', 'Sleep Apnea', 'Ear Pain', 'Uterine Perforation', 'Respiratory', 'Urinary Frequency', 'Small Intestinal Anastomotic Leak', 'Aphonia', 'Jejunal Hemorrhage', 'Laryngopharyngeal Dysesthesia', 'Atrial Fibrillation', 'Peripheral Ischemia', 'Papulopustular Rash', 'Intraoperative Head and Neck Injury', 'Hypertension', 'Joint Effusion', 'Muscle Weakness Right-Sided', 'Enterocolitis', 'Electrocardiogram QT Corrected Interval Prolonged', 'Jejunal Perforation', 'Constipation', 'Premature Menopause', 'Prostatic Hemorrhage', 'Stenosis of Gastrointestinal Stoma', 'Gastrointestinal Anastomotic Leak', 'Telangiectasia', 'Hypothermia', 'Acidosis', 'Testicular Hemorrhage', 'Pharyngeal Fistula', 'Hallucinations', 'Hepatic Necrosis', 'Sick Sinus Syndrome', 'Weight Gain', 'Ovarian Hemorrhage', 'Irregular Menstruation', 'Oral Dysesthesia', 'Visceral Arterial Ischemia', 'Lymphocele', 'Bladder Anastomotic Leak', 'Phantom Pain', 'Intestinal Stoma Leak', 'Libido Decreased', 'Pain of Skin', 'Jejunal Obstruction', 'Pancreatitis', 'Unequal Limb Length', 'Scleral Disorder', 'Gastric Anastomotic Leak', 'Jejunal Stenosis', 'Abdominal Infection', 'Bone Pain', 'Tracheostomy Site Bleeding', 'Malabsorption', 'Rectal Fistula', 'Bronchopulmonary Hemorrhage', 'Anorexia', 'Duodenal Fistula', 'Metabolism and Nutrition Disorders Other', 'Iron Overload', 'Intraoperative Venous Injury', 'Euphoria', 'Laryngeal Mucositis', 'Hyperkalemia', 'Hypoparathyroidism', 'Concentration Impairment', 'Postoperative Thoracic Procedure Complication', 'Fetal Growth Retardation', 'Pelvic Infection', 'Jejunal Fistula', 'Hematuria', 'Muscle Weakness Upper Limb', 'Gallbladder Perforation', 'Sepsis', 'Genital Edema', 'Musculoskeletal Deformity', 'Diarrhea', 'Muscle Weakness Left-Sided', 'Body Odor', 'Blood Antidiuretic Hormone Abnormal', 'Anaphylaxis', 'Toothache', 'Psychosis', 'Laryngeal Edema', 'Psychiatric Disorders Other', 'Dermatitis Radiation', 'Hemoglobin Increased', 'Esophageal Obstruction', 'Pancreatic Hemorrhage', 'Neck Edema', 'Vaginal Fistula', 'Fracture', 'Respiratory Failure', 'Vasculitis', 'Tumor Pain', 'Vaginal Perforation', 'Delusions', 'Dyspepsia', 'Myocardial Infarction', 'Pancreatic Necrosis', 'Cough', 'Ataxia', 'Eye Pain', 'Skin Hypopigmentation', 'Vitreous Hemorrhage', 'Small Intestinal Mucositis', 'Hypokalemia', 'Renal Colic', 'Phlebitis Infective', 'Sinusitis', 'Vaginal Dryness', 'Urostomy Stenosis', 'Rectal Obstruction', 'Otitis Media', 'Mediastinal Hemorrhage', 'Rectal Mucositis', 'Pharyngeal Hemorrhage', 'Pneumothorax', 'Purpura', 'Upper Respiratory Infection', 'Superior Vena Cava Syndrome', 'Oral Pain', 'Intraoperative Gastrointestinal Injury', 'Wrist Fracture', 'Atelectasis', 'CPK Increased', 'Erythema Multiforme', 'Hypomagnesemia', 'Extraocular Muscle Paresis', 'Esophageal Necrosis', 'Laryngospasm', 'Alanine Aminotransferase Increased', 'Urinary Tract Infection', 'Allergic Rhinitis', 'Intraoperative Renal Injury', 'Middle Ear Inflammation', 'Vaginal Hemorrhage', 'Female Genital Tract Fistula', 'Urticaria', 'Dizziness', 'Flank Pain', 'dysphagia', 'Proteinuria', 'Hiccups', 'Irritability', 'Myelitis', 'Right Ventricular Dysfunction', 'Musculoskeletal and Connective Tissue Disorders Other', 'Delayed Puberty', 'Vital Capacity Abnormal', 'Periodontal Disease', 'Atrioventricular Block First Degree', 'Fetal Death', 'Delayed Orgasm', 'Surgical and Medical Procedures Other', 'Lip Pain', 'Meningitis', 'Tooth Infection', 'Esophageal Perforation', 'Pericardial Tamponade', 'Pulmonary Fibrosis', 'Exostosis', 'Intraoperative Neurological Injury', 'Hot Flashes', 'Laryngeal Obstruction', 'Movements Involuntary', 'Hyperuricemia', 'Neck Soft Tissue Necrosis', 'Gallbladder Pain', 'Neuralgia', 'Gastric Hemorrhage', 'Bullous Dermatitis', 'Vasovagal Reaction', 'Superficial Thrombophlebitis', 'Urostomy Leak', 'Retinal Detachment', 'Osteoporosis', 'Spasticity', 'Precocious Puberty', 'Anal Ulcer', 'Transient Ischemic Attacks', 'Menorrhagia', 'Stroke', 'Skin Induration', 'Febrile Neutropenia', 'Feminization Acquired', 'Retinoic Acid Syndrome', 'Retroperitoneal Hemorrhage', 'Urine Discoloration', 'Left Ventricular Systolic Dysfunction', 'Colonic Hemorrhage', 'Cranial Nerve Infection', 'Eye Disorders Other', 'Duodenal Perforation', 'Mobitz Type I', 'Chills', 'Dysesthesia', 'Virilization', 'Aspiration', 'Gastrointestinal Stoma Necrosis', 'Eye Infection', 'Peripheral Sensory Neuropathy', 'Hemoglobinuria', 'Small Intestine Infection', 'Intraoperative Arterial Injury', 'Alopecia', 'Retinopathy', 'Fibrinogen Decreased', 'Olfactory Nerve Disorder', 'Vaginal Obstruction', 'Gastric Stenosis', 'Hypoglycemia', 'Skin Hyperpigmentation', 'Urinary Retention', 'Aspartate Aminotransferase Increased', 'Hypersomnia', 'Penile Pain', 'Conduction Disorder', 'Arterial Injury', 'Brachial Plexopathy', 'Esophageal Pain', 'Infusion Related Reaction', 'Peritoneal Necrosis', 'Enterocolitis Infectious', 'Ischemia Cerebrovascular', 'Mania', 'Puerperium and Perinatal Conditions Other', 'Treatment Related Secondary Malignancy', 'Pleuritic Pain', 'Trigeminal Nerve Disorder', 'Encephalopathy', 'Cecal Hemorrhage', 'Accessory Nerve Disorder', 'Gingival Pain', 'Hemolytic Uremic Syndrome', 'Blurred Vision', 'Dry Skin', 'Ventricular Fibrillation', 'Memory Impairment', 'Lethargy', 'Paroxysmal Atrial Tachycardia', 'Fallopian Tube Anastomotic Leak', 'Infusion Site Extravasation', 'Pulmonary Edema', 'Malaise', 'Tracheal Stenosis', 'Leukocytosis', 'Dry Mouth', 'Mediastinal Infection', 'Lymph Gland Infection', 'Intraoperative Hemorrhage', 'Non-Cardiac Chest Pain', 'Sinus Bradycardia', 'Abdominal Pain', 'Amnesia', 'Papilledema', 'Vaginal Anastomotic Leak', 'Oral Hemorrhage', 'Vaginal Inflammation', 'Alcohol Intolerance', 'INR Increased', 'Intraoperative Reproductive Tract Injury', 'Fever', 'Urinary Incontinence', 'Ileus', 'Renal Hemorrhage', 'Retinal Tear', 'Tracheal Mucositis', 'Agitation', 'Adult Respiratory Distress Syndrome', 'Gum Infection', 'Bloating', 'Mucosal Infection', 'Small Intestinal Obstruction', 'Skin Atrophy', 'Spinal Fracture', 'Colonic Perforation', 'Familial and Genetic Disorders Other', 'Hypohidrosis', 'Anorgasmia', 'Bladder Perforation', 'Gastritis', 'Blood Bilirubin Increased', 'Hyponatremia', 'Pelvic Pain', 'Lordosis', 'Nausea', 'Device Related Infection', 'Uterine Fistula', 'Esophagitis', 'Laryngeal Inflammation', 'Tooth Development Disorder', 'Extrapyramidal Disorder', 'Bone Marrow Hypocellular', 'Stomal Ulcer', 'Hyperhidrosis', 'Abducens Nerve Disorder', 'Aortic Valve Disease', 'Ovarian Rupture', 'Gastrointestinal Pain', 'Lower Gastrointestinal Hemorrhage', 'Cytokine Release Syndrome', 'Arthralgia', 'Duodenal Obstruction', 'Hepatic Hemorrhage', 'Prolapse of Urostomy', 'Colonic Ulcer', 'Gynecomastia', 'Acute Coronary Syndrome', 'Fecal Incontinence', 'Serum Amylase Increased', 'Postnasal Drip', 'Injection Site Reaction', 'Intraoperative Breast Injury', 'Small Intestinal Perforation', 'Social Circumstances Other', 'wheezing', 'Hearing Impaired', 'Pelvic Soft Tissue Necrosis', 'Facial Pain', 'Rash Acneiform', 'Prostatic Obstruction', 'Dry Eye', 'Ileal Obstruction', 'Ileal Stenosis', 'Restlessness', 'Vascular Access Complication', 'Vulval Infection', 'Intraoperative Hepatobiliary Injury', 'Hirsutism', 'Tooth Discoloration', 'Suicidal Ideation', 'Muscle Weakness Trunk', 'Night Blindness', 'Obesity', 'Vaginal Pain', 'Arteritis Infective', 'Testicular Disorder', 'Vaginal Infection', 'Anal Necrosis', 'Glossopharyngeal Nerve Disorder', 'Anorectal Infection', 'Intraoperative Endocrine Injury', 'Pelvic Floor Muscle Weakness', 'Bronchial Obstruction', 'Poisoning and Procedural Complications Other', 'Vomiting', 'Leukemia Secondary to Oncology Chemotherapy', 'Hypotension', 'Carbon Monoxide Diffusing Capacity Decreased', 'Gastric Perforation', 'Localized Edema', 'Rectal Ulcer', 'Oculomotor Nerve Disorder', 'Pharyngolaryngeal Pain', 'Injury to Carotid Artery', 'Venous Injury', 'Death NOS', 'Gastric Fistula', 'Ear and Labyrinth Disorders Other', 'Intraoperative Musculoskeletal Injury', 'Thrombotic Thrombocytopenic Purpura', 'GGT Increased', 'Periorbital Infection', 'Kyphosis', 'Paresthesia', 'Growth Accelerated', 'Pruritus', 'Flu Like Symptoms', 'Tracheal Hemorrhage', 'Spermatic Cord Obstruction', 'Urine Output Decreased', 'Immune System Disorders Other', 'Rectal Perforation', 'Intraoperative Cardiac Injury', 'Cardiac Troponin I Increased', 'Gastroparesis', 'Tracheal Fistula', 'Thromboembolic Event', 'Somnolence', 'Pharyngitis', 'Anal Stenosis', 'Flatulence', 'Sore Throat', 'Pancreatic Duct Stenosis', 'Small Intestinal Stenosis', 'Biliary Anastomotic Leak', 'Tremor', 'Edema Face', 'Fibrosis Deep Connective Tissue', 'Seizure', 'Ileal Fistula', 'Recurrent Laryngeal Nerve Palsy', 'Pharyngeal Anastomotic Leak', 'Ureteric Anastomotic Leak', 'Esophageal Ulcer', 'Infective Myositis', 'Pleural Infection', 'Cervicitis Infection', 'Injury to Superior Vena Cava', 'Cataract', 'Fallopian Tube Obstruction', 'Portal Vein Thrombosis', 'Hemolysis', 'Flushing', 'Lip Infection', 'Urinary Tract Pain', 'Bronchial Stricture', 'Asystole', 'Mitral Valve Disease', 'Delirium', 'Hyperparathyroidism', 'Pulmonary Fistula', 'Duodenal Hemorrhage', 'Colonic Fistula', 'Ventricular Arrhythmia', 'Gallbladder Obstruction', 'Headache', 'Gallbladder Necrosis', 'Gastric Necrosis', 'Nail Discoloration', 'Stevens-Johnson Syndrome', 'Blood Gonadotrophin Abnormal', 'Hypermagnesemia', 'Thoracic and Mediastinal Disorders Other', 'Skin and Subcutaneous Tissue Disorders Other', 'Colonic Obstruction', 'Gastrointestinal Fistula', 'Anal Pain', 'Peritoneal Infection', 'Hypertriglyceridemia', 'Skin Ulceration', 'Hematosalpinx', 'Meningismus', 'Palpitations', 'Hypertrichosis', 'Palmar-Plantar Erythrodysesthesia Syndrome', 'Myelodysplastic Syndrome', 'External Ear Inflammation', 'Arthritis', 'Esophageal Infection', 'Rectal Necrosis', 'Intra-Abdominal Hemorrhage', 'Intraoperative Skin Injury', 'Pericardial Effusion', 'Encephalomyelitis Infection', 'Chronic Kidney Disease', 'Intraoperative Splenic Injury', 'Lymphedema', 'Pericarditis', 'Fallopian Tube Perforation', 'Vertigo', 'Congenital', 'Presyncope', 'Anxiety', 'Endocarditis Infective', 'Blood and Lymphatic System Disorders Other', 'Eyelid Function Disorder', 'Endophthalmitis', 'Postoperative Hemorrhage', 'Portal Hypertension', 'Splenic Infection', 'Lipohypertrophy', 'Penile Infection', 'Nail Ridging', 'Colonic Stenosis', 'Laryngeal Hemorrhage', 'Head Soft Tissue Necrosis', 'Spleen Disorder', 'Nail Loss', 'Urostomy Obstruction', 'Hepatic Infection', 'Adrenal Insufficiency', 'Appendicitis Perforated', 'Hoarseness', 'Pain', 'Confusion', 'Prolapse of Intestinal Stoma', 'Vascular Disorders Other', 'Ventricular Tachycardia', 'Gallbladder Infection', 'Gastric Ulcer', 'Injury to Jugular Vein', 'Joint Range of Motion Decreased Cervical Spine', 'Soft Tissue Necrosis Upper Limb', 'Dyspareunia', 'Muscle Weakness Lower Limb', 'Facial Muscle Weakness', 'Ovulation Pain', 'Intraoperative Ocular Injury', 'Voice Alteration', 'Hyperthyroidism', 'Catheter Related Infection', 'Reversible Posterior Leukoencephalopathy Syndrome', 'Cholesterol High', 'Malignant and Unspecified (Incl Cysts and Polyps) Other', 'Tinnitus', 'Edema Cerebral', 'Urinary Urgency', 'Nasal Congestion', 'Anal Mucositis', 'Obstruction Gastric', 'Tracheitis', 'Endocrine Disorders Other', 'External Ear Pain', 'Sinus Pain', 'Soft Tissue Infection', 'Acoustic Nerve Disorder NOS', 'Blood Prolactin Abnormal', 'Capillary Leak Syndrome', 'Biliary Fistula', 'Injury', 'Scrotal Infection', 'Vagus Nerve Disorder', 'Esophageal Hemorrhage', 'Pneumonitis', 'Hemorrhoidal Hemorrhage', 'Vaginal Stricture', 'Ileal Ulcer', 'Phlebitis', 'Forced Expiratory Volume Decreased', 'Epistaxis', 'Alkalosis', 'Tumor Lysis Syndrome', 'Neoplasms Benign', 'Periorbital Edema', 'Renal Calculi', 'Chest Pain Cardiac', 'Duodenal Stenosis', 'Bronchopleural Fistula', 'Upper Gastrointestinal Hemorrhage', 'Uterine Obstruction', 'Hypercalcemia', 'Constrictive Pericarditis', 'Platelet Count Decreased', 'Colitis', 'Tracheal Obstruction', 'Bone Infection', 'Salivary Gland Infection', 'Urethral Infection', 'Lactation Disorder', 'Bronchial Fistula', 'Fatigue', 'Intraoperative Ear Injury', 'Uveitis', 'Suicide Attempt', 'Allergic Reaction', 'Prostate Infection', 'Mobitz (Type) II Atrioventricular Block', 'Pancreatic Enzymes Decreased', 'Autoimmune Disorder', 'Erythroderma', 'Syncope', 'Watering Eyes', 'Mucositis Oral', 'Lung Infection', 'Corneal Ulcer', 'Stridor', 'Investigations Other', 'Hepatobiliary Disorders Other', 'Corneal Infection', 'Depression', 'Depressed Level of Consciousness', 'Productive Cough', 'Pleural Effusion', 'Hemorrhoids', 'Tricuspid Valve Disease', 'Atrioventricular Block Complete', 'Intraoperative Respiratory Injury', 'Gastroesophageal Reflux Disease', 'Hypoxia', 'Premature Delivery', 'Superficial Soft Tissue Fibrosis', 'Vaginal Discharge', 'White Blood Cell Decreased', 'Azoospermia', 'Peripheral Motor Neuropathy', 'Wound Dehiscence', 'Menopause', 'Perineal Pain', 'Pancreatic Anastomotic Leak', 'Gait Disturbance', 'Cystitis Noninfective', 'Rectal Stenosis', 'Buttock Pain', 'Weight Loss', 'Pregnancy', 'Breast Infection', 'Paronychia', 'Myocarditis', 'Hepatic Failure', 'Reproductive System and Breast Disorders Other', 'Scrotal Pain', 'Encephalitis Infection', 'Osteonecrosis of Jaw', 'Chylothorax', 'Urostomy Site Bleeding', 'Intestinal Stoma Obstruction', 'Supraventricular Tachycardia', 'Laryngeal Fistula', 'Joint Range of Motion Decreased Lumbar Spine', 'Pulmonary Valve Disease', 'Infections and Infestations Other', 'Libido Increased', 'Dehydration', 'Avascular Necrosis', 'Chest Wall Pain', 'Proctitis', 'Optic Nerve Disorder', 'Pharyngeal Mucositis', 'Neck Pain', 'Salivary Duct Inflammation', 'Hepatitis Viral', 'Growth Hormone Abnormal', 'Heart Failure', 'Edema Limbs', 'Urinary Fistula', 'Esophageal Varices Hemorrhage', 'Nystagmus', 'Oral Cavity Fistula', 'Conjunctivitis', 'Cognitive Disturbance', 'Serum Sickness', 'Ankle Fracture', 'Urinary Tract Obstruction', 'Trismus', 'Bladder Spasm', 'Gallbladder Fistula', 'Cardiac Disorders Other', 'Joint Infection', 'Joint Range of Motion Decreased', 'Rash Maculo-Papular', 'Hypoglossal Nerve Disorder', 'Bronchospasm', 'Abdominal Distension', 'Toxic Epidermal Necrolysis', 'Anal Fistula', 'Rectal Hemorrhage', 'Intestinal Stoma Site Bleeding', 'Fat Atrophy', 'Hepatic Pain', 'Hip Fracture', 'Pancreas Infection', 'Gastrointestinal Disorders Other', 'Haptoglobin Decreased', 'dyspnea', 'Otitis Externa', 'Restrictive Cardiomyopathy', 'Hydrocephalus', 'Bladder Infection', 'Wound Complication', 'Glucose Intolerance', 'Flashing Lights', 'Spermatic Cord Anastomotic Leak', 'Keratitis', 'Kidney Infection', 'Alkaline Phosphatase Increased', 'Atrial Flutter', 'Fallopian Tube Stenosis', 'Kidney Anastomotic Leak', 'Arachnoiditis', 'Hypoalbuminemia', 'General Disorders and Administration Site Conditions Other', 'Stomach Pain', 'Prostatic Pain', 'Lymph Node Pain', 'Myalgia', 'Enterovesical Fistula', 'Large Intestinal Anastomotic Leak', 'Cardiac Troponin T Increased', 'Esophageal Anastomotic Leak', 'Fall', 'Duodenal Infection', 'Hypocalcemia', 'Vas Deferens Anastomotic Leak', 'Abdominal Soft Tissue Necrosis', 'Bile Duct Stenosis', 'Floaters', 'Insomnia', 'Apnea', 'Ileal Hemorrhage', 'Disseminated Intravascular Coagulation', 'Myositis', 'Ovarian Infection', 'Sinus Tachycardia', 'Erectile Dysfunction', 'Edema Trunk', 'Esophageal Stenosis', 'Acute Kidney Injury', 'Bruising', 'Small Intestine Ulcer', 'Dysmenorrhea', 'Personality Change', 'Biliary Tract Infection', 'Laryngitis', 'Vestibular Disorder', 'CD4 Lymphocytes Decreased', 'Central Nervous System Necrosis', 'Burn', 'Cushingoid', 'Activated Partial Thromboplastin Time Prolonged', 'Dysarthria', 'Renal and Urinary Disorders Other', 'Peripheral Nerve Infection', 'Nail Infection', 'Ileal Perforation', 'Wound Infection', 'Rhinitis Infective', 'Neutrophil Count Decreased', 'Nervous System Disorders Other', 'Appendicitis', 'Pyramidal Tract Syndrome', 'Scalp Pain', 'Death Neonatal', 'Intraoperative Urinary Injury', 'Pharyngeal Stenosis', 'Hyperglycemia', 'Rectal Anastomotic Leak', 'Testicular Pain', 'Duodenal Ulcer', 'Sinus Disorder', 'Cholecystitis', 'Salivary Gland Fistula', 'Pulmonary Hypertension', 'Uterine Infection', 'Skin Infection', 'Pain in Extremity', 'Injury to Inferior Vena Cava', 'Ascites', 'Hematoma', 'Sneezing', 'Akathisia', 'Conjunctivitis Infective', 'Hypernatremia', 'Nipple Deformity', 'Aortic Injury', 'Retinal Vascular Disorder', 'Bronchial Infection', 'Hypothyroidism', 'Radiation Recall Reaction (Dermatologic)', 'Anal Hemorrhage', 'Radiculitis', 'Multi-Organ Failure', 'Ejaculation Disorder', 'Ejection Fraction Decreased', 'Perforation Bile Duct', 'Anemia', 'Typhlitis', 'Oligospermia', 'Dysphasia', 'Photosensitivity', 'Uterine Anastomotic Leak', 'Pharyngeal Necrosis', 'Breast Atrophy', 'Seroma', 'Rectal Pain', 'Wolff-Parkinson-White Syndrome', 'Cecal Infection', 'Rash Pustular', 'Dysgeusia', 'Photophobia', 'Jejunal Ulcer', 'Dental Caries', 'Vaginismus', 'Unintended Pregnancy', 'Uterine Pain', 'Cheilitis', 'IVth Nerve Disorder', 'Lipase Increased', 'Creatinine Increased', 'Generalized Muscle Weakness', 'Sudden Death NOS', 'Esophageal Fistula', 'Glaucoma', 'Back Pain', 'Hypophosphatemia', 'Cerebrospinal Fluid Leakage', 'Growth Suppression', 'Breast Pain', 'Leukoencephalopathy', 'Blood Corticotrophin Decreased', 'Lymphocyte Count Increased', 'Uterine Hemorrhage', 'Cardiac Arrest', 'Pleural Hemorrhage', 'Spermatic Cord Hemorrhage', 'Scoliosis', '']",,FollowUp -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,FollowUp -Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['Not Reported', 'Yes - Progression or Recurrence', 'no', 'unknown']",,FollowUp -FEV1 Ref Pre Bronch Percent,FEV1 Ref Pre Bronch Percent,FEV1RefPreBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.,False,,,,FollowUp -Weight,Weight,Weight,The weight of the patient measured in kilograms.,False,,,,FollowUp +Body Surface Area,Body Surface Area,BodySurfaceArea,Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.,False,,,,FollowUp +ECOG Performance Status,ECOG Performance Status,ECOGPerformanceStatus,The ECOG functional performance status of the patient/participant.,False,,"['""3""', '""2""', '""1""', '""4""', '""5.0""', '""4.0""', '""0""', 'unknown', '""1.0""', '""2.0""', '""0.0""', 'Not Reported', '""3.0""', '""5""', '']",,FollowUp +Diabetes Treatment Type,Diabetes Treatment Type,DiabetesTreatmentType,Text term used to describe the types of treatment used to manage diabetes.,False,,"['Alpha-Glucosidase Inhibitor', 'Insulin', 'Biguanide', 'Oral Hypoglycemic', 'unknown', 'Other', 'Diet', 'Injected Insulin', 'Sulfonylurea', 'Thiazolidinedione', 'Not Reported', '']",,FollowUp +Reflux Treatment Type,Reflux Treatment Type,RefluxTreatmentType,Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).,False,,"['No Treatment', 'Surgically Treated', 'Medically Treated', 'Proton Pump Inhibitors', 'H2 Blockers', 'unknown', 'Antacids', 'Not Applicable', 'Not Reported', '']",,FollowUp FEV 1 FVC Pre Bronch Percent,FEV 1 FVC Pre Bronch Percent,FEV1FVCPreBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) pre-bronchodilator.,False,,,,FollowUp -Cause of Response,Cause of Response,CauseofResponse,The text term used to describe the suspected cause or reason for the patient disease response.,False,,,,FollowUp -Pregnancy Outcome,Pregnancy Outcome,PregnancyOutcome,The text term used to describe the type of pregnancy the patient had,False,,"['Miscarriage', 'unknown', 'Induced Abortion', 'Ectopic Pregnancy', 'Live Birth', 'Not Reported', 'Stillbirth', '']",,FollowUp -Recist Targeted Regions Sum,Recist Targeted Regions Sum,RecistTargetedRegionsSum,"Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.",False,,,,FollowUp -Scan Tracer Used,Scan Tracer Used,ScanTracerUsed,The text term used to describe the type of tracer used during the imaging or scan of the patient.,False,,"['Acetate', 'Sodium Fluoride', 'PSMA', 'Axumin', 'Choline', '']",,FollowUp -HAART Treatment Indicator,HAART Treatment Indicator,HAARTTreatmentIndicator,The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,FollowUp -Imaging Type,Imaging Type,ImagingType,The text term used to describe the type of imaging or scan performed on the patient.,False,,"['99mTc Bone Scintigraphy', 'MRI', 'CT Scan', 'PET', '']",,FollowUp -Recist Targeted Regions Number,Recist Targeted Regions Number,RecistTargetedRegionsNumber,"Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria",False,,,,FollowUp -Barretts Esophagus Goblet Cells Present,Barretts Esophagus Goblet Cells Present,BarrettsEsophagusGobletCellsPresent,Presence or absennce of Barretts esophagus goblet cells.,False,,"['no', 'yes', '']",,FollowUp -Viral Hepatitis Serologies,Viral Hepatitis Serologies,ViralHepatitisSerologies,Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.,False,,"['HBV Surface Antibody', 'HCV Genotype', 'HBV Genotype', 'HBV Core Antibody', 'unknown', 'Hepatitis C Antibody', 'Hepatitis C Virus RNA', 'Not Reported', 'HBV DNA', 'Hepatitis B Surface Antigen', '']",,FollowUp -Height,Height,Height,The height of the patient in centimeters.,False,,,,FollowUp -Risk Factor,Risk Factor,RiskFactor,The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Headache', 'Undescended Testis', 'Oral Contraceptives', 'Chronic Hepatitis', 'Myasthenia Gravis', 'Steatosis', 'Lynch Syndrome', 'Hematologic Disorder NOS', 'Intestinal Metaplasia', 'Nonalcoholic Steatohepatitis', 'Allergy Meat', 'Fibrosis', 'Diverticulitis', 'Hemihypertrophy', 'Allergy Seafood', 'Pancreatitis', 'Alcoholic Liver Disease', 'Parasitic Disease of Biliary Tract', 'Colon Polyps', 'Wagr Syndrome', 'Hepatitis C Infection', 'Sarcoidosis', 'Iron Overload', ""Barrett's Esophagus"", 'Hepatitis B Infection', 'Allergy Dairy or Lactose', 'Tattoo', 'unknown', 'Li-Fraumeni Syndrome', 'Allergy Cat', 'Beckwith-Wiedemann', 'Cholelithiasis', 'Thyroid Nodular Hyperplasia', 'Endosalpingiosis', 'Serous tubal intraepithelial carcinoma (STIC)', 'Hypospadias', 'Allergy Processed Foods', 'Primary Sclerosing Cholangitis', 'Recurrent Pyogenic Cholangitis', 'Allergy Ant', 'Rubinstein-Taybi Syndrome', 'High Grade Dysplasia', 'Endometriosis', 'Allergy Nuts', 'Allergy Fruit', 'Fanconi Anemia', 'Tobacco Smokeless', 'Diabetes NOS', 'Denys-Drash Syndrome', 'Cirrhosis', 'Familial Adenomatous Polyposis', ""Gilbert's Syndrome"", 'Allergy Animal NOS', 'Diabetes Type II', ""Behcet's Disease"", 'Obesity', 'Gorlin Syndrome', 'Common variable immune deficiency (CVID)', 'Eczema', 'Lymphocytic Thyroiditis', 'Allergy Wasp', 'Rheumatoid Arthritis', 'Alpha-1 Antitrypsin Deficiency', 'Not Reported', 'Allergy Mold or Dust', 'Gastric Polyp(s)', 'Tobacco Smoking', 'Nonalcoholic Fatty Liver Disease', ""Hashimoto's Thyroiditis"", 'Diabetes Type I', 'Reflux Disease', 'Alcohol Consumption', 'Helicobacter Pylori-Associated Gastritis', 'Sensory Changes', 'Hepatic Encephalopathy', 'Hepatitis NOS', 'Epstein-Barr Virus', 'Allergy Dog', 'Allergy Eggs', 'Low Grade Dysplasia', 'Allergy Food NOS', 'Tobacco NOS', 'Allergy Bee', 'Cancer', 'Hemochromatosis', 'Seizure', 'Vision Changes', 'Autoimmune Atrophic Chronic Gastritis', 'Diet', 'Turcot Syndrome', 'Human Papillomavirus Infection', 'Hay Fever', 'HIV', '']",,FollowUp -Nadir CD4 Count,Nadir CD4 Count,NadirCD4Count,Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).,False,,,,FollowUp -Days to Imaging,Days to Imaging,DaystoImaging,Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable',False,,,,FollowUp -Disease Response,Disease Response,DiseaseResponse,Code assigned to describe the patient's response or outcome to the disease.,False,,"['DU-Disease Unchanged', 'TE-Too Early', 'Non-CR/Non-PD-Non-CR/Non-PD', 'PR-Partial Response', 'MR-Minimal/Marginal response', 'PSR-Pseudoresponse', 'PPD-Pseudoprogression', 'VGPR-Very Good Partial Response', 'WT-With Tumor', 'CR-Complete Response', 'unknown', 'SPD-Surgical Progression', 'NR-No Response', 'MX-Mixed Response', 'NPB-No Palliative Benefit', 'PA-Palliative Therapy', 'RD-Responsive Disease', 'CPD-Clinical Progression', 'AJ-Adjuvant Therapy', 'IMR-Immunoresponse', 'RPD-Radiographic Progressive Disease', 'PD-Progressive Disease', 'PB-Palliative Benefit', 'PLD-Persistent Locoregional Disease', 'PDM-Persistent Distant Metastasis', 'BED-Biochemical Evidence of Disease', 'TF-Tumor Free', 'IPD-Immunoprogression', 'RP-Response', 'sCR-Stringent Complete Response', 'CRU-Complete Response Unconfirmed', 'SD-Stable Disease', 'Not Reported', '']",,FollowUp -FEV1 Ref Post Bronch Percent,FEV1 Ref Post Bronch Percent,FEV1RefPostBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.,False,,,,FollowUp -AIDS Risk Factors,AIDS Risk Factors,AIDSRiskFactors,The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.,False,,"['Herpes Simplex Virus', 'Toxoplasmosis', 'Wasting Syndrome', 'Candidiasis', 'Coccidioidomycosis', 'Mycobacterium tuberculosis', 'Nocardiosis', 'Isosporiasis', 'NOS', 'pneumonia', 'Mycobacterium', 'Cryptococcosis', 'Progressive Multifocal Leukoencephalopathy', 'Encephalopathy', 'Cytomegalovirus', 'Pneumocystis Pneumonia', 'Histoplasmosis', 'Salmonella Septicemia', 'Mycobacterium avium Complex', '']",,FollowUp -Pancreatitis Onset Year,Pancreatitis Onset Year,PancreatitisOnsetYear,Date of onset of pancreatitis.,False,,,,FollowUp -Hysterectomy Type,Hysterectomy Type,HysterectomyType,The text term used to describe the type of hysterectomy the patient had.,False,,"['Radical Hysterectomy', 'Not performed', 'unknown', 'Simple Hysterectomy', 'Not Reported', 'Hysterectomy NOS', '']",,FollowUp -Reflux Treatment Type,Reflux Treatment Type,RefluxTreatmentType,Text term used to describe the types of treatment used to manage gastroesophageal reflux disease (GERD).,False,,"['Antacids', 'Not Applicable', 'unknown', 'Medically Treated', 'H2 Blockers', 'Proton Pump Inhibitors', 'No Treatment', 'Surgically Treated', 'Not Reported', '']",,FollowUp -Hysterectomy Margins Involved,Hysterectomy Margins Involved,HysterectomyMarginsInvolved,The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.,False,,"['None', 'Microscopic Parametrium', 'unknown', 'Macroscopic Parametrium', 'Vagina', 'Not Reported', 'Bladder', '']",,FollowUp +Karnofsky Performance Status,Karnofsky Performance Status,KarnofskyPerformanceStatus,Text term used to describe the classification used of the functional capabilities of a person.,False,,"['""10""', '""80""', '""40""', '""70""', '""0""', '""100""', 'unknown', '""30""', '""60""', '""50""', 'Not Reported', '""20""', '""90""', '']",,FollowUp +Adverse Event Grade,Adverse Event Grade,AdverseEventGrade,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['Grade 3', 'Grade 1', 'Grade 5', 'Grade 2', 'Grade 4', '']",,FollowUp +Viral Hepatitis Serologies,Viral Hepatitis Serologies,ViralHepatitisSerologies,Text term that describes the kind of serological laboratory test used to determine the patient's hepatitus status.,False,,"['HBV Surface Antibody', 'Hepatitis C Virus RNA', 'HBV Genotype', 'HBV Core Antibody', 'unknown', 'HCV Genotype', 'HBV DNA', 'Hepatitis B Surface Antigen', 'Not Reported', 'Hepatitis C Antibody', '']",,FollowUp +Days to Adverse Event,Days to Adverse Event,DaystoAdverseEvent,Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable',False,,,,FollowUp +FEV1 Ref Pre Bronch Percent,FEV1 Ref Pre Bronch Percent,FEV1RefPreBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second pre-bronchodilator.,False,,,,FollowUp +Imaging Result,Imaging Result,ImagingResult,The text term used to describe the result of the imaging or scan performed on the patient.,False,,"['Not Performed', 'positive', 'Indeterminate', 'unknown', 'negative', 'Not Reported', '']",,FollowUp +Hysterectomy Type,Hysterectomy Type,HysterectomyType,The text term used to describe the type of hysterectomy the patient had.,False,,"['Simple Hysterectomy', 'Not performed', 'Hysterectomy NOS', 'unknown', 'Not Reported', 'Radical Hysterectomy', '']",,FollowUp +CDC HIV Risk Factors,CDC HIV Risk Factors,CDCHIVRiskFactors,"The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.",False,,"['None', 'unknown', 'Intravenous Drug User', 'Heterosexual Contact', 'Not Reported', 'Hemophiliac', 'Transfusion Recipient', 'Homosexual Contact', '']",,FollowUp BMI,BMI,BMI,A calculated numerical quantity that represents an individual's weight to height ratio.,False,,,,FollowUp -Evidence of Recurrence Type,Evidence of Recurrence Type,EvidenceofRecurrenceType,The text term used to describe the type of evidence used to determine whether the patient's disease recurred,False,,"['Positive Biomarkers', 'Convincing Image Source', 'Biopsy with Histologic Confirmation', '']",,FollowUp -Body Surface Area,Body Surface Area,BodySurfaceArea,Numeric value used to represent the 2-dimensional extent of the body surface relating height to weight.,False,,,,FollowUp +Height,Height,Height,The height of the patient in centimeters.,False,,,,FollowUp Days to Comorbidity,Days to Comorbidity,DaystoComorbidity,Number of days between the date used for index and the date the patient was diagnosed with a comorbidity. If not applicable please enter 'Not Applicable',False,,,,FollowUp -FEV1 FVC Post Bronch Percent,FEV1 FVC Post Bronch Percent,FEV1FVCPostBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.,False,,,,FollowUp -Comorbidity Method of Diagnosis,Comorbidity Method of Diagnosis,ComorbidityMethodofDiagnosis,The text term used to describe the method used to diagnose the patient's comorbidity disease.,False,,"['Histology', 'Pathology', 'unknown', 'Not Reported', 'Radiology', '']",,FollowUp -Menopause Status,Menopause Status,MenopauseStatus,Text term used to describe the patient's menopause status.,False,,"['Postmenopausal', 'unknown', 'Premenopausal', 'Not Reported', 'Perimenopausal', '']",,FollowUp -ECOG Performance Status,ECOG Performance Status,ECOGPerformanceStatus,The ECOG functional performance status of the patient/participant.,False,,"['""4.0""', '""2.0""', '""3.0""', 'unknown', '""5""', '""2""', '""4""', '""0.0""', '""5.0""', '""1""', 'Not Reported', '""1.0""', '""3""', '""0""', '']",,FollowUp -Days to Follow Up,Days to Follow Up,DaystoFollowUp,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable',True,,,,FollowUp -Immunosuppressive Treatment Type,Immunosuppressive Treatment Type,ImmunosuppressiveTreatmentType,The text term used to describe the type of immunosuppresive treatment the patient received.,False,,"['Other', 'None', 'Methotrexate', 'Cyclophosphamide', 'Anti-TNFTherapy', 'unknown', 'Not Reported', 'Azathioprine', '']",,FollowUp -Imaging Result,Imaging Result,ImagingResult,The text term used to describe the result of the imaging or scan performed on the patient.,False,,"['Indeterminate', 'unknown', 'Not Performed', 'negative', 'Not Reported', 'positive', '']",,FollowUp -Risk Factor Treatment,Risk Factor Treatment,RiskFactorTreatment,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,FollowUp +Risk Factor,Risk Factor,RiskFactor,The text term used to describe a risk factor the patient had at the time of or prior to their diagnosis.,False,,"[""Behcet's Disease"", 'Parasitic Disease of Biliary Tract', 'Tobacco NOS', 'Endosalpingiosis', 'Oral Contraceptives', 'Hepatitis B Infection', 'Li-Fraumeni Syndrome', 'Diet', 'Fanconi Anemia', 'Diabetes NOS', 'Headache', 'Allergy Wasp', 'Lynch Syndrome', 'Autoimmune Atrophic Chronic Gastritis', 'Sarcoidosis', 'Diabetes Type II', 'Allergy Mold or Dust', 'Beckwith-Wiedemann', 'Nonalcoholic Steatohepatitis', 'Intestinal Metaplasia', 'Allergy Cat', 'Hepatitis C Infection', 'Alpha-1 Antitrypsin Deficiency', 'Fibrosis', 'Vision Changes', 'Low Grade Dysplasia', 'Human Papillomavirus Infection', 'Diverticulitis', ""Hashimoto's Thyroiditis"", 'Steatosis', 'Cholelithiasis', 'Thyroid Nodular Hyperplasia', 'Hematologic Disorder NOS', 'Helicobacter Pylori-Associated Gastritis', 'Alcohol Consumption', 'Chronic Hepatitis', 'Hepatic Encephalopathy', 'Not Reported', 'Turcot Syndrome', 'Denys-Drash Syndrome', 'Cirrhosis', 'Allergy Fruit', 'Hemochromatosis', 'Colon Polyps', 'Allergy Processed Foods', 'Tobacco Smoking', 'Allergy Seafood', 'Gorlin Syndrome', 'Recurrent Pyogenic Cholangitis', 'Sensory Changes', 'Obesity', 'Tobacco Smokeless', 'Nonalcoholic Fatty Liver Disease', 'Allergy Ant', 'Common variable immune deficiency (CVID)', 'Hypospadias', 'HIV', 'Allergy Bee', 'unknown', 'Allergy Meat', 'Pancreatitis', 'Epstein-Barr Virus', 'High Grade Dysplasia', 'Iron Overload', 'Primary Sclerosing Cholangitis', 'Familial Adenomatous Polyposis', 'Allergy Food NOS', 'Hay Fever', 'Allergy Dairy or Lactose', 'Hepatitis NOS', 'Myasthenia Gravis', 'Gastric Polyp(s)', 'Allergy Eggs', 'Seizure', ""Barrett's Esophagus"", 'Hemihypertrophy', 'Allergy Nuts', 'Serous tubal intraepithelial carcinoma (STIC)', 'Endometriosis', 'Alcoholic Liver Disease', 'Reflux Disease', 'Cancer', 'Undescended Testis', 'Rubinstein-Taybi Syndrome', 'Tattoo', 'Allergy Animal NOS', ""Gilbert's Syndrome"", 'Allergy Dog', 'Eczema', 'Wagr Syndrome', 'Rheumatoid Arthritis', 'Diabetes Type I', 'Lymphocytic Thyroiditis', '']",,FollowUp +Cause of Response,Cause of Response,CauseofResponse,The text term used to describe the suspected cause or reason for the patient disease response.,False,,,,FollowUp +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,FollowUp HIV Viral Load,HIV Viral Load,HIVViralLoad,"Numeric value that represents the concentration of an analyte or aliquot extracted from the sample or sample portion, measured in milligrams per milliliter.",False,,,,FollowUp -Karnofsky Performance Status,Karnofsky Performance Status,KarnofskyPerformanceStatus,Text term used to describe the classification used of the functional capabilities of a person.,False,,"['""10""', '""50""', '""40""', '""70""', '""30""', 'unknown', '""20""', '""60""', '""80""', 'Not Reported', '""100""', '""0""', '""90""', '']",,FollowUp -CDC HIV Risk Factors,CDC HIV Risk Factors,CDCHIVRiskFactors,"The text term used to describe a risk factor for human immunodeficiency virus, as described by the Center for Disease Control.",False,,"['Heterosexual Contact', 'None', 'Transfusion Recipient', 'Hemophiliac', 'unknown', 'Intravenous Drug User', 'Homosexual Contact', 'Not Reported', '']",,FollowUp -Hepatitis Sustained Virological Response,Hepatitis Sustained Virological Response,HepatitisSustainedVirologicalResponse,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,FollowUp -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,FollowUp -Adverse Event Grade,Adverse Event Grade,AdverseEventGrade,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['Grade 4', 'Grade 3', 'Grade 2', 'Grade 5', 'Grade 1', '']",,FollowUp -Comorbidity,Comorbidity,Comorbidity,"The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.",False,,"['Tyrosinemia', 'Joint Replacement', 'Bone Fracture(s)', 'Headache', 'Lupus', 'Gout', 'HIV / AIDS', 'Adenomatous Polyposis Coli', 'Liver Cirrhosis (Liver Disease)', 'Osteoporosis or Osteopenia', 'Avascular Necrosis', 'Connective Tissue Disorder', 'Chronic Hepatitis', 'Other Cancer Within 5 Years', 'Intraductal Papillary Mucinous Neoplasm', 'Atrial Fibrillation', 'Kidney Disease', 'Rheumatologic Disease', 'Myasthenia Gravis', 'Arthritis', 'Steatosis', 'Hypertension', 'Lynch Syndrome', 'Nonalcoholic Steatohepatitis', 'Coronary Artery Disease', 'Inflammatory Bowel Disease', 'Tuberculosis', 'Fibrosis', 'Liver Toxicity (Non-Infectious)', 'Pulmonary Hemorrhage', 'Hyperlipidemia', 'Diabetes', 'Diverticulitis', 'Cerebrovascular Disease', 'Blood Clots', 'Hemihypertrophy', 'Anxiety', 'Adrenocortical Insufficiency', 'Type II', 'H. pylori Infection', 'Pancreatitis', 'Colon Polyps', 'Cataracts', 'Wagr Syndrome', 'Hepatitis C Infection', 'Neuroendocrine Tumor', 'Insulin Controlled Diabetes', 'Sarcoidosis', 'Iron Overload', ""Barrett's Esophagus"", 'Hepatitis B Infection', 'Deep Vein Thrombosis / Thromboembolism', 'Common Variable Immunodeficiency', 'unknown', 'Li-Fraumeni Syndrome', 'Other Pulmonary Complications', 'Hepatitis', 'Allergies', 'Beckwith-Wiedemann', 'COPD', 'Diet Controlled Diabetes', 'Peripheral Neuropathy', 'Dyslipidemia', 'Cholelithiasis', 'Hepatitis A Infection', 'Diabetic Neuropathy', 'Ischemic Heart Disease', 'Hypospadias', 'Hereditary Non-polyposis Colon Cancer', 'Low Grade Liver Dysplastic Nodule', 'Primary Sclerosing Cholangitis', 'Myocardial Infarction', 'Biliary Disorder', 'Alpha-1 Antitrypsin', 'Rubinstein-Taybi Syndrome', 'Renal Failure (Requiring Dialysis)', 'Ulcerative Colitis', 'Osteoarthritis', 'Fanconi Anemia', 'Pain (Various)', 'Smoking', 'Organ transplant (site)', 'Other Nonmalignant Systemic Disease', 'Asthma', 'Denys-Drash Syndrome', 'Glycogen Storage Disease', 'Cirrhosis', 'Basal Cell Carcinoma', 'Familial Adenomatous Polyposis', 'Gonadal Dysfunction', 'Arrhythmia', 'Adenocarcinoma', 'Transient Ischemic Attack', 'MAI', 'Cryptogenic Organizing Pneumonia', 'Hypercalcemia', 'Peutz-Jeghers Disease', 'Sleep apnea', ""Behcet's Disease"", 'Peripheral Vascular Disease', 'Obesity', 'Gorlin Syndrome', 'Heart Disease', 'Hyperglycemia', 'Psoriasis', 'Eczema', 'Hypercholesterolemia', 'High Grade Liver Dysplastic Nodule', 'ITP', 'Rheumatoid Arthritis', 'Not Reported', 'DVT/PE', 'Pregnancy in Patient or Partner', 'Congestive Heart Failure (CHF)', ""Hashimoto's Thyroiditis"", 'Hypothyroidism', 'Bronchitis', 'Depression', 'Anemia', 'Acute Renal Failure', 'Pulmonary Fibrosis', 'Other', 'Epstein-Barr Virus', 'Gastroesophageal Reflux Disease', 'unknown Etiology', 'Chronic Renal Failure', 'Celiac Disease', 'Stroke', 'GERD', 'Epilepsy', 'Herpes', 'HUS/TTP', 'Peptic Ulcer (Ulcer)', 'Seizure', 'Calcium Channel Blockers', 'Hemorrhagic Cystitis', 'Renal Dialysis', 'Glaucoma', 'Turcot Syndrome', 'Human Papillomavirus Infection', 'Renal Insufficiency', ""Crohn's Disease"", 'Interstitial Pneumontis or ARDS', 'Cancer', '']",,FollowUp -Days to Adverse Event,Days to Adverse Event,DaystoAdverseEvent,Number of days between the date used for index and the date of the patient's adverse event. If not applicable please enter 'Not Applicable',False,,,,FollowUp +Barretts Esophagus Goblet Cells Present,Barretts Esophagus Goblet Cells Present,BarrettsEsophagusGobletCellsPresent,Presence or absennce of Barretts esophagus goblet cells.,False,,"['yes', 'no', '']",,FollowUp +Comorbidity Method of Diagnosis,Comorbidity Method of Diagnosis,ComorbidityMethodofDiagnosis,The text term used to describe the method used to diagnose the patient's comorbidity disease.,False,,"['Pathology', 'Histology', 'unknown', 'Radiology', 'Not Reported', '']",,FollowUp +Menopause Status,Menopause Status,MenopauseStatus,Text term used to describe the patient's menopause status.,False,,"['Postmenopausal', 'Premenopausal', 'unknown', 'Perimenopausal', 'Not Reported', '']",,FollowUp +HAART Treatment Indicator,HAART Treatment Indicator,HAARTTreatmentIndicator,The text term used to indicate whether the patient received Highly Active Antiretroviral Therapy (HAART).,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,FollowUp CD4 Count,CD4 Count,CD4Count,The text term used to describe the outcome of the procedure to determine the amount of the CD4 expressing cells in a sample.,False,,,,FollowUp -HPV Positive Type,HPV Positive Type,HPVPositiveType,Text classification to represent the strain or type of human papillomavirus identified in an individual.,False,,"['""16""', '""73""', '""52""', '""68""', '""63""', 'Other', '""39""', 'unknown', '""56""', '""31""', '""35""', '""66""', '""58""', '""82""', '""70""', '""33""', '""18""', '""51""', '""26""', '""53""', '""59""', 'Not Reported', '""45""', '']",,FollowUp +Days to Imaging,Days to Imaging,DaystoImaging,Number of days between the date used for index and the date the imaging or scan was performed on the patient. If not applicable please enter 'Not Applicable',False,,,,FollowUp +Scan Tracer Used,Scan Tracer Used,ScanTracerUsed,The text term used to describe the type of tracer used during the imaging or scan of the patient.,False,,"['Acetate', 'Choline', 'PSMA', 'Axumin', 'Sodium Fluoride', '']",,FollowUp DLCO Ref Predictive Percent,DLCO Ref Predictive Percent,DLCORefPredictivePercent,"The value, as a percentage of predicted lung volume, measuring the amount of carbon monoxide detected in a patient's lungs.",False,,,,FollowUp -Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Olfactory nerve', 'Overlapping lesion of bladder', 'Anterior floor of mouth', 'Bone marrow', 'Other specified parts of female genital organs', 'Parametrium', 'Overlapping lesion of lung', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Branchial cleft', 'Lower gum', 'Renal pelvis', 'skin NOS', 'Overlapping lesion of accessory sinuses', 'Gastric antrum', 'Overlapping lesion of cervix uteri', 'Nasal cavity', 'Peripheral nerves and autonomic nervous system of thorax', 'Autonomic nervous system NOS', 'Overlapping lesion of nasopharynx', 'Lateral wall of oropharynx', 'Upper-inner quadrant of breast', 'Thymus', 'Posterior mediastinum', 'Anus NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Stomach NOS', 'Broad ligament', 'Cloacogenic zone', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Lateral wall of bladder', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Biliary tract NOS', 'Anterior 2/3 of tongue NOS', 'Testis NOS', 'Overlapping lesion of ill-defined sites', 'Uterine adnexa', 'Fundus uteri', 'Central portion of breast', 'Overlapping lesion of skin', 'Lateral wall of nasopharynx', 'Nipple', 'Overlapping lesion of urinary organs', 'Soft palate NOS', 'Main bronchus', 'Trachea', 'Upper lobe lung', 'Anterior wall of nasopharynx', 'Specified parts of peritoneum', 'Body of penis', 'Tonsillar fossa', 'Overlapping lesion of breast', 'Adrenal gland NOS', 'Hepatic flexure of colon', 'Aortic body and other paraganglia', 'Frontal lobe', 'Pleura NOS', 'Lateral floor of mouth', 'Intrathoracic lymph nodes', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Pylorus', 'Skin of lip NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peripheral nerves and autonomic nervous system of abdomen', 'Waldeyer ring', 'Axillary tail of breast', 'Cervical esophagus', 'Not Reported', 'Round ligament', 'Anterior mediastinum', 'Cecum', 'Cerebrum', 'Cerebellum NOS', 'Ureteric orifice', 'Abdomen NOS', 'Brain NOS', 'Major salivary gland NOS', 'Thyroid gland', 'Overlapping lesion of rectum anus and anal canal', 'Upper-outer quadrant of breast', 'Peritoneum NOS', 'Male genital organs NOS', 'Cranial nerve NOS', 'Gum NOS', 'Ethmoid sinus', 'Subglottis', 'Meninges NOS', 'Nasopharynx NOS', 'Spinal cord', 'Clitoris', 'Labium majus', 'Urachus', 'Duodenum', 'Short bones of upper limb and associated joints', 'Posterior wall of oropharynx', 'Vulva NOS', 'Thorax NOS', 'Temporal lobe', 'Maxillary sinus', 'Middle third of esophagus', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of pancreas', 'Overlapping lesion of tonsil', 'Overlapping lesion of floor of mouth', 'Accessory sinus NOS', 'External lower lip', 'Vagina NOS', 'Parathyroid gland', 'Overlapping lesions of oropharynx', 'Overlapping lesion of esophagus', 'Overlapping lesion of colon', 'Base of tongue NOS', 'Overlapping lesion of vulva', 'Isthmus uteri', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of digestive system', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Ill-defined sites within respiratory system', 'Lower-inner quadrant of breast', 'Fundus of stomach', 'Prostate gland', 'Spinal meninges', 'Supraglottis', 'Bladder neck', 'Connective subcutaneous and other soft tissues of abdomen', 'Mandible', 'Blood', 'Anal canal', 'Overlapping lesion of penis', 'Nervous system NOS', 'Lymph node NOS', 'Overlapping lesion of corpus uteri', 'Retroperitoneum', 'Pharynx NOS', 'Rib sternum clavicle and associated joints', 'Lower-outer quadrant of breast', 'Intrahepatic bile duct', 'Appendix', 'Lymph nodes of multiple regions', 'Occipital lobe', 'Cervix uteri', 'Fallopian tube', 'Endometrium', 'Ventricle NOS', 'Ampulla of Vater', 'Pineal gland', 'Pelvis NOS', 'Skin of scalp and neck', 'Brain stem', 'Islets of Langerhans', 'Endocervix', 'Upper limb NOS', 'Dome of bladder', 'Thoracic esophagus', 'Vertebral column', 'Short bones of lower limb and associated joints', 'Tongue NOS', 'Overlapping lesion of male genital organs', 'Exocervix', 'Splenic flexure of colon', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Upper gum', 'Labium minus', 'Glottis', 'Overlapping lesion of lip', 'Mucosa of lower lip', 'Optic nerve', 'Kidney NOS', 'Pancreatic duct', 'Breast NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Meckel diverticulum', 'Overlapping lesion of biliary tract', 'Overlapping lesion of tongue', 'Larynx NOS', 'Ileum', 'Pancreas NOS', 'Overlapping lesion of stomach', 'Abdominal esophagus', 'Intestinal tract NOS', 'Frontal sinus', 'Cardia NOS', 'Liver', 'Tonsillar pillar', 'Bone of limb NOS', 'Cauda equina', 'Other specified parts of male genital organs', 'Upper respiratory tract NOS', 'unknown primary site', 'Small intestine NOS', 'Upper third of esophagus', 'Connective subcutaneous and other soft tissues of thorax', 'Sigmoid colon', 'Lymph nodes of head face and neck', 'Pyriform sinus', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Lung NOS', 'Border of tongue', 'Tonsil NOS', 'Rectum NOS', 'Parietal lobe', 'Hypopharynx NOS', 'Heart', 'Mouth NOS', 'Hematopoietic system NOS', 'Superior wall of nasopharynx', 'Endocrine gland NOS', 'Craniopharyngeal duct', 'Overlapping lesion of heart mediastinum and pleura', 'Lymph nodes of axilla or arm', 'Head face or neck NOS', 'Medulla of adrenal gland', 'Lymph nodes of inguinal region or leg', 'Female genital tract NOS', 'Glans penis', 'skin of lower limb and hip', 'Body of stomach', 'Reticuloendothelial system NOS', 'Choroid', 'External upper lip', 'Prepuce', 'Posterior wall of nasopharynx', 'Urinary system NOS', 'Conjunctiva', 'Rectosigmoid junction', 'Intra-abdominal lymph nodes', 'Lingual tonsil', 'External lip NOS', 'Parotid gland', 'Bones of skull and face and associated joints', 'Dorsal surface of tongue NOS', 'Lip NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of endocrine glands and related structures', 'Middle ear', 'Bladder NOS', 'Bone NOS', 'Trigone of bladder', 'Gallbladder', 'Descended testis', 'Orbit NOS', 'Descending colon', 'Spleen', 'Retromolar area', 'Ureter', 'skin of upper limb and shoulder', 'Pelvic lymph nodes', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Eye NOS', 'Myometrium', 'Lower third of esophagus', 'Body of pancreas', 'Mediastinum NOS', 'Sublingual gland', 'Anterior surface of epiglottis', 'Hard palate', 'Overlapping lesion of major salivary glands', 'Scrotum NOS', 'Ventral surface of tongue NOS', 'Submandibular gland', 'Oropharynx NOS', 'Lower limb NOS', 'Overlapping lesion of brain', 'Overlapping lesion of larynx', 'Cornea NOS', 'Corpus uteri', 'External ear', 'Commissure of lip', 'unknown', 'Cheek mucosa', 'Overlapping lesion of hypopharynx', 'Pituitary gland', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Ascending colon', 'Epididymis', 'Esophagus NOS', 'Overlapping lesion of other and unspecified parts of mouth', 'Laryngeal cartilage', 'Skin of trunk', 'Transverse colon', 'Penis NOS', 'Ovary', 'Anterior wall of bladder', 'Carotid body', 'Colon NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Jejunum', 'Spermatic cord', 'Long bones of lower limb and associated joints', 'Undescended testis', 'Head of pancreas', 'Vestibule of mouth', 'Middle lobe lung', 'Posterior wall of bladder', 'Overlapping lesion of eye and adnexa', 'Overlapping lesion of palate', 'Overlapping lesion of lip oral cavity and pharynx', 'Cerebral meninges', 'Sphenoid sinus', 'Gastrointestinal tract NOS', 'Uvula', 'Other specified parts of pancreas', 'Uterus NOS', 'Tail of pancreas', 'Acoustic nerve', 'Lacrimal gland', 'Cortex of adrenal gland', 'Palate NOS', 'Extrahepatic bile duct', 'Vallecula', 'Ciliary body', 'Hypopharyngeal aspect of aryepiglottic fold', 'Greater curvature of stomach NOS', 'Overlapping lesion of female genital organs', 'Retina', 'Other ill-defined sites', 'Posterior wall of hypopharynx', 'Urethra', 'Overlapping lesion of small intestine', 'Peripheral nerves and autonomic nervous system of pelvis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Postcricoid region', 'Lower lobe lung', 'Skin of other and unspecified parts of face', 'Mucosa of lip NOS', 'Eyelid', 'Mucosa of upper lip', 'Paraurethral gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Placenta', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp -Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp +Disease Response,Disease Response,DiseaseResponse,Code assigned to describe the patient's response or outcome to the disease.,False,,"['CPD-Clinical Progression', 'IPD-Immunoprogression', 'MX-Mixed Response', 'DU-Disease Unchanged', 'RD-Responsive Disease', 'CR-Complete Response', 'BED-Biochemical Evidence of Disease', 'AJ-Adjuvant Therapy', 'PDM-Persistent Distant Metastasis', 'PPD-Pseudoprogression', 'PSR-Pseudoresponse', 'TF-Tumor Free', 'PD-Progressive Disease', 'sCR-Stringent Complete Response', 'SPD-Surgical Progression', 'NR-No Response', 'TE-Too Early', 'unknown', 'NPB-No Palliative Benefit', 'PR-Partial Response', 'PLD-Persistent Locoregional Disease', 'Not Reported', 'RPD-Radiographic Progressive Disease', 'PB-Palliative Benefit', 'SD-Stable Disease', 'VGPR-Very Good Partial Response', 'PA-Palliative Therapy', 'WT-With Tumor', 'MR-Minimal/Marginal response', 'Non-CR/Non-PD-Non-CR/Non-PD', 'CRU-Complete Response Unconfirmed', 'RP-Response', 'IMR-Immunoresponse', '']",,FollowUp +FEV1 FVC Post Bronch Percent,FEV1 FVC Post Bronch Percent,FEV1FVCPostBronchPercent,Percentage value to represent result of Forced Expiratory Volume in 1 second (FEV1) divided by the Forced Vital Capacity (FVC) post-bronchodilator.,False,,,,FollowUp +Weight,Weight,Weight,The weight of the patient measured in kilograms.,False,,,,FollowUp +Evidence of Recurrence Type,Evidence of Recurrence Type,EvidenceofRecurrenceType,The text term used to describe the type of evidence used to determine whether the patient's disease recurred,False,,"['Biopsy with Histologic Confirmation', 'Positive Biomarkers', 'Convincing Image Source', '']",,FollowUp +Recist Targeted Regions Number,Recist Targeted Regions Number,RecistTargetedRegionsNumber,"Numeric value that represents the number of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria",False,,,,FollowUp +HPV Positive Type,HPV Positive Type,HPVPositiveType,Text classification to represent the strain or type of human papillomavirus identified in an individual.,False,,"['""58""', '""52""', '""33""', '""16""', '""26""', '""56""', 'Other', '""31""', '""59""', '""66""', '""39""', '""68""', '""82""', '""45""', '""70""', '""18""', '""73""', 'unknown', '""53""', '""63""', 'Not Reported', '""35""', '""51""', '']",,FollowUp +Pancreatitis Onset Year,Pancreatitis Onset Year,PancreatitisOnsetYear,Date of onset of pancreatitis.,False,,,,FollowUp +Nadir CD4 Count,Nadir CD4 Count,NadirCD4Count,Numeric value that represents the lowest point to which the CD4 count has dropped (nadir).,False,,,,FollowUp +Hysterectomy Margins Involved,Hysterectomy Margins Involved,HysterectomyMarginsInvolved,The text term used to indicate whether the patient's disease was determined to be involved based on the surgical margins of the hysterectomy.,False,,"['Vagina', 'None', 'Microscopic Parametrium', 'unknown', 'Bladder', 'Not Reported', 'Macroscopic Parametrium', '']",,FollowUp +Comorbidity,Comorbidity,Comorbidity,"The text term used to describe a comorbidity disease, which coexists with the patient's malignant disease.",False,,"['Other Cancer Within 5 Years', 'Diabetes', 'Pulmonary Fibrosis', ""Behcet's Disease"", 'Ischemic Heart Disease', 'Cerebrovascular Disease', 'Anxiety', 'Organ transplant (site)', 'Lupus', 'Hepatitis B Infection', 'Li-Fraumeni Syndrome', 'High Grade Liver Dysplastic Nodule', 'Ulcerative Colitis', 'Fanconi Anemia', 'HIV / AIDS', 'Insulin Controlled Diabetes', 'Headache', 'Alpha-1 Antitrypsin', 'Epilepsy', 'Lynch Syndrome', 'Interstitial Pneumontis or ARDS', 'Peptic Ulcer (Ulcer)', 'Peripheral Neuropathy', 'Osteoarthritis', 'Sarcoidosis', 'Arrhythmia', 'Psoriasis', 'Peutz-Jeghers Disease', 'Beckwith-Wiedemann', 'Liver Toxicity (Non-Infectious)', 'Hypothyroidism', 'Nonalcoholic Steatohepatitis', 'Arthritis', 'Hepatitis C Infection', 'MAI', 'Coronary Artery Disease', 'Hereditary Non-polyposis Colon Cancer', 'Adenocarcinoma', 'Fibrosis', 'Human Papillomavirus Infection', 'Avascular Necrosis', 'Bronchitis', 'Liver Cirrhosis (Liver Disease)', 'Cataracts', 'Kidney Disease', 'Other Pulmonary Complications', 'Diverticulitis', 'Celiac Disease', 'Renal Dialysis', ""Hashimoto's Thyroiditis"", 'Hypercholesterolemia', 'Steatosis', 'Asthma', 'Adrenocortical Insufficiency', 'Cholelithiasis', 'Glaucoma', 'Intraductal Papillary Mucinous Neoplasm', 'Sleep apnea', 'Hyperglycemia', 'Type II', 'Chronic Hepatitis', 'Blood Clots', 'Not Reported', 'H. pylori Infection', 'Dyslipidemia', 'Low Grade Liver Dysplastic Nodule', 'Calcium Channel Blockers', 'Turcot Syndrome', 'Denys-Drash Syndrome', 'Cirrhosis', 'COPD', 'Inflammatory Bowel Disease', 'Colon Polyps', 'ITP', 'Stroke', 'Common Variable Immunodeficiency', 'Pain (Various)', 'Peripheral Vascular Disease', 'Tyrosinemia', 'Gorlin Syndrome', 'Allergies', 'Obesity', 'Neuroendocrine Tumor', 'Depression', 'Other Nonmalignant Systemic Disease', 'Heart Disease', 'Hepatitis A Infection', 'Pulmonary Hemorrhage', 'Deep Vein Thrombosis / Thromboembolism', 'HUS/TTP', 'Gonadal Dysfunction', 'Hypospadias', 'Acute Renal Failure', 'Chronic Renal Failure', 'Atrial Fibrillation', 'Tuberculosis', 'Rheumatologic Disease', 'Transient Ischemic Attack', 'GERD', 'unknown', 'Hyperlipidemia', 'Hypertension', 'Gout', 'Pancreatitis', 'Epstein-Barr Virus', 'Iron Overload', 'Hepatitis', 'Primary Sclerosing Cholangitis', 'Hemorrhagic Cystitis', 'Congestive Heart Failure (CHF)', 'Diet Controlled Diabetes', 'Familial Adenomatous Polyposis', 'Smoking', 'Glycogen Storage Disease', 'DVT/PE', 'Renal Failure (Requiring Dialysis)', 'Hypercalcemia', 'Myasthenia Gravis', 'Biliary Disorder', 'Myocardial Infarction', 'Seizure', 'Pregnancy in Patient or Partner', ""Barrett's Esophagus"", 'Other', 'Diabetic Neuropathy', 'Connective Tissue Disorder', 'Hemihypertrophy', ""Crohn's Disease"", 'Basal Cell Carcinoma', 'Cancer', 'Anemia', 'Rubinstein-Taybi Syndrome', 'Bone Fracture(s)', 'Cryptogenic Organizing Pneumonia', 'Osteoporosis or Osteopenia', 'Eczema', 'Joint Replacement', 'Herpes', 'Adenomatous Polyposis Coli', 'Wagr Syndrome', 'Rheumatoid Arthritis', 'Renal Insufficiency', 'Gastroesophageal Reflux Disease', 'unknown Etiology', '']",,FollowUp +Days to Follow Up,Days to Follow Up,DaystoFollowUp,Number of days between the date used for index and the date of the patient's last follow-up appointment or contact. If not applicable please enter 'Not Applicable',True,,,,FollowUp +Adverse Event,Adverse Event,AdverseEvent,Text that represents the Common Terminology Criteria for Adverse Events low level term name for an adverse event.,False,,"['Pulmonary Fibrosis', 'Fallopian Tube Stenosis', 'Thromboembolic Event', 'Tricuspid Valve Disease', 'Anxiety', 'Colonic Hemorrhage', 'Lymphocyte Count Decreased', 'Gastric Perforation', 'Cytokine Release Syndrome', 'Prolapse of Intestinal Stoma', 'Genital Edema', 'Vaginal Anastomotic Leak', 'Wolff-Parkinson-White Syndrome', 'Anorectal Infection', 'Vaginal Infection', 'Duodenal Hemorrhage', 'Hip Fracture', 'Psychosis', 'Sinus Pain', 'Neck Pain', 'Headache', 'Urinary Tract Infection', 'Paronychia', 'Hallucinations', 'Gastric Hemorrhage', 'Hyperhidrosis', 'Meningismus', 'Scalp Pain', 'Arachnoiditis', 'Urinary Tract Pain', 'Hoarseness', 'Duodenal Ulcer', 'Uterine Fistula', 'Growth Hormone Abnormal', 'Cecal Infection', 'Mucositis Oral', 'Colonic Obstruction', 'Optic Nerve Disorder', 'Pancreatic Necrosis', 'Urinary Incontinence', 'Perforation Bile Duct', 'Urostomy Obstruction', 'Retroperitoneal Hemorrhage', 'Avascular Necrosis', 'Sore Throat', 'Osteonecrosis of Jaw', 'Cerebrospinal Fluid Leakage', 'Hepatic Necrosis', 'Reproductive System and Breast Disorders Other', 'Myocarditis', 'Gastrointestinal Anastomotic Leak', 'Jejunal Ulcer', 'Esophageal Perforation', 'Duodenal Fistula', 'Salivary Gland Infection', 'Injection Site Reaction', 'Proteinuria', 'Corneal Ulcer', 'Familial and Genetic Disorders Other', 'Abdominal Infection', 'Puerperium and Perinatal Conditions Other', 'Scoliosis', 'Neuralgia', 'Oligospermia', 'Pleural Effusion', 'Hyperthyroidism', 'Pharyngeal Necrosis', 'Uterine Hemorrhage', 'Voice Alteration', 'Dysphasia', 'Pruritus', 'Skin Ulceration', 'Pulmonary Valve Disease', 'Spinal Fracture', 'Adrenal Insufficiency', 'Urostomy Leak', 'Retinopathy', 'Gastrointestinal Stoma Necrosis', 'Duodenal Stenosis', 'Sinus Tachycardia', 'Small Intestinal Perforation', 'Aortic Valve Disease', 'Retinal Tear', 'Reversible Posterior Leukoencephalopathy Syndrome', 'Brachial Plexopathy', 'Acidosis', 'Cecal Hemorrhage', 'Jejunal Perforation', 'Tracheal Obstruction', 'Muscle Weakness Trunk', 'Injury to Jugular Vein', 'Prostate Infection', 'Body Odor', 'Lymph Gland Infection', 'Supraventricular Tachycardia', 'Intestinal Stoma Site Bleeding', 'Malignant and Unspecified (Incl Cysts and Polyps) Other', 'Pancreatic Enzymes Decreased', 'Radiation Recall Reaction (Dermatologic)', 'Dysmenorrhea', 'Hot Flashes', 'Skin Induration', 'Toothache', 'Facial Pain', 'Atrial Fibrillation', 'Breast Pain', 'Movements Involuntary', 'Vaginal Discharge', 'Ovarian Rupture', 'Catheter Related Infection', 'Vertigo', 'Intraoperative Renal Injury', 'Glossopharyngeal Nerve Disorder', 'Hemorrhoids', 'Lordosis', 'Rhinitis Infective', 'Fracture', 'Hypoglossal Nerve Disorder', 'Hypoparathyroidism', 'Pancreatitis', 'Pulmonary Edema', 'Venous Injury', 'Renal and Urinary Disorders Other', 'Injury', 'Lactation Disorder', 'Wound Complication', 'Laryngeal Hemorrhage', 'Retinal Vascular Disorder', 'Poisoning and Procedural Complications Other', 'Gallbladder Obstruction', 'Laryngeal Fistula', 'Fallopian Tube Perforation', 'Ileal Stenosis', 'Mobitz (Type) II Atrioventricular Block', 'Large Intestinal Anastomotic Leak', 'Rash Acneiform', 'Pharyngeal Anastomotic Leak', 'Head Soft Tissue Necrosis', 'Tooth Infection', 'Lymphedema', 'Intestinal Stoma Obstruction', 'Flushing', 'Urticaria', 'Hyperparathyroidism', 'Erythroderma', 'Hyperuricemia', 'Retinal Detachment', 'Intraoperative Cardiac Injury', 'Fibrinogen Decreased', 'Hydrocephalus', 'Skin and Subcutaneous Tissue Disorders Other', 'Insomnia', 'Salivary Duct Inflammation', 'Pneumonitis', 'Night Blindness', 'Sleep Apnea', 'Urostomy Site Bleeding', 'Malaise', 'Tracheal Fistula', 'Intraoperative Urinary Injury', 'Hypocalcemia', 'Anemia', 'Pain', 'External Ear Pain', 'Stridor', 'Transient Ischemic Attacks', 'Cheilitis', 'Mitral Valve Disease', 'Delusions', 'Palpitations', 'Joint Infection', 'Ileal Fistula', 'Portal Vein Thrombosis', 'Radiculitis', 'Respiratory Failure', 'Gastroesophageal Reflux Disease', 'Intraoperative Gastrointestinal Injury', 'Skin Atrophy', 'Superficial Soft Tissue Fibrosis', 'Pleural Infection', 'Vas Deferens Anastomotic Leak', 'Renal Calculi', 'Tracheal Hemorrhage', 'Psychiatric Disorders Other', 'Stomal Ulcer', 'Death Neonatal', 'Alkaline Phosphatase Increased', 'Neck Soft Tissue Necrosis', 'Sepsis', 'Pelvic Infection', 'Left Ventricular Systolic Dysfunction', 'Trigeminal Nerve Disorder', 'Eye Pain', 'Ileal Hemorrhage', 'Bile Duct Stenosis', 'Aspartate Aminotransferase Increased', 'Ear Pain', 'Growth Accelerated', 'Irregular Menstruation', 'Aspiration', 'Anorgasmia', 'Perineal Pain', 'Fall', 'Intraoperative Arterial Injury', 'Myositis', 'Vascular Disorders Other', 'Heart Failure', 'Ovarian Hemorrhage', 'Gallbladder Fistula', 'Esophageal Obstruction', 'Intraoperative Musculoskeletal Injury', 'Hypersomnia', 'Ileus', 'INR Increased', 'Toxic Epidermal Necrolysis', 'Chest Pain Cardiac', 'Paroxysmal Atrial Tachycardia', 'Abducens Nerve Disorder', 'Chest Wall Pain', 'Muscle Weakness Right-Sided', 'Watering Eyes', 'Arteritis Infective', 'Gastrointestinal Pain', 'Dehydration', 'Fallopian Tube Obstruction', 'Hypothyroidism', 'Pharyngolaryngeal Pain', 'Urinary Tract Obstruction', 'Arthritis', 'Weight Loss', 'Intraoperative Skin Injury', 'Fever', 'Phlebitis Infective', 'Rectal Obstruction', 'Retinoic Acid Syndrome', 'Superficial Thrombophlebitis', 'Urine Output Decreased', 'Pharyngeal Hemorrhage', 'Rectal Pain', 'Testicular Hemorrhage', 'Intraoperative Breast Injury', 'Hemolysis', 'Visceral Arterial Ischemia', 'Biliary Tract Infection', 'Hypohidrosis', 'GGT Increased', 'Intra-Abdominal Hemorrhage', 'Peripheral Nerve Infection', 'Esophagitis', 'Vasovagal Reaction', 'Memory Impairment', 'Corneal Infection', 'Biliary Anastomotic Leak', 'Vaginal Pain', 'Cholesterol High', 'Concentration Impairment', 'Infective Myositis', 'Rash Maculo-Papular', 'Tracheitis', 'Libido Decreased', 'Pericardial Tamponade', 'Photosensitivity', 'Creatinine Increased', 'Blood Corticotrophin Decreased', 'Irritability', 'Apnea', 'Soft Tissue Necrosis Upper Limb', 'Alopecia', 'Flu Like Symptoms', 'Lipase Increased', 'Hypoxia', 'Dry Eye', 'Gingival Pain', 'Unequal Limb Length', 'Kyphosis', 'Unintended Pregnancy', 'Hypertrichosis', 'Bloating', 'Tracheal Mucositis', 'Edema Cerebral', 'Anal Ulcer', 'Restlessness', 'Scleral Disorder', 'Eyelid Function Disorder', 'Laryngitis', 'Trismus', 'Enterocolitis', 'Diarrhea', 'Hepatic Failure', 'IVth Nerve Disorder', 'Fallopian Tube Anastomotic Leak', 'Hypoalbuminemia', 'Obesity', 'Pericarditis', 'Pulmonary Fistula', 'Wound Dehiscence', 'Alcohol Intolerance', 'Intraoperative Hepatobiliary Injury', 'Death NOS', 'Anal Stenosis', 'Pancreatic Duct Stenosis', 'Capillary Leak Syndrome', 'Menorrhagia', 'Periorbital Edema', 'Stevens-Johnson Syndrome', 'Central Nervous System Necrosis', 'Malabsorption', 'Endocarditis Infective', 'Uveitis', 'Ventricular Arrhythmia', 'Bladder Spasm', 'Lymphocyte Count Increased', 'Hypertension', 'Pancreatic Anastomotic Leak', 'Vital Capacity Abnormal', 'Joint Effusion', 'Hearing Impaired', 'Injury to Carotid Artery', 'Duodenal Infection', 'Penile Pain', 'Social Circumstances Other', 'wheezing', 'Conduction Disorder', 'Iron Overload', 'Abdominal Distension', 'Intraoperative Reproductive Tract Injury', 'Oral Pain', 'Leukocytosis', 'Cholecystitis', 'Investigations Other', 'Abdominal Pain', 'Oculomotor Nerve Disorder', 'Neutrophil Count Decreased', 'Hypomagnesemia', 'Nail Discoloration', 'Agitation', 'Hypercalcemia', 'Esophageal Stenosis', 'Nasal Congestion', 'Kidney Infection', 'Eye Infection', 'Delayed Puberty', 'Vascular Access Complication', 'Joint Range of Motion Decreased', 'Acute Kidney Injury', 'Lymph Leakage', 'Hypokalemia', 'Nystagmus', 'Pain of Skin', 'Delayed Orgasm', 'Duodenal Obstruction', 'Seizure', 'Adult Respiratory Distress Syndrome', 'Intracranial Hemorrhage', 'Bronchopleural Fistula', 'Alkalosis', 'Back Pain', 'Pyramidal Tract Syndrome', 'Bone Infection', 'Bladder Anastomotic Leak', 'Presyncope', 'Stoma Site Infection', 'Laryngeal Obstruction', 'Confusion', 'Anal Hemorrhage', 'Gastric Anastomotic Leak', 'Acoustic Nerve Disorder NOS', 'Esophageal Fistula', 'White Blood Cell Decreased', 'Nail Ridging', 'Spleen Disorder', 'Gastrointestinal Fistula', 'Alanine Aminotransferase Increased', 'Uterine Pain', 'Rectal Anastomotic Leak', 'Vaginal Obstruction', 'Vaginal Perforation', 'Rectal Necrosis', 'Papilledema', 'Fecal Incontinence', 'Small Intestinal Stenosis', 'Vitreous Hemorrhage', 'Fatigue', 'Vaginismus', 'Uterine Perforation', 'Bruising', 'Cardiac Arrest', 'Esophageal Infection', 'Bronchopulmonary Hemorrhage', 'Surgical and Medical Procedures Other', 'Sinus Bradycardia', 'Oral Cavity Fistula', 'Bladder Infection', 'Appendicitis Perforated', 'Accessory Nerve Disorder', 'Dermatitis Radiation', 'Papulopustular Rash', 'Intraoperative Splenic Injury', 'Postnasal Drip', 'Azoospermia', 'Spermatic Cord Obstruction', 'Dental Caries', 'Injury to Inferior Vena Cava', 'Delirium', 'Precocious Puberty', 'Sneezing', 'Encephalitis Infection', 'Constipation', 'Ureteric Anastomotic Leak', 'Musculoskeletal Deformity', 'Joint Range of Motion Decreased Cervical Spine', 'Restrictive Cardiomyopathy', 'Blood Prolactin Abnormal', 'External Ear Inflammation', 'Cervicitis Infection', 'Nervous System Disorders Other', 'Paresthesia', 'Peritoneal Necrosis', 'Respiratory', 'Renal Hemorrhage', 'Skin Hyperpigmentation', 'Testicular Disorder', 'Cardiac Troponin I Increased', 'Gait Disturbance', 'Jejunal Obstruction', 'Ventricular Fibrillation', 'Sudden Death NOS', 'Hematosalpinx', 'Osteoporosis', 'Autoimmune Disorder', 'Hypotension', 'Hyponatremia', 'Hypernatremia', 'Allergic Reaction', 'Lung Infection', 'Colitis', 'Mediastinal Hemorrhage', 'Atrial Flutter', 'Fibrosis Deep Connective Tissue', 'Gallbladder Infection', 'Pleural Hemorrhage', 'Bladder Perforation', 'Periodontal Disease', 'Pharyngitis', 'Esophageal Necrosis', 'Jejunal Hemorrhage', 'Otitis Externa', 'Bronchial Stricture', 'Ankle Fracture', 'Infusion Site Extravasation', 'Rectal Hemorrhage', 'Soft Tissue Necrosis Lower Limb', 'Glucose Intolerance', 'Immune System Disorders Other', 'Peripheral Motor Neuropathy', 'Neoplasms Benign', 'Recurrent Laryngeal Nerve Palsy', 'Infusion Related Reaction', 'Cognitive Disturbance', 'Hepatic Hemorrhage', 'Colonic Stenosis', 'Small Intestinal Anastomotic Leak', 'Hyperkalemia', 'Jejunal Stenosis', 'Urinary Urgency', 'Carbon Monoxide Diffusing Capacity Decreased', 'Middle Ear Inflammation', 'Stroke', 'Menopause', 'Gastroparesis', 'Sinusitis', 'Small Intestinal Mucositis', 'Tracheal Stenosis', 'Abdominal Soft Tissue Necrosis', 'Dry Mouth', 'Soft Tissue Infection', 'Urostomy Stenosis', 'Depression', 'Somnolence', 'Lip Pain', 'Bronchial Infection', 'Esophageal Anastomotic Leak', 'Lower Gastrointestinal Hemorrhage', 'Constrictive Pericarditis', 'Mucosal Infection', 'Urinary Frequency', 'Telangiectasia', 'Ovarian Infection', 'Ileal Obstruction', 'Tinnitus', 'Gastritis', 'Dysarthria', 'Hypothermia', 'Lymphocele', 'Vaginal Stricture', 'Upper Respiratory Infection', 'Leukoencephalopathy', 'Typhlitis', 'Tumor Lysis Syndrome', 'Vulval Infection', 'Atelectasis', 'Aphonia', 'Lymph Node Pain', 'Flatulence', 'Dysesthesia', 'Scrotal Pain', 'Cushingoid', 'Aortic Injury', 'Muscle Weakness Lower Limb', 'Periorbital Infection', 'Gallbladder Necrosis', 'Hemolytic Uremic Syndrome', 'Jejunal Fistula', 'Splenic Infection', 'Muscle Weakness Left-Sided', 'Allergic Rhinitis', 'Wrist Fracture', 'Superior Vena Cava Syndrome', 'Prostatic Obstruction', 'Rash Pustular', 'Facial Muscle Weakness', 'Localized Edema', 'Facial Nerve Disorder', 'Fetal Death', 'Personality Change', 'Pharyngeal Mucositis', 'Scrotal Infection', 'Peritoneal Infection', 'Erythema Multiforme', 'Urethral Infection', 'Uterine Infection', 'CD4 Lymphocytes Decreased', 'Amnesia', 'Flank Pain', 'Chylothorax', 'Myelitis', 'Phantom Pain', 'Rectal Fistula', 'Myocardial Infarction', 'Hematoma', 'Intraoperative Ear Injury', 'Spermatic Cord Hemorrhage', 'Colonic Ulcer', 'Epistaxis', 'Febrile Neutropenia', 'Upper Gastrointestinal Hemorrhage', 'Ventricular Tachycardia', 'Feminization Acquired', 'Generalized Muscle Weakness', 'Extraocular Muscle Paresis', 'Joint Range of Motion Decreased Lumbar Spine', 'Device Related Infection', 'Gastrointestinal Disorders Other', 'Salivary Gland Fistula', 'Spermatic Cord Anastomotic Leak', 'Productive Cough', 'Small Intestine Infection', 'Tooth Discoloration', 'Bone Pain', 'Urine Discoloration', 'Meningitis', 'Forced Expiratory Volume Decreased', 'Burn', 'Blood and Lymphatic System Disorders Other', 'Chronic Kidney Disease', 'Weight Gain', 'Encephalomyelitis Infection', 'Floaters', 'Metabolism and Nutrition Disorders Other', 'Conjunctivitis Infective', 'Nail Loss', 'Dizziness', 'Acute Coronary Syndrome', 'Anal Fistula', 'Vomiting', 'Sick Sinus Syndrome', 'Laryngeal Mucositis', 'Oral Dysesthesia', 'Pelvic Pain', 'Cranial Nerve Infection', 'Cough', 'Pleuritic Pain', 'Small Intestinal Obstruction', 'Anorexia', 'Vestibular Disorder', 'Esophageal Hemorrhage', 'Electrocardiogram QT Corrected Interval Prolonged', 'Hemoglobin Increased', 'Breast Atrophy', 'Intraoperative Head and Neck Injury', 'Suicidal Ideation', 'Pancreatic Fistula', 'Laryngeal Edema', 'Stenosis of Gastrointestinal Stoma', 'Buttock Pain', 'Growth Suppression', 'Hepatobiliary Disorders Other', 'Mania', 'Peripheral Ischemia', 'Edema Face', 'Dry Skin', 'Vasculitis', 'Appendicitis', 'Intraoperative Ocular Injury', 'Tracheostomy Site Bleeding', 'Treatment Related Secondary Malignancy', 'Tremor', 'Conjunctivitis', 'Endophthalmitis', 'Cataract', 'Nipple Deformity', 'Erectile Dysfunction', 'Oral Hemorrhage', 'Gastric Necrosis', 'Edema Limbs', 'General Disorders and Administration Site Conditions Other', 'Pericardial Effusion', 'Hepatic Infection', 'Intraoperative Venous Injury', 'Urinary Retention', 'Peripheral Sensory Neuropathy', 'Hepatitis Viral', 'Stomach Pain', 'Disseminated Intravascular Coagulation', 'Prolapse of Urostomy', 'Encephalopathy', 'Fetal Growth Retardation', 'Vaginal Inflammation', 'Proctitis', 'Vaginal Hemorrhage', 'Gallbladder Perforation', 'Esophageal Ulcer', 'Skin Hypopigmentation', 'Blood Bilirubin Increased', 'Female Genital Tract Fistula', 'Hiccups', 'Injury to Superior Vena Cava', 'Rectal Stenosis', 'Ejection Fraction Decreased', 'Glaucoma', 'Palmar-Plantar Erythrodysesthesia Syndrome', 'Uterine Anastomotic Leak', 'Postoperative Thoracic Procedure Complication', 'Laryngeal Inflammation', 'Laryngospasm', 'Gastric Fistula', 'Hypophosphatemia', 'Testicular Pain', 'Pelvic Floor Muscle Weakness', 'Pain in Extremity', 'Myelodysplastic Syndrome', 'Seroma', 'Hyperglycemia', 'Portal Hypertension', 'Arterial Injury', 'Thoracic and Mediastinal Disorders Other', 'Pharyngeal Stenosis', 'Small Intestine Ulcer', 'Breast Infection', 'Gallbladder Pain', 'Muscle Weakness Upper Limb', 'Akathisia', 'Esophageal Varices Hemorrhage', 'Hepatic Pain', 'Leukemia Secondary to Oncology Chemotherapy', 'Biliary Fistula', 'Ileal Ulcer', 'Urethral Anastomotic Leak', 'Congenital', 'Ischemia Cerebrovascular', 'Anal Necrosis', 'Penile Infection', 'Hypertriglyceridemia', 'Rectal Mucositis', 'Anal Pain', 'Hematuria', 'Ear and Labyrinth Disorders Other', 'Bone Marrow Hypocellular', 'Pulmonary Hypertension', 'Bullous Dermatitis', 'Euphoria', 'Non-Cardiac Chest Pain', 'Vaginal Dryness', 'Pelvic Soft Tissue Necrosis', 'Mobitz Type I', 'Ascites', 'Spasticity', 'Laryngopharyngeal Dysesthesia', 'Prostatic Hemorrhage', 'Suicide Attempt', 'Vagus Nerve Disorder', 'Fat Atrophy', 'Tooth Development Disorder', 'Bronchospasm', 'Depressed Level of Consciousness', 'Hemorrhoidal Hemorrhage', 'Intraoperative Neurological Injury', 'Premature Menopause', 'Infections and Infestations Other', 'Hirsutism', 'Rectal Ulcer', 'Extrapyramidal Disorder', 'Ovulation Pain', 'Chills', 'Premature Delivery', 'Blurred Vision', 'Anaphylaxis', 'CPK Increased', 'Ileal Perforation', 'Pneumothorax', 'Renal Colic', 'Right Ventricular Dysfunction', 'Dyspareunia', 'Duodenal Perforation', 'dyspnea', 'Flashing Lights', 'Tumor Pain', 'Hypoglycemia', 'Gastric Ulcer', 'Colonic Fistula', 'Atrioventricular Block First Degree', 'Intraoperative Hemorrhage', 'Urinary Fistula', 'Keratitis', 'Postoperative Hemorrhage', 'Myalgia', 'Gastric Stenosis', 'Obstruction Gastric', 'Purpura', 'Lethargy', 'Colonic Perforation', 'Rectal Perforation', 'Blood Gonadotrophin Abnormal', 'Musculoskeletal and Connective Tissue Disorders Other', 'Serum Sickness', 'Activated Partial Thromboplastin Time Prolonged', 'Pancreatic Hemorrhage', 'dysphagia', 'Nail Infection', 'Virilization', 'Haptoglobin Decreased', 'Sinus Disorder', 'Eye Disorders Other', 'Intraoperative Respiratory Injury', 'Phlebitis', 'Anal Mucositis', 'Multi-Organ Failure', 'Esophageal Pain', 'Bronchial Obstruction', 'Gynecomastia', 'Hypermagnesemia', 'Gum Infection', 'Cardiac Disorders Other', 'Laryngeal Stenosis', 'Intraoperative Endocrine Injury', 'Vaginal Fistula', 'Kidney Anastomotic Leak', 'Mediastinal Infection', 'Ataxia', 'Wound Infection', 'Nausea', 'Asystole', 'Skin Infection', 'Libido Increased', 'Edema Trunk', 'Serum Amylase Increased', 'Pancreas Infection', 'Arthralgia', 'Cystitis Noninfective', 'Lipohypertrophy', 'Cardiac Troponin T Increased', 'Ejaculation Disorder', 'Exostosis', 'Syncope', 'Pharyngeal Fistula', 'Olfactory Nerve Disorder', 'Thrombotic Thrombocytopenic Purpura', 'Prostatic Pain', 'Blood Antidiuretic Hormone Abnormal', 'Atrioventricular Block Complete', 'Endocrine Disorders Other', 'Intestinal Stoma Leak', 'Enterovesical Fistula', 'Platelet Count Decreased', 'Photophobia', 'Neck Edema', 'Lip Infection', 'Otitis Media', 'Dyspepsia', 'Uterine Obstruction', 'Enterocolitis Infectious', 'Dysgeusia', 'Pregnancy', 'Bronchial Fistula', 'Hemoglobinuria', '']",,FollowUp +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,FollowUp +Pregnancy Outcome,Pregnancy Outcome,PregnancyOutcome,The text term used to describe the type of pregnancy the patient had,False,,"['Miscarriage', 'Ectopic Pregnancy', 'Live Birth', 'unknown', 'Stillbirth', 'Not Reported', 'Induced Abortion', '']",,FollowUp +AIDS Risk Factors,AIDS Risk Factors,AIDSRiskFactors,The text term used to describe a risk factor of the acquired immunodeficiency syndrome (AIDS) that the patient either had at time time of the study or experienced in the past.,False,,"['Encephalopathy', 'Cytomegalovirus', 'Herpes Simplex Virus', 'Pneumocystis Pneumonia', 'Mycobacterium tuberculosis', 'Isosporiasis', 'NOS', 'Toxoplasmosis', 'Nocardiosis', 'Mycobacterium avium Complex', 'Cryptococcosis', 'Salmonella Septicemia', 'Candidiasis', 'pneumonia', 'Progressive Multifocal Leukoencephalopathy', 'Mycobacterium', 'Wasting Syndrome', 'Coccidioidomycosis', 'Histoplasmosis', '']",,FollowUp +Hepatitis Sustained Virological Response,Hepatitis Sustained Virological Response,HepatitisSustainedVirologicalResponse,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,FollowUp +Immunosuppressive Treatment Type,Immunosuppressive Treatment Type,ImmunosuppressiveTreatmentType,The text term used to describe the type of immunosuppresive treatment the patient received.,False,,"['None', 'Azathioprine', 'Cyclophosphamide', 'Methotrexate', 'Anti-TNFTherapy', 'unknown', 'Other', 'Not Reported', '']",,FollowUp +Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['Not Reported', 'Yes - Progression or Recurrence', 'no', 'unknown']",,FollowUp +Recist Targeted Regions Sum,Recist Targeted Regions Sum,RecistTargetedRegionsSum,"Numeric value that represents the sum of baseline target lesions, as described by the Response Evaluation Criteria in Solid Tumours (RECIST) criteria.",False,,,,FollowUp +Risk Factor Treatment,Risk Factor Treatment,RiskFactorTreatment,The yes/no/unknown indicator used to describe whether the patient received treatment for a risk factor the patient had at the time of or prior to their diagnosis.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,FollowUp +FEV1 Ref Post Bronch Percent,FEV1 Ref Post Bronch Percent,FEV1RefPostBronchPercent,The percentage comparison to a normal value reference range of the volume of air that a patient can forcibly exhale from the lungs in one second post-bronchodilator.,False,,,,FollowUp +Hormonal Contraceptive Use,Hormonal Contraceptive Use,HormonalContraceptiveUse,The text term used to indicate whether the patient used hormonal contraceptives.,False,,"['Former User', 'Current User', 'unknown', 'Never Used', 'Not Reported', '']",,FollowUp +Imaging Type,Imaging Type,ImagingType,The text term used to describe the type of imaging or scan performed on the patient.,False,,"['CT Scan', 'PET', 'MRI', '99mTc Bone Scintigraphy', '']",,FollowUp Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp Days to Progression,Days to Progression,DaystoProgression,Number of days between the date used for index and the date the patient's disease progressed. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp -Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Distant', 'unknown', 'Local', 'Regional', 'Not Reported', 'Biochemical', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp -Lymphatic Invasion Present,Lymphatic Invasion Present,LymphaticInvasionPresent,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement",False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,Diagnosis -Mitotic Count,Mitotic Count,MitoticCount,"The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.",False,,,,Diagnosis -Lymph Nodes Tested,Lymph Nodes Tested,LymphNodesTested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,False,,,,Diagnosis -Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",False,,"['G2', 'Intermediate Grade', 'G3', 'GB', 'High Grade', 'Not Applicable', 'GX', 'G4', 'unknown', 'G1', 'Low Grade', 'Not Reported', '']",,Diagnosis -Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Olfactory nerve', 'Overlapping lesion of bladder', 'Anterior floor of mouth', 'Bone marrow', 'Other specified parts of female genital organs', 'Parametrium', 'Overlapping lesion of lung', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Branchial cleft', 'Lower gum', 'Renal pelvis', 'skin NOS', 'Overlapping lesion of accessory sinuses', 'Gastric antrum', 'Overlapping lesion of cervix uteri', 'Nasal cavity', 'Peripheral nerves and autonomic nervous system of thorax', 'Autonomic nervous system NOS', 'Overlapping lesion of nasopharynx', 'Lateral wall of oropharynx', 'Upper-inner quadrant of breast', 'Thymus', 'Posterior mediastinum', 'Anus NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Stomach NOS', 'Broad ligament', 'Paraspinal', 'Cloacogenic zone', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Lateral wall of bladder', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Biliary tract NOS', 'Anterior 2/3 of tongue NOS', 'Testis NOS', 'Overlapping lesion of ill-defined sites', 'Uterine adnexa', 'Fundus uteri', 'Central portion of breast', 'Overlapping lesion of skin', 'Lateral wall of nasopharynx', 'Nipple', 'Overlapping lesion of urinary organs', 'Soft palate NOS', 'Main bronchus', 'Trachea', 'Upper lobe lung', 'Anterior wall of nasopharynx', 'Specified parts of peritoneum', 'Body of penis', 'Tonsillar fossa', 'Overlapping lesion of breast', 'Adrenal gland NOS', 'Hepatic flexure of colon', 'Aortic body and other paraganglia', 'Frontal lobe', 'Pleura NOS', 'Lateral floor of mouth', 'Intrathoracic lymph nodes', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Pylorus', 'Skin of lip NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peripheral nerves and autonomic nervous system of abdomen', 'Waldeyer ring', 'Axillary tail of breast', 'Cervical esophagus', 'Not Reported', 'Round ligament', 'Anterior mediastinum', 'Cecum', 'Cerebrum', 'Cerebellum NOS', 'Ureteric orifice', 'Abdomen NOS', 'Brain NOS', 'Major salivary gland NOS', 'Thyroid gland', 'Overlapping lesion of rectum anus and anal canal', 'Upper-outer quadrant of breast', 'Peritoneum NOS', 'Male genital organs NOS', 'Cranial nerve NOS', 'Gum NOS', 'Ethmoid sinus', 'Subglottis', 'Meninges NOS', 'Nasopharynx NOS', 'Spinal cord', 'Clitoris', 'Labium majus', 'Urachus', 'Duodenum', 'Short bones of upper limb and associated joints', 'Posterior wall of oropharynx', 'Vulva NOS', 'Thorax NOS', 'Temporal lobe', 'Maxillary sinus', 'Middle third of esophagus', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of pancreas', 'Overlapping lesion of tonsil', 'Overlapping lesion of floor of mouth', 'Accessory sinus NOS', 'External lower lip', 'Vagina NOS', 'Parathyroid gland', 'Overlapping lesions of oropharynx', 'Overlapping lesion of esophagus', 'Overlapping lesion of colon', 'Base of tongue NOS', 'Overlapping lesion of vulva', 'Isthmus uteri', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of digestive system', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Ill-defined sites within respiratory system', 'Lower-inner quadrant of breast', 'Fundus of stomach', 'Prostate gland', 'Spinal meninges', 'Supraglottis', 'Bladder neck', 'Connective subcutaneous and other soft tissues of abdomen', 'Mandible', 'Blood', 'Anal canal', 'Overlapping lesion of penis', 'Nervous system NOS', 'Lymph node NOS', 'Overlapping lesion of corpus uteri', 'Retroperitoneum', 'Pharynx NOS', 'Rib sternum clavicle and associated joints', 'Lower-outer quadrant of breast', 'Intrahepatic bile duct', 'Appendix', 'Lymph nodes of multiple regions', 'Occipital lobe', 'Cervix uteri', 'Fallopian tube', 'Endometrium', 'Ventricle NOS', 'Ampulla of Vater', 'Pineal gland', 'Pelvis NOS', 'Skin of scalp and neck', 'Brain stem', 'Islets of Langerhans', 'Endocervix', 'Upper limb NOS', 'Dome of bladder', 'Thoracic esophagus', 'Vertebral column', 'Short bones of lower limb and associated joints', 'Tongue NOS', 'Overlapping lesion of male genital organs', 'Exocervix', 'Splenic flexure of colon', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Upper gum', 'Labium minus', 'Glottis', 'Overlapping lesion of lip', 'Mucosa of lower lip', 'Optic nerve', 'Kidney NOS', 'Pancreatic duct', 'Breast NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Meckel diverticulum', 'Overlapping lesion of biliary tract', 'Overlapping lesion of tongue', 'Larynx NOS', 'Ileum', 'Pancreas NOS', 'Overlapping lesion of stomach', 'Abdominal esophagus', 'Intestinal tract NOS', 'Frontal sinus', 'Cardia NOS', 'Liver', 'Tonsillar pillar', 'Bone of limb NOS', 'Cauda equina', 'Other specified parts of male genital organs', 'Upper respiratory tract NOS', 'unknown primary site', 'Small intestine NOS', 'Upper third of esophagus', 'Connective subcutaneous and other soft tissues of thorax', 'Sigmoid colon', 'Lymph nodes of head face and neck', 'Pyriform sinus', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Lung NOS', 'Border of tongue', 'Tonsil NOS', 'Rectum NOS', 'Parietal lobe', 'Hypopharynx NOS', 'Heart', 'Mouth NOS', 'Hematopoietic system NOS', 'Superior wall of nasopharynx', 'Endocrine gland NOS', 'Craniopharyngeal duct', 'Overlapping lesion of heart mediastinum and pleura', 'Lymph nodes of axilla or arm', 'Head face or neck NOS', 'Medulla of adrenal gland', 'Lymph nodes of inguinal region or leg', 'Female genital tract NOS', 'Glans penis', 'skin of lower limb and hip', 'Body of stomach', 'Reticuloendothelial system NOS', 'Choroid', 'External upper lip', 'Prepuce', 'Posterior wall of nasopharynx', 'Urinary system NOS', 'Conjunctiva', 'Rectosigmoid junction', 'Intra-abdominal lymph nodes', 'Lingual tonsil', 'External lip NOS', 'Parotid gland', 'Bones of skull and face and associated joints', 'Dorsal surface of tongue NOS', 'Lip NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of endocrine glands and related structures', 'Middle ear', 'Bladder NOS', 'Bone NOS', 'Trigone of bladder', 'Gallbladder', 'Descended testis', 'Orbit NOS', 'Descending colon', 'Spleen', 'Retromolar area', 'Ureter', 'Pelvic lymph nodes', 'skin of upper limb and shoulder', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Eye NOS', 'Myometrium', 'Lower third of esophagus', 'Body of pancreas', 'Mediastinum NOS', 'Sublingual gland', 'Anterior surface of epiglottis', 'Hard palate', 'Overlapping lesion of major salivary glands', 'Scrotum NOS', 'Ventral surface of tongue NOS', 'Submandibular gland', 'Oropharynx NOS', 'Lower limb NOS', 'Overlapping lesion of brain', 'Overlapping lesion of larynx', 'Cornea NOS', 'Corpus uteri', 'External ear', 'Commissure of lip', 'unknown', 'Cheek mucosa', 'Overlapping lesion of hypopharynx', 'Pituitary gland', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Ascending colon', 'Epididymis', 'Esophagus NOS', 'Overlapping lesion of other and unspecified parts of mouth', 'Laryngeal cartilage', 'Skin of trunk', 'Transverse colon', 'Penis NOS', 'Ovary', 'Anterior wall of bladder', 'Carotid body', 'Colon NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Jejunum', 'Spermatic cord', 'Long bones of lower limb and associated joints', 'Undescended testis', 'Head of pancreas', 'Vestibule of mouth', 'Middle lobe lung', 'Posterior wall of bladder', 'Overlapping lesion of eye and adnexa', 'Overlapping lesion of palate', 'Overlapping lesion of lip oral cavity and pharynx', 'Cerebral meninges', 'Sphenoid sinus', 'Gastrointestinal tract NOS', 'Uvula', 'Other specified parts of pancreas', 'Uterus NOS', 'Tail of pancreas', 'Acoustic nerve', 'Lacrimal gland', 'Cortex of adrenal gland', 'Palate NOS', 'Extrahepatic bile duct', 'Vallecula', 'Ciliary body', 'Hypopharyngeal aspect of aryepiglottic fold', 'Greater curvature of stomach NOS', 'Overlapping lesion of female genital organs', 'Retina', 'Other ill-defined sites', 'Posterior wall of hypopharynx', 'Urethra', 'Overlapping lesion of small intestine', 'Peripheral nerves and autonomic nervous system of pelvis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Postcricoid region', 'Lower lobe lung', 'Skin of other and unspecified parts of face', 'Mucosa of lip NOS', 'Eyelid', 'Mucosa of upper lip', 'Paraurethral gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Placenta']",,Diagnosis -Laterality,Laterality,Laterality,"For tumors in paired organs, designates the side on which the cancer originates.",False,,"['Unilateral', 'Bilateral', 'Left', 'unknown', 'Not Reported', 'Midline', 'Right', '']",,Diagnosis -AJCC Pathologic Stage,AJCC Pathologic Stage,AJCCPathologicStage,"The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.",False,,"['Stage X', 'Stage IA1', 'Stage IC', 'Stage II', 'Stage 0a', 'Stage IIIC1', 'Stage III', 'Stage IIIA', 'Stage IIA2', 'Stage 0', 'Stage IIA1', 'Stage I', 'Stage IB1', 'unknown', 'Stage IA2', 'Stage Tis', 'Stage IIA', 'Stage IIC', 'Stage IIB', 'Stage IB', 'Stage IIIC2', 'Stage IVA', 'Stage IIIB', 'Stage IVB', 'Stage IIIC', 'Stage 0is', 'Stage IB2', 'Stage IIC1', 'Stage IVC', 'Stage IA', 'Stage IV', 'Not Reported', 'Stage IS', '']",,Diagnosis -Method of Diagnosis,Method of Diagnosis,MethodofDiagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,False,,"['Pap Smear', 'Blood Draw', 'Physical Exam', 'Bone Marrow Aspirate', 'Pathologic Review', 'Cystoscopy', 'Other', 'Debulking', 'unknown', 'Laparotomy', 'Incisional Biopsy', 'Thoracentesis', 'Diagnostic Imaging', 'Dilation and Curettage Procedure', 'Surgical Resection', 'Biopsy', 'Core Biopsy', 'Fine Needle Aspiration', 'Excisional Biopsy', 'Autopsy', 'Enucleation', 'Cytology', 'Ultrasound Guided Biopsy', 'Not Reported', 'Laparoscopy', '']",,Diagnosis -Best Overall Response,Best Overall Response,BestOverallResponse,The best improvement achieved throughout the entire course of protocol treatment.,False,,"['DU-Disease Unchanged', 'TE-Too Early', 'Non-CR/Non-PD-Non-CR/Non-PD', 'PR-Partial Response', 'PSR-Pseudoresponse', 'PPD-Pseudoprogression', 'VGPR-Very Good Partial Response', 'CR-Complete Response', 'SPD-Surgical Progression', 'NR-No Response', 'MX-Mixed Response', 'NPB-No Palliative Benefit', 'PA-Palliative Therapy', 'RD-Responsive Disease', 'CPD-Clinical Progression', 'AJ-Adjuvant Therapy', 'IMR-Immunoresponse', 'RPD-Radiographic Progressive Disease', 'PD-Progressive Disease', 'PB-Palliative Benefit', 'IPD-Immunoprogression', 'RP-Response', 'sCR-Stringent Complete Response', 'CRU-Complete Response Unconfirmed', 'SD-Stable Disease', 'MR-Minimal/Marginal Response', '']",,Diagnosis +Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Distant', 'Local', 'Regional', 'unknown', 'Biochemical', 'Not Reported', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp +Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Urethra', 'Connective subcutaneous and other soft tissues of pelvis', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp +Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",FollowUp +Days to Diagnosis,Days to Diagnosis,DaystoDiagnosis,Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable',False,,,,Diagnosis +Gleason Grade Tertiary,Gleason Grade Tertiary,GleasonGradeTertiary,The text term used to describe the tertiary pattern as described by the Gleason Grading System.,False,,"['Pattern 5', 'Pattern 4', '']",,Diagnosis +Best Overall Response,Best Overall Response,BestOverallResponse,The best improvement achieved throughout the entire course of protocol treatment.,False,,"['CPD-Clinical Progression', 'IPD-Immunoprogression', 'MX-Mixed Response', 'DU-Disease Unchanged', 'RD-Responsive Disease', 'CR-Complete Response', 'PPD-Pseudoprogression', 'AJ-Adjuvant Therapy', 'PSR-Pseudoresponse', 'MR-Minimal/Marginal Response', 'PD-Progressive Disease', 'sCR-Stringent Complete Response', 'SPD-Surgical Progression', 'NR-No Response', 'TE-Too Early', 'NPB-No Palliative Benefit', 'PR-Partial Response', 'RPD-Radiographic Progressive Disease', 'PB-Palliative Benefit', 'SD-Stable Disease', 'VGPR-Very Good Partial Response', 'PA-Palliative Therapy', 'Non-CR/Non-PD-Non-CR/Non-PD', 'CRU-Complete Response Unconfirmed', 'RP-Response', 'IMR-Immunoresponse', '']",,Diagnosis +Medulloblastoma Molecular Classification,Medulloblastoma Molecular Classification,MedulloblastomaMolecularClassification,The text term used to describe the classification of medulloblastoma tumors based on molecular features.,False,,"['Non-WNT/non-SHH Activated', 'WNT-Activated', 'unknown', 'Not Reported', 'SHH-Activated', 'Not Determined', '']",,Diagnosis +INSS Stage,INSS Stage,INSSStage,"Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).",False,,"['Stage 2A', 'Stage 4S', 'unknown', 'Stage 4', 'Stage 1', 'Stage 3', 'Stage 2B', 'Not Reported', '']",,Diagnosis +Cog Rhabdomyosarcoma Risk Group,Cog Rhabdomyosarcoma Risk Group,CogRhabdomyosarcomaRiskGroup,"Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).",False,,"['Intermediate Risk', 'unknown', 'Low Risk', 'Not Reported', 'High Risk', '']",,Diagnosis +ISS Stage,ISS Stage,ISSStage,The multiple myeloma disease stage at diagnosis.,False,,"['II', 'I', 'unknown', 'III', 'Not Reported', '']",,Diagnosis +Pregnant at Diagnosis,Pregnant at Diagnosis,PregnantatDiagnosis,The text term used to indicate whether the patient was pregnant at the time they were diagnosed.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Diagnosis +Last Known Disease Status,Last Known Disease Status,LastKnownDiseaseStatus,Text term that describes the last known state or condition of an individual's neoplasm.,True,,"['Tumor free', 'Not Allowed To Collect', 'Loco-regional recurrence/progression', 'Distant met recurrence/progression', 'With tumor', 'Biochemical evidence of disease without structural correlate', 'Not Applicable', 'Not Reported', 'unknown tumor status']",,Diagnosis +Residual Disease,Residual Disease,ResidualDisease,Text terms to describe the status of a tissue margin following surgical resection.,False,,"['R2', 'RX', 'R1', 'R0', 'unknown', 'Not Reported', '']",,Diagnosis +INPC Histologic Group,INPC Histologic Group,INPCHistologicGroup,"The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.",False,,"['Not Reported', 'Unfavorable', 'Favorable', 'unknown', '']",,Diagnosis +Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['Not Reported', 'Yes - Progression or Recurrence', 'no', 'unknown']",,Diagnosis +Mitosis Karyorrhexis Index,Mitosis Karyorrhexis Index,MitosisKaryorrhexisIndex,Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).,False,,"['High', 'unknown', 'Intermediate', 'Low', 'Not Reported', '']",,Diagnosis +Micropapillary Features,Micropapillary Features,MicropapillaryFeatures,The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.,False,,"['Not Reported', 'Absent', 'Present', 'unknown', '']",,Diagnosis +INPC Grade,INPC Grade,INPCGrade,"Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).",False,,"['unknown', 'Differentiating', 'Poorly Differentiated', 'Undifferentiated', 'Not Reported', '']",,Diagnosis +AJCC Pathologic N,AJCC Pathologic N,AJCCPathologicN,The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.,False,,"['N2b', 'N1b', 'N0', 'N1c', 'N1', 'N1bI', 'N1bIV', 'NX', 'N2', 'N3', 'N2a', 'N0 (mol+)', 'N3b', 'N3c', 'N0 (mol-)', 'N1a', 'N1bII', 'unknown', 'N4', 'N0 (i+)', 'N2c', 'Not Reported', 'N3a', 'N1bIII', 'N0 (i-)', 'N1mi', '']",,Diagnosis Tumor Depth,Tumor Depth,TumorDepth,"Numeric value that represents the depth of tumor invasion, measured in millimeters (mm).",False,,,,Diagnosis -Tissue or Organ of Origin,Tissue or Organ of Origin,TissueorOrganofOrigin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Olfactory nerve', 'Overlapping lesion of bladder', 'Anterior floor of mouth', 'Bone marrow', 'Other specified parts of female genital organs', 'Parametrium', 'Overlapping lesion of lung', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Branchial cleft', 'Lower gum', 'Renal pelvis', 'skin NOS', 'Overlapping lesion of accessory sinuses', 'Gastric antrum', 'Overlapping lesion of cervix uteri', 'Nasal cavity', 'Peripheral nerves and autonomic nervous system of thorax', 'Autonomic nervous system NOS', 'Overlapping lesion of nasopharynx', 'Lateral wall of oropharynx', 'Upper-inner quadrant of breast', 'Thymus', 'Posterior mediastinum', 'Anus NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Stomach NOS', 'Broad ligament', 'Paraspinal', 'Cloacogenic zone', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Lateral wall of bladder', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Biliary tract NOS', 'Anterior 2/3 of tongue NOS', 'Testis NOS', 'Overlapping lesion of ill-defined sites', 'Uterine adnexa', 'Fundus uteri', 'Central portion of breast', 'Overlapping lesion of skin', 'Lateral wall of nasopharynx', 'Nipple', 'Overlapping lesion of urinary organs', 'Soft palate NOS', 'Main bronchus', 'Trachea', 'Upper lobe lung', 'Anterior wall of nasopharynx', 'Specified parts of peritoneum', 'Body of penis', 'Tonsillar fossa', 'Overlapping lesion of breast', 'Adrenal gland NOS', 'Hepatic flexure of colon', 'Aortic body and other paraganglia', 'Frontal lobe', 'Pleura NOS', 'Lateral floor of mouth', 'Intrathoracic lymph nodes', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Pylorus', 'Skin of lip NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peripheral nerves and autonomic nervous system of abdomen', 'Waldeyer ring', 'Axillary tail of breast', 'Cervical esophagus', 'Not Reported', 'Round ligament', 'Anterior mediastinum', 'Cecum', 'Cerebrum', 'Cerebellum NOS', 'Ureteric orifice', 'Abdomen NOS', 'Brain NOS', 'Major salivary gland NOS', 'Thyroid gland', 'Overlapping lesion of rectum anus and anal canal', 'Upper-outer quadrant of breast', 'Peritoneum NOS', 'Male genital organs NOS', 'Cranial nerve NOS', 'Gum NOS', 'Ethmoid sinus', 'Subglottis', 'Meninges NOS', 'Nasopharynx NOS', 'Spinal cord', 'Clitoris', 'Labium majus', 'Urachus', 'Duodenum', 'Short bones of upper limb and associated joints', 'Posterior wall of oropharynx', 'Vulva NOS', 'Thorax NOS', 'Temporal lobe', 'Maxillary sinus', 'Middle third of esophagus', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of pancreas', 'Overlapping lesion of tonsil', 'Overlapping lesion of floor of mouth', 'Accessory sinus NOS', 'External lower lip', 'Vagina NOS', 'Parathyroid gland', 'Overlapping lesions of oropharynx', 'Overlapping lesion of esophagus', 'Overlapping lesion of colon', 'Base of tongue NOS', 'Overlapping lesion of vulva', 'Isthmus uteri', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of digestive system', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Ill-defined sites within respiratory system', 'Lower-inner quadrant of breast', 'Fundus of stomach', 'Prostate gland', 'Spinal meninges', 'Supraglottis', 'Bladder neck', 'Connective subcutaneous and other soft tissues of abdomen', 'Mandible', 'Blood', 'Anal canal', 'Overlapping lesion of penis', 'Nervous system NOS', 'Lymph node NOS', 'Overlapping lesion of corpus uteri', 'Retroperitoneum', 'Pharynx NOS', 'Rib sternum clavicle and associated joints', 'Lower-outer quadrant of breast', 'Intrahepatic bile duct', 'Appendix', 'Lymph nodes of multiple regions', 'Occipital lobe', 'Cervix uteri', 'Fallopian tube', 'Endometrium', 'Ventricle NOS', 'Ampulla of Vater', 'Pineal gland', 'Pelvis NOS', 'Skin of scalp and neck', 'Brain stem', 'Islets of Langerhans', 'Endocervix', 'Upper limb NOS', 'Dome of bladder', 'Thoracic esophagus', 'Vertebral column', 'Short bones of lower limb and associated joints', 'Tongue NOS', 'Overlapping lesion of male genital organs', 'Exocervix', 'Splenic flexure of colon', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Upper gum', 'Labium minus', 'Glottis', 'Overlapping lesion of lip', 'Mucosa of lower lip', 'Optic nerve', 'Kidney NOS', 'Pancreatic duct', 'Breast NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Meckel diverticulum', 'Overlapping lesion of biliary tract', 'Overlapping lesion of tongue', 'Larynx NOS', 'Ileum', 'Pancreas NOS', 'Overlapping lesion of stomach', 'Abdominal esophagus', 'Intestinal tract NOS', 'Frontal sinus', 'Cardia NOS', 'Liver', 'Tonsillar pillar', 'Bone of limb NOS', 'Cauda equina', 'Other specified parts of male genital organs', 'Upper respiratory tract NOS', 'unknown primary site', 'Small intestine NOS', 'Upper third of esophagus', 'Connective subcutaneous and other soft tissues of thorax', 'Sigmoid colon', 'Lymph nodes of head face and neck', 'Pyriform sinus', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Lung NOS', 'Border of tongue', 'Tonsil NOS', 'Rectum NOS', 'Parietal lobe', 'Hypopharynx NOS', 'Heart', 'Mouth NOS', 'Hematopoietic system NOS', 'Superior wall of nasopharynx', 'Endocrine gland NOS', 'Craniopharyngeal duct', 'Overlapping lesion of heart mediastinum and pleura', 'Lymph nodes of axilla or arm', 'Head face or neck NOS', 'Medulla of adrenal gland', 'Lymph nodes of inguinal region or leg', 'Female genital tract NOS', 'Glans penis', 'skin of lower limb and hip', 'Body of stomach', 'Reticuloendothelial system NOS', 'Choroid', 'External upper lip', 'Prepuce', 'Posterior wall of nasopharynx', 'Urinary system NOS', 'Conjunctiva', 'Rectosigmoid junction', 'Intra-abdominal lymph nodes', 'Lingual tonsil', 'External lip NOS', 'Parotid gland', 'Bones of skull and face and associated joints', 'Dorsal surface of tongue NOS', 'Lip NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of endocrine glands and related structures', 'Middle ear', 'Bladder NOS', 'Bone NOS', 'Trigone of bladder', 'Gallbladder', 'Descended testis', 'Orbit NOS', 'Descending colon', 'Spleen', 'Retromolar area', 'Ureter', 'Pelvic lymph nodes', 'skin of upper limb and shoulder', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Eye NOS', 'Myometrium', 'Lower third of esophagus', 'Body of pancreas', 'Mediastinum NOS', 'Sublingual gland', 'Anterior surface of epiglottis', 'Hard palate', 'Overlapping lesion of major salivary glands', 'Scrotum NOS', 'Ventral surface of tongue NOS', 'Submandibular gland', 'Oropharynx NOS', 'Lower limb NOS', 'Overlapping lesion of brain', 'Overlapping lesion of larynx', 'Cornea NOS', 'Corpus uteri', 'External ear', 'Commissure of lip', 'unknown', 'Cheek mucosa', 'Overlapping lesion of hypopharynx', 'Pituitary gland', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Ascending colon', 'Epididymis', 'Esophagus NOS', 'Overlapping lesion of other and unspecified parts of mouth', 'Laryngeal cartilage', 'Skin of trunk', 'Transverse colon', 'Penis NOS', 'Ovary', 'Anterior wall of bladder', 'Carotid body', 'Colon NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Jejunum', 'Spermatic cord', 'Long bones of lower limb and associated joints', 'Undescended testis', 'Head of pancreas', 'Vestibule of mouth', 'Middle lobe lung', 'Posterior wall of bladder', 'Overlapping lesion of eye and adnexa', 'Overlapping lesion of palate', 'Overlapping lesion of lip oral cavity and pharynx', 'Cerebral meninges', 'Sphenoid sinus', 'Gastrointestinal tract NOS', 'Uvula', 'Other specified parts of pancreas', 'Uterus NOS', 'Tail of pancreas', 'Acoustic nerve', 'Lacrimal gland', 'Cortex of adrenal gland', 'Palate NOS', 'Extrahepatic bile duct', 'Vallecula', 'Ciliary body', 'Hypopharyngeal aspect of aryepiglottic fold', 'Greater curvature of stomach NOS', 'Overlapping lesion of female genital organs', 'Retina', 'Other ill-defined sites', 'Posterior wall of hypopharynx', 'Urethra', 'Overlapping lesion of small intestine', 'Peripheral nerves and autonomic nervous system of pelvis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Postcricoid region', 'Lower lobe lung', 'Skin of other and unspecified parts of face', 'Mucosa of lip NOS', 'Eyelid', 'Mucosa of upper lip', 'Paraurethral gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Placenta']",,Diagnosis -IRS Group,IRS Group,IRSGroup,"Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['Group IV', 'Group IIc', 'Group III', 'unknown', 'Group II', 'Group IIa', 'Group IIIb', 'Group Ib', 'Group Ia', 'Not Reported', 'Group I', 'Group IIIa', '']",,Diagnosis -Vascular Invasion Present,Vascular Invasion Present,VascularInvasionPresent,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,False,,"['Not Allowed To Collect', 'no', 'unknown', 'Not Reported', 'Yes - Vascular Invasion Present', '']",,Diagnosis -Residual Disease,Residual Disease,ResidualDisease,Text terms to describe the status of a tissue margin following surgical resection.,False,,"['R0', 'unknown', 'RX', 'R1', 'Not Reported', 'R2', '']",,Diagnosis -Gleason Grade Group,Gleason Grade Group,GleasonGradeGroup,"The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Group 2', 'Group 5', 'Group 4', 'Group 3', 'Group 1', '']",,Diagnosis -AJCC Pathologic N,AJCC Pathologic N,AJCCPathologicN,The codes that represent the stage of cancer based on the nodes present (N stage) according to criteria based on multiple editions of the AJCC's Cancer Staging Manual.,False,,"['N2c', 'N3b', 'N0', 'N3', 'N2a', 'N1a', 'N1c', 'N3c', 'unknown', 'N2b', 'N0 (i+)', 'NX', 'N2', 'N1bIV', 'N1', 'N1bII', 'N0 (i-)', 'N3a', 'N1bI', 'N0 (mol-)', 'N1b', 'N0 (mol+)', 'N4', 'Not Reported', 'N1mi', 'N1bIII', '']",,Diagnosis -Synchronous Malignancy,Synchronous Malignancy,SynchronousMalignancy,"A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.",False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,Diagnosis -Greatest Tumor Dimension,Greatest Tumor Dimension,GreatestTumorDimension,Numeric value that represents the measurement of the widest portion of the tumor in centimeters.,False,,,,Diagnosis -Year of Diagnosis,Year of Diagnosis,YearofDiagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,False,,,,Diagnosis -Lymph Node Involved Site,Lymph Node Involved Site,LymphNodeInvolvedSite,The text term used to describe the anatomic site of lymph node involvement.,False,,"['Hilar', 'Splenic', 'NOS', 'Epitrochlear', 'Cervical', 'Axillary', 'Iliac', 'unknown', 'Iliac-external', 'Supraclavicular', 'Iliac-common', 'Paraaortic', 'None', 'Parotid', 'Popliteal', 'Retroperitoneal', 'Inguinal', 'Submandibular', 'Mesenteric', 'Mediastinal', 'Not Reported', 'Occipital', 'Femoral', '']",,Diagnosis -INRG Stage,INRG Stage,INRGStage,"The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).",False,,"['M', 'L2', 'Ms', 'unknown', 'Not Reported', 'L1', '']",,Diagnosis +Metastasis at Diagnosis Site,Metastasis at Diagnosis Site,MetastasisatDiagnosisSite,Text term to identify an anatomic site in which metastatic disease involvement is found.,False,,"['Soft Tissue', 'Cerebrospinal Fluid', 'Brain', 'Mediastinum', 'Ascites', 'Scalp', 'Lymph Node NOS', 'Abdomen', 'Peritoneum', 'Skin', 'Bone Marrow', 'Omentum', 'Pleura', 'Pelvis', 'Colon', 'Adrenal Gland', 'Small Intestine', 'Spinal Cord', 'Ovary', 'Central Nervous System', 'Lung', 'Distant Nodes', 'Bone', 'unknown', 'Peritoneal Cavity', 'Not Reported', 'Inguinal', 'Distant Organ', 'Kidney', 'Groin', 'Lymph Node', 'Axillary', 'Liver', '']",,Diagnosis +AJCC Clinical M,AJCC Clinical M,AJCCClinicalM,Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['M1c', 'M1a', 'M1b', 'M0', 'unknown', 'MX', 'Not Reported', 'M1', 'cM0 (i+)', '']",,Diagnosis +Perineural Invasion Present,Perineural Invasion Present,PerineuralInvasionPresent,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Diagnosis +AJCC Pathologic Stage,AJCC Pathologic Stage,AJCCPathologicStage,"The extent of a cancer, especially whether the disease has spread from the original site to other parts of the body based on AJCC staging criteria.",False,,"['Stage IIA1', 'Stage IVA', 'Stage IIB', 'Stage IB1', 'Stage X', 'Stage IIA2', 'Stage IS', 'Stage 0is', 'Stage IC', 'Stage IV', 'Stage Tis', 'Stage 0', 'Stage IIIB', 'Stage IVB', 'Stage IIIC1', 'Stage IA', 'Stage 0a', 'Stage IB', 'Stage IIA', 'Stage IIIC2', 'Stage IIIC', 'unknown', 'Not Reported', 'Stage IIC1', 'Stage I', 'Stage IA2', 'Stage IB2', 'Stage IIC', 'Stage II', 'Stage IIIA', 'Stage IA1', 'Stage III', 'Stage IVC', '']",,Diagnosis +Lymphatic Invasion Present,Lymphatic Invasion Present,LymphaticInvasionPresent,"A yes/no indicator to ask if small or thin-walled vessel invasion is present, indicating lymphatic involvement",False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Diagnosis Breslow Thickness,Breslow Thickness,BreslowThickness,"The number that describes the distance, in millimeters, between the upper layer of the epidermis and the deepest point of tumor penetration.",False,,,,Diagnosis -AJCC Clinical T,AJCC Clinical T,AJCCClinicalT,Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['T3d', 'T2', 'T1c', 'T4b', 'T1a', 'T1a2', 'T3b', 'T4', 'T1b2', 'Tis (LCIS)', ""Tis (Paget's)"", 'T2a2', 'T2c', 'T2d', 'TX', 'unknown', 'Tis (DCIS)', 'Tis', 'T1b', 'T2a', 'T2a1', 'T4e', 'T4c', 'T3c', 'T4a', 'T3', 'T3a', 'T1', 'T1a1', 'Ta', 'T2b', 'T1mi', 'T4d', 'T1b1', 'T0', 'Not Reported', '']",,Diagnosis -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Diagnosis -Progression or Recurrence,Progression or Recurrence,ProgressionorRecurrence,Yes/No/unknown indicator to identify whether a patient has had a new tumor event after initial treatment.,True,,"['Not Reported', 'Yes - Progression or Recurrence', 'no', 'unknown']",,Diagnosis -ISS Stage,ISS Stage,ISSStage,The multiple myeloma disease stage at diagnosis.,False,,"['unknown', 'II', 'Not Reported', 'I', 'III', '']",,Diagnosis -Perineural Invasion Present,Perineural Invasion Present,PerineuralInvasionPresent,A yes/no indicator to ask if perineural invasion or infiltration of tumor or cancer is present.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,Diagnosis -AJCC Clinical Stage,AJCC Clinical Stage,AJCCClinicalStage,"Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.",False,,"['Stage X', 'Stage IA1', 'Stage IC', 'Stage II', 'Stage 0a', 'Stage IIIC1', 'Stage III', 'Stage IIIA', 'Stage IIA2', 'Stage 0', 'Stage IIA1', 'Stage I', 'Stage IB1', 'unknown', 'Stage IA2', 'Stage Tis', 'Stage IIA', 'Stage IIC', 'Stage IIB', 'Stage IB', 'Stage IIIC2', 'Stage IVA', 'Stage IIIB', 'Stage IVB', 'Stage IIIC', 'Stage 0is', 'Stage IB2', 'Stage IIC1', 'Stage IVC', 'Stage IA', 'Stage IV', 'Not Reported', 'Stage IS', '']",,Diagnosis -Non Nodal Regional Disease,Non Nodal Regional Disease,NonNodalRegionalDisease,The text term used to describe whether the patient had non-nodal regional disease.,False,,"['Present', 'Indeterminate', 'unknown', 'Absent', 'Not Reported', '']",,Diagnosis +Prior Malignancy,Prior Malignancy,PriorMalignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,False,,"['Not Allowed To Collect', 'no', 'unknown', 'Not Reported', 'yes', '']",,Diagnosis +AJCC Clinical Stage,AJCC Clinical Stage,AJCCClinicalStage,"Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer.",False,,"['Stage IIA1', 'Stage IVA', 'Stage IIB', 'Stage IB1', 'Stage X', 'Stage IIA2', 'Stage IS', 'Stage 0is', 'Stage IC', 'Stage IV', 'Stage Tis', 'Stage 0', 'Stage IIIB', 'Stage IVB', 'Stage IIIC1', 'Stage IA', 'Stage 0a', 'Stage IB', 'Stage IIA', 'Stage IIIC2', 'Stage IIIC', 'unknown', 'Not Reported', 'Stage IIC1', 'Stage I', 'Stage IA2', 'Stage IB2', 'Stage IIC', 'Stage II', 'Stage IIIA', 'Stage IA1', 'Stage III', 'Stage IVC', '']",,Diagnosis +Primary Diagnosis,Primary Diagnosis,PrimaryDiagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Bile duct adenocarcinoma', 'Classical Hodgkin lymphoma lymphocyte depletion reticular', 'Gastrin cell tumor malignant', 'Pagetoid reticulosis', 'Mixed pineal tumor', 'Squamous cell carcinoma clear cell type', 'Pancreatic endocrine tumor malignant', 'Carcinoma undifferentiated NOS', 'Bronchiolo-alveolar carcinoma Clara cell and goblet cell type', 'Tumor NOS', 'Malignant lymphoma large B-cell NOS', 'Pituitary carcinoma NOS', 'c-ALL', 'Secondary carcinoma', 'Splenic diffuse red pulp small B-cell lymphoma', 'Carcinoma in situ in a polyp NOS', 'Malignant lymphoma lymphocytic diffuse NOS', 'Medullary osteosarcoma', 'Capillary lymphangioma', 'Malignant melanoma in congenital melanocytic nevus', 'Combined large cell neuroendocrine carcinoma', 'Osteoblastoma malignant', 'Basal cell adenocarcinoma', 'Hodgkin lymphoma nodular sclerosis NOS', 'Transitional carcinoma', 'Renal carcinoma collecting duct type', 'Papillary adenocarcinoma NOS', 'Bile duct adenoma', 'Lobular carcinoma in situ NOS', 'Nevus NOS', 'Classical Hodgkin lymphoma nodular sclerosis grade 1', 'Papillary carcinoma NOS', 'Glioma NOS', 'Mixed adenocarcinoma and epidermoid carcinoma', 'Malignant lymphoma large B-cell diffuse NOS', 'T-cell lymphoma NOS', 'Hepatocarcinoma', 'Pigmented basal cell carcinoma', 'Classical Hodgkin lymphoma lymphocyte-rich', 'Diffuse astrocytoma IDH-mutant', 'Paraganglioma benign', 'Tumor metastatic', 'Liver cell adenoma', 'Renal medullary carcinoma', 'Cervical intraepithelial neoplasia low grade', 'Neoplasm malignant uncertain whether primary or metastatic', 'Neurofibromatosis NOS', 'Unclassified tumor uncertain whether benign or malignant', 'Acute myelomonocytic leukemia', 'Classical Hodgkin lymphoma nodular sclerosis cellular phase', 'Papilloma NOS', 'Familial adenomatous polyposis', 'Malignant lymphoma immunoblastic NOS', 'Intraductal and lobular carcinoma', 'Adenocarcinoma NOS', 'Undifferentiated pleomorphic sarcoma', 'Hodgkin sarcoma', 'Malignant lymphoma NOS', 'Melanoma in situ', 'Rodent ulcer', 'Cervical intraepithelial neoplasia grade III', 'Endometrioid carcinoma NOS', 'Ewing sarcoma', 'Malignant melanoma in Hutchinson melanotic freckle', 'Infiltrating basal cell carcinoma NOS', 'Ependymoma NOS', 'Combined small cell-large carcinoma', 'Papillomatosis NOS', 'Chronic myelomonocytic leukemia Type 1', 'Epithelial tumor malignant', 'Nephroblastoma NOS', 'Adenocarcinoma in situ NOS', 'Adult rhabdomyoma', 'Papillary microcarcinoma', 'Carcinoma in situ NOS', 'Papillary squamous cell carcinoma', 'Epidermoid carcinoma NOS', 'Interstitial cell tumor NOS', 'Melanotic psammomatous MPNST', 'Capillary hemangioma', 'Tubular adenocarcinoma', 'Combined small cell carcinoma', 'Classical Hodgkin lymphoma nodular sclerosis grade 2', 'Adenocarcinoma in situ mucinous', 'Paget disease and infiltrating duct carcinoma of breast', 'Intraductal carcinoma solid type', 'Esophageal squamous intraepithelial neoplasia (dysplasia) low grade', 'Precursor B-cell lymphoblastic leukemia', 'Papillary adenoma NOS', 'Diffuse large B-cell lymphoma NOS', 'Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL)', 'Adenocarcinoma in situ in tubular adenoma', 'Central neurocytoma', 'Tubulopapillary adenocarcinoma', 'Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive', 'Small cell sarcoma', 'Malignant melanoma NOS', 'Lymphoma NOS', 'Chronic myelomonocytic leukemia Type II', 'Melanoameloblastoma', 'Carcinoma in situ in adenomatous polyp', 'Rhabdoid tumor NOS', 'Bronchiolo-alveolar carcinoma non-mucinous', 'Liposarcoma NOS', 'Combined hepatocellular carcinoma and cholangiocarcinoma', 'Carcinoma NOS', 'Eosinophilic leukemia', 'Intraductal carcinoma clinging', 'Non-Hodgkin lymphoma NOS', 'Neurofibroma NOS', 'Bronchiolo-alveolar carcinoma indeterminate type', 'Mixed small cell carcinoma', 'Acute lymphoblastic leukemia precursor cell type', 'Adenocarcinoma in polypoid adenoma', 'Endometrioid adenocarcinoma NOS', 'Intravascular B-cell lymphoma', 'Myeloma NOS', 'Malignant lymphoma small B lymphocytic NOS', 'Hepatocellular adenoma', 'Pro-B ALL', 'Chronic lymphatic leukemia', 'B lymphoblastic leukemia/lymphoma with hyperdiploidy', 'Pigmented nevus NOS', 'Acute myeloid leukemia minimal differentiation', 'Adenocarcinoma of anal ducts', 'Bronchio-alveolar carcinoma mixed mucinous and non-mucinous', 'Dermal nevus', 'Glioma malignant', 'Intraductal tubular-papillary neoplasm low grade', 'Eosinophil adenoma', 'Tubular carcinoma', 'Mixed pancreatic endocrine and exocrine tumor malignant', 'Hodgkin lymphoma NOS', 'Tubulovillous adenoma NOS', 'Malignant melanoma in precancerous melanosis', 'Precursor T-cell lymphoblastic lymphoma', 'Adenocarcinoma intestinal type', 'Sclerosing hepatic carcinoma', 'Adenocarcinoma metastatic NOS', 'Therapy related myeloid neoplasm', 'Malignant lymphoma non-Hodgkin NOS', 'Mixed squamous cell and glandular papilloma', 'Epithelial tumor benign', 'Rhabdosarcoma', 'Composite Hodgkin and non-Hodgkin lymphoma', 'Hodgkin paragranuloma NOS', 'Paget disease and intraductal carcinoma of breast', 'Interstitial cell tumor benign', 'Pancreatobiliary neoplasm non-invasive', 'Carcinoma in a polyp NOS', 'Hepatoid adenocarcinoma', 'Basal cell tumor', 'Pancreatoblastoma', 'Chronic myeloproliferative disease NOS', 'Lymphoblastoma', 'Tumor embolus', 'Tumor benign', 'Inflammatory carcinoma', 'Small cell neuroendocrine carcinoma', 'High-grade serous carcinoma', 'Papillary squamous cell carcinoma in situ', 'B lymphoblastic leukemia/lymphoma NOS', 'Papillary cystadenoma NOS', 'Malignant lymphoma nodular NOS', 'T lymphoblastic leukemia/lymphoma', 'Acute promyelocytic leukemia NOS', 'Precursor B-cell lymphoblastic lymphoma', 'Adenocarcinoma in tubular adenoma', 'Skin appendage carcinoma', 'Eosinophil adenocarcinoma', 'Pancreatobiliary-type carcinoma', 'Acute myeloid leukemia MLL', 'Basal cell carcinoma NOS', 'Adenocarcinoma in situ in adenomatous polyp', 'Gastrin cell tumor', 'Malignant melanoma regressing', 'B cell lymphoma NOS', 'Cementoma NOS', 'Astrocytoma low grade', 'Astrocytoma NOS', 'Intraductal micropapillary carcinoma', 'Hepatocholangiocarcinoma', 'Renal cell carcinoma spindle cell', 'Neoplasm metastatic', 'Basophil adenoma', 'Papillary glioneuronal tumor', 'Endometrioid adenoma NOS', 'Monocytic leukemia NOS', 'Papillary adenocarcinoma follicular variant', 'Prostatic intraepithelial neoplasia grade III', 'B-ALL', 'Glioblastoma', 'B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL)', 'Splenic marginal zone lymphoma NOS', 'Hodgkin disease NOS', 'Classical Hodgkin lymphoma nodular sclerosis NOS', 'Intraductal adenocarcinoma noninfiltrating NOS', 'Melanocytoma NOS', 'Precursor cell lymphoblastic leukemia NOS', 'Non-invasive low grade serous carcinoma', 'Intraductal carcinoma NOS', 'Kaposi sarcoma', 'Malignant lymphoma mixed cell type nodular', 'Malignant lymphoma Hodgkin', 'Small congenital nevus', 'Tumor cells NOS', 'Renal cell carcinoma unclassified', 'Ductal carcinoma in situ NOS', 'Medullary carcinoma NOS', 'Astrocytoma anaplastic', 'Esophageal glandular dysplasia (intraepithelial neoplasia) low grade', 'Adenocarcinoma combined with other types of carcinoma', 'Rhabdomyosarcoma NOS', 'Adenocarcinoma in situ non-mucinous', 'Teratoma NOS', 'Classical Hodgkin lymphoma lymphocyte depletion NOS', 'Adenocarcinoma in a polyp NOS', 'Meningioma malignant', 'Neuroendocrine carcinoma NOS', 'Meningeal melanocytoma', 'Adenocarcinoma of anal glands', 'Neoplasm uncertain whether benign or malignant', 'Acute basophilic leukaemia', 'Undifferentiated uterine sarcoma', 'Gastrinoma malignant', 'Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis', 'B-cell lymphocytic leukemia/small lymphocytic lymphoma', 'Hepatoid carcinoma', 'Typical carcinoid', 'Papillary and follicular carcinoma', 'Rhabdomyoma NOS', 'Melanotic neurofibroma', 'Tubular androblastoma NOS', 'Undifferentiated spindle cell sarcoma', 'Adenocarcinoma diffuse type', 'Combined small cell-adenocarcinoma', 'Non-lymphocytic leukemia NOS', 'Undifferentiated epithelioid sarcoma', 'Papillary carcinoma in situ', 'Intraductal papillary carcinoma', 'Papillary meningioma', 'Carcinoma diffuse type', 'Bronchial adenoma carcinoid', 'Bronchiolar carcinoma', 'Duct cell carcinoma', 'Spindle cell melanoma NOS', 'Infiltrating duct and colloid carcinoma', 'Diffuse astrocytoma IDH-wildtype', 'Myelocytic leukemia NOS', 'Chronic myeloid leukemia NOS', 'Tubulo-papillary adenoma', 'Intraepidermal carcinoma NOS', 'Bile duct cystadenocarcinoma', 'Melanocytoma eyeball', 'Chronic neutrophilic leukemia', 'Mixed tumor NOS', 'Papillotubular adenoma', 'Tumor malignant NOS', 'Gastrinoma NOS', 'Diffuse astrocytoma low grade', 'Undifferentiated high-grade pleomorphic sarcoma', 'Preleukemia', 'Chronic granulocytic leukemia BCR/ABL', 'Duct carcinoma desmoplastic type', 'Duct adenocarcinoma NOS', 'Meningioma anaplastic', 'Undifferentiated sarcoma', 'Ductal carcinoma NOS', 'Lobular adenocarcinoma', 'Paraganglioma NOS', 'Adenocarcinoma pancreatobiliary type', 'Pituitary adenoma NOS', 'Tumorlet benign', 'Epidermoid carcinoma in situ NOS', 'Neoplasm secondary', 'Pleomorphic lobular carcinoma in situ', 'Teratoma malignant NOS', 'Chondrosarcoma grade 2/3', 'Duct carcinoma NOS', 'Malignant melanoma in giant pigmented nevus', 'Rhabdoid sarcoma', 'Malignant melanoma in junctional nevus', 'Endometrioid adenofibroma NOS', 'Tumor cells benign', 'Pleomorphic carcinoma', 'Unclassified tumor malignant uncertain whether primary or metastatic', 'Bronchial adenoma NOS', 'Hodgkin granuloma', 'Acute lymphoblastic leukemia mature B-cell type', 'Neoplasm benign', 'Infiltrating duct and cribriform carcinoma', 'Intraductal tubular-papillary neoplasm high grade', 'Melanotic MPNST', 'Pulmonary adenomatosis', 'Transitional cell carcinoma in situ', 'Malignant lymphoma mixed cell type diffuse', 'Central neuroblastoma', 'Rhabdomyosarcoma with ganglionic differentiation', 'Meningeal melanoma', 'Preleukemic syndrome', 'Pancreatic endocrine tumor nonfunctioning', 'Intraductal tubulopapillary neoplasm', 'Primary amyloidosis', 'Eosinophilic granuloma', 'Not Reported', 'Sarcoma NOS', 'Haemangioblastoma', 'Adenocarcinoma in villous adenoma', 'Precancerous melanosis NOS', 'Myeloid leukemia NOS', 'Adenocarcinoid tumor', 'Squamous cell carcinoma adenoid', 'Large cell carcinoma NOS', 'Malignant lymphoma lymphoblastic NOS', 'Pleomorphic liposarcoma', 'Mixed medullary-follicular carcinoma', 'Gastrointestinal stromal tumor malignant', 'Pancreatic endocrine tumor benign', 'Papillary serous cystadenoma NOS', 'Transitional cell carcinoma', 'Diffuse melanocytosis', 'Carcinoma metastatic NOS', 'Neoplasm malignant', 'Melanotic progonoma', 'Lobular carcinoma NOS', 'Carcinoma in pleomorphic adenoma', 'Esophageal glandular dysplasia (intraepithelial neoplasia) high grade', 'Non-small cell carcinoma', 'Burkitt tumor', 'Basal cell epithelioma', 'Bronchial adenoma cylindroid', 'Secretory carcinoma of breast', 'Chronic monocytic leukemia', 'Melanoma malignant of soft parts', 'Papillotubular adenocarcinoma', 'Chronic lymphocytic leukemia', 'Esophageal intraepithelial neoplasia high grade', 'Undifferentiated leukaemia', 'Adenocarcinoma in situ in a polyp NOS', 'Paget disease mammary', 'Intradermal nevus', 'Tubular androblastoma with lipid storage', 'Papilloma of bladder', 'Liposarcoma well differentiated', 'Acute lymphatic leukemia', 'Acute lymphoid leukemia', 'Unclassified tumor malignant', 'Carcinosarcoma NOS', 'Adenocarcinoma endocervical type', 'Mucous adenocarcinoma', 'Pancreatic microadenoma', 'Papillary transitional cell carcinoma', 'Papillary tumor of the pineal region', 'Serous surface papillary carcinoma', 'Spindle cell carcinoma NOS', 'Meningioma NOS', 'Tubular adenoma NOS', 'Cancer', 'Renal cell adenocarcinoma', 'Bile duct carcinoma', 'Cerebellar liponeurocytoma', 'Classical Hodgkin lymphoma mixed cellularity NOS', 'Paget disease of breast', 'Adenocarcinoma in adenomatous polyp', 'Acute leukemia NOS', 'Pigmented adenoma', 'Medulloblastoma NOS', 'Papillary serous adenocarcinoma', 'Neuroblastoma NOS', 'Hepatocellular carcinoma NOS', 'Bronchiolar adenocarcinoma', 'Bronchiolo-alveolar carcinoma Clara cell', 'Malignant lymphoma lymphocytic NOS', 'Inflammatory adenocarcinoma', 'Micropapillary carcinoma NOS', 'Juvenile myelomonocytic leukemia', 'Multiple myeloma', 'Pancreatic endocrine tumor NOS', 'Intracystic papilloma', 'Intraductal carcinoma and lobular carcinoma in situ', 'Lobular carcinoma noninfiltrating', 'Burkitt-like lymphoma', 'Carcinoma intestinal type', 'Squamous cell carcinoma NOS', 'Tumor cells malignant', 'Chronic myelogenous leukemia BCR-ABL positive', 'Melanotic schwannoma', 'Renal cell carcinoma chromophobe type', 'Bronchiolo-alveolar adenocarcinoma NOS', 'Bronchiolo-alveolar carcinoma goblet cell type', 'Carcinoma anaplastic NOS', 'Splenic lymphoma with villous lymphocytes', 'Melanotic medulloblastoma', 'Splenic B-cell lymphoma/leukemia unclassifiable', 'Chronic myelomonocytic leukemia in transformation', 'Liposarcoma differentiated', 'Splenic marginal zone B-cell lymphoma', 'Acute myeloid leukemia NOS', 'Hodgkin lymphoma mixed cellularity NOS', 'Endometrial sarcoma NOS', 'Acinar cell carcinoma', 'Bile duct cystadenoma', 'Cerebellar sarcoma NOS', 'Tubulocystic renal cell carcinoma', 'Liver cell carcinoma', 'Chronic myeloproliferative disorder', 'Unclassified tumor benign', 'Duct adenoma NOS', 'Pleomorphic lipoma', 'Neurosarcoma', 'Osteosarcoma NOS', 'Papillomatosis glandular', 'Medullary adenocarcinoma', 'Melanotic neuroectodermal tumor', 'Tumor cells uncertain whether benign or malignant', 'Peripheral T-cell lymphoma NOS', 'Acute lymphocytic leukemia', 'Papillary renal cell carcinoma', 'Acute lymphoblastic leukemia-lymphoma NOS', 'Papillary urothelial carcinoma', 'Tumor secondary', 'Pleomorphic lobular carcinoma', 'Lymphocytic leukemia NOS', 'Esophageal squamous intraepithelial neoplasia (dysplasia) high grade', 'Small cell carcinoma NOS', 'Basal cell adenoma', 'Neurofibrosarcoma', 'Paraganglioma malignant', 'Malignant lymphoma diffuse NOS', 'Mixed medullary-papillary carcinoma', 'Myoepithelioma', 'Bronchiolo-alveolar carcinoma NOS', 'Papillary epidermoid carcinoma', 'Malignancy', 'Intraepidermal squamous cell carcinoma Bowen type', 'Chronic myelocytic leukemia NOS', 'Paget disease extramammary', 'Bronchio-alveolar carcinoma mucinous', 'Osteoblastoma NOS', 'Chronic lymphoid leukemia', 'T-cell large granular lymphocytic leukemia', 'Bronchial-associated lymphoid tissue lymphoma', 'Melanocytic nevus', 'Dysplastic nevus', 'Neoplasm NOS', 'Undifferentiated round cell sarcoma', 'Tubulolobular carcinoma', 'Pulmonary artery intimal sarcoma', 'Papillary adenofibroma', 'Interstitial cell tumor malignant', 'Chronic myelomonocytic leukemia NOS', 'Infiltrating duct carcinoma NOS', 'Serous cystadenocarcinoma NOS', 'Malignant lymphoma large cell NOS', 'Intraductal papillary adenocarcinoma with invasion', 'Renal cell carcinoma sarcomatoid', 'Malignant lymphoma mixed cell type follicular', 'Adult T-cell lymphoma', 'Lobular and ductal carcinoma', 'Small cell osteosarcoma', 'Adult T-cell lymphoma/leukemia', 'Mixed tumor malignant NOS', 'Papillary serous cystadenocarcinoma', 'Lymphoblastic leukemia NOS', 'T-cell large granular lymphocytosis', 'Precursor T-cell lymphoblastic leukemia', 'unknown', 'Squamous cell carcinoma in situ NOS', 'Burkitt lymphoma NOS (Includes all variants)', 'Haemangiosarcoma', 'Basophil adenocarcinoma', 'Acute lymphoblastic leukemia NOS', 'Melanoma NOS', 'Burkitt cell leukemia', 'Unclassified tumor borderline malignancy', 'Dermatofibroma NOS', 'Combined small cell-squamous cell carcinoma', 'Intraductal papillary adenocarcinoma NOS', 'Rhabdoid meningioma', 'Lymphatic leukemic NOS', 'Carcinoma in adenomatous polyp', 'Malignant lymphoma lymphocytic nodular NOS', 'Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive', 'Renal cell carcinoma NOS', 'Mammary carcinoma in situ', 'Acute leukemia Burkitt type', 'Chronic granulocytic leukemia NOS', 'Peripheral T-cell lymphoma large cell', 'Mixed adenocarcinoma and squamous cell carcinoma', 'Neuroepithelioma NOS', 'Pro-T ALL', 'Nonpigmented nevus', 'Basophil carcinoma', 'Chondroma NOS', 'Tubular carcinoid', 'Intraductal carcinoma noninfiltrating NOS', 'Chronic leukemia NOS', 'Oat cell carcinoma', 'Ganglioglioma NOS', 'Eosinophil carcinoma', 'Mucosal-associated lymphoid tissue lymphoma', 'Combined/mixed carcinoid and adenocarcinoma', 'Pleomorphic adenoma', 'Pulmonary blastoma', 'Sclerosing hemangioma']",,Diagnosis Gross Tumor Weight,Gross Tumor Weight,GrossTumorWeight,"Numeric value used to describe the gross pathologic tumor weight, measured in grams.",False,,,,Diagnosis -Lymph Nodes Positive,Lymph Nodes Positive,LymphNodesPositive,The number of lymph nodes involved with disease as determined by pathologic examination.,False,,,,Diagnosis -Gleason Grade Tertiary,Gleason Grade Tertiary,GleasonGradeTertiary,The text term used to describe the tertiary pattern as described by the Gleason Grading System.,False,,"['Pattern 4', 'Pattern 5', '']",,Diagnosis +Margin Distance,Margin Distance,MarginDistance,Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.,False,,,,Diagnosis +Tumor Confined to Organ of Origin,Tumor Confined to Organ of Origin,TumorConfinedtoOrganofOrigin,The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Diagnosis +Gleason Grade Group,Gleason Grade Group,GleasonGradeGroup,"The text term used to describe the overall grouping of grades defined by the Gleason grading classification, which is used to determine the aggressiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Group 2', 'Group 5', 'Group 4', 'Group 1', 'Group 3', '']",,Diagnosis +Anaplasia Present,Anaplasia Present,AnaplasiaPresent,Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.,False,,"['Yes - Anaplasia Present', 'Not Reported', 'no', 'unknown', '']",,Diagnosis +IRS Stage,IRS Stage,IRSStage,"The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['3', '2', 'unknown', '1', 'Not Reported', '4', '']",,Diagnosis +AJCC Pathologic T,AJCC Pathologic T,AJCCPathologicT,"Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).",False,,"['T1c', 'Ta', 'T1a1', 'T0', 'T1mi', ""Tis (Paget's)"", 'T2', 'T3d', 'T1a', 'T3c', 'Tis (LCIS)', 'T1a2', 'T4b', 'T2a', 'T1b2', 'T2b', 'Tis (DCIS)', 'T4a', 'T3b', 'T1b', 'T3', 'unknown', 'T2c', 'Not Reported', 'Tis', 'T4e', 'T2d', 'T3a', 'T4', 'T4d', 'T1', 'TX', 'T2a1', 'T1b1', 'T2a2', 'T4c', '']",,Diagnosis +Vascular Invasion Type,Vascular Invasion Type,VascularInvasionType,Text term that represents the type of vascular tumor invasion.,False,,"['Extramural', 'Micro', 'unknown', 'Intramural', 'Macro', 'No Vascular Invasion', 'Not Reported', '']",,Diagnosis Morphology,Morphology,Morphology,"The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data.",True,,,,Diagnosis -Metastasis at Diagnosis Site,Metastasis at Diagnosis Site,MetastasisatDiagnosisSite,Text term to identify an anatomic site in which metastatic disease involvement is found.,False,,"['Liver', 'Omentum', 'Kidney', 'Lymph Node NOS', 'Peritoneum', 'Spinal Cord', 'Brain', 'Colon', 'Abdomen', 'Cerebrospinal Fluid', 'Pleura', 'Axillary', 'unknown', 'Distant Nodes', 'Bone Marrow', 'Bone', 'Central Nervous System', 'Peritoneal Cavity', 'Pelvis', 'Adrenal Gland', 'Scalp', 'Skin', 'Distant Organ', 'Groin', 'Ovary', 'Lymph Node', 'Soft Tissue', 'Lung', 'Inguinal', 'Small Intestine', 'Mediastinum', 'Ascites', 'Not Reported', '']",,Diagnosis -First Symptom Prior to Diagnosis,First Symptom Prior to Diagnosis,FirstSymptomPriortoDiagnosis,Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.,False,,"['Motor or Movement Changes', 'Seizures', 'unknown', 'Visual Changes', 'Headaches', 'Not Reported', 'Altered Mental Status', 'Sensory Changes', '']",,Diagnosis -Cog Rhabdomyosarcoma Risk Group,Cog Rhabdomyosarcoma Risk Group,CogRhabdomyosarcomaRiskGroup,"Text term used to describe the classification of rhabdomyosarcoma, as defined by the Children's Oncology Group (COG).",False,,"['High Risk', 'Intermediate Risk', 'unknown', 'Low Risk', 'Not Reported', '']",,Diagnosis -AJCC Pathologic T,AJCC Pathologic T,AJCCPathologicT,"Code of pathological T (primary tumor) to define the size or contiguous extension of the primary tumor (T), using staging criteria from the American Joint Committee on Cancer (AJCC).",False,,"['T3d', 'T2', 'T1c', 'T4b', 'T1a', 'T1a2', 'T3b', 'T4', 'T1b2', 'Tis (LCIS)', ""Tis (Paget's)"", 'T2a2', 'T2c', 'T2d', 'TX', 'unknown', 'Tis (DCIS)', 'Tis', 'T1b', 'T2a', 'T2a1', 'T4e', 'T4c', 'T3c', 'T4a', 'T3', 'T3a', 'T1', 'T1a1', 'Ta', 'T2b', 'T1mi', 'T4d', 'T1b1', 'T0', 'Not Reported', '']",,Diagnosis -Supratentorial Localization,Supratentorial Localization,SupratentorialLocalization,Text term to specify the location of the supratentorial tumor.,False,,"['Deep Gray', 'White Matter', 'Cerebral Cortex', 'unknown', 'Spinal Cord', 'Not Reported', '']",,Diagnosis -Days to Diagnosis,Days to Diagnosis,DaystoDiagnosis,Number of days between the date used for index and the date the patient was diagnosed with the malignant disease. If not applicable please enter 'Not Applicable',False,,,,Diagnosis -Pregnant at Diagnosis,Pregnant at Diagnosis,PregnantatDiagnosis,The text term used to indicate whether the patient was pregnant at the time they were diagnosed.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,Diagnosis -INPC Grade,INPC Grade,INPCGrade,"Text term used to describe the classification of neuroblastic differentiation within neuroblastoma tumors, as defined by the International Neuroblastoma Pathology Classification (INPC).",False,,"['Poorly Differentiated', 'Undifferentiated', 'unknown', 'Differentiating', 'Not Reported', '']",,Diagnosis -Medulloblastoma Molecular Classification,Medulloblastoma Molecular Classification,MedulloblastomaMolecularClassification,The text term used to describe the classification of medulloblastoma tumors based on molecular features.,False,,"['Not Determined', 'WNT-Activated', 'Non-WNT/non-SHH Activated', 'unknown', 'Not Reported', 'SHH-Activated', '']",,Diagnosis -Prior Malignancy,Prior Malignancy,PriorMalignancy,The yes/no/unknown indicator used to describe the patient's history of prior cancer diagnosis.,False,,"['Not Allowed To Collect', 'no', 'unknown', 'Not Reported', 'yes', '']",,Diagnosis -Ovarian Surface Involvement,Ovarian Surface Involvement,OvarianSurfaceInvolvement,The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.,False,,"['Present', 'Indeterminate', 'unknown', 'Absent', 'Not Reported', '']",,Diagnosis -Primary Gleason Grade,Primary Gleason Grade,PrimaryGleasonGrade,"The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 4', 'Pattern 5', 'Pattern 2', 'Pattern 1', 'Pattern 3', '']",,Diagnosis -Anaplasia Present Type,Anaplasia Present Type,AnaplasiaPresentType,"The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.",False,,"['Present', 'Diffuse', 'unknown', 'Absent', 'Sclerosis', 'Equivocal', 'Focal', 'Not Reported', '']",,Diagnosis -Metastasis at Diagnosis,Metastasis at Diagnosis,MetastasisatDiagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,False,,"['Regional Metastasis', 'Distant Metastasis', 'unknown', 'No Metastasis', 'Metastasis NOS', 'Not Reported', '']",,Diagnosis -Primary Diagnosis,Primary Diagnosis,PrimaryDiagnosis,"Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Lobular carcinoma NOS', 'Infiltrating duct and colloid carcinoma', 'Central neurocytoma', 'Inflammatory carcinoma', 'Neuroendocrine carcinoma NOS', 'Intraductal carcinoma solid type', 'Non-invasive low grade serous carcinoma', 'Melanocytoma eyeball', 'Undifferentiated high-grade pleomorphic sarcoma', 'Malignant melanoma regressing', 'Adenocarcinoma in villous adenoma', 'Esophageal glandular dysplasia (intraepithelial neoplasia) low grade', 'Central neuroblastoma', 'Monocytic leukemia NOS', 'Multiple myeloma', 'Rhabdoid tumor NOS', 'Neurofibroma NOS', 'Infiltrating duct and cribriform carcinoma', 'Papillotubular adenocarcinoma', 'Non-lymphocytic leukemia NOS', 'Intravascular B-cell lymphoma', 'Osteoblastoma malignant', 'Combined small cell-squamous cell carcinoma', 'Tumor NOS', 'Small cell sarcoma', 'Bile duct cystadenocarcinoma', 'Oat cell carcinoma', 'Gastrointestinal stromal tumor malignant', 'Bronchial adenoma NOS', 'Combined small cell carcinoma', 'Hepatocellular adenoma', 'Secretory carcinoma of breast', 'Unclassified tumor uncertain whether benign or malignant', 'Infiltrating basal cell carcinoma NOS', 'Teratoma malignant NOS', 'Intraductal carcinoma and lobular carcinoma in situ', 'Basophil adenocarcinoma', 'Carcinoma in pleomorphic adenoma', 'Adenocarcinoma in situ in a polyp NOS', 'Epithelial tumor benign', 'Acute promyelocytic leukemia NOS', 'Tumor cells NOS', 'Meningioma anaplastic', 'Small cell neuroendocrine carcinoma', 'Adenocarcinoma diffuse type', 'Bronchiolo-alveolar carcinoma goblet cell type', 'Esophageal squamous intraepithelial neoplasia (dysplasia) high grade', 'Diffuse melanocytosis', 'Bile duct adenoma', 'Duct adenocarcinoma NOS', 'Intraductal tubulopapillary neoplasm', 'Acute lymphoblastic leukemia precursor cell type', 'Chronic granulocytic leukemia BCR/ABL', 'Diffuse large B-cell lymphoma NOS', 'Bronchial-associated lymphoid tissue lymphoma', 'T-cell large granular lymphocytosis', 'Hodgkin paragranuloma NOS', 'Splenic marginal zone lymphoma NOS', 'Myelocytic leukemia NOS', 'Ganglioglioma NOS', 'Pro-B ALL', 'Undifferentiated sarcoma', 'Nephroblastoma NOS', 'Melanoma malignant of soft parts', 'Liposarcoma NOS', 'Malignant lymphoma lymphocytic diffuse NOS', 'Sclerosing hemangioma', 'Kaposi sarcoma', 'Precursor cell lymphoblastic leukemia NOS', 'Chronic myelomonocytic leukemia NOS', 'Interstitial cell tumor benign', 'Carcinoma NOS', 'Mixed tumor NOS', 'Basophil carcinoma', 'Liver cell adenoma', 'B-ALL', 'Papillary squamous cell carcinoma', 'Papillary serous adenocarcinoma', 'Tubulocystic renal cell carcinoma', 'Undifferentiated epithelioid sarcoma', 'Rodent ulcer', 'Diffuse astrocytoma low grade', 'Acute myeloid leukemia MLL', 'Not Reported', 'Bronchiolar carcinoma', 'Pancreatic endocrine tumor benign', 'Malignant lymphoma lymphoblastic NOS', 'High-grade serous carcinoma', 'Mixed adenocarcinoma and squamous cell carcinoma', 'Chondrosarcoma grade 2/3', 'Liver cell carcinoma', 'Squamous cell carcinoma clear cell type', 'Malignant lymphoma mixed cell type follicular', 'Papilloma of bladder', 'Pancreatoblastoma', 'Precursor B-cell lymphoblastic lymphoma', 'Pancreatobiliary neoplasm non-invasive', 'Melanoameloblastoma', 'Hodgkin lymphoma NOS', 'Pituitary carcinoma NOS', 'Intraductal tubular-papillary neoplasm low grade', 'Chronic lymphatic leukemia', 'Haemangiosarcoma', 'Interstitial cell tumor NOS', 'Papillary renal cell carcinoma', 'Squamous cell carcinoma adenoid', 'Transitional cell carcinoma in situ', 'Precursor T-cell lymphoblastic leukemia', 'Diffuse astrocytoma IDH-wildtype', 'Glioma NOS', 'Melanotic medulloblastoma', 'Combined small cell-adenocarcinoma', 'Adenocarcinoma in adenomatous polyp', 'Carcinoma in adenomatous polyp', 'Hepatoid adenocarcinoma', 'Cerebellar liponeurocytoma', 'Preleukemic syndrome', 'Typical carcinoid', 'Mixed squamous cell and glandular papilloma', 'Pulmonary blastoma', 'Meningioma NOS', 'Hodgkin lymphoma mixed cellularity NOS', 'Malignant lymphoma lymphocytic nodular NOS', 'Rhabdomyoma NOS', 'Neuroepithelioma NOS', 'Astrocytoma low grade', 'Chronic lymphoid leukemia', 'Skin appendage carcinoma', 'Gastrinoma NOS', 'Neoplasm metastatic', 'Tumor cells benign', 'Acute lymphoid leukemia', 'Bile duct carcinoma', 'Precancerous melanosis NOS', 'Intraductal carcinoma clinging', 'Pleomorphic lipoma', 'Papilloma NOS', 'Carcinoma metastatic NOS', 'Neuroblastoma NOS', 'B cell lymphoma NOS', 'Bronchiolo-alveolar adenocarcinoma NOS', 'Adenocarcinoid tumor', 'Tubulovillous adenoma NOS', 'Chronic granulocytic leukemia Philadelphia chromosome (Ph1) positive', 'Adult T-cell lymphoma', 'T-cell large granular lymphocytic leukemia', 'Spindle cell melanoma NOS', 'Combined hepatocellular carcinoma and cholangiocarcinoma', 'Endometrioid adenofibroma NOS', 'Unclassified tumor malignant uncertain whether primary or metastatic', 'Myoepithelioma', 'Chronic lymphocytic leukemia B-cell type (includes all variants of BCLL)', 'Mixed adenocarcinoma and epidermoid carcinoma', 'Splenic diffuse red pulp small B-cell lymphoma', 'Eosinophilic leukemia', 'Esophageal squamous intraepithelial neoplasia (dysplasia) low grade', 'Pulmonary artery intimal sarcoma', 'Lobular adenocarcinoma', 'Carcinosarcoma NOS', 'Tumor cells malignant', 'Hodgkin sarcoma', 'Pulmonary adenomatosis', 'Pancreatobiliary-type carcinoma', 'Peripheral T-cell lymphoma NOS', 'Adenocarcinoma in polypoid adenoma', 'Sclerosing hepatic carcinoma', 'Haemangioblastoma', 'Tubular adenocarcinoma', 'Gastrin cell tumor malignant', 'Chronic lymphocytic leukemia', 'Lobular carcinoma in situ NOS', 'Pigmented adenoma', 'Squamous cell carcinoma NOS', 'Osteoblastoma NOS', 'Rhabdomyosarcoma NOS', 'Rhabdosarcoma', 'Papillary carcinoma in situ', 'Capillary hemangioma', 'Intraepidermal squamous cell carcinoma Bowen type', 'Paraganglioma malignant', 'Tubular carcinoid', 'Bile duct adenocarcinoma', 'Malignant melanoma in precancerous melanosis', 'Lymphatic leukemic NOS', 'Rhabdomyosarcoma with ganglionic differentiation', 'Infiltrating duct carcinoma NOS', 'Adenocarcinoma in situ non-mucinous', 'Acute lymphoblastic leukemia-lymphoma NOS', 'Chronic myelocytic leukemia NOS', 'Tumor malignant NOS', 'Epithelial tumor malignant', 'Neoplasm malignant', 'Carcinoma in situ NOS', 'Lobular and ductal carcinoma', 'Tubular adenoma NOS', 'Tubular carcinoma', 'Malignant lymphoma lymphocytic NOS', 'Bronchial adenoma carcinoid', 'Neoplasm uncertain whether benign or malignant', 'Acute lymphatic leukemia', 'Malignant lymphoma nodular NOS', 'Preleukemia', 'Classical Hodgkin lymphoma nodular sclerosis NOS', 'Splenic B-cell lymphoma/leukemia unclassifiable', 'Serous cystadenocarcinoma NOS', 'Dysplastic nevus', 'Malignant melanoma NOS', 'Papillary glioneuronal tumor', 'Renal cell carcinoma spindle cell', 'Pigmented basal cell carcinoma', 'Tumor secondary', 'B lymphoblastic leukemia/lymphoma with hyperdiploidy', 'Pleomorphic carcinoma', 'Malignant melanoma in congenital melanocytic nevus', 'Cerebellar sarcoma NOS', 'Myeloid leukemia NOS', 'Neurofibromatosis NOS', 'Bronchio-alveolar carcinoma mixed mucinous and non-mucinous', 'Eosinophil carcinoma', 'Carcinoma undifferentiated NOS', 'Bronchiolo-alveolar carcinoma Clara cell and goblet cell type', 'Combined large cell neuroendocrine carcinoma', 'Neoplasm benign', 'Hodgkin lymphoma nodular sclerosis NOS', 'Intraductal carcinoma noninfiltrating NOS', 'Undifferentiated uterine sarcoma', 'Adenocarcinoma metastatic NOS', 'B lymphoblastic leukemia/lymphoma with hypodiploidy (Hypodiploid ALL)', 'Liposarcoma differentiated', 'Adenocarcinoma in tubular adenoma', 'Adult rhabdomyoma', 'Intraductal papillary adenocarcinoma NOS', 'Adenocarcinoma of anal glands', 'Renal cell carcinoma sarcomatoid', 'Malignant lymphoma non-Hodgkin NOS', 'Papillary serous cystadenocarcinoma', 'Small cell osteosarcoma', 'Chronic leukemia NOS', 'Duct cell carcinoma', 'Tubular androblastoma with lipid storage', 'Adenocarcinoma in situ in adenomatous polyp', 'Pleomorphic adenoma', 'Papillary adenocarcinoma follicular variant', 'Eosinophilic granuloma', 'Acute myeloid leukemia NOS', 'Cancer', 'Endometrioid adenoma NOS', 'Papillary microcarcinoma', 'Micropapillary carcinoma NOS', 'Renal carcinoma collecting duct type', 'Epidermoid carcinoma in situ NOS', 'Classical Hodgkin lymphoma nodular sclerosis grade 2', 'Esophageal glandular dysplasia (intraepithelial neoplasia) high grade', 'Malignant lymphoma mixed cell type diffuse', 'Unclassified tumor benign', 'Therapy related myeloid neoplasm', 'Adenocarcinoma endocervical type', 'Sarcoma NOS', 'Lymphocytic leukemia NOS', 'Burkitt-like lymphoma', 'Melanotic progonoma', 'Peripheral T-cell lymphoma large cell', 'Paget disease and intraductal carcinoma of breast', 'Paget disease of breast', 'Intraductal tubular-papillary neoplasm high grade', 'Basal cell tumor', 'Adenocarcinoma of anal ducts', 'Astrocytoma NOS', 'Malignant melanoma in giant pigmented nevus', 'Papillary adenoma NOS', 'Malignant lymphoma mixed cell type nodular', 'Intraductal papillary adenocarcinoma with invasion', 'Glioblastoma', 'Dermatofibroma NOS', 'Pancreatic microadenoma', 'Malignant lymphoma small B lymphocytic NOS', 'Cervical intraepithelial neoplasia low grade', 'Bronchiolo-alveolar carcinoma non-mucinous', 'Dermal nevus', 'Papillary carcinoma NOS', 'Adenocarcinoma in situ NOS', 'Papillary squamous cell carcinoma in situ', 'Paget disease extramammary', 'Chronic myelomonocytic leukemia Type 1', 'Malignant lymphoma large B-cell NOS', 'Chronic myeloproliferative disorder', 'Bronchial adenoma cylindroid', 'Mixed medullary-papillary carcinoma', 'Juvenile myelomonocytic leukemia', 'Tubular androblastoma NOS', 'Carcinoma in situ in adenomatous polyp', 'Mixed tumor malignant NOS', 'Adult T-cell lymphoma/leukemia', 'Malignant lymphoma Hodgkin', 'Capillary lymphangioma', 'Papillomatosis NOS', 'Prostatic intraepithelial neoplasia grade III', 'Malignant lymphoma NOS', 'Tubulo-papillary adenoma', 'Carcinoma in a polyp NOS', 'Astrocytoma anaplastic', 'Papillotubular adenoma', 'Papillary adenocarcinoma NOS', 'Medullary osteosarcoma', 'Bile duct cystadenoma', 'c-ALL', 'Teratoma NOS', 'Acute myeloid leukemia minimal differentiation', 'Bronchio-alveolar carcinoma mucinous', 'Melanotic schwannoma', 'Mixed pancreatic endocrine and exocrine tumor malignant', 'Precursor T-cell lymphoblastic lymphoma', 'Interstitial cell tumor malignant', 'Paraganglioma benign', 'Mixed pineal tumor', 'Chronic myeloproliferative disease NOS', 'Eosinophil adenocarcinoma', 'Medullary adenocarcinoma', 'Hodgkin granuloma', 'Intracystic papilloma', 'Burkitt tumor', 'Non-small cell carcinoma', 'B lymphoblastic leukemia/lymphoma NOS', 'Medulloblastoma NOS', 'Liposarcoma well differentiated', 'Tumor embolus', 'Acute leukemia NOS', 'Chondroma NOS', 'Melanotic neuroectodermal tumor', 'Classical Hodgkin lymphoma lymphocyte depletion diffuse fibrosis', 'Intraductal and lobular carcinoma', 'Acute leukemia Burkitt type', 'Papillary cystadenoma NOS', 'T lymphoblastic leukemia/lymphoma', 'Carcinoma intestinal type', 'Rhabdoid sarcoma', 'Small cell carcinoma NOS', 'Acute lymphocytic leukemia', 'Duct adenoma NOS', 'Malignant lymphoma large B-cell diffuse NOS', 'Precursor B-cell lymphoblastic leukemia', 'Splenic marginal zone B-cell lymphoma', 'Undifferentiated leukaemia', 'Eosinophil adenoma', 'Neoplasm NOS', 'Classical Hodgkin lymphoma mixed cellularity NOS', 'Bronchiolo-alveolar carcinoma NOS', 'Secondary carcinoma', 'Tumor cells uncertain whether benign or malignant', 'Melanoma in situ', 'Chronic granulocytic leukemia NOS', 'Tumorlet benign', 'Melanotic psammomatous MPNST', 'Lymphoblastic leukemia NOS', 'Intraductal papillary carcinoma', 'Classical Hodgkin lymphoma lymphocyte depletion NOS', 'Squamous cell carcinoma in situ NOS', 'Lymphoma NOS', 'Transitional cell carcinoma', 'Intraductal micropapillary carcinoma', 'Chronic monocytic leukemia', 'Pleomorphic lobular carcinoma', 'Basal cell epithelioma', 'Bronchiolo-alveolar carcinoma indeterminate type', 'Classical Hodgkin lymphoma nodular sclerosis grade 1', 'Malignant lymphoma diffuse NOS', 'Endometrioid carcinoma NOS', 'Renal cell carcinoma unclassified', 'Paget disease mammary', 'Intraepidermal carcinoma NOS', 'Mucosal-associated lymphoid tissue lymphoma', 'Malignant melanoma in Hutchinson melanotic freckle', 'Ductal carcinoma NOS', 'Papillomatosis glandular', 'Neurosarcoma', 'Carcinoma anaplastic NOS', 'Cementoma NOS', 'Lobular carcinoma noninfiltrating', 'Bronchiolar adenocarcinoma', 'Paget disease and infiltrating duct carcinoma of breast', 'Pancreatic endocrine tumor malignant', 'Primary amyloidosis', 'Acute lymphoblastic leukemia mature B-cell type', 'Transitional carcinoma', 'Malignant melanoma in junctional nevus', 'Papillary urothelial carcinoma', 'Pleomorphic liposarcoma', 'Undifferentiated spindle cell sarcoma', 'Duct carcinoma desmoplastic type', 'Inflammatory adenocarcinoma', 'Unclassified tumor borderline malignancy', 'Familial adenomatous polyposis', 'Diffuse astrocytoma IDH-mutant', 'Tumor benign', 'Melanocytoma NOS', 'Mucous adenocarcinoma', 'Chronic myelomonocytic leukemia in transformation', 'Mammary carcinoma in situ', 'Hepatocellular carcinoma NOS', 'Malignancy', 'Bronchiolo-alveolar carcinoma Clara cell', 'Chronic myelogenous leukemia Philadelphia chromosome (Ph 1) positive', 'Classical Hodgkin lymphoma nodular sclerosis cellular phase', 'Burkitt cell leukemia', 'Hepatocarcinoma', 'Pro-T ALL', 'Combined/mixed carcinoid and adenocarcinoma', 'T-cell lymphoma NOS', 'Intradermal nevus', 'Serous surface papillary carcinoma', 'Meningeal melanocytoma', 'Combined small cell-large carcinoma', 'Pagetoid reticulosis', 'Basophil adenoma', 'Burkitt lymphoma NOS (Includes all variants)', 'Splenic lymphoma with villous lymphocytes', 'Acute lymphoblastic leukemia NOS', 'Malignant lymphoma large cell NOS', 'Spindle cell carcinoma NOS', 'Epidermoid carcinoma NOS', 'Glioma malignant', 'Basal cell adenoma', 'Pancreatic endocrine tumor nonfunctioning', 'Chronic myelomonocytic leukemia Type II', 'Tubulolobular carcinoma', 'Basal cell carcinoma NOS', 'Duct carcinoma NOS', 'Cervical intraepithelial neoplasia grade III', 'Hepatocholangiocarcinoma', 'Tubulopapillary adenocarcinoma', 'Neoplasm malignant uncertain whether primary or metastatic', 'unknown', 'Pituitary adenoma NOS', 'Papillary adenofibroma', 'B-cell lymphocytic leukemia/small lymphocytic lymphoma', 'Adenocarcinoma intestinal type', 'Medullary carcinoma NOS', 'Pancreatic endocrine tumor NOS', 'Meningioma malignant', 'Intraductal adenocarcinoma noninfiltrating NOS', 'Papillary meningioma', 'Renal cell carcinoma chromophobe type', 'Lymphoblastoma', 'Tumor metastatic', 'Osteosarcoma NOS', 'Papillary transitional cell carcinoma', 'Adenocarcinoma combined with other types of carcinoma', 'Melanoma NOS', 'Neoplasm secondary', 'Melanotic MPNST', 'Melanotic neurofibroma', 'Carcinoma in situ in a polyp NOS', 'Chronic neutrophilic leukemia', 'Adenocarcinoma NOS', 'Chronic myeloid leukemia NOS', 'Hepatoid carcinoma', 'Adenocarcinoma in a polyp NOS', 'Mixed medullary-follicular carcinoma', 'Paraganglioma NOS', 'Malignant lymphoma immunoblastic NOS', 'Papillary epidermoid carcinoma', 'Classical Hodgkin lymphoma lymphocyte depletion reticular', 'Adenocarcinoma in situ mucinous', 'Chronic myelogenous leukemia BCR-ABL positive', 'Renal medullary carcinoma', 'Myeloma NOS', 'Renal cell adenocarcinoma', 'Papillary and follicular carcinoma', 'Papillary serous cystadenoma NOS', 'Mixed small cell carcinoma', 'Non-Hodgkin lymphoma NOS', 'Composite Hodgkin and non-Hodgkin lymphoma', 'Melanocytic nevus', 'Nevus NOS', 'Undifferentiated pleomorphic sarcoma', 'Neurofibrosarcoma', 'Carcinoma diffuse type', 'Ewing sarcoma', 'Unclassified tumor malignant', 'Renal cell carcinoma NOS', 'Meningeal melanoma', 'Endometrioid adenocarcinoma NOS', 'Esophageal intraepithelial neoplasia high grade', 'Classical Hodgkin lymphoma lymphocyte-rich', 'Undifferentiated round cell sarcoma', 'Endometrial sarcoma NOS', 'Rhabdoid meningioma', 'Adenocarcinoma pancreatobiliary type', 'Ductal carcinoma in situ NOS', 'Small congenital nevus', 'Papillary tumor of the pineal region', 'Gastrin cell tumor', 'Intraductal carcinoma NOS', 'Acute basophilic leukaemia', 'Adenocarcinoma in situ in tubular adenoma', 'Ependymoma NOS', 'Large cell carcinoma NOS', 'Acute myelomonocytic leukemia', 'Pleomorphic lobular carcinoma in situ', 'Nonpigmented nevus', 'Gastrinoma malignant', 'Hodgkin disease NOS', 'Pigmented nevus NOS', 'Basal cell adenocarcinoma', 'Acinar cell carcinoma']",,Diagnosis -Tumor Focality,Tumor Focality,TumorFocality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,False,,"['Not Reported', 'Unifocal', 'Multifocal', 'unknown', '']",,Diagnosis -Tumor Largest Dimension Diameter,Tumor Largest Dimension Diameter,TumorLargestDimensionDiameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",False,,,,Diagnosis -International Prognostic Index,International Prognostic Index,InternationalPrognosticIndex,"The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.",False,,"['Low-Intermediate Risk', 'High-Intermediate Risk', 'High Risk', 'Low Risk', '']",,Diagnosis -Tumor Confined to Organ of Origin,Tumor Confined to Organ of Origin,TumorConfinedtoOrganofOrigin,The yes/no/unknown indicator used to describe whether the tumor is confined to the organ where it originated and did not spread to a proximal or distant location within the body.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,Diagnosis -AJCC Clinical M,AJCC Clinical M,AJCCClinicalM,Extent of the distant metastasis for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['M1c', 'M1', 'MX', 'cM0 (i+)', 'M1a', 'unknown', 'Not Reported', 'M0', 'M1b', '']",,Diagnosis -Vascular Invasion Type,Vascular Invasion Type,VascularInvasionType,Text term that represents the type of vascular tumor invasion.,False,,"['Extramural', 'Macro', 'unknown', 'No Vascular Invasion', 'Not Reported', 'Intramural', 'Micro', '']",,Diagnosis -AJCC Pathologic M,AJCC Pathologic M,AJCCPathologicM,"Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).",False,,"['M1c', 'M1', 'MX', 'cM0 (i+)', 'M1a', 'unknown', 'Not Reported', 'M0', 'M1b', '']",,Diagnosis -IGCCCG Stage,IGCCCG Stage,IGCCCGStage,"The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.",False,,"['Intermediate Prognosis', 'Good Prognosis', 'Poor Prognosis', 'unknown', 'Not Reported', '']",,Diagnosis +Supratentorial Localization,Supratentorial Localization,SupratentorialLocalization,Text term to specify the location of the supratentorial tumor.,False,,"['Spinal Cord', 'Cerebral Cortex', 'unknown', 'White Matter', 'Deep Gray', 'Not Reported', '']",,Diagnosis +IRS Group,IRS Group,IRSGroup,"Text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['Group II', 'Group IIc', 'Group III', 'Group Ib', 'Group IIIb', 'unknown', 'Group I', 'Group IV', 'Group IIIa', 'Not Reported', 'Group Ia', 'Group IIa', '']",,Diagnosis +Primary Gleason Grade,Primary Gleason Grade,PrimaryGleasonGrade,"The text term used to describe the primary Gleason score, which describes the pattern of cells making up the largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 1', 'Pattern 4', 'Pattern 5', 'Pattern 2', 'Pattern 3', '']",,Diagnosis +AJCC Clinical T,AJCC Clinical T,AJCCClinicalT,Extent of the primary cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['T1c', 'Ta', 'T1a1', 'T0', 'T1mi', ""Tis (Paget's)"", 'T2', 'T3d', 'T1a', 'T3c', 'Tis (LCIS)', 'T1a2', 'T4b', 'T2a', 'T1b2', 'T2b', 'Tis (DCIS)', 'T4a', 'T3b', 'T1b', 'T3', 'unknown', 'T2c', 'Not Reported', 'Tis', 'T4e', 'T2d', 'T3a', 'T4', 'T4d', 'T1', 'TX', 'T2a1', 'T1b1', 'T2a2', 'T4c', '']",,Diagnosis +Anaplasia Present Type,Anaplasia Present Type,AnaplasiaPresentType,"The text term used to describe the morphologic findings indicating the presence of a malignant cellular infiltrate characterized by the presence of large pleomorphic cells, necrosis, and high mitotic activity in a tissue sample.",False,,"['Diffuse', 'unknown', 'Equivocal', 'Absent', 'Present', 'Sclerosis', 'Not Reported', 'Focal', '']",,Diagnosis +Laterality,Laterality,Laterality,"For tumors in paired organs, designates the side on which the cancer originates.",False,,"['Right', 'Midline', 'Bilateral', 'unknown', 'Unilateral', 'Not Reported', 'Left', '']",,Diagnosis +Non Nodal Tumor Deposits,Non Nodal Tumor Deposits,NonNodalTumorDeposits,The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Diagnosis +WHO CNS Grade,WHO CNS Grade,WHOCNSGrade,WHO CNS Grade,False,,"['Grade I', 'Grade III', 'Grade Not Assigned', 'unknown', 'Grade IV', 'Grade II', 'Not Reported', '']",,Diagnosis +Mitotic Count,Mitotic Count,MitoticCount,"The number of mitoses identified under the microscope in tumors. The method of counting varies, according to the specific tumor examined. Usually, the mitotic count is determined based on the number of mitoses per high power field (40X) or 10 high power fields.",False,,,,Diagnosis +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Diagnosis +AJCC Clinical N,AJCC Clinical N,AJCCClinicalN,Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['N2b', 'N1b', 'N0', 'N1c', 'N1', 'N1bI', 'N1bIV', 'NX', 'N2', 'N3', 'N2a', 'N0 (mol+)', 'N3b', 'N3c', 'N0 (mol-)', 'N1a', 'N1bII', 'unknown', 'N4', 'N0 (i+)', 'N2c', 'Not Reported', 'N3a', 'N1bIII', 'N0 (i-)', 'N1mi', '']",,Diagnosis +Margins Involved Site,Margins Involved Site,MarginsInvolvedSite,The text term used to describe the anatomic sites that were involved in the survival margins.,False,,"['Gerota Fascia', 'Renal', 'Renal Sinus', 'Renal Capsule', 'Perinephric Fat', 'Renal Vein', 'Parenchyma', 'Ureter', '']",,Diagnosis +Peritoneal Fluid Cytological Status,Peritoneal Fluid Cytological Status,PeritonealFluidCytologicalStatus,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,False,,"['Unsatisfactory', 'Malignant', 'unknown', 'Non-Malignant', 'Atypical', 'Not Reported', '']",,Diagnosis +Metastasis at Diagnosis,Metastasis at Diagnosis,MetastasisatDiagnosis,The text term used to describe the extent of metastatic disease present at diagnosis.,False,,"['No Metastasis', 'unknown', 'Regional Metastasis', 'Metastasis NOS', 'Distant Metastasis', 'Not Reported', '']",,Diagnosis +Classification of Tumor,Classification of Tumor,ClassificationofTumor,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,False,,"['Not Allowed To Collect', 'Metastasis', 'Recurrence', 'unknown', 'Other', 'Not Reported', 'Primary', '']",,Diagnosis +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Diagnosis +Ovarian Specimen Status,Ovarian Specimen Status,OvarianSpecimenStatus,The text term used to describe the physical condition of the involved ovary.,False,,"['Ovarian Capsule Fragmented', 'Ovarian Capsule Ruptured', 'unknown', 'Ovarian Capsule Intact', 'Not Reported', '']",,Diagnosis +IGCCCG Stage,IGCCCG Stage,IGCCCGStage,"The text term used to describe the International Germ Cell Cancer Collaborative Group (IGCCCG), a grouping used to further classify metastatic testicular tumors.",False,,"['Intermediate Prognosis', 'unknown', 'Good Prognosis', 'Not Reported', 'Poor Prognosis', '']",,Diagnosis Days to Last Follow up,Days to Last Follow up,DaystoLastFollowup,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'",True,,,,Diagnosis Prior Treatment,Prior Treatment,PriorTreatment,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected.,False,,"['Not Allowed To Collect', 'no', 'unknown', 'Not Reported', 'yes', '']",,Diagnosis +Ovarian Surface Involvement,Ovarian Surface Involvement,OvarianSurfaceInvolvement,The text term that describes whether the surface tissue (outer boundary) of the ovary shows evidence of involvement or presence of cancer.,False,,"['Indeterminate', 'unknown', 'Absent', 'Present', 'Not Reported', '']",,Diagnosis +WHO NTE Grade,WHO NTE Grade,WHONTEGrade,WHO NTE Grade,False,,"['G3', 'unknown', 'G2', 'G1', 'Not Reported', 'GX', '']",,Diagnosis +Tumor Grade,Tumor Grade,TumorGrade,"Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.",False,,"['GB', 'Low Grade', 'unknown', 'G3', 'G4', 'High Grade', 'G2', 'G1', 'Not Applicable', 'Not Reported', 'Intermediate Grade', 'GX', '']",,Diagnosis +INRG Stage,INRG Stage,INRGStage,"The text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Risk Group (INRG).",False,,"['L2', 'Ms', 'L1', 'unknown', 'Not Reported', 'M', '']",,Diagnosis +AJCC Pathologic M,AJCC Pathologic M,AJCCPathologicM,"Code to represent the defined absence or presence of distant spread or metastases (M) to locations via vascular channels or lymphatics beyond the regional lymph nodes, using criteria established by the American Joint Committee on Cancer (AJCC).",False,,"['M1c', 'M1a', 'M1b', 'M0', 'unknown', 'MX', 'Not Reported', 'M1', 'cM0 (i+)', '']",,Diagnosis +Method of Diagnosis,Method of Diagnosis,MethodofDiagnosis,Text term used to describe the method used to confirm the patients malignant diagnosis.,False,,"['Pap Smear', 'Diagnostic Imaging', 'Surgical Resection', 'Blood Draw', 'Cystoscopy', 'Thoracentesis', 'Pathologic Review', 'Excisional Biopsy', 'Bone Marrow Aspirate', 'Laparotomy', 'Laparoscopy', 'Other', 'Debulking', 'Cytology', 'Core Biopsy', 'unknown', 'Not Reported', 'Biopsy', 'Incisional Biopsy', 'Physical Exam', 'Fine Needle Aspiration', 'Enucleation', 'Autopsy', 'Ultrasound Guided Biopsy', 'Dilation and Curettage Procedure', '']",,Diagnosis +Non Nodal Regional Disease,Non Nodal Regional Disease,NonNodalRegionalDisease,The text term used to describe whether the patient had non-nodal regional disease.,False,,"['Indeterminate', 'unknown', 'Absent', 'Present', 'Not Reported', '']",,Diagnosis Age at Diagnosis,Age at Diagnosis,AgeatDiagnosis,Age at the time of diagnosis expressed in number of days since birth.,True,,,,Diagnosis -Peritoneal Fluid Cytological Status,Peritoneal Fluid Cytological Status,PeritonealFluidCytologicalStatus,The text term used to describe the malignant status of the peritoneal fluid determined by cytologic testing.,False,,"['Atypical', 'Malignant', 'Unsatisfactory', 'Non-Malignant', 'unknown', 'Not Reported', '']",,Diagnosis -Margin Distance,Margin Distance,MarginDistance,Numeric value (in centimeters) that represents the distance between the tumor and the surgical margin.,False,,,,Diagnosis -Micropapillary Features,Micropapillary Features,MicropapillaryFeatures,The yes/no/unknown indicator used to describe whether micropapillary features were determined to be present.,False,,"['Not Reported', 'Absent', 'Present', 'unknown', '']",,Diagnosis -INPC Histologic Group,INPC Histologic Group,INPCHistologicGroup,"The text term used to describe the classification of neuroblastomas distinguishing between favorable and unfavorable histologic groups. The histologic score, defined by the International Neuroblastoma Pathology Classification (INPC), is based on age, mitosis-karyorrhexis index (MKI), stromal content and degree of tumor cell differentiation.",False,,"['Not Reported', 'Favorable', 'Unfavorable', 'unknown', '']",,Diagnosis -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Diagnosis -INSS Stage,INSS Stage,INSSStage,"Text term used to describe the staging classification of neuroblastic tumors, as defined by the International Neuroblastoma Staging System (INSS).",False,,"['Stage 2B', 'Stage 3', 'Stage 2A', 'unknown', 'Stage 1', 'Not Reported', 'Stage 4S', 'Stage 4', '']",,Diagnosis -Cog Neuroblastoma Risk Group,Cog Neuroblastoma Risk Group,CogNeuroblastomaRiskGroup,Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.,False,,"['High Risk', 'Intermediate Risk', 'unknown', 'Low Risk', 'Not Reported', '']",,Diagnosis -AJCC Clinical N,AJCC Clinical N,AJCCClinicalN,Extent of the regional lymph node involvement for the cancer based on evidence obtained from clinical assessment parameters determined prior to treatment.,False,,"['N2c', 'N3b', 'N0', 'N3', 'N2a', 'N1a', 'N1c', 'N3c', 'unknown', 'N2b', 'N0 (i+)', 'NX', 'N2', 'N1bIV', 'N1', 'N1bII', 'N0 (i-)', 'N3a', 'N1bI', 'N0 (mol-)', 'N1b', 'N0 (mol+)', 'N4', 'Not Reported', 'N1mi', 'N1bIII', '']",,Diagnosis -Ovarian Specimen Status,Ovarian Specimen Status,OvarianSpecimenStatus,The text term used to describe the physical condition of the involved ovary.,False,,"['Ovarian Capsule Intact', 'unknown', 'Ovarian Capsule Fragmented', 'Not Reported', 'Ovarian Capsule Ruptured', '']",,Diagnosis -Classification of Tumor,Classification of Tumor,ClassificationofTumor,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint.,False,,"['Other', 'Metastasis', 'Primary', 'Not Allowed To Collect', 'unknown', 'Not Reported', 'Recurrence', '']",,Diagnosis -Mitosis Karyorrhexis Index,Mitosis Karyorrhexis Index,MitosisKaryorrhexisIndex,Text term that represents the component of the International Neuroblastoma Pathology Classification (INPC) for mitosis-karyorrhexis index (MKI).,False,,"['Low', 'unknown', 'Intermediate', 'Not Reported', 'High', '']",,Diagnosis -Days to Last Known Disease Status,Days to Last Known Disease Status,DaystoLastKnownDiseaseStatus,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'",True,,,,Diagnosis -Last Known Disease Status,Last Known Disease Status,LastKnownDiseaseStatus,Text term that describes the last known state or condition of an individual's neoplasm.,True,,"['unknown tumor status', 'Not Allowed To Collect', 'Not Applicable', 'Distant met recurrence/progression', 'With tumor', 'Loco-regional recurrence/progression', 'Not Reported', 'Tumor free', 'Biochemical evidence of disease without structural correlate']",,Diagnosis -Margins Involved Site,Margins Involved Site,MarginsInvolvedSite,The text term used to describe the anatomic sites that were involved in the survival margins.,False,,"['Parenchyma', 'Renal Capsule', 'Renal Sinus', 'Gerota Fascia', 'Ureter', 'Renal', 'Renal Vein', 'Perinephric Fat', '']",,Diagnosis -Secondary Gleason Grade,Secondary Gleason Grade,SecondaryGleasonGrade,"The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 4', 'Pattern 5', 'Pattern 2', 'Pattern 1', 'Pattern 3', '']",,Diagnosis -IRS Stage,IRS Stage,IRSStage,"The text term used to describe the classification of rhabdomyosarcoma tumors, as defined by the Intergroup Rhabdomyosarcoma Study (IRS).",False,,"['2', '4', '3', 'unknown', 'Not Reported', '1', '']",,Diagnosis -Non Nodal Tumor Deposits,Non Nodal Tumor Deposits,NonNodalTumorDeposits,The yes/no/unknown indicator used to describe the presence of tumor deposits in the pericolic or perirectal fat or in adjacent mesentery away from the leading edge of the tumor.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,Diagnosis -WHO CNS Grade,WHO CNS Grade,WHOCNSGrade,WHO CNS Grade,False,,"['Grade III', 'Grade IV', 'Grade Not Assigned', 'unknown', 'Grade I', 'Grade II', 'Not Reported', '']",,Diagnosis -WHO NTE Grade,WHO NTE Grade,WHONTEGrade,WHO NTE Grade,False,,"['G2', 'G3', 'GX', 'unknown', 'G1', 'Not Reported', '']",,Diagnosis +Precancerous Condition Type,Precancerous Condition Type,PrecancerousConditionType,The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).,False,,"['Scar - no residual melanoma', 'Normal', 'Adenocarcinoma in situ - mucinous', 'Adenocarcinoma in situ - non mucinous', 'Melanoma in situ', 'Severe dysplasia', 'Normal WDA', 'Superficial spreading', 'Lentigo maligna type', 'Squamous carcinoma in situ', 'Invasive melanoma - nevoid', 'Invasive melanoma - desmoplastic', 'Hamartoma', 'Invasive melanoma - superficial spreading', 'Neuroendocrine cell hyperplasia', 'Benign tumor NOS', 'Other', 'Persistent melanoma in situ', 'Invasive melanoma - lentigo maligna', 'Mild dysplasia', 'Acral-lentiginous', 'Not Applicable', 'Prostatic Intraepithelial Neoplasia', 'Melanocytic hyperplasia', 'Pancreatic Intraductal Papillary-Mucinous Neoplasm', 'Reserve cell hyperplasia', 'Invasive melanoma - acral lentiginous', 'Moderate dysplasia', 'Melanoma in situ arising in a giant congenital nevus', 'Atypical Adenomatous Lung Hyperplasia', 'Invasive melanoma', 'Squamous metaplasia - mature', 'Atypical adenomatous hyperplasia', 'Atypical melanocytic proliferation', 'Invasive melanoma - nodular type', 'Squamous metaplasia - immature', 'No diagnosis possible', 'Melanoma in situ not otherwise classified', 'Pancreatic Intraepithelial Neoplasia', 'Ductal Carcinoma In Situ', 'Carcinoma NOS', '']",,Diagnosis +Vascular Invasion Present,Vascular Invasion Present,VascularInvasionPresent,The yes/no indicator to ask if large vessel or venous invasion was detected by surgery or presence in a tumor specimen.,False,,"['Not Allowed To Collect', 'no', 'unknown', 'Not Reported', 'Yes - Vascular Invasion Present', '']",,Diagnosis +Lymph Nodes Positive,Lymph Nodes Positive,LymphNodesPositive,The number of lymph nodes involved with disease as determined by pathologic examination.,False,,,,Diagnosis +Tissue or Organ of Origin,Tissue or Organ of Origin,TissueorOrganofOrigin,"The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Paraspinal', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Connective subcutaneous and other soft tissues of pelvis', 'Urethra', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas']",,Diagnosis +Synchronous Malignancy,Synchronous Malignancy,SynchronousMalignancy,"A yes/no/unknown indicator used to describe whether the patient had an additional malignant diagnosis at the same time the tumor used for sequencing was diagnosed. If both tumors were sequenced, both tumors would have synchronous malignancies.",False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Diagnosis +Cog Neuroblastoma Risk Group,Cog Neuroblastoma Risk Group,CogNeuroblastomaRiskGroup,Text term that represents the categorization of patients on the basis of prognostic factors per a system developed by Children's Oncology Group (COG). Risk level is used to assign treatment intensity.,False,,"['Intermediate Risk', 'unknown', 'Low Risk', 'Not Reported', 'High Risk', '']",,Diagnosis Percent Tumor Invasion,Percent Tumor Invasion,PercentTumorInvasion,The percentage of tumor cells spread locally in a malignant neoplasm through infiltration or destruction of adjacent tissue.,False,,,,Diagnosis -Anaplasia Present,Anaplasia Present,AnaplasiaPresent,Yes/no/unknown/Not Reported indicator used to describe whether anaplasia was present at the time of diagnosis.,False,,"['Not Reported', 'no', 'Yes - Anaplasia Present', 'unknown', '']",,Diagnosis -Precancerous Condition Type,Precancerous Condition Type,PrecancerousConditionType,The classification of pre-cancerous cells found in a specific collection of data being studied by the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL).,False,,"['Severe dysplasia', 'Scar - no residual melanoma', 'Acral-lentiginous', 'Hamartoma', 'Ductal Carcinoma In Situ', 'Melanoma in situ', 'Invasive melanoma - desmoplastic', 'Normal', 'Other', 'Reserve cell hyperplasia', 'Prostatic Intraepithelial Neoplasia', 'Squamous carcinoma in situ', 'Melanocytic hyperplasia', 'Carcinoma NOS', 'Melanoma in situ arising in a giant congenital nevus', 'Moderate dysplasia', 'Benign tumor NOS', 'Adenocarcinoma in situ - non mucinous', 'Lentigo maligna type', 'No diagnosis possible', 'Invasive melanoma', 'Mild dysplasia', 'Adenocarcinoma in situ - mucinous', 'Invasive melanoma - superficial spreading', 'Squamous metaplasia - mature', 'Squamous metaplasia - immature', 'Atypical Adenomatous Lung Hyperplasia', 'Superficial spreading', 'Pancreatic Intraductal Papillary-Mucinous Neoplasm', 'Persistent melanoma in situ', 'Not Applicable', 'Invasive melanoma - lentigo maligna', 'Invasive melanoma - acral lentiginous', 'Normal WDA', 'Atypical melanocytic proliferation', 'Atypical adenomatous hyperplasia', 'Pancreatic Intraepithelial Neoplasia', 'Invasive melanoma - nevoid', 'Neuroendocrine cell hyperplasia', 'Invasive melanoma - nodular type', 'Melanoma in situ not otherwise classified', '']",,Diagnosis +Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",True,,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Paraspinal', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Connective subcutaneous and other soft tissues of pelvis', 'Urethra', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas']",,Diagnosis +Secondary Gleason Grade,Secondary Gleason Grade,SecondaryGleasonGrade,"The text term used to describe the secondary Gleason score, which describes the pattern of cells making up the second largest area of the tumor. The primary and secondary Gleason pattern grades are combined to determine the patient's Gleason grade group, which is used to determine the aggresiveness of prostate cancer. Note that this grade describes the entire prostatectomy specimen and is not specific to the sample used for sequencing.",False,,"['Pattern 1', 'Pattern 4', 'Pattern 5', 'Pattern 2', 'Pattern 3', '']",,Diagnosis +Lymph Nodes Tested,Lymph Nodes Tested,LymphNodesTested,The number of lymph nodes tested to determine whether lymph nodes were involved with disease as determined by a pathologic examination.,False,,,,Diagnosis +Greatest Tumor Dimension,Greatest Tumor Dimension,GreatestTumorDimension,Numeric value that represents the measurement of the widest portion of the tumor in centimeters.,False,,,,Diagnosis +Year of Diagnosis,Year of Diagnosis,YearofDiagnosis,Numeric value to represent the year of an individual's initial pathologic diagnosis of cancer.,False,,,,Diagnosis +Tumor Focality,Tumor Focality,TumorFocality,The text term used to describe whether the patient's disease originated in a single location or multiple locations.,False,,"['Unifocal', 'Not Reported', 'Multifocal', 'unknown', '']",,Diagnosis +AJCC Staging System Edition,AJCC Staging System Edition,AJCCStagingSystemEdition,"The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.",False,,"['1st', '7th', '6th', '5th', '4th', 'unknown', '3rd', '2nd', 'Not Reported', '8th', '']",,Diagnosis +Days to Last Known Disease Status,Days to Last Known Disease Status,DaystoLastKnownDiseaseStatus,"Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. If not applicable please enter 'Not Applicable'",True,,,,Diagnosis +First Symptom Prior to Diagnosis,First Symptom Prior to Diagnosis,FirstSymptomPriortoDiagnosis,Text term used to describe the patient's first symptom experienced prior to diagnosis and thought to be related to the disease.,False,,"['Visual Changes', 'Sensory Changes', 'Headaches', 'Motor or Movement Changes', 'Altered Mental Status', 'unknown', 'Not Reported', 'Seizures', '']",,Diagnosis +Tumor Largest Dimension Diameter,Tumor Largest Dimension Diameter,TumorLargestDimensionDiameter,"Numeric value used to describe the maximum diameter or dimension of the primary tumor, measured in centimeters.",False,,,,Diagnosis Gleason Patterns Percent,Gleason Patterns Percent,GleasonPatternsPercent,"Numeric value that represents the percentage of Patterns 4 and 5, which is used when the Gleason score is greater than 7 to predict prognosis.",False,,,,Diagnosis -AJCC Staging System Edition,AJCC Staging System Edition,AJCCStagingSystemEdition,"The text term used to describe the version or edition of the American Joint Committee on Cancer Staging Handbooks, a publication by the group formed for the purpose of developing a system of staging for cancer that is acceptable to the American medical profession and is compatible with other accepted classifications.",False,,"['1st', '7th', '3rd', '5th', '8th', 'unknown', '4th', 'Not Reported', '6th', '2nd', '']",,Diagnosis -Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Olfactory nerve', 'Overlapping lesion of bladder', 'Anterior floor of mouth', 'Bone marrow', 'Other specified parts of female genital organs', 'Parametrium', 'Overlapping lesion of lung', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Branchial cleft', 'Lower gum', 'Renal pelvis', 'skin NOS', 'Overlapping lesion of accessory sinuses', 'Gastric antrum', 'Overlapping lesion of cervix uteri', 'Nasal cavity', 'Peripheral nerves and autonomic nervous system of thorax', 'Autonomic nervous system NOS', 'Overlapping lesion of nasopharynx', 'Lateral wall of oropharynx', 'Upper-inner quadrant of breast', 'Thymus', 'Posterior mediastinum', 'Anus NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Stomach NOS', 'Broad ligament', 'Cloacogenic zone', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Lateral wall of bladder', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Biliary tract NOS', 'Anterior 2/3 of tongue NOS', 'Testis NOS', 'Overlapping lesion of ill-defined sites', 'Uterine adnexa', 'Fundus uteri', 'Central portion of breast', 'Overlapping lesion of skin', 'Lateral wall of nasopharynx', 'Nipple', 'Overlapping lesion of urinary organs', 'Soft palate NOS', 'Main bronchus', 'Trachea', 'Upper lobe lung', 'Anterior wall of nasopharynx', 'Specified parts of peritoneum', 'Body of penis', 'Tonsillar fossa', 'Overlapping lesion of breast', 'Adrenal gland NOS', 'Hepatic flexure of colon', 'Aortic body and other paraganglia', 'Frontal lobe', 'Pleura NOS', 'Lateral floor of mouth', 'Intrathoracic lymph nodes', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Pylorus', 'Skin of lip NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peripheral nerves and autonomic nervous system of abdomen', 'Waldeyer ring', 'Axillary tail of breast', 'Cervical esophagus', 'Not Reported', 'Round ligament', 'Anterior mediastinum', 'Cecum', 'Cerebrum', 'Cerebellum NOS', 'Ureteric orifice', 'Abdomen NOS', 'Brain NOS', 'Major salivary gland NOS', 'Thyroid gland', 'Overlapping lesion of rectum anus and anal canal', 'Upper-outer quadrant of breast', 'Peritoneum NOS', 'Male genital organs NOS', 'Cranial nerve NOS', 'Gum NOS', 'Ethmoid sinus', 'Subglottis', 'Meninges NOS', 'Nasopharynx NOS', 'Spinal cord', 'Clitoris', 'Labium majus', 'Urachus', 'Duodenum', 'Short bones of upper limb and associated joints', 'Posterior wall of oropharynx', 'Vulva NOS', 'Thorax NOS', 'Temporal lobe', 'Maxillary sinus', 'Middle third of esophagus', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of pancreas', 'Overlapping lesion of tonsil', 'Overlapping lesion of floor of mouth', 'Accessory sinus NOS', 'External lower lip', 'Vagina NOS', 'Parathyroid gland', 'Overlapping lesions of oropharynx', 'Overlapping lesion of esophagus', 'Overlapping lesion of colon', 'Base of tongue NOS', 'Overlapping lesion of vulva', 'Isthmus uteri', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of digestive system', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Ill-defined sites within respiratory system', 'Lower-inner quadrant of breast', 'Fundus of stomach', 'Prostate gland', 'Spinal meninges', 'Supraglottis', 'Bladder neck', 'Connective subcutaneous and other soft tissues of abdomen', 'Mandible', 'Blood', 'Anal canal', 'Overlapping lesion of penis', 'Nervous system NOS', 'Lymph node NOS', 'Overlapping lesion of corpus uteri', 'Retroperitoneum', 'Pharynx NOS', 'Rib sternum clavicle and associated joints', 'Lower-outer quadrant of breast', 'Intrahepatic bile duct', 'Appendix', 'Lymph nodes of multiple regions', 'Occipital lobe', 'Cervix uteri', 'Fallopian tube', 'Endometrium', 'Ventricle NOS', 'Ampulla of Vater', 'Pineal gland', 'Pelvis NOS', 'Skin of scalp and neck', 'Brain stem', 'Islets of Langerhans', 'Endocervix', 'Upper limb NOS', 'Dome of bladder', 'Thoracic esophagus', 'Vertebral column', 'Short bones of lower limb and associated joints', 'Tongue NOS', 'Overlapping lesion of male genital organs', 'Exocervix', 'Splenic flexure of colon', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Upper gum', 'Labium minus', 'Glottis', 'Overlapping lesion of lip', 'Mucosa of lower lip', 'Optic nerve', 'Kidney NOS', 'Pancreatic duct', 'Breast NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Meckel diverticulum', 'Overlapping lesion of biliary tract', 'Overlapping lesion of tongue', 'Larynx NOS', 'Ileum', 'Pancreas NOS', 'Overlapping lesion of stomach', 'Abdominal esophagus', 'Intestinal tract NOS', 'Frontal sinus', 'Cardia NOS', 'Liver', 'Tonsillar pillar', 'Bone of limb NOS', 'Cauda equina', 'Other specified parts of male genital organs', 'Upper respiratory tract NOS', 'unknown primary site', 'Small intestine NOS', 'Upper third of esophagus', 'Connective subcutaneous and other soft tissues of thorax', 'Sigmoid colon', 'Lymph nodes of head face and neck', 'Pyriform sinus', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Lung NOS', 'Border of tongue', 'Tonsil NOS', 'Rectum NOS', 'Parietal lobe', 'Hypopharynx NOS', 'Heart', 'Mouth NOS', 'Hematopoietic system NOS', 'Superior wall of nasopharynx', 'Endocrine gland NOS', 'Craniopharyngeal duct', 'Overlapping lesion of heart mediastinum and pleura', 'Lymph nodes of axilla or arm', 'Head face or neck NOS', 'Medulla of adrenal gland', 'Lymph nodes of inguinal region or leg', 'Female genital tract NOS', 'Glans penis', 'skin of lower limb and hip', 'Body of stomach', 'Reticuloendothelial system NOS', 'Choroid', 'External upper lip', 'Prepuce', 'Posterior wall of nasopharynx', 'Urinary system NOS', 'Conjunctiva', 'Rectosigmoid junction', 'Intra-abdominal lymph nodes', 'Lingual tonsil', 'External lip NOS', 'Parotid gland', 'Bones of skull and face and associated joints', 'Dorsal surface of tongue NOS', 'Lip NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of endocrine glands and related structures', 'Middle ear', 'Bladder NOS', 'Bone NOS', 'Trigone of bladder', 'Gallbladder', 'Descended testis', 'Orbit NOS', 'Descending colon', 'Spleen', 'Retromolar area', 'Ureter', 'skin of upper limb and shoulder', 'Pelvic lymph nodes', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Eye NOS', 'Myometrium', 'Lower third of esophagus', 'Body of pancreas', 'Mediastinum NOS', 'Sublingual gland', 'Anterior surface of epiglottis', 'Hard palate', 'Overlapping lesion of major salivary glands', 'Scrotum NOS', 'Ventral surface of tongue NOS', 'Submandibular gland', 'Oropharynx NOS', 'Lower limb NOS', 'Overlapping lesion of brain', 'Overlapping lesion of larynx', 'Cornea NOS', 'Corpus uteri', 'External ear', 'Commissure of lip', 'unknown', 'Cheek mucosa', 'Overlapping lesion of hypopharynx', 'Pituitary gland', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Ascending colon', 'Epididymis', 'Esophagus NOS', 'Overlapping lesion of other and unspecified parts of mouth', 'Laryngeal cartilage', 'Skin of trunk', 'Transverse colon', 'Penis NOS', 'Ovary', 'Anterior wall of bladder', 'Carotid body', 'Colon NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Jejunum', 'Spermatic cord', 'Long bones of lower limb and associated joints', 'Undescended testis', 'Head of pancreas', 'Vestibule of mouth', 'Middle lobe lung', 'Posterior wall of bladder', 'Overlapping lesion of eye and adnexa', 'Overlapping lesion of palate', 'Overlapping lesion of lip oral cavity and pharynx', 'Cerebral meninges', 'Sphenoid sinus', 'Gastrointestinal tract NOS', 'Uvula', 'Other specified parts of pancreas', 'Uterus NOS', 'Tail of pancreas', 'Acoustic nerve', 'Lacrimal gland', 'Cortex of adrenal gland', 'Palate NOS', 'Extrahepatic bile duct', 'Vallecula', 'Ciliary body', 'Hypopharyngeal aspect of aryepiglottic fold', 'Greater curvature of stomach NOS', 'Overlapping lesion of female genital organs', 'Retina', 'Other ill-defined sites', 'Posterior wall of hypopharynx', 'Urethra', 'Overlapping lesion of small intestine', 'Peripheral nerves and autonomic nervous system of pelvis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Postcricoid region', 'Lower lobe lung', 'Skin of other and unspecified parts of face', 'Mucosa of lip NOS', 'Eyelid', 'Mucosa of upper lip', 'Paraurethral gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Placenta', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis -Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis +Lymph Node Involved Site,Lymph Node Involved Site,LymphNodeInvolvedSite,The text term used to describe the anatomic site of lymph node involvement.,False,,"['Mesenteric', 'Cervical', 'Submandibular', 'Hilar', 'Paraaortic', 'Popliteal', 'Splenic', 'Iliac', 'NOS', 'Mediastinal', 'Supraclavicular', 'None', 'unknown', 'Parotid', 'Epitrochlear', 'Femoral', 'Not Reported', 'Retroperitoneal', 'Inguinal', 'Occipital', 'Iliac-common', 'Iliac-external', 'Axillary', '']",,Diagnosis +International Prognostic Index,International Prognostic Index,InternationalPrognosticIndex,"The text term used to describe the International Prognostic Index, which classifies the prognosis of patients with aggressive non-Hodgkin's lymphoma.",False,,"['High-Intermediate Risk', 'Low-Intermediate Risk', 'Low Risk', 'High Risk', '']",,Diagnosis Days to Progression Free,Days to Progression Free,DaystoProgressionFree,Number of days between the date used for index and the date the patient's disease was formally confirmed as progression-free. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis Days to Progression,Days to Progression,DaystoProgression,Number of days between the date used for index and the date the patient's disease progressed. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis -Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Distant', 'unknown', 'Local', 'Regional', 'Not Reported', 'Biochemical', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis -Treatment Dose Units,Treatment Dose Units,TreatmentDoseUnits,The text term used to describe the dose units of an agent the patient received.,False,,"['Gy', 'cGy', '']",,Therapy -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Therapy -Treatment Anatomic Site,Treatment Anatomic Site,TreatmentAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,,"['Olfactory nerve', 'Overlapping lesion of bladder', 'Anterior floor of mouth', 'Bone marrow', 'Other specified parts of female genital organs', 'Parametrium', 'Overlapping lesion of lung', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Branchial cleft', 'Lower gum', 'Renal pelvis', 'skin NOS', 'Overlapping lesion of accessory sinuses', 'Gastric antrum', 'Overlapping lesion of cervix uteri', 'Nasal cavity', 'Peripheral nerves and autonomic nervous system of thorax', 'Autonomic nervous system NOS', 'Overlapping lesion of nasopharynx', 'Lateral wall of oropharynx', 'Upper-inner quadrant of breast', 'Thymus', 'Posterior mediastinum', 'Anus NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Stomach NOS', 'Broad ligament', 'Cloacogenic zone', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Lateral wall of bladder', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Biliary tract NOS', 'Anterior 2/3 of tongue NOS', 'Testis NOS', 'Overlapping lesion of ill-defined sites', 'Uterine adnexa', 'Fundus uteri', 'Central portion of breast', 'Overlapping lesion of skin', 'Lateral wall of nasopharynx', 'Nipple', 'Overlapping lesion of urinary organs', 'Soft palate NOS', 'Main bronchus', 'Trachea', 'Upper lobe lung', 'Anterior wall of nasopharynx', 'Specified parts of peritoneum', 'Body of penis', 'Tonsillar fossa', 'Overlapping lesion of breast', 'Adrenal gland NOS', 'Hepatic flexure of colon', 'Aortic body and other paraganglia', 'Frontal lobe', 'Pleura NOS', 'Lateral floor of mouth', 'Intrathoracic lymph nodes', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Pylorus', 'Skin of lip NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peripheral nerves and autonomic nervous system of abdomen', 'Waldeyer ring', 'Axillary tail of breast', 'Cervical esophagus', 'Not Reported', 'Round ligament', 'Anterior mediastinum', 'Cecum', 'Cerebrum', 'Cerebellum NOS', 'Ureteric orifice', 'Abdomen NOS', 'Brain NOS', 'Major salivary gland NOS', 'Thyroid gland', 'Overlapping lesion of rectum anus and anal canal', 'Upper-outer quadrant of breast', 'Peritoneum NOS', 'Male genital organs NOS', 'Cranial nerve NOS', 'Gum NOS', 'Ethmoid sinus', 'Subglottis', 'Meninges NOS', 'Nasopharynx NOS', 'Spinal cord', 'Clitoris', 'Labium majus', 'Urachus', 'Duodenum', 'Short bones of upper limb and associated joints', 'Posterior wall of oropharynx', 'Vulva NOS', 'Thorax NOS', 'Temporal lobe', 'Maxillary sinus', 'Middle third of esophagus', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of pancreas', 'Overlapping lesion of tonsil', 'Overlapping lesion of floor of mouth', 'Accessory sinus NOS', 'External lower lip', 'Vagina NOS', 'Parathyroid gland', 'Overlapping lesions of oropharynx', 'Overlapping lesion of esophagus', 'Overlapping lesion of colon', 'Base of tongue NOS', 'Overlapping lesion of vulva', 'Isthmus uteri', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of digestive system', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Ill-defined sites within respiratory system', 'Lower-inner quadrant of breast', 'Fundus of stomach', 'Prostate gland', 'Spinal meninges', 'Supraglottis', 'Bladder neck', 'Connective subcutaneous and other soft tissues of abdomen', 'Mandible', 'Blood', 'Anal canal', 'Overlapping lesion of penis', 'Nervous system NOS', 'Lymph node NOS', 'Overlapping lesion of corpus uteri', 'Retroperitoneum', 'Pharynx NOS', 'Rib sternum clavicle and associated joints', 'Lower-outer quadrant of breast', 'Intrahepatic bile duct', 'Appendix', 'Lymph nodes of multiple regions', 'Occipital lobe', 'Cervix uteri', 'Fallopian tube', 'Endometrium', 'Ventricle NOS', 'Ampulla of Vater', 'Pineal gland', 'Pelvis NOS', 'Skin of scalp and neck', 'Brain stem', 'Islets of Langerhans', 'Endocervix', 'Upper limb NOS', 'Dome of bladder', 'Thoracic esophagus', 'Vertebral column', 'Short bones of lower limb and associated joints', 'Tongue NOS', 'Overlapping lesion of male genital organs', 'Exocervix', 'Splenic flexure of colon', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Upper gum', 'Labium minus', 'Glottis', 'Overlapping lesion of lip', 'Mucosa of lower lip', 'Optic nerve', 'Kidney NOS', 'Pancreatic duct', 'Breast NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Meckel diverticulum', 'Overlapping lesion of biliary tract', 'Overlapping lesion of tongue', 'Larynx NOS', 'Ileum', 'Pancreas NOS', 'Overlapping lesion of stomach', 'Abdominal esophagus', 'Intestinal tract NOS', 'Frontal sinus', 'Cardia NOS', 'Liver', 'Tonsillar pillar', 'Bone of limb NOS', 'Cauda equina', 'Other specified parts of male genital organs', 'Upper respiratory tract NOS', 'unknown primary site', 'Small intestine NOS', 'Upper third of esophagus', 'Connective subcutaneous and other soft tissues of thorax', 'Sigmoid colon', 'Lymph nodes of head face and neck', 'Pyriform sinus', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Lung NOS', 'Border of tongue', 'Tonsil NOS', 'Rectum NOS', 'Parietal lobe', 'Hypopharynx NOS', 'Heart', 'Mouth NOS', 'Hematopoietic system NOS', 'Superior wall of nasopharynx', 'Endocrine gland NOS', 'Craniopharyngeal duct', 'Overlapping lesion of heart mediastinum and pleura', 'Lymph nodes of axilla or arm', 'Head face or neck NOS', 'Medulla of adrenal gland', 'Lymph nodes of inguinal region or leg', 'Female genital tract NOS', 'Glans penis', 'skin of lower limb and hip', 'Body of stomach', 'Reticuloendothelial system NOS', 'Choroid', 'External upper lip', 'Prepuce', 'Posterior wall of nasopharynx', 'Urinary system NOS', 'Conjunctiva', 'Rectosigmoid junction', 'Intra-abdominal lymph nodes', 'Lingual tonsil', 'External lip NOS', 'Parotid gland', 'Bones of skull and face and associated joints', 'Dorsal surface of tongue NOS', 'Lip NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of endocrine glands and related structures', 'Middle ear', 'Bladder NOS', 'Bone NOS', 'Trigone of bladder', 'Gallbladder', 'Descended testis', 'Orbit NOS', 'Descending colon', 'Spleen', 'Retromolar area', 'Ureter', 'Pelvic lymph nodes', 'skin of upper limb and shoulder', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Eye NOS', 'Myometrium', 'Lower third of esophagus', 'Body of pancreas', 'Mediastinum NOS', 'Sublingual gland', 'Anterior surface of epiglottis', 'Hard palate', 'Overlapping lesion of major salivary glands', 'Scrotum NOS', 'Ventral surface of tongue NOS', 'Submandibular gland', 'Oropharynx NOS', 'Lower limb NOS', 'Overlapping lesion of brain', 'Overlapping lesion of larynx', 'Cornea NOS', 'Corpus uteri', 'External ear', 'Commissure of lip', 'unknown', 'Cheek mucosa', 'Overlapping lesion of hypopharynx', 'Pituitary gland', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Ascending colon', 'Epididymis', 'Esophagus NOS', 'Overlapping lesion of other and unspecified parts of mouth', 'Laryngeal cartilage', 'Skin of trunk', 'Transverse colon', 'Penis NOS', 'Ovary', 'Anterior wall of bladder', 'Carotid body', 'Colon NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Jejunum', 'Spermatic cord', 'Long bones of lower limb and associated joints', 'Undescended testis', 'Head of pancreas', 'Vestibule of mouth', 'Middle lobe lung', 'Posterior wall of bladder', 'Overlapping lesion of eye and adnexa', 'Overlapping lesion of palate', 'Overlapping lesion of lip oral cavity and pharynx', 'Cerebral meninges', 'Sphenoid sinus', 'Gastrointestinal tract NOS', 'Uvula', 'Other specified parts of pancreas', 'Uterus NOS', 'Tail of pancreas', 'Acoustic nerve', 'Lacrimal gland', 'Cortex of adrenal gland', 'Palate NOS', 'Extrahepatic bile duct', 'Vallecula', 'Ciliary body', 'Hypopharyngeal aspect of aryepiglottic fold', 'Greater curvature of stomach NOS', 'Overlapping lesion of female genital organs', 'Retina', 'Other ill-defined sites', 'Posterior wall of hypopharynx', 'Urethra', 'Overlapping lesion of small intestine', 'Peripheral nerves and autonomic nervous system of pelvis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Postcricoid region', 'Lower lobe lung', 'Skin of other and unspecified parts of face', 'Mucosa of lip NOS', 'Eyelid', 'Mucosa of upper lip', 'Paraurethral gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Placenta', '']",,Therapy -Regimen or Line of Therapy,Regimen or Line of Therapy,RegimenorLineofTherapy,The text term used to describe the regimen or line of therapy.,False,,,,Therapy +Progression or Recurrence Type,Progression or Recurrence Type,ProgressionorRecurrenceType,The text term used to describe the type of progressive or recurrent disease or relapsed disease.,False,True,"['Distant', 'Local', 'Regional', 'unknown', 'Biochemical', 'Not Reported', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis +Progression or Recurrence Anatomic Site,Progression or Recurrence Anatomic Site,ProgressionorRecurrenceAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,True,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Urethra', 'Connective subcutaneous and other soft tissues of pelvis', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas', '']","['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis +Days to Recurrence,Days to Recurrence,DaystoRecurrence,Number of days between the date used for index and the date the patient's disease recurred. If not applicable please enter 'Not Applicable',False,True,,"['Progression or Recurrence is ""Yes - Progression or Recurrence""']",Diagnosis +Chemo Concurrent to Radiation,Chemo Concurrent to Radiation,ChemoConcurrenttoRadiation,The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Therapy Days to Treatment End,Days to Treatment End,DaystoTreatmentEnd,Number of days between the date used for index and the date the treatment ended. If not applicable please enter 'Not Applicable',False,,,,Therapy -Treatment Outcome,Treatment Outcome,TreatmentOutcome,Text term that describes the patient's final outcome after the treatment was administered.,False,,"['Stable Disease', 'Partial Response', 'No Measurable Disease', 'Complete Response', 'unknown', 'Persistent Disease', 'No Response', 'Progressive Disease', 'Treatment Ongoing', 'Very Good Partial Response', 'Not Reported', 'Treatment Stopped Due to Toxicity', 'Mixed Response', '']",,Therapy -Treatment Arm,Treatment Arm,TreatmentArm,Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.,False,,"['E4512', 'A081105', 'EA5142', '']",,Therapy -Initial Disease Status,Initial Disease Status,InitialDiseaseStatus,The text term used to describe the status of the patient's malignancy when the treatment began.,False,,"['Initial Diagnosis', 'Recurrent Disease', 'Residual Disease', 'unknown', 'Progressive Disease', 'Not Reported', '']",,Therapy +Regimen or Line of Therapy,Regimen or Line of Therapy,RegimenorLineofTherapy,The text term used to describe the regimen or line of therapy.,False,,,,Therapy +Treatment Intent Type,Treatment Intent Type,TreatmentIntentType,Text term to identify the reason for the administration of a treatment regimen. [Manually-curated],False,,"['Cancer Control', 'Neoadjuvant', 'Prevention', 'unknown', 'Adjuvant', 'Palliative', 'Not Reported', 'Cure', '']",,Therapy +Treatment Anatomic Site,Treatment Anatomic Site,TreatmentAnatomicSite,The text term used to describe the anatomic site of resection; biopsy; tissue or organ of biospecimen origin; progression or recurrent disease; treatment,False,,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Connective subcutaneous and other soft tissues of pelvis', 'Urethra', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas', '']",,Therapy Days to Treatment Start,Days to Treatment Start,DaystoTreatmentStart,Number of days between the date used for index and the date the treatment started. If not applicable please enter 'Not Applicable',False,,,,Therapy -Treatment Effect,Treatment Effect,TreatmentEffect,The text term used to describe the pathologic effect a treatment(s) had on the tumor.,False,,"['Incomplete Necrosis (Viable Tumor Present)', 'unknown', 'Complete Necrosis (No Viable Tumor)', 'Not Reported', 'No Necrosis', '']",,Therapy -Reason Treatment Ended,Reason Treatment Ended,ReasonTreatmentEnded,The text term used to describe the reason a specific treatment or regimen ended.,False,,"['Other', 'Adverse Therapy Event', 'Disease Progression', 'Withdrawal by Subject', 'Death', 'Course of Therapy Completed', '']",,Therapy -Therapeutic Agents,Therapeutic Agents,TherapeuticAgents,Text identification of the individual agent(s) used as part of a treatment regimen.,False,,,,Therapy +Initial Disease Status,Initial Disease Status,InitialDiseaseStatus,The text term used to describe the status of the patient's malignancy when the treatment began.,False,,"['Residual Disease', 'Recurrent Disease', 'unknown', 'Not Reported', 'Initial Diagnosis', 'Progressive Disease', '']",,Therapy +Number of Cycles,Number of Cycles,NumberofCycles,The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.,False,,,,Therapy +Treatment Effect,Treatment Effect,TreatmentEffect,The text term used to describe the pathologic effect a treatment(s) had on the tumor.,False,,"['Incomplete Necrosis (Viable Tumor Present)', 'No Necrosis', 'Complete Necrosis (No Viable Tumor)', 'unknown', 'Not Reported', '']",,Therapy +Treatment Arm,Treatment Arm,TreatmentArm,Text term used to describe the treatment arm assigned to a patient at the time eligibility is determined.,False,,"['EA5142', 'E4512', 'A081105', '']",,Therapy +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,Therapy Treatment Dose,Treatment Dose,TreatmentDose,The numeric value used to describe the dose of an agent the patient received.,False,,,,Therapy -Chemo Concurrent to Radiation,Chemo Concurrent to Radiation,ChemoConcurrenttoRadiation,The text term used to describe whether the patient was receiving chemotherapy concurrent to radiation.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,Therapy -Treatment or Therapy,Treatment or Therapy,TreatmentorTherapy,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,Therapy +Treatment Effect Indicator,Treatment Effect Indicator,TreatmentEffectIndicator,The text term used to indicate whether the treatment had an effect on the patient.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Therapy +Reason Treatment Ended,Reason Treatment Ended,ReasonTreatmentEnded,The text term used to describe the reason a specific treatment or regimen ended.,False,,"['Disease Progression', 'Adverse Therapy Event', 'Death', 'Withdrawal by Subject', 'Other', 'Course of Therapy Completed', '']",,Therapy +Treatment Outcome,Treatment Outcome,TreatmentOutcome,Text term that describes the patient's final outcome after the treatment was administered.,False,,"['No Response', 'Treatment Ongoing', 'Mixed Response', 'No Measurable Disease', 'Very Good Partial Response', 'Treatment Stopped Due to Toxicity', 'unknown', 'Persistent Disease', 'Stable Disease', 'Not Reported', 'Complete Response', 'Partial Response', 'Progressive Disease', '']",,Therapy +Treatment or Therapy,Treatment or Therapy,TreatmentorTherapy,A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,Therapy +Treatment Frequency,Treatment Frequency,TreatmentFrequency,The text term used to describe the frequency the patient received an agent or regimen.,False,,"['Four Times Daily', 'Five Times Daily', 'Twice Daily', 'unknown', 'Three Times Daily', 'Twice Weekly', 'Every Hour', 'Once Weekly', 'Not Reported', 'Every Other Day', 'Every 24 Hours', '']",,Therapy Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Therapy +Therapeutic Agents,Therapeutic Agents,TherapeuticAgents,Text identification of the individual agent(s) used as part of a treatment regimen.,False,,,,Therapy +Treatment Dose Units,Treatment Dose Units,TreatmentDoseUnits,The text term used to describe the dose units of an agent the patient received.,False,,"['Gy', 'cGy', '']",,Therapy Treatment Type,Treatment Type,TreatmentType,Text term that describes the kind of treatment administered.,False,,,,Therapy -Treatment Intent Type,Treatment Intent Type,TreatmentIntentType,Text term to identify the reason for the administration of a treatment regimen. [Manually-curated],False,,"['Prevention', 'unknown', 'Cancer Control', 'Adjuvant', 'Not Reported', 'Palliative', 'Neoadjuvant', 'Cure', '']",,Therapy -Treatment Effect Indicator,Treatment Effect Indicator,TreatmentEffectIndicator,The text term used to indicate whether the treatment had an effect on the patient.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,Therapy -Treatment Frequency,Treatment Frequency,TreatmentFrequency,The text term used to describe the frequency the patient received an agent or regimen.,False,,"['Twice Daily', 'Every Other Day', 'Once Weekly', 'Three Times Daily', 'Five Times Daily', 'unknown', 'Every 24 Hours', 'Twice Weekly', 'Four Times Daily', 'Every Hour', 'Not Reported', '']",,Therapy -Number of Cycles,Number of Cycles,NumberofCycles,The numeric value used to describe the number of cycles of a specific treatment or regimen the patient received.,False,,,,Therapy -Specialized Molecular Test,Specialized Molecular Test,SpecializedMolecularTest,Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MolecularTest -Blood Test Normal Range Upper,Blood Test Normal Range Upper,BloodTestNormalRangeUpper,Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.,False,,,,MolecularTest -Clinical Biospecimen Type,Clinical Biospecimen Type,ClinicalBiospecimenType,"The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['Uninvolved Tissue NOS', 'Embryonic Tissue', 'Muscle Tissue', 'Nerve Tissue', 'Tissue NOS', 'Buffy Coat', 'Buccal Mucosa', 'Cerebrospinal Fluid', 'unknown', 'Feces', 'Bone Marrow', 'Saliva', 'Embryonic Fluid', 'Connective Tissue', 'Skin', 'Urine', 'Blood', 'Granulocyte', 'Pleural Fluid', 'Serum', 'Soft Tissue', 'Not Reported', 'Peritoneal Fluid', 'Plasma', '']",,MolecularTest -Chromosome,Chromosome,Chromosome,"The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['chr6', 'chr5', 'chr4', 'chr15', 'chr20', 'chr11', 'chr2', 'chr22', 'chr1', 'unknown', 'chr9', 'chr12', 'chr18', 'chr10', 'chr8', 'chr17', 'chrY', 'chr13', 'chr7', 'chr21', 'chr16', 'chr14', 'chr19', 'chrM', 'chr23', 'chrX', 'Not Reported', 'chr3', '']",,MolecularTest -Molecular Consequence,Molecular Consequence,MolecularConsequence,The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Stop Gain', 'Intergenic Variant', '3 Prime UTR Variant', 'Incomplete Terminal Codon Variant', 'Non-coding Transcript Variant', 'Splice Region Variant', 'Downstream Gene Variant', '5 Prime UTR Variant', 'Inframe Deletion', 'Non-coding Transcript Exon Variant', 'NMD Transcript Variant', 'Synonymous Variant', 'Transcript Amplification', 'Transcript Ablation', 'Feature Elongation', 'TFBS Amplification', 'Start Lost', 'Upstream Gene Variant', 'Frameshift Variant', 'Mature miRNA Variant', 'Feature Truncation', 'Stop Lost', 'Stop Retained Variant', 'Protein Altering Variant', 'Splice Donor Variant', 'Missense Variant', 'Regulatory Region Variant', 'Coding Sequence Variant', 'TF Binding Site Variant', 'Intron Variant', 'Splice Acceptor Variant', 'Regulatory Region Ablation', 'Inframe Insertion', 'Regulatory Region Amplification', 'TFBS Ablation', '']",,MolecularTest -Test Result,Test Result,TestResult,The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Abnormal NOS', 'Loss of Expression', 'Test Value Reported', 'Not Applicable', 'Low', 'unknown', 'Copy Number Reported', 'negative', 'Intermediate', 'Equivocal', 'Not Reported', 'Overexpressed', 'Normal', 'High', 'positive']",,MolecularTest -Variant Type,Variant Type,VariantType,The text term used to describe the type of genetic variation.,False,,"['Methylation', 'Partial Methylation', 'Repeated Sequences', 'Substitution', 'Inversion', 'Conversion', 'Amplification', 'Splice', 'Other', 'Loss', 'Deletion', 'Chrimerism', 'unknown', 'Gain', 'Rearrangement', 'Insertion', 'Mosaicism', 'Translocation', 'Deletion-Insertion', 'Extension', 'Duplication', 'Hypermethylation', 'Alleles', 'Not Reported', '']",,MolecularTest -Antigen,Antigen,Antigen,The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['HLA-DR', 'CD34', 'CD5', 'CD25', 'CD79A', 'CD3', 'CD19', 'CD138', 'Mesothelin', 'CD14', 'CEA', 'unknown', 'CD117', 'CD33', 'CD56', 'CD10', 'NSE', 'CCND1', 'CD15', 'CD7', 'Squamous Cell Carcinoma Antigen', 'BCL6', 'CA19-9', 'CD30', 'CD22', 'CD23', 'CD45', 'Not Reported', 'CA-125', 'CD20', '']",,MolecularTest -Test Analyte Type,Test Analyte Type,TestAnalyteType,The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['miRNA', 'Protein Analyte', 'mRNA', 'unknown', 'DNA', 'Total RNA', 'Not Reported', '']",,MolecularTest -Test Value,Test Value,TestValue,The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here,False,,,,MolecularTest -Exon,Exon,Exon,"Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest -Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,MolecularTest -Pathogenicity,Pathogenicity,Pathogenicity,The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).,False,,"['Likely Benign', 'Pathogenic', 'Uncertain Significance', 'Benign', 'Likely Pathogenic', '']",,MolecularTest -Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,MolecularTest -Blood Test Normal Range Lower,Blood Test Normal Range Lower,BloodTestNormalRangeLower,Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.,False,,,,MolecularTest -Molecular Analysis Method,Molecular Analysis Method,MolecularAnalysisMethod,The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Flow Cytometry', 'FISH', 'Southern Blotting', 'Other', 'unknown', 'RNA Sequencing', 'Karyotype', 'WGS', 'ISH', 'Microarray', 'WXS', 'Sequencing NOS', 'IHC', 'RT-PCR', 'Cytogenetics NOS', 'Comparative Genomic Hybridization', 'Targeted Sequencing', 'Not Applicable', 'Microsatellite Analysis', 'Nuclear Staining', 'Not Reported']",,MolecularTest -Variant Origin,Variant Origin,VariantOrigin,The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Germline', 'unknown', 'Somatic', '']",,MolecularTest -Second Gene Symbol,Second Gene Symbol,SecondGeneSymbol,"The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest Gene Symbol,Gene Symbol,GeneSymbol,"The text term used to describe a gene targeted or included in molecular analysis. For rearrangements, this is should be used to represent the reference gene. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",True,,,,MolecularTest -Cell Count,Cell Count,CellCount,Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -AA Change,AA Change,AAChange,Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -Locus,Locus,Locus,Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.,False,,,,MolecularTest -Test Units,Test Units,TestUnits,The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -Histone Variant,Histone Variant,HistoneVariant,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['H2A.Z.2', 'H3.Y', 'H2A.Z.1', 'H3.5', 'H2A.X', 'unknown', 'mH2A', 'mH2A.1', 'H2A-Bbd', 'H3.1', 'mH2A.2', 'H3t (H3.4)', 'H3.X', 'CENP-A', 'H3.2', 'H2A.Z', 'H2A.Z.2.2', 'Not Reported', 'H3.3', '']",,MolecularTest -Histone Family,Histone Family,HistoneFamily,"The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.",False,,"['H2A', 'H3', 'H4', 'unknown', 'H2B', 'Not Reported', 'H1', '']",,MolecularTest -Mismatch Repair Mutation,Mismatch Repair Mutation,MismatchRepairMutation,The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Not Reported', 'no', 'yes', 'unknown', '']",,MolecularTest +Loci Abnormal Count,Loci Abnormal Count,LociAbnormalCount,Numeric value used to describe the number of loci determined to be abnormal.,False,,,,MolecularTest +Mismatch Repair Mutation,Mismatch Repair Mutation,MismatchRepairMutation,The yes/no/unknown indicator used to describe whether the mutation included in molecular testing was known to have an affect on the mismatch repair process. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Not Reported', 'yes', 'no', 'unknown', '']",,MolecularTest Second Exon,Second Exon,SecondExon,"The second exon number involved in molecular variation. If a specific genetic variant is being reported, this property can be used to capture the second exon where that variant is located. This property is typically used for a translocation where two different locations are involved in the variation.",False,,,,MolecularTest -Intron,Intron,Intron,"Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.",False,,,,MolecularTest +AA Change,AA Change,AAChange,Alphanumeric value used to describe the amino acid change for a specific genetic variant. Example: R116Q. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest +Stop Days from Index,Stop Days from Index,StopDaysfromIndex,"Number of days from the date of birth (index date) to the end date of the event (e.g. exposure to environmental factor, treatment start, etc.). Note: if the event occurs at a single time point, e.g. a diagnosis or a lab test, the values for this column is 'Not Applicable'",False,,,,MolecularTest +Test Result,Test Result,TestResult,The text term used to describe the result of the molecular test. If the test result was a numeric value see test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['High', 'Normal', 'Abnormal NOS', 'Copy Number Reported', 'positive', 'Test Value Reported', 'unknown', 'negative', 'Intermediate', 'Equivocal', 'Overexpressed', 'Low', 'Not Applicable', 'Not Reported', 'Loss of Expression']",,MolecularTest +Laboratory Test,Laboratory Test,LaboratoryTest,"The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.",False,,"['Eosinophil', 'Immunoglobulin M', 'Basophil', 'Platelets', 'Immunoglobulin A', 'Circulating Tumor Cells', 'Human Chorionic Gonadotropin', 'M Protein', 'Lymphoblasts', 'Kappa', 'NOS', 'Creatinine', 'Blood Urea Nitrogen', 'Albumin', 'Total Bilirubin', 'Human Papillomavirus', 'Absolute Neutrophil', 'C-Reactive Protein', 'Myeloblasts', 'Prolymphocytes', 'Promyelocytes', 'Metamyelocytes', 'Segmented Neutrophil', 'Neutrophil Bands', 'Hematocrit', 'Beta 2 Microglobulin', 'Cellularity', 'Immunoglobulin G', 'Leukocytes', 'Lambda', 'Testosterone', 'Alpha Fetoprotein', 'unknown', 'Calcium', 'Not Reported', 'Hemoglobin', 'Total Protein', 'Promonocytes', 'Epstein-Barr Virus', 'Luteinizing Hormone', 'Myelocytes', 'Lactate Dehydrogenase', 'Serum Free Immunoglobulin Light Chain', 'B-cell genotyping', 'Glucose', 'HPV-E6/E7', 'Lymphocytes', '']",,MolecularTest +Copy Number,Copy Number,CopyNumber,"Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest Loci Count,Loci Count,LociCount,Numeric value used to describe the number of loci tested.,False,,,,MolecularTest +Ploidy,Ploidy,Ploidy,Text term used to describe the number of sets of homologous chromosomes.,False,,"['unknown', 'Hypodiploid', 'Near Diploid', 'Tetraploid', 'Diploid', 'Not Reported', 'Aneuploid', 'Hyperdiploid', '']",,MolecularTest +Histone Family,Histone Family,HistoneFamily,"The text term used to describe the family, or classification of a group of basic proteins found in chromatin, called histones.",False,,"['H1', 'unknown', 'H3', 'H2B', 'H2A', 'H4', 'Not Reported', '']",,MolecularTest +Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Clonal', 'Non-clonal', '']",,MolecularTest Transcript,Transcript,Transcript,Alphanumeric value used to describe the transcript of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest -Laboratory Test,Laboratory Test,LaboratoryTest,"The text term used to describe the medical testing used to diagnose, treat or further understand a patient's disease.",False,,"['Neutrophil Bands', 'Metamyelocytes', 'Myelocytes', 'Leukocytes', 'Kappa', 'Promyelocytes', 'NOS', 'Myeloblasts', 'Luteinizing Hormone', 'M Protein', 'Prolymphocytes', 'Total Protein', 'Epstein-Barr Virus', 'Creatinine', 'Promonocytes', 'Lymphoblasts', 'unknown', 'Glucose', 'Testosterone', 'Basophil', 'Cellularity', 'Lambda', 'Segmented Neutrophil', 'Calcium', 'HPV-E6/E7', 'Human Chorionic Gonadotropin', 'Blood Urea Nitrogen', 'B-cell genotyping', 'Lymphocytes', 'C-Reactive Protein', 'Absolute Neutrophil', 'Circulating Tumor Cells', 'Serum Free Immunoglobulin Light Chain', 'Hemoglobin', 'Lactate Dehydrogenase', 'Immunoglobulin M', 'Total Bilirubin', 'Albumin', 'Alpha Fetoprotein', 'Eosinophil', 'Immunoglobulin A', 'Human Papillomavirus', 'Hematocrit', 'Platelets', 'Not Reported', 'Immunoglobulin G', 'Beta 2 Microglobulin', '']",,MolecularTest -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MolecularTest -Loci Abnormal Count,Loci Abnormal Count,LociAbnormalCount,Numeric value used to describe the number of loci determined to be abnormal.,False,,,,MolecularTest -Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Non-clonal', 'Clonal', '']",,MolecularTest -Ploidy,Ploidy,Ploidy,Text term used to describe the number of sets of homologous chromosomes.,False,,"['Hypodiploid', 'Aneuploid', 'Diploid', 'unknown', 'Near Diploid', 'Hyperdiploid', 'Tetraploid', 'Not Reported', '']",,MolecularTest -Zygosity,Zygosity,Zygosity,The text term used to describe the zygosity of a specific genetic variant.,False,,"['Homozygous', 'Nullizygous', 'unknown', 'Hemizygous', 'Heterozygous', 'Not Reported', '']",,MolecularTest +Locus,Locus,Locus,Alphanumeric value used to describe the locus of a specific genetic variant. Example: NM_001126114.,False,,,,MolecularTest +Blood Test Normal Range Lower,Blood Test Normal Range Lower,BloodTestNormalRangeLower,Numeric value used to describe the lower limit of the normal range used to describe a healthy individual at the institution where the test was completed.,False,,,,MolecularTest +Blood Test Normal Range Upper,Blood Test Normal Range Upper,BloodTestNormalRangeUpper,Numeric value used to describe the upper limit of the normal range used to describe a healthy individual at the institution where the test was completed.,False,,,,MolecularTest +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MolecularTest +Molecular Analysis Method,Molecular Analysis Method,MolecularAnalysisMethod,The text term used to describe the method used for molecular analysis. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,True,,"['Microsatellite Analysis', 'Flow Cytometry', 'Karyotype', 'IHC', 'Southern Blotting', 'RT-PCR', 'Sequencing NOS', 'FISH', 'Other', 'Not Applicable', 'Targeted Sequencing', 'RNA Sequencing', 'unknown', 'Comparative Genomic Hybridization', 'Not Reported', 'WGS', 'Microarray', 'Cytogenetics NOS', 'Nuclear Staining', 'ISH', 'WXS']",,MolecularTest +Chromosome,Chromosome,Chromosome,"The text term used to describe a chromosome targeted or included in molecular testing. If a specific genetic variant is being reported, this property can be used to capture the chromosome where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['chr8', 'chrY', 'chrM', 'chr13', 'chr19', 'chr23', 'chr6', 'chr9', 'chr18', 'chr22', 'chr2', 'chr1', 'chr12', 'chr5', 'chr11', 'chr15', 'chr10', 'unknown', 'chr4', 'chr3', 'chr20', 'Not Reported', 'chr17', 'chr16', 'chr21', 'chr7', 'chr14', 'chrX', '']",,MolecularTest +Cell Count,Cell Count,CellCount,Numeric value used to describe the number of cells used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest +Pathogenicity,Pathogenicity,Pathogenicity,The text used to describe a variant's level of involvement in the cause of the patient's disease according to the standards outlined by the American College of Medical Genetics and Genomics (ACMG).,False,,"['Uncertain Significance', 'Benign', 'Likely Benign', 'Likely Pathogenic', 'Pathogenic', '']",,MolecularTest +Test Units,Test Units,TestUnits,The text term used to describe the units of the test value for a molecular test. This property is used in conjunction with test_value. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest +Second Gene Symbol,Second Gene Symbol,SecondGeneSymbol,"The text term used to describe a secondary gene targeted or included in molecular analysis. For rearrangements, this is should represent the location of the variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +Variant Origin,Variant Origin,VariantOrigin,The text term used to describe the biological origin of a specific genetic variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Somatic', 'Germline', 'unknown', '']",,MolecularTest Cytoband,Cytoband,Cytoband,"Alphanumeric value used to describe the cytoband or chromosomal location targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the cytoband where the variant is located. Format: [chromosome][chromosome arm].[band+sub-bands]. Example: 17p13.1. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +Zygosity,Zygosity,Zygosity,The text term used to describe the zygosity of a specific genetic variant.,False,,"['Nullizygous', 'unknown', 'Hemizygous', 'Homozygous', 'Heterozygous', 'Not Reported', '']",,MolecularTest +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MolecularTest Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,MolecularTest -Copy Number,Copy Number,CopyNumber,"Numeric value used to describe the number of times a section of the genome is repeated or copied within an insertion, duplication or deletion variant. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +Intron,Intron,Intron,"Intron number targeted or included in molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the intron where that variant is located.",False,,,,MolecularTest +Variant Type,Variant Type,VariantType,The text term used to describe the type of genetic variation.,False,,"['Inversion', 'Mosaicism', 'Gain', 'Substitution', 'Extension', 'Insertion', 'Partial Methylation', 'Translocation', 'Other', 'Conversion', 'Deletion', 'Hypermethylation', 'Deletion-Insertion', 'unknown', 'Rearrangement', 'Not Reported', 'Loss', 'Alleles', 'Splice', 'Chrimerism', 'Repeated Sequences', 'Amplification', 'Duplication', 'Methylation', '']",,MolecularTest +Test Analyte Type,Test Analyte Type,TestAnalyteType,The text term used to describe the type of analyte used for molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Total RNA', 'DNA', 'mRNA', 'unknown', 'Protein Analyte', 'Not Reported', 'miRNA', '']",,MolecularTest +Test Value,Test Value,TestValue,The text term or numeric value used to describe a specific result of a molecular test. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here,False,,,,MolecularTest +Start Days from Index,Start Days from Index,StartDaysfromIndex,"Number of days from the date of birth (index date) to the date of an event (e.g. exposure to environmental factor, treatment start, etc.). If not applicable please enter 'Not Applicable'",True,,,,MolecularTest +Molecular Consequence,Molecular Consequence,MolecularConsequence,The text term used to describe the molecular consequence of genetic variation. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Upstream Gene Variant', 'Regulatory Region Amplification', 'Stop Gain', 'Transcript Amplification', 'Non-coding Transcript Exon Variant', 'Stop Retained Variant', 'Coding Sequence Variant', 'Inframe Insertion', 'Synonymous Variant', 'Intergenic Variant', 'Splice Region Variant', 'Splice Donor Variant', '5 Prime UTR Variant', 'Regulatory Region Ablation', 'Mature miRNA Variant', 'Missense Variant', 'Protein Altering Variant', 'Incomplete Terminal Codon Variant', 'TFBS Ablation', 'Regulatory Region Variant', 'Inframe Deletion', '3 Prime UTR Variant', 'Splice Acceptor Variant', 'Frameshift Variant', 'Feature Truncation', 'Start Lost', 'Intron Variant', 'NMD Transcript Variant', 'TFBS Amplification', 'TF Binding Site Variant', 'Non-coding Transcript Variant', 'Stop Lost', 'Downstream Gene Variant', 'Feature Elongation', 'Transcript Ablation', '']",,MolecularTest +Antigen,Antigen,Antigen,The text term used to describe an antigen included in molecular testing. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['CD3', 'CD10', 'CD56', 'CEA', 'CD23', 'CD22', 'NSE', 'Mesothelin', 'CA19-9', 'CD79A', 'CD138', 'CD30', 'CD117', 'CA-125', 'HLA-DR', 'CD25', 'Squamous Cell Carcinoma Antigen', 'BCL6', 'unknown', 'CD14', 'CD7', 'Not Reported', 'CD5', 'CD34', 'CCND1', 'CD33', 'CD20', 'CD19', 'CD45', 'CD15', '']",,MolecularTest +Histone Variant,Histone Variant,HistoneVariant,"The text term used to describe a specific histone variants, which are proteins that substitute for the core canonical histones.",False,,"['H2A.Z.1', 'mH2A.2', 'mH2A', 'H3.X', 'H3.Y', 'H3.2', 'H2A.Z.2.2', 'H3.3', 'H3t (H3.4)', 'H3.5', 'unknown', 'Not Reported', 'H2A.Z.2', 'H3.1', 'H2A.X', 'H2A.Z', 'mH2A.1', 'H2A-Bbd', 'CENP-A', '']",,MolecularTest +Exon,Exon,Exon,"Exon number targeted or included in a molecular analysis. If a specific genetic variant is being reported, this property can be used to capture the exon where that variant is located. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,,,MolecularTest +Specialized Molecular Test,Specialized Molecular Test,SpecializedMolecularTest,Text term used to describe a specific test that is not covered in the list of molecular analysis methods. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,,,MolecularTest +Clinical Biospecimen Type,Clinical Biospecimen Type,ClinicalBiospecimenType,"The text term used to describe the biological material used for testing, diagnostic, treatment or research purposes. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.",False,,"['Saliva', 'Blood', 'Buccal Mucosa', 'Embryonic Tissue', 'Soft Tissue', 'Tissue NOS', 'Buffy Coat', 'Peritoneal Fluid', 'Cerebrospinal Fluid', 'Granulocyte', 'Nerve Tissue', 'Skin', 'Muscle Tissue', 'Bone Marrow', 'Serum', 'Plasma', 'Embryonic Fluid', 'Uninvolved Tissue NOS', 'unknown', 'Not Reported', 'Urine', 'Pleural Fluid', 'Feces', 'Connective Tissue', '']",,MolecularTest +Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Urine Biospecimen Type', 'Stool Biospecimen Type', 'Analyte Biospecimen Type', 'Ascites Biospecimen Type', 'Fluids Biospecimen Type', 'Cells Biospecimen Type', 'Bone Marrow Biospecimen Type', 'Sputum Biospecimen Type', 'Blood Biospecimen Type', 'Tissue Biospecimen Type', 'Mouth Rinse Biospecimen Type']",,Biospecimen +Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Surgical Resection', 'Fine Needle Aspirate', 'Excision', 'Endoscopic biopsy', 'Induced sputum', 'Other Acquisition Method', 'Punch Biopsy', 'Fluid collection', 'Lymphadenectomy - Regional Nodes', 'BAL (bronchial alveolar lavage)', 'Core needle biopsy', 'Shave Biopsy', 'Forceps biopsy', 'Biopsy', 'Sentinel Node Biopsy', 'Blood draw', 'Not specified', 'Non induced sputum', 'Cytobrush', 'Autopsy', 'Re-excision']",,Biospecimen +Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['TCL lysis buffer', 'NP40 lysis buffer', 'Formalin', 'Dimethylacetamide', 'Methacarn', 'Unfixed', 'Alcohol', 'Polaxamer', 'Cryo-store', 'Other', ""Carnoy's Fixative"", 'RNAlater', 'Acetone', 'Saline', 'PAXgene tissue', 'None', 'unknown', 'OCT media', 'Carbodiimide', 'Glutaraldehyde', '95% Ethanol', 'Para-benzoquinone', 'Dimidoester']",,Biospecimen Processing Location,Processing Location,ProcessingLocation,"Site with an HTAN center where specimen processing occurs, if applicable. Any identifier used within the center to identify processing location. No PHI/PII is allowed.",False,,,,Biospecimen -Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Cells Biospecimen Type', 'Analyte Biospecimen Type', 'Mouth Rinse Biospecimen Type', 'Ascites Biospecimen Type', 'Blood Biospecimen Type', 'Stool Biospecimen Type', 'Urine Biospecimen Type', 'Bone Marrow Biospecimen Type', 'Sputum Biospecimen Type', 'Tissue Biospecimen Type', 'Fluids Biospecimen Type']",,Biospecimen -Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['Ambient temperature', 'Frozen at -20C', 'Frozen in vapor phase', 'Frozen at -150C', 'Cut slide', '4C in vacuum chamber', 'Frozen at -80C', 'Frozen at -70C', 'unknown', 'Paraffin block', 'RNAlater at 4C', 'RNAlater at -20C', 'Refrigerated at 4 degrees', 'Frozen in liquid nitrogen', 'Fresh', 'Refrigerated vacuum chamber', 'RNAlater at 25C', 'Not Applicable', 'Desiccant at 4C']",,Biospecimen -Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['95% Ethanol', 'Dimidoester', 'Cryo-store', 'Saline', 'Other', 'Formalin', 'OCT media', 'Dimethylacetamide', 'unknown', 'TCL lysis buffer', 'Methacarn', 'Unfixed', 'Glutaraldehyde', 'None', 'Acetone', 'Para-benzoquinone', 'Alcohol', 'Carbodiimide', 'PAXgene tissue', 'RNAlater', ""Carnoy's Fixative"", 'Polaxamer', 'NP40 lysis buffer']",,Biospecimen -Degree of Dysplasia,Degree of Dysplasia,DegreeofDysplasia,Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.,False,,"['Severe dysplasia', 'unknown', 'Mild dysplasia', 'Normal or basal cell hyperplasia or metaplasia', 'Carcinoma in Situ', 'Moderate dysplasia', '']",,Biospecimen -Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['Melanoma in situ - lentigo maligna type', 'Severe dysplasia', 'Invasive melanoma - other', 'Squamous Carcinoma in situ', 'Melanoma in situ - arising in a giant congenital nevus', 'Scar - no residual melanoma', 'Melanoma in situ - not otherwise classified', 'Hamartoma', 'Melanoma in situ - acral-lentiginous', 'Invasive melanoma - desmoplastic', 'Reserve cell hyperplasia', 'Melanocytic hyperplasia', 'Carcinoma NOS', 'Moderate dysplasia', 'Benign tumor NOS', 'Adenocarcinoma in situ - non mucinous', 'No diagnosis possible', 'Mild dysplasia', 'Adenocarcinoma in situ - mucinous', 'Invasive melanoma - superficial spreading', 'Squamous metaplasia - mature', 'Squamous metaplasia - immature', 'Persistent melanoma in situ', 'Invasive melanoma - lentigo maligna', 'Invasive melanoma - acral lentiginous', 'Normal WDA', 'Atypical melanocytic proliferation', 'Atypical adenomatous hyperplasia', 'Melanoma in situ - superficial spreading', 'Invasive melanoma - nevoid', 'Invasive melanoma - nodular type', '']",,Biospecimen -Percent Necrosis,Percent Necrosis,PercentNecrosis,Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.,False,,,,Biospecimen -Number Proliferating Cells,Number Proliferating Cells,NumberProliferatingCells,Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).,False,,,,Biospecimen -Dysplasia Fraction,Dysplasia Fraction,DysplasiaFraction,Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5],False,,,,Biospecimen -Histology Assessment Medium,Histology Assessment Medium,HistologyAssessmentMedium,The method of assessment used to characterize histology,False,,"['Other', 'Microscopy', 'unknown', 'Digital', '']",,Biospecimen +Percent Lymphocyte Infiltration,Percent Lymphocyte Infiltration,PercentLymphocyteInfiltration,Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.,False,,,,Biospecimen +Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,Biospecimen Percent Inflam Infiltration,Percent Inflam Infiltration,PercentInflamInfiltration,"Numeric value to represent local response to cellular injury, marked by capillary dilatation, edema and leukocyte infiltration; clinically, inflammation is manifest by redness, heat, pain, swelling and loss of function, with the need to heal damaged tissue.",False,,,,Biospecimen -Histology Assessment By,Histology Assessment By,HistologyAssessmentBy,Text term describing who (in what role) made the histological assessments of the sample,False,,"['Other', 'Pathologist', 'unknown', 'Research Scientist', '']",,Biospecimen -Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable',True,,,,Biospecimen -Slicing Method,Slicing Method,SlicingMethod,Imaging specific: the method by which the tissue was sliced.,False,,"['Other', 'Tissue molds', 'Sliding microtome', 'Vibratome', 'unknown', 'Cryosectioning', 'Sectioning', 'Not Reported', '']",,Biospecimen -Percent Granulocyte Infiltration,Percent Granulocyte Infiltration,PercentGranulocyteInfiltration,Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.,False,,,,Biospecimen +Fiducial Marker,Fiducial Marker,FiducialMarker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,False,,"['Grid Slides - Hemocytometer', 'unknown', 'Other', 'Adhesive Markers', 'Fluorescent Beads', 'Nuclear Stain - DAPI', 'Not Reported', '']",,Biospecimen +Histology Assessment By,Histology Assessment By,HistologyAssessmentBy,Text term describing who (in what role) made the histological assessments of the sample,False,,"['Pathologist', 'Other', 'Research Scientist', 'unknown', '']",,Biospecimen Percent Tumor Nuclei,Percent Tumor Nuclei,PercentTumorNuclei,Numeric value to represent the percentage of tumor nuclei in a malignant neoplasm sample or specimen.,False,,,,Biospecimen -Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Fluid collection', 'Re-excision', 'Lymphadenectomy - Regional Nodes', 'Non induced sputum', 'Core needle biopsy', 'Endoscopic biopsy', 'Sentinel Node Biopsy', 'BAL (bronchial alveolar lavage)', 'Not specified', 'Surgical Resection', 'Biopsy', 'Fine Needle Aspirate', 'Forceps biopsy', 'Autopsy', 'Excision', 'Punch Biopsy', 'Induced sputum', 'Cytobrush', 'Blood draw', 'Other Acquisition Method', 'Shave Biopsy']",,Biospecimen -Site Data Source,Site Data Source,SiteDataSource,"Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.",False,,,,Biospecimen -Lysis Buffer,Lysis Buffer,LysisBuffer,scRNA-seq specific: Type of lysis buffer used,False,,,,Biospecimen -Tumor Infiltrating Lymphocytes,Tumor Infiltrating Lymphocytes,TumorInfiltratingLymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],False,,,,Biospecimen -Percent Neutrophil Infiltration,Percent Neutrophil Infiltration,PercentNeutrophilInfiltration,Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.,False,,,,Biospecimen -Fiducial Marker,Fiducial Marker,FiducialMarker,Imaging specific: fiducial markers for the alignment of images taken across multiple rounds of imaging.,False,,"['Other', 'Fluorescent Beads', 'Grid Slides - Hemocytometer', 'unknown', 'Nuclear Stain - DAPI', 'Not Reported', 'Adhesive Markers', '']",,Biospecimen -Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,Biospecimen -Percent Normal Cells,Percent Normal Cells,PercentNormalCells,Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.,False,,,,Biospecimen +Percent Eosinophil Infiltration,Percent Eosinophil Infiltration,PercentEosinophilInfiltration,Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.,False,,,,Biospecimen Percent Tumor Cells,Percent Tumor Cells,PercentTumorCells,Numeric value that represents the percentage of infiltration by tumor cells in a sample.,False,,,,Biospecimen +Dysplasia Fraction,Dysplasia Fraction,DysplasiaFraction,Resulting value to represent the number of pieces of dysplasia divided by the total number of pieces. [Text: max length 5],False,,,,Biospecimen +Percent Granulocyte Infiltration,Percent Granulocyte Infiltration,PercentGranulocyteInfiltration,Numeric value to represent the percentage of infiltration by granulocytes in a tumor sample or specimen.,False,,,,Biospecimen +Tumor Infiltrating Lymphocytes,Tumor Infiltrating Lymphocytes,TumorInfiltratingLymphocytes,Measure of Tumor-Infiltrating Lymphocytes [Number],False,,,,Biospecimen +Method of Nucleic Acid Isolation,Method of Nucleic Acid Isolation,MethodofNucleicAcidIsolation,"Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]",False,,,,Biospecimen +HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,Biospecimen +Degree of Dysplasia,Degree of Dysplasia,DegreeofDysplasia,Information related to the presence of cells that look abnormal under a microscope but are not cancer. Records the degree of dysplasia for the cyst or lesion under consideration.,False,,"['Moderate dysplasia', 'Severe dysplasia', 'unknown', 'Normal or basal cell hyperplasia or metaplasia', 'Mild dysplasia', 'Carcinoma in Situ', '']",,Biospecimen Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,Biospecimen -HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Biospecimen -Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,Biospecimen +Percent Necrosis,Percent Necrosis,PercentNecrosis,Numeric value to represent the percentage of cell death in a malignant tumor sample or specimen.,False,,,,Biospecimen +Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['Ambient temperature', 'Frozen at -80C', 'Cut slide', '4C in vacuum chamber', 'Desiccant at 4C', 'RNAlater at 25C', 'Frozen at -150C', 'Frozen at -70C', 'Frozen in liquid nitrogen', 'Not Applicable', 'Paraffin block', 'unknown', 'RNAlater at -20C', 'Refrigerated at 4 degrees', 'Refrigerated vacuum chamber', 'RNAlater at 4C', 'Fresh', 'Frozen at -20C', 'Frozen in vapor phase']",,Biospecimen Processing Days from Index,Processing Days from Index,ProcessingDaysfromIndex,Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable',True,,,,Biospecimen +Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['Scar - no residual melanoma', 'Adenocarcinoma in situ - mucinous', 'Adenocarcinoma in situ - non mucinous', 'Severe dysplasia', 'Melanoma in situ - acral-lentiginous', 'Normal WDA', 'Invasive melanoma - nevoid', 'Melanoma in situ - not otherwise classified', 'Invasive melanoma - desmoplastic', 'Hamartoma', 'Invasive melanoma - superficial spreading', 'Benign tumor NOS', 'Invasive melanoma - other', 'Persistent melanoma in situ', 'Invasive melanoma - lentigo maligna', 'Mild dysplasia', 'Melanocytic hyperplasia', 'Reserve cell hyperplasia', 'Invasive melanoma - acral lentiginous', 'Moderate dysplasia', 'Melanoma in situ - arising in a giant congenital nevus', 'Squamous Carcinoma in situ', 'Squamous metaplasia - mature', 'Atypical adenomatous hyperplasia', 'Melanoma in situ - lentigo maligna type', 'Atypical melanocytic proliferation', 'Invasive melanoma - nodular type', 'Squamous metaplasia - immature', 'No diagnosis possible', 'Melanoma in situ - superficial spreading', 'Carcinoma NOS', '']",,Biospecimen Percent Stromal Cells,Percent Stromal Cells,PercentStromalCells,"Numeric value to represent the percentage of reactive cells that are present in a malignant tumor sample or specimen but are not malignant such as fibroblasts, vascular structures, etc.",False,,,,Biospecimen +Slicing Method,Slicing Method,SlicingMethod,Imaging specific: the method by which the tissue was sliced.,False,,"['Sliding microtome', 'Vibratome', 'unknown', 'Other', 'Sectioning', 'Tissue molds', 'Not Reported', 'Cryosectioning', '']",,Biospecimen +Percent Monocyte Infiltration,Percent Monocyte Infiltration,PercentMonocyteInfiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,False,,,,Biospecimen +Percent Normal Cells,Percent Normal Cells,PercentNormalCells,Numeric value to represent the percentage of normal cell content in a malignant tumor sample or specimen.,False,,,,Biospecimen +Lysis Buffer,Lysis Buffer,LysisBuffer,scRNA-seq specific: Type of lysis buffer used,False,,,,Biospecimen +Percent Neutrophil Infiltration,Percent Neutrophil Infiltration,PercentNeutrophilInfiltration,Numeric value to represent the percentage of infiltration by neutrophils in a tumor sample or specimen.,False,,,,Biospecimen +Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['None', 'PBS', 'RPMI', 'RPMI+Serum', 'DMEM+Serum', 'PBS+Serum', 'DMEM', '']",,Biospecimen +Mounting Medium,Mounting Medium,MountingMedium,"The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media",False,,"['Antifade with DAPI', 'Antifade without DAPI', 'PBS', 'Aqueous water based', 'Xylene', 'unknown', 'Not Reported', 'Non-Aqueous Solvent based', 'Toluene', '']",,Biospecimen Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Biospecimen -Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['None', 'DMEM', 'PBS', 'DMEM+Serum', 'PBS+Serum', 'RPMI+Serum', 'RPMI', '']",,Biospecimen -Mounting Medium,Mounting Medium,MountingMedium,"The solution in which the specimen is embedded, generally under a cover glass. It may be liquid, gum or resinous, soluble in water, alcohol or other solvents and be sealed from the external atmosphere by non-soluble ringing media",False,,"['Non-Aqueous Solvent based', 'Toluene', 'Aqueous water based', 'Antifade with DAPI', 'unknown', 'Antifade without DAPI', 'Not Reported', 'Xylene', 'PBS', '']",,Biospecimen -Percent Lymphocyte Infiltration,Percent Lymphocyte Infiltration,PercentLymphocyteInfiltration,Numeric value to represent the percentage of infiltration by lymphocytes in a solid tissue normal sample or specimen.,False,,,,Biospecimen -HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,Biospecimen -Method of Nucleic Acid Isolation,Method of Nucleic Acid Isolation,MethodofNucleicAcidIsolation,"Bulk RNA & DNA-seq specific: method used for nucleic acid isolation. E.g. Qiagen Allprep, Qiagen miRNAeasy. [Text - max length 100]",False,,,,Biospecimen -Percent Eosinophil Infiltration,Percent Eosinophil Infiltration,PercentEosinophilInfiltration,Numeric value to represent the percentage of infiltration by eosinophils in a tumor sample or specimen.,False,,,,Biospecimen +HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Biospecimen +Site Data Source,Site Data Source,SiteDataSource,"Text to identify the data source for the specimen/sample from within the HTAN center, if applicable. Any identifier used within the center to identify data sources. No PHI/PII is allowed.",False,,,,Biospecimen +Number Proliferating Cells,Number Proliferating Cells,NumberProliferatingCells,Numeric value that represents the count of proliferating cells determined during pathologic review of the sample slide(s).,False,,,,Biospecimen +Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,Biospecimen Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,Biospecimen -Percent Monocyte Infiltration,Percent Monocyte Infiltration,PercentMonocyteInfiltration,Numeric value to represent the percentage of monocyte infiltration in a sample or specimen.,False,,,,Biospecimen -Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['RNA Analyte', 'protein', 'cfDNA Analyte', 'DNA Analyte', 'PBMCs', 'metabolite', 'Total RNA Analyte', 'Serum Analyte', 'lipid', 'Tissue Block Analyte', 'PBMCs or Plasma or Serum Analyte', 'cDNA Libraries Analyte', 'Tissue Section Analyte', 'Plasma', '']","['Biospecimen is ""Analyte""']",Biospecimen -Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Other', 'Uncharged', 'Coverslip', 'Not applicable', 'Charged', '']","['Biospecimen is ""Analyte""']",Biospecimen -Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,True,,"['Biospecimen is ""Analyte""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Not Shipped', 'Ice Pack', 'Ambient Pack', 'Specimen at Room Temperature', 'Other Shipping Environment', 'Dry Ice', 'Cold Pack', 'Liquid Nitrogen', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Blood""']",Biospecimen -Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,,"['Biospecimen is ""Analyte""']",Biospecimen -Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,True,"['4C wet ice', 'Ambient air', 'unknown', 'Dry Ice', 'Negative -20C', 'Cold Ischemia', 'Liquid Nitrogen', 'Warm Ischemia', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,,"['Biospecimen is ""Analyte""']",Biospecimen -Sectioning Days from Index,Sectioning Days from Index,SectioningDaysfromIndex,Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable',False,True,,"['Biospecimen is ""Analyte""']",Biospecimen -Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Normal distant', 'Additional Primary', 'Metastatic', 'Primary', 'Post therapy', 'Premalignant - in situ', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Premalignant', 'Recurrent', 'Post therapy neoadjuvant', 'Not analyzed', 'Post therapy adjuvant', 'Local recurrence', 'Normal', 'Normal adjacent', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Not Applicable', 'Bilateral', 'Left', 'unknown', 'Not Reported', 'Right', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen +Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable',True,,,,Biospecimen +Histology Assessment Medium,Histology Assessment Medium,HistologyAssessmentMedium,The method of assessment used to characterize histology,False,,"['Other', 'Microscopy', 'Digital', 'unknown', '']",,Biospecimen Histologic Morphology Code,Histologic Morphology Code,HistologicMorphologyCode,"The microscopic anatomy of normal and abnormal cells and tissues of the specimen as captured in the morphology codes of the International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). Example - 8010/0",False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen Total Volume,Total Volume,TotalVolume,Numeric value for the total amount of sample or specimen,False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,False,True,"['Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Cryopreservation in dry ice - dead tissue', 'Negative 80 Deg C', 'unknown', 'Frozen', 'Formalin fixed-buffered', 'Fresh dissociated and single cell sorted', 'Cryopreservation in liquid nitrogen - dead tissue', 'Snap Frozen', 'Formalin fixed-unbuffered', 'Cryopreservation in liquid nitrogen - live cells', 'Fresh dissociated and single cell sorted into plates', 'Fresh', 'Cryopreserved', 'Formalin fixed paraffin embedded - FFPE', 'Not Reported', 'Methacarn fixed paraffin embedded - MFPE', 'Liquid Nitrogen', 'OCT', 'Fresh dissociated', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Olfactory nerve', 'Overlapping lesion of bladder', 'Anterior floor of mouth', 'Bone marrow', 'Other specified parts of female genital organs', 'Parametrium', 'Overlapping lesion of lung', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Branchial cleft', 'Lower gum', 'Renal pelvis', 'skin NOS', 'Overlapping lesion of accessory sinuses', 'Gastric antrum', 'Overlapping lesion of cervix uteri', 'Nasal cavity', 'Peripheral nerves and autonomic nervous system of thorax', 'Autonomic nervous system NOS', 'Overlapping lesion of nasopharynx', 'Lateral wall of oropharynx', 'Upper-inner quadrant of breast', 'Thymus', 'Posterior mediastinum', 'Anus NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Stomach NOS', 'Broad ligament', 'Paraspinal', 'Cloacogenic zone', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Lateral wall of bladder', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Biliary tract NOS', 'Anterior 2/3 of tongue NOS', 'Testis NOS', 'Overlapping lesion of ill-defined sites', 'Uterine adnexa', 'Fundus uteri', 'Central portion of breast', 'Overlapping lesion of skin', 'Lateral wall of nasopharynx', 'Nipple', 'Overlapping lesion of urinary organs', 'Soft palate NOS', 'Main bronchus', 'Trachea', 'Upper lobe lung', 'Anterior wall of nasopharynx', 'Specified parts of peritoneum', 'Body of penis', 'Tonsillar fossa', 'Overlapping lesion of breast', 'Adrenal gland NOS', 'Hepatic flexure of colon', 'Aortic body and other paraganglia', 'Frontal lobe', 'Pleura NOS', 'Lateral floor of mouth', 'Intrathoracic lymph nodes', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Pylorus', 'Skin of lip NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peripheral nerves and autonomic nervous system of abdomen', 'Waldeyer ring', 'Axillary tail of breast', 'Cervical esophagus', 'Not Reported', 'Round ligament', 'Anterior mediastinum', 'Cecum', 'Cerebrum', 'Cerebellum NOS', 'Ureteric orifice', 'Abdomen NOS', 'Brain NOS', 'Major salivary gland NOS', 'Thyroid gland', 'Overlapping lesion of rectum anus and anal canal', 'Upper-outer quadrant of breast', 'Peritoneum NOS', 'Male genital organs NOS', 'Cranial nerve NOS', 'Gum NOS', 'Ethmoid sinus', 'Subglottis', 'Meninges NOS', 'Nasopharynx NOS', 'Spinal cord', 'Clitoris', 'Labium majus', 'Urachus', 'Duodenum', 'Short bones of upper limb and associated joints', 'Posterior wall of oropharynx', 'Vulva NOS', 'Thorax NOS', 'Temporal lobe', 'Maxillary sinus', 'Middle third of esophagus', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of pancreas', 'Overlapping lesion of tonsil', 'Overlapping lesion of floor of mouth', 'Accessory sinus NOS', 'External lower lip', 'Vagina NOS', 'Parathyroid gland', 'Overlapping lesions of oropharynx', 'Overlapping lesion of esophagus', 'Overlapping lesion of colon', 'Base of tongue NOS', 'Overlapping lesion of vulva', 'Isthmus uteri', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of digestive system', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Ill-defined sites within respiratory system', 'Lower-inner quadrant of breast', 'Fundus of stomach', 'Prostate gland', 'Spinal meninges', 'Supraglottis', 'Bladder neck', 'Connective subcutaneous and other soft tissues of abdomen', 'Mandible', 'Blood', 'Anal canal', 'Overlapping lesion of penis', 'Nervous system NOS', 'Lymph node NOS', 'Overlapping lesion of corpus uteri', 'Retroperitoneum', 'Pharynx NOS', 'Rib sternum clavicle and associated joints', 'Lower-outer quadrant of breast', 'Intrahepatic bile duct', 'Appendix', 'Lymph nodes of multiple regions', 'Occipital lobe', 'Cervix uteri', 'Fallopian tube', 'Endometrium', 'Ventricle NOS', 'Ampulla of Vater', 'Pineal gland', 'Pelvis NOS', 'Skin of scalp and neck', 'Brain stem', 'Islets of Langerhans', 'Endocervix', 'Upper limb NOS', 'Dome of bladder', 'Thoracic esophagus', 'Vertebral column', 'Short bones of lower limb and associated joints', 'Tongue NOS', 'Overlapping lesion of male genital organs', 'Exocervix', 'Splenic flexure of colon', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Upper gum', 'Labium minus', 'Glottis', 'Overlapping lesion of lip', 'Mucosa of lower lip', 'Optic nerve', 'Kidney NOS', 'Pancreatic duct', 'Breast NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Meckel diverticulum', 'Overlapping lesion of biliary tract', 'Overlapping lesion of tongue', 'Larynx NOS', 'Ileum', 'Pancreas NOS', 'Overlapping lesion of stomach', 'Abdominal esophagus', 'Intestinal tract NOS', 'Frontal sinus', 'Cardia NOS', 'Liver', 'Tonsillar pillar', 'Bone of limb NOS', 'Cauda equina', 'Other specified parts of male genital organs', 'Upper respiratory tract NOS', 'unknown primary site', 'Small intestine NOS', 'Upper third of esophagus', 'Connective subcutaneous and other soft tissues of thorax', 'Sigmoid colon', 'Lymph nodes of head face and neck', 'Pyriform sinus', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Lung NOS', 'Border of tongue', 'Tonsil NOS', 'Rectum NOS', 'Parietal lobe', 'Hypopharynx NOS', 'Heart', 'Mouth NOS', 'Hematopoietic system NOS', 'Superior wall of nasopharynx', 'Endocrine gland NOS', 'Craniopharyngeal duct', 'Overlapping lesion of heart mediastinum and pleura', 'Lymph nodes of axilla or arm', 'Head face or neck NOS', 'Medulla of adrenal gland', 'Lymph nodes of inguinal region or leg', 'Female genital tract NOS', 'Glans penis', 'skin of lower limb and hip', 'Body of stomach', 'Reticuloendothelial system NOS', 'Choroid', 'External upper lip', 'Prepuce', 'Posterior wall of nasopharynx', 'Urinary system NOS', 'Conjunctiva', 'Rectosigmoid junction', 'Intra-abdominal lymph nodes', 'Lingual tonsil', 'External lip NOS', 'Parotid gland', 'Bones of skull and face and associated joints', 'Dorsal surface of tongue NOS', 'Lip NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of endocrine glands and related structures', 'Middle ear', 'Bladder NOS', 'Bone NOS', 'Trigone of bladder', 'Gallbladder', 'Descended testis', 'Orbit NOS', 'Descending colon', 'Spleen', 'Retromolar area', 'Ureter', 'Pelvic lymph nodes', 'skin of upper limb and shoulder', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Eye NOS', 'Myometrium', 'Lower third of esophagus', 'Body of pancreas', 'Mediastinum NOS', 'Sublingual gland', 'Anterior surface of epiglottis', 'Hard palate', 'Overlapping lesion of major salivary glands', 'Scrotum NOS', 'Ventral surface of tongue NOS', 'Submandibular gland', 'Oropharynx NOS', 'Lower limb NOS', 'Overlapping lesion of brain', 'Overlapping lesion of larynx', 'Cornea NOS', 'Corpus uteri', 'External ear', 'Commissure of lip', 'unknown', 'Cheek mucosa', 'Overlapping lesion of hypopharynx', 'Pituitary gland', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Ascending colon', 'Epididymis', 'Esophagus NOS', 'Overlapping lesion of other and unspecified parts of mouth', 'Laryngeal cartilage', 'Skin of trunk', 'Transverse colon', 'Penis NOS', 'Ovary', 'Anterior wall of bladder', 'Carotid body', 'Colon NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Jejunum', 'Spermatic cord', 'Long bones of lower limb and associated joints', 'Undescended testis', 'Head of pancreas', 'Vestibule of mouth', 'Middle lobe lung', 'Posterior wall of bladder', 'Overlapping lesion of eye and adnexa', 'Overlapping lesion of palate', 'Overlapping lesion of lip oral cavity and pharynx', 'Cerebral meninges', 'Sphenoid sinus', 'Gastrointestinal tract NOS', 'Uvula', 'Other specified parts of pancreas', 'Uterus NOS', 'Tail of pancreas', 'Acoustic nerve', 'Lacrimal gland', 'Cortex of adrenal gland', 'Palate NOS', 'Extrahepatic bile duct', 'Vallecula', 'Ciliary body', 'Hypopharyngeal aspect of aryepiglottic fold', 'Greater curvature of stomach NOS', 'Overlapping lesion of female genital organs', 'Retina', 'Other ill-defined sites', 'Posterior wall of hypopharynx', 'Urethra', 'Overlapping lesion of small intestine', 'Peripheral nerves and autonomic nervous system of pelvis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Postcricoid region', 'Lower lobe lung', 'Skin of other and unspecified parts of face', 'Mucosa of lip NOS', 'Eyelid', 'Mucosa of upper lip', 'Paraurethral gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Placenta', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen +Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Paraspinal', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Connective subcutaneous and other soft tissues of pelvis', 'Urethra', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen +Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,False,True,"['Fresh dissociated and single cell sorted', 'Fresh dissociated', 'Cryopreservation in dry ice - dead tissue', 'Liquid Nitrogen', 'Cryopreserved', 'Fresh dissociated and single cell sorted into plates', 'Formalin fixed-buffered', 'Formalin fixed-unbuffered', 'OCT', 'unknown', 'Cryopreservation in liquid nitrogen - dead tissue', 'Cryopreservation in liquid nitrogen - live cells', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Not Reported', 'Frozen', 'Formalin fixed paraffin embedded - FFPE', 'Fresh', 'Snap Frozen', 'Negative 80 Deg C', 'Methacarn fixed paraffin embedded - MFPE', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen Portion Weight,Portion Weight,PortionWeight,"Numeric value that represents the sample portion weight, measured in milligrams.",False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen +Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Right', 'unknown', 'Bilateral', 'Not Applicable', 'Not Reported', 'Left', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen +Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Analyte""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen +Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,True,"['Warm Ischemia', '4C wet ice', 'Ambient air', 'Negative -20C', 'unknown', 'Liquid Nitrogen', 'Dry Ice', 'Cold Ischemia', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Analyte""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen +Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Normal', 'Metastatic', 'Post therapy neoadjuvant', 'Premalignant - in situ', 'Post therapy adjuvant', 'Atypia - hyperplasia', 'Not analyzed', 'Normal adjacent', 'Recurrent', 'Additional Primary', 'Not Otherwise Specified', 'Post therapy', 'Local recurrence', 'Primary', 'Premalignant', 'Normal distant', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen +Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,,"['Biospecimen is ""Analyte""']",Biospecimen +Sectioning Days from Index,Sectioning Days from Index,SectioningDaysfromIndex,Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable',False,True,,"['Biospecimen is ""Analyte""']",Biospecimen +Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Uncharged', 'Charged', 'Coverslip', 'Other', 'Not applicable', '']","['Biospecimen is ""Analyte""']",Biospecimen +Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Ambient Pack', 'Specimen at Room Temperature', 'Other Shipping Environment', 'Liquid Nitrogen', 'Not Shipped', 'Ice Pack', 'Dry Ice', 'Cold Pack', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Blood""']",Biospecimen +Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['lipid', 'Tissue Section Analyte', 'PBMCs or Plasma or Serum Analyte', 'metabolite', 'RNA Analyte', 'cfDNA Analyte', 'Total RNA Analyte', 'Tissue Block Analyte', 'DNA Analyte', 'cDNA Libraries Analyte', 'PBMCs', 'protein', 'Plasma', 'Serum Analyte', '']","['Biospecimen is ""Analyte""']",Biospecimen +Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,,"['Biospecimen is ""Analyte""']",Biospecimen +Biospecimen Dimension 3,Biospecimen Dimension 3,BiospecimenDimension3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen Biospecimen Dimension 2,Biospecimen Dimension 2,BiospecimenDimension2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen Section Number in Sequence,Section Number in Sequence,SectionNumberinSequence,"Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen -Biospecimen Dimension 3,Biospecimen Dimension 3,BiospecimenDimension3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen Biospecimen Dimension 1,Biospecimen Dimension 1,BiospecimenDimension1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",Biospecimen Acquisition Method Other Specify,Acquisition Method Other Specify,AcquisitionMethodOtherSpecify,A custom acquisition method [Text - max length 100 characters],False,True,,"['Acquisition is ""Other Acquisition Method""']",Biospecimen -Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['square centimeter', 'cubic millimeter', 'mL', '']",,Biospecimen +Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['cubic millimeter', 'mL', 'square centimeter', '']",,Biospecimen Dimensions Unit,Dimensions Unit,DimensionsUnit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)",False,,"['mm', 'cm', '']",,Biospecimen -Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Cells Biospecimen Type', 'Analyte Biospecimen Type', 'Mouth Rinse Biospecimen Type', 'Ascites Biospecimen Type', 'Blood Biospecimen Type', 'Stool Biospecimen Type', 'Urine Biospecimen Type', 'Bone Marrow Biospecimen Type', 'Sputum Biospecimen Type', 'Tissue Biospecimen Type', 'Fluids Biospecimen Type']",,SRRSBiospecimen -Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['Ambient temperature', 'Frozen at -20C', 'Frozen in vapor phase', 'Frozen at -150C', 'Cut slide', '4C in vacuum chamber', 'Frozen at -80C', 'Frozen at -70C', 'unknown', 'Paraffin block', 'RNAlater at 4C', 'RNAlater at -20C', 'Refrigerated at 4 degrees', 'Frozen in liquid nitrogen', 'Fresh', 'Refrigerated vacuum chamber', 'RNAlater at 25C', 'Not Applicable', 'Desiccant at 4C']",,SRRSBiospecimen -Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['95% Ethanol', 'Dimidoester', 'Cryo-store', 'Saline', 'Other', 'Formalin', 'OCT media', 'Dimethylacetamide', 'unknown', 'TCL lysis buffer', 'Methacarn', 'Unfixed', 'Glutaraldehyde', 'None', 'Acetone', 'Para-benzoquinone', 'Alcohol', 'Carbodiimide', 'PAXgene tissue', 'RNAlater', ""Carnoy's Fixative"", 'Polaxamer', 'NP40 lysis buffer']",,SRRSBiospecimen -Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['Melanoma in situ - lentigo maligna type', 'Severe dysplasia', 'Invasive melanoma - other', 'Squamous Carcinoma in situ', 'Melanoma in situ - arising in a giant congenital nevus', 'Scar - no residual melanoma', 'Melanoma in situ - not otherwise classified', 'Hamartoma', 'Melanoma in situ - acral-lentiginous', 'Invasive melanoma - desmoplastic', 'Reserve cell hyperplasia', 'Melanocytic hyperplasia', 'Carcinoma NOS', 'Moderate dysplasia', 'Benign tumor NOS', 'Adenocarcinoma in situ - non mucinous', 'No diagnosis possible', 'Mild dysplasia', 'Adenocarcinoma in situ - mucinous', 'Invasive melanoma - superficial spreading', 'Squamous metaplasia - mature', 'Squamous metaplasia - immature', 'Persistent melanoma in situ', 'Invasive melanoma - lentigo maligna', 'Invasive melanoma - acral lentiginous', 'Normal WDA', 'Atypical melanocytic proliferation', 'Atypical adenomatous hyperplasia', 'Melanoma in situ - superficial spreading', 'Invasive melanoma - nevoid', 'Invasive melanoma - nodular type', '']",,SRRSBiospecimen -Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,,,,SRRSBiospecimen -Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable',True,,,,SRRSBiospecimen -Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,True,,"['Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Cryopreservation in dry ice - dead tissue', 'Negative 80 Deg C', 'unknown', 'Frozen', 'Formalin fixed-buffered', 'Fresh dissociated and single cell sorted', 'Cryopreservation in liquid nitrogen - dead tissue', 'Snap Frozen', 'Formalin fixed-unbuffered', 'Cryopreservation in liquid nitrogen - live cells', 'Fresh dissociated and single cell sorted into plates', 'Fresh', 'Cryopreserved', 'Formalin fixed paraffin embedded - FFPE', 'Not Reported', 'Methacarn fixed paraffin embedded - MFPE', 'Liquid Nitrogen', 'OCT', 'Fresh dissociated']",,SRRSBiospecimen -Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Fluid collection', 'Re-excision', 'Lymphadenectomy - Regional Nodes', 'Non induced sputum', 'Core needle biopsy', 'Endoscopic biopsy', 'Sentinel Node Biopsy', 'BAL (bronchial alveolar lavage)', 'Not specified', 'Surgical Resection', 'Biopsy', 'Fine Needle Aspirate', 'Forceps biopsy', 'Autopsy', 'Excision', 'Punch Biopsy', 'Induced sputum', 'Cytobrush', 'Blood draw', 'Other Acquisition Method', 'Shave Biopsy']",,SRRSBiospecimen +Biospecimen Type,Biospecimen Type,BiospecimenType,Biospecimen Type,True,,"['Urine Biospecimen Type', 'Stool Biospecimen Type', 'Analyte Biospecimen Type', 'Ascites Biospecimen Type', 'Fluids Biospecimen Type', 'Cells Biospecimen Type', 'Bone Marrow Biospecimen Type', 'Sputum Biospecimen Type', 'Blood Biospecimen Type', 'Tissue Biospecimen Type', 'Mouth Rinse Biospecimen Type']",,SRRSBiospecimen +Acquisition Method Type,Acquisition Method Type,AcquisitionMethodType,Records the method of acquisition or source for the specimen under consideration.,True,,"['Surgical Resection', 'Fine Needle Aspirate', 'Excision', 'Endoscopic biopsy', 'Induced sputum', 'Other Acquisition Method', 'Punch Biopsy', 'Fluid collection', 'Lymphadenectomy - Regional Nodes', 'BAL (bronchial alveolar lavage)', 'Core needle biopsy', 'Shave Biopsy', 'Forceps biopsy', 'Biopsy', 'Sentinel Node Biopsy', 'Blood draw', 'Not specified', 'Non induced sputum', 'Cytobrush', 'Autopsy', 'Re-excision']",,SRRSBiospecimen Histologic Morphology Code,Histologic Morphology Code,HistologicMorphologyCode,"The microscopic anatomy of normal and abnormal cells and tissues of the specimen as captured in the morphology codes of the International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). Example - 8010/0",True,,,,SRRSBiospecimen -Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,,"['4C wet ice', 'Ambient air', 'unknown', 'Dry Ice', 'Negative -20C', 'Cold Ischemia', 'Liquid Nitrogen', 'Warm Ischemia', '']",,SRRSBiospecimen +Fixative Type,Fixative Type,FixativeType,Text term to identify the type of fixative used to preserve a tissue specimen,True,,"['TCL lysis buffer', 'NP40 lysis buffer', 'Formalin', 'Dimethylacetamide', 'Methacarn', 'Unfixed', 'Alcohol', 'Polaxamer', 'Cryo-store', 'Other', ""Carnoy's Fixative"", 'RNAlater', 'Acetone', 'Saline', 'PAXgene tissue', 'None', 'unknown', 'OCT media', 'Carbodiimide', 'Glutaraldehyde', '95% Ethanol', 'Para-benzoquinone', 'Dimidoester']",,SRRSBiospecimen +Preservation Method,Preservation Method,PreservationMethod,Text term that represents the method used to preserve the sample.,True,,"['Fresh dissociated and single cell sorted', 'Fresh dissociated', 'Cryopreservation in dry ice - dead tissue', 'Liquid Nitrogen', 'Cryopreserved', 'Fresh dissociated and single cell sorted into plates', 'Formalin fixed-buffered', 'Formalin fixed-unbuffered', 'OCT', 'unknown', 'Cryopreservation in liquid nitrogen - dead tissue', 'Cryopreservation in liquid nitrogen - live cells', 'Fresh dissociated and single cell sorted into plates in NP40 buffer', 'Not Reported', 'Frozen', 'Formalin fixed paraffin embedded - FFPE', 'Fresh', 'Snap Frozen', 'Negative 80 Deg C', 'Methacarn fixed paraffin embedded - MFPE']",,SRRSBiospecimen Adjacent Biospecimen IDs,Adjacent Biospecimen IDs,AdjacentBiospecimenIDs,"List of HTAN Identifiers (separated by commas) of adjacent biospecimens cut from the same sample; for example HTA3_3000_3, HTA3_3000_4, ...",False,,,,SRRSBiospecimen +HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,SRRSBiospecimen Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSBiospecimen -Additional Topography,Additional Topography,AdditionalTopography,Topography not included in the ICD-O-3 Topography codes.,False,,"['skin of palm', 'skin of sole', 'skin of back', 'skin of upper limb and shoulder', 'skin of scalp', 'skin of lip', 'skin of abdomen', 'skin of eye lid', 'skin NOS', 'skin of nose', 'skin of neck', 'skin of scrotum', 'skin of vulva', 'skin of ear', 'Skin of trunk', 'skin of chest', 'Peri-tumoral Airway', 'Hilar Airway', 'skin of penis', 'skin of lower limb and hip', 'skin of other parts of face', 'Not Reported', 'skin of breast', '']",,SRRSBiospecimen -HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSBiospecimen -Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,SRRSBiospecimen +Storage Method,Storage Method,StorageMethod,The method by which a biomaterial was stored after preservation or before another protocol was used.,True,,"['Ambient temperature', 'Frozen at -80C', 'Cut slide', '4C in vacuum chamber', 'Desiccant at 4C', 'RNAlater at 25C', 'Frozen at -150C', 'Frozen at -70C', 'Frozen in liquid nitrogen', 'Not Applicable', 'Paraffin block', 'unknown', 'RNAlater at -20C', 'Refrigerated at 4 degrees', 'Refrigerated vacuum chamber', 'RNAlater at 4C', 'Fresh', 'Frozen at -20C', 'Frozen in vapor phase']",,SRRSBiospecimen Processing Days from Index,Processing Days from Index,ProcessingDaysfromIndex,Number of days from the research participant's index date that the biospecimen was processed. If not applicable please enter 'Not Applicable',True,,,,SRRSBiospecimen -Topography Code,Topography Code,TopographyCode,"Topography Code, indicating site within the body, based on ICD-O-3.",False,,"['C47.3', 'C49.0', 'C57.4', 'C50.9', 'C02.4', 'C57.3', 'C71.6', 'C15.9', 'C72.2', 'C57.1', 'C34.2', 'C16.9', 'C54.2', 'C75.5', 'C31.3', 'C38.1', 'C74.0', 'C04.8', 'C41.9', 'C75.3', 'C75.4', 'C55.9', 'C17.9', 'C65.9', 'C47.9', 'C14.8', 'C05.0', 'C21.0', 'C68.9', 'C41.4', 'C47.1', 'C44.4', 'C14.2', 'C49.3', 'C18.4', 'C47.0', 'C50.6', 'C41.2', 'C30.0', 'C72.8', 'C71.8', 'C66.9', 'C13.9', 'C15.2', 'C16.5', 'C40.9', 'C50.8', 'C34.9', 'C23.9', 'C41.8', 'C41.0', 'C22.0', 'C17.0', 'C11.1', 'C54.3', 'C14.0', 'C69.4', 'C63.9', 'C71.5', 'C54.8', 'Not Reported', 'C25.9', 'C18.5', 'C07.9', 'C25.8', 'C76.0', 'C37.9', 'C42.2', 'C11.8', 'C02.1', 'C34.0', 'C31.1', 'C18.2', 'C05.2', 'C02.8', 'C49.1', 'C10.1', 'C50.2', 'C44.0', 'C10.3', 'C18.1', 'C34.3', 'C00.0', 'C76.1', 'C17.2', 'C44.7', 'C03.0', 'C51.8', 'C63.1', 'C25.7', 'C54.1', 'C11.2', 'C18.3', 'C71.7', 'C49.8', 'C77.3', 'C70.9', 'C31.2', 'C69.3', 'C69.1', 'C72.5', 'C04.9', 'C25.0', 'C51.0', 'C39.0', 'C10.0', 'C44.6', 'C18.9', 'C48.1', 'C08.1', 'C69.5', 'C17.1', 'C16.3', 'C73.9', 'C49.2', 'C72.4', 'C32.9', 'C31.8', 'C09.0', 'C10.8', 'C03.1', 'C24.0', 'C22.1', 'C77.4', 'C63.2', 'C53.1', 'C77.0', 'C42.0', 'C44.1', 'C31.0', 'C06.1', 'C21.1', 'C77.9', 'C30.1', 'C62.9', 'C10.4', 'C76.7', 'C16.2', 'C16.4', 'C64.9', 'C42.3', 'C08.0', 'C24.1', 'C57.8', 'C00.5', 'C60.1', 'C26.0', 'C68.1', 'C15.3', 'C80.9', 'C76.5', 'C68.0', 'C05.8', 'C56.9', 'C11.9', 'C17.3', 'C54.0', 'C38.8', 'C03.9', 'C02.3', 'C16.8', 'C08.8', 'C71.0', 'C41.1', 'C20.9', 'C16.0', 'C42.1', 'C67.9', 'C05.9', 'C39.9', 'C13.8', 'C25.4', 'C13.1', 'C15.5', 'C57.0', 'C77.1', 'C71.1', 'C51.2', 'C60.2', 'C63.8', 'C38.3', 'C18.7', 'C75.9', 'C51.1', 'C69.9', 'C16.1', 'C47.6', 'C15.8', 'C60.8', 'C67.1', 'C41.3', 'C05.1', 'C25.3', 'C01.9', 'C00.3', 'C49.4', 'C67.6', 'C34.1', 'C67.2', 'C62.0', 'C08.9', 'C24.9', 'C57.7', 'C42.4', 'C13.0', 'C15.0', 'C63.0', 'C44.3', 'C53.8', 'C38.4', 'C26.9', 'C25.2', 'C18.8', 'C21.8', 'C76.3', 'C62.1', 'C44.2', 'C13.2', 'C11.3', 'C70.0', 'C32.0', 'C11.0', 'C17.8', 'C50.1', 'C74.9', 'C48.2', 'C02.0', 'C32.3', 'C72.0', 'C06.8', 'C33.9', 'C47.4', 'C67.8', 'C50.5', 'C68.8', 'C32.8', 'C61.9', 'C16.6', 'C71.2', 'C71.3', 'C60.9', 'C77.2', 'C69.8', 'C15.4', 'C15.1', 'C09.8', 'C67.7', 'C74.1', 'C06.2', 'C25.1', 'C67.0', 'C63.7', 'C18.6', 'C00.2', 'C57.2', 'C51.9', 'C77.8', 'C77.5', 'C00.6', 'C47.2', 'C24.8', 'C57.9', 'C72.9', 'C75.8', 'unknown', 'C47.5', 'C67.4', 'C72.3', 'C18.0', 'C26.8', 'C39.8', 'C32.1', 'C71.4', 'C50.3', 'C69.2', 'C48.0', 'C19.9', 'C06.9', 'C49.5', 'C21.2', 'C69.0', 'C12.9', 'C02.2', 'C38.0', 'C00.4', 'C04.1', 'C00.8', 'C32.2', 'C72.1', 'C40.1', 'C75.2', 'C76.4', 'C70.1', 'C52.9', 'C09.1', 'C75.0', 'C49.9', 'C40.8', 'C60.0', 'C71.9', 'C02.9', 'C49.6', 'C50.0', 'C47.8', 'C04.0', 'C69.6', 'C40.0', 'C00.1', 'C34.8', 'C50.4', 'C76.8', 'C76.2', 'C31.9', 'C38.2', 'C40.3', 'C53.9', 'C09.9', 'C75.1', 'C54.9', 'C53.0', 'C06.0', 'C44.5', 'C48.8', 'C10.9', 'C10.2', '']",,SRRSBiospecimen +Additional Topography,Additional Topography,AdditionalTopography,Topography not included in the ICD-O-3 Topography codes.,False,,"['skin of back', 'skin of lower limb and hip', 'skin of vulva', 'skin of chest', 'skin of nose', 'skin of lip', 'skin of other parts of face', 'skin NOS', 'skin of ear', 'skin of abdomen', 'skin of palm', 'skin of eye lid', 'skin of neck', 'Hilar Airway', 'skin of penis', 'skin of upper limb and shoulder', 'Peri-tumoral Airway', 'Not Reported', 'skin of breast', 'skin of scrotum', 'skin of sole', 'Skin of trunk', 'skin of scalp', '']",,SRRSBiospecimen +Preinvasive Morphology,Preinvasive Morphology,PreinvasiveMorphology,"Histologic Morphology not included in ICD-O-3 morphology codes, for preinvasive lesions included in the HTAN",False,,"['Scar - no residual melanoma', 'Adenocarcinoma in situ - mucinous', 'Adenocarcinoma in situ - non mucinous', 'Severe dysplasia', 'Melanoma in situ - acral-lentiginous', 'Normal WDA', 'Invasive melanoma - nevoid', 'Melanoma in situ - not otherwise classified', 'Invasive melanoma - desmoplastic', 'Hamartoma', 'Invasive melanoma - superficial spreading', 'Benign tumor NOS', 'Invasive melanoma - other', 'Persistent melanoma in situ', 'Invasive melanoma - lentigo maligna', 'Mild dysplasia', 'Melanocytic hyperplasia', 'Reserve cell hyperplasia', 'Invasive melanoma - acral lentiginous', 'Moderate dysplasia', 'Melanoma in situ - arising in a giant congenital nevus', 'Squamous Carcinoma in situ', 'Squamous metaplasia - mature', 'Atypical adenomatous hyperplasia', 'Melanoma in situ - lentigo maligna type', 'Atypical melanocytic proliferation', 'Invasive melanoma - nodular type', 'Squamous metaplasia - immature', 'No diagnosis possible', 'Melanoma in situ - superficial spreading', 'Carcinoma NOS', '']",,SRRSBiospecimen +Ischemic Time,Ischemic Time,IschemicTime,"Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. Integer value.",False,,,,SRRSBiospecimen +Topography Code,Topography Code,TopographyCode,"Topography Code, indicating site within the body, based on ICD-O-3.",False,,"['C63.9', 'C16.6', 'C17.0', 'C72.4', 'C16.0', 'C44.2', 'C00.3', 'C40.1', 'C69.0', 'C67.1', 'C44.3', 'C69.3', 'C75.3', 'C09.8', 'C53.0', 'C18.7', 'C47.0', 'C44.7', 'C21.0', 'C77.4', 'C05.2', 'C47.5', 'C60.2', 'C47.1', 'C24.9', 'C25.8', 'C40.8', 'C10.3', 'C69.1', 'C17.2', 'C04.0', 'C69.6', 'C49.2', 'C11.3', 'C71.4', 'C57.9', 'C14.0', 'C31.1', 'C34.2', 'C72.2', 'C40.9', 'C09.9', 'C11.2', 'C15.8', 'C47.4', 'C41.1', 'C44.5', 'C71.1', 'C41.8', 'C75.0', 'C42.1', 'C34.0', 'C50.4', 'C57.3', 'C38.2', 'C10.9', 'C39.0', 'C70.9', 'C50.1', 'C18.9', 'C49.0', 'C34.3', 'C01.9', 'C73.9', 'C77.5', 'C21.1', 'C00.2', 'C42.3', 'C17.1', 'C72.3', 'C31.8', 'C69.4', 'C15.2', 'C49.4', 'C39.8', 'C09.1', 'C03.1', 'C18.4', 'C38.0', 'C18.1', 'C50.5', 'C42.2', 'C76.4', 'C70.0', 'C02.8', 'C51.2', 'C00.1', 'C14.8', 'C76.5', 'C41.9', 'C10.8', 'C10.2', 'C57.7', 'C31.3', 'C67.8', 'C71.2', 'C11.0', 'C60.1', 'C02.3', 'C16.9', 'C26.8', 'C40.3', 'C77.8', 'C10.1', 'C02.9', 'C51.9', 'C02.2', 'C08.1', 'C44.1', 'C16.1', 'C60.0', 'C75.1', 'C18.2', 'C00.0', 'C72.5', 'C13.8', 'C69.8', 'C51.0', 'C04.1', 'C60.8', 'C68.0', 'C18.8', 'C12.9', 'C04.9', 'C23.9', 'C18.3', 'C13.1', 'C32.8', 'C54.2', 'C06.9', 'C15.3', 'C16.5', 'C15.4', 'C34.1', 'C32.1', 'C00.6', 'C70.1', 'C71.9', 'C31.0', 'C06.2', 'C03.9', 'C32.0', 'C11.8', 'C49.1', 'C72.1', 'C67.2', 'C17.3', 'C09.0', 'C41.0', 'C48.2', 'C77.2', 'C49.3', 'C76.3', 'C16.3', 'C22.0', 'C75.5', 'C48.8', 'C76.0', 'C75.9', 'C54.8', 'C14.2', 'C72.9', 'C44.0', 'C50.6', 'C08.0', 'C55.9', 'C68.1', 'C24.1', 'C62.0', 'C06.1', 'C76.7', 'C48.0', 'C05.1', 'C00.8', 'C15.5', 'C63.0', 'C67.4', 'C24.8', 'C54.9', 'C08.9', 'C38.3', 'C26.9', 'C34.8', 'C25.1', 'C15.9', 'C00.4', 'C26.0', 'C16.4', 'C19.9', 'C18.0', 'C54.0', 'C76.8', 'C63.7', 'C56.9', 'C62.9', 'C11.1', 'C53.8', 'C21.2', 'C63.8', 'Not Reported', 'C10.0', 'C25.7', 'C42.0', 'C71.3', 'C69.9', 'C44.4', 'C57.1', 'C77.9', 'C67.0', 'C05.9', 'C57.8', 'C16.2', 'C34.9', 'C71.8', 'C13.2', 'C51.1', 'C25.3', 'C11.9', 'C41.4', 'C18.6', 'C76.1', 'C41.2', 'C21.8', 'C80.9', 'C75.8', 'C31.9', 'C38.1', 'C37.9', 'C25.0', 'C71.6', 'C25.4', 'C75.2', 'C41.3', 'C49.8', 'C64.9', 'C49.9', 'C47.2', 'C16.8', 'C54.1', 'C22.1', 'C32.3', 'C63.1', 'C72.0', 'C17.8', 'C00.5', 'C02.1', 'C50.2', 'C52.9', 'C40.0', 'C33.9', 'C13.9', 'C57.4', 'C77.1', 'C24.0', 'C57.0', 'C47.9', 'C25.2', 'C71.0', 'C66.9', 'C02.0', 'C50.8', 'C69.5', 'C31.2', 'C71.5', 'C30.1', 'C74.1', 'C38.8', 'C30.0', 'C47.8', 'C60.9', 'C75.4', 'C03.0', 'C17.9', 'C05.8', 'C54.3', 'C77.0', 'C74.9', 'C08.8', 'C25.9', 'C71.7', 'C68.8', 'C67.7', 'C53.1', 'C67.9', 'C67.6', 'C04.8', 'C53.9', 'C13.0', 'C76.2', 'C18.5', 'C02.4', 'unknown', 'C20.9', 'C42.4', 'C61.9', 'C05.0', 'C49.6', 'C07.9', 'C63.2', 'C65.9', 'C47.3', 'C62.1', 'C49.5', 'C57.2', 'C72.8', 'C74.0', 'C06.8', 'C44.6', 'C48.1', 'C69.2', 'C50.3', 'C50.9', 'C15.0', 'C39.9', 'C77.3', 'C06.0', 'C10.4', 'C47.6', 'C68.9', 'C15.1', 'C51.8', 'C50.0', 'C38.4', 'C32.2', 'C32.9', '']",,SRRSBiospecimen +Ischemic Temperature,Ischemic Temperature,IschemicTemperature,Specify whether specimen experienced warm or cold ischemia.,False,,"['Warm Ischemia', '4C wet ice', 'Ambient air', 'Negative -20C', 'unknown', 'Liquid Nitrogen', 'Dry Ice', 'Cold Ischemia', '']",,SRRSBiospecimen +Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['None', 'PBS', 'RPMI', 'RPMI+Serum', 'DMEM+Serum', 'PBS+Serum', 'DMEM', '']",,SRRSBiospecimen Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSBiospecimen -Collection Media,Collection Media,CollectionMedia,Material Specimen is collected into post procedure,False,,"['None', 'DMEM', 'PBS', 'DMEM+Serum', 'PBS+Serum', 'RPMI+Serum', 'RPMI', '']",,SRRSBiospecimen -HTAN Parent ID,HTAN Parent ID,HTANParentID,HTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.,True,,,,SRRSBiospecimen +Source HTAN Biospecimen ID,Source HTAN Biospecimen ID,SourceHTANBiospecimenID,This is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).,False,,,,SRRSBiospecimen +HTAN Biospecimen ID,HTAN Biospecimen ID,HTANBiospecimenID,HTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSBiospecimen Timepoint Label,Timepoint Label,TimepointLabel,"Label to identify the time point at which the clinical data or biospecimen was obtained (e.g. Baseline, End of Treatment, Overall survival, Final). NO PHI/PII INFORMATION IS ALLOWED.",True,,,,SRRSBiospecimen -Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['RNA Analyte', 'protein', 'cfDNA Analyte', 'DNA Analyte', 'PBMCs', 'metabolite', 'Total RNA Analyte', 'Serum Analyte', 'lipid', 'Tissue Block Analyte', 'PBMCs or Plasma or Serum Analyte', 'cDNA Libraries Analyte', 'Tissue Section Analyte', 'Plasma', '']","['Biospecimen is ""Analyte""']",SRRSBiospecimen -Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Other', 'Uncharged', 'Coverslip', 'Not applicable', 'Charged', '']","['Biospecimen is ""Analyte""']",SRRSBiospecimen -Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Not Shipped', 'Ice Pack', 'Ambient Pack', 'Specimen at Room Temperature', 'Other Shipping Environment', 'Dry Ice', 'Cold Pack', 'Liquid Nitrogen', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Blood""']",SRRSBiospecimen -Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen -Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen -Sectioning Days from Index,Sectioning Days from Index,SectioningDaysfromIndex,Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable',False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen -Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Normal distant', 'Additional Primary', 'Metastatic', 'Primary', 'Post therapy', 'Premalignant - in situ', 'Atypia - hyperplasia', 'Not Otherwise Specified', 'Premalignant', 'Recurrent', 'Post therapy neoadjuvant', 'Not analyzed', 'Post therapy adjuvant', 'Local recurrence', 'Normal', 'Normal adjacent', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen -Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Not Applicable', 'Bilateral', 'Left', 'unknown', 'Not Reported', 'Right', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen +Collection Days from Index,Collection Days from Index,CollectionDaysfromIndex,Number of days from the research participant's index date that the biospecimen was obtained. If not applicable please enter 'Not Applicable',True,,,,SRRSBiospecimen Total Volume,Total Volume,TotalVolume,Numeric value for the total amount of sample or specimen,False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen -Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Olfactory nerve', 'Overlapping lesion of bladder', 'Anterior floor of mouth', 'Bone marrow', 'Other specified parts of female genital organs', 'Parametrium', 'Overlapping lesion of lung', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Branchial cleft', 'Lower gum', 'Renal pelvis', 'skin NOS', 'Overlapping lesion of accessory sinuses', 'Gastric antrum', 'Overlapping lesion of cervix uteri', 'Nasal cavity', 'Peripheral nerves and autonomic nervous system of thorax', 'Autonomic nervous system NOS', 'Overlapping lesion of nasopharynx', 'Lateral wall of oropharynx', 'Upper-inner quadrant of breast', 'Thymus', 'Posterior mediastinum', 'Anus NOS', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Stomach NOS', 'Broad ligament', 'Paraspinal', 'Cloacogenic zone', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Lateral wall of bladder', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Biliary tract NOS', 'Anterior 2/3 of tongue NOS', 'Testis NOS', 'Overlapping lesion of ill-defined sites', 'Uterine adnexa', 'Fundus uteri', 'Central portion of breast', 'Overlapping lesion of skin', 'Lateral wall of nasopharynx', 'Nipple', 'Overlapping lesion of urinary organs', 'Soft palate NOS', 'Main bronchus', 'Trachea', 'Upper lobe lung', 'Anterior wall of nasopharynx', 'Specified parts of peritoneum', 'Body of penis', 'Tonsillar fossa', 'Overlapping lesion of breast', 'Adrenal gland NOS', 'Hepatic flexure of colon', 'Aortic body and other paraganglia', 'Frontal lobe', 'Pleura NOS', 'Lateral floor of mouth', 'Intrathoracic lymph nodes', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Pylorus', 'Skin of lip NOS', 'Lesser curvature of stomach NOS', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Peripheral nerves and autonomic nervous system of abdomen', 'Waldeyer ring', 'Axillary tail of breast', 'Cervical esophagus', 'Not Reported', 'Round ligament', 'Anterior mediastinum', 'Cecum', 'Cerebrum', 'Cerebellum NOS', 'Ureteric orifice', 'Abdomen NOS', 'Brain NOS', 'Major salivary gland NOS', 'Thyroid gland', 'Overlapping lesion of rectum anus and anal canal', 'Upper-outer quadrant of breast', 'Peritoneum NOS', 'Male genital organs NOS', 'Cranial nerve NOS', 'Gum NOS', 'Ethmoid sinus', 'Subglottis', 'Meninges NOS', 'Nasopharynx NOS', 'Spinal cord', 'Clitoris', 'Labium majus', 'Urachus', 'Duodenum', 'Short bones of upper limb and associated joints', 'Posterior wall of oropharynx', 'Vulva NOS', 'Thorax NOS', 'Temporal lobe', 'Maxillary sinus', 'Middle third of esophagus', 'Overlapping lesion of brain and central nervous system', 'Overlapping lesion of pancreas', 'Overlapping lesion of tonsil', 'Overlapping lesion of floor of mouth', 'Accessory sinus NOS', 'External lower lip', 'Vagina NOS', 'Parathyroid gland', 'Overlapping lesions of oropharynx', 'Overlapping lesion of esophagus', 'Overlapping lesion of colon', 'Base of tongue NOS', 'Overlapping lesion of vulva', 'Isthmus uteri', 'Long bones of upper limb scapula and associated joints', 'Overlapping lesion of digestive system', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Ill-defined sites within respiratory system', 'Lower-inner quadrant of breast', 'Fundus of stomach', 'Prostate gland', 'Spinal meninges', 'Supraglottis', 'Bladder neck', 'Connective subcutaneous and other soft tissues of abdomen', 'Mandible', 'Blood', 'Anal canal', 'Overlapping lesion of penis', 'Nervous system NOS', 'Lymph node NOS', 'Overlapping lesion of corpus uteri', 'Retroperitoneum', 'Pharynx NOS', 'Rib sternum clavicle and associated joints', 'Lower-outer quadrant of breast', 'Intrahepatic bile duct', 'Appendix', 'Lymph nodes of multiple regions', 'Occipital lobe', 'Cervix uteri', 'Fallopian tube', 'Endometrium', 'Ventricle NOS', 'Ampulla of Vater', 'Pineal gland', 'Pelvis NOS', 'Skin of scalp and neck', 'Brain stem', 'Islets of Langerhans', 'Endocervix', 'Upper limb NOS', 'Dome of bladder', 'Thoracic esophagus', 'Vertebral column', 'Short bones of lower limb and associated joints', 'Tongue NOS', 'Overlapping lesion of male genital organs', 'Exocervix', 'Splenic flexure of colon', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Upper gum', 'Labium minus', 'Glottis', 'Overlapping lesion of lip', 'Mucosa of lower lip', 'Optic nerve', 'Kidney NOS', 'Pancreatic duct', 'Breast NOS', 'Pelvic bones sacrum coccyx and associated joints', 'Meckel diverticulum', 'Overlapping lesion of biliary tract', 'Overlapping lesion of tongue', 'Larynx NOS', 'Ileum', 'Pancreas NOS', 'Overlapping lesion of stomach', 'Abdominal esophagus', 'Intestinal tract NOS', 'Frontal sinus', 'Cardia NOS', 'Liver', 'Tonsillar pillar', 'Bone of limb NOS', 'Cauda equina', 'Other specified parts of male genital organs', 'Upper respiratory tract NOS', 'unknown primary site', 'Small intestine NOS', 'Upper third of esophagus', 'Connective subcutaneous and other soft tissues of thorax', 'Sigmoid colon', 'Lymph nodes of head face and neck', 'Pyriform sinus', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Lung NOS', 'Border of tongue', 'Tonsil NOS', 'Rectum NOS', 'Parietal lobe', 'Hypopharynx NOS', 'Heart', 'Mouth NOS', 'Hematopoietic system NOS', 'Superior wall of nasopharynx', 'Endocrine gland NOS', 'Craniopharyngeal duct', 'Overlapping lesion of heart mediastinum and pleura', 'Lymph nodes of axilla or arm', 'Head face or neck NOS', 'Medulla of adrenal gland', 'Lymph nodes of inguinal region or leg', 'Female genital tract NOS', 'Glans penis', 'skin of lower limb and hip', 'Body of stomach', 'Reticuloendothelial system NOS', 'Choroid', 'External upper lip', 'Prepuce', 'Posterior wall of nasopharynx', 'Urinary system NOS', 'Conjunctiva', 'Rectosigmoid junction', 'Intra-abdominal lymph nodes', 'Lingual tonsil', 'External lip NOS', 'Parotid gland', 'Bones of skull and face and associated joints', 'Dorsal surface of tongue NOS', 'Lip NOS', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of endocrine glands and related structures', 'Middle ear', 'Bladder NOS', 'Bone NOS', 'Trigone of bladder', 'Gallbladder', 'Descended testis', 'Orbit NOS', 'Descending colon', 'Spleen', 'Retromolar area', 'Ureter', 'Pelvic lymph nodes', 'skin of upper limb and shoulder', 'Floor of mouth NOS', 'Connective subcutaneous and other soft tissues NOS', 'Eye NOS', 'Myometrium', 'Lower third of esophagus', 'Body of pancreas', 'Mediastinum NOS', 'Sublingual gland', 'Anterior surface of epiglottis', 'Hard palate', 'Overlapping lesion of major salivary glands', 'Scrotum NOS', 'Ventral surface of tongue NOS', 'Submandibular gland', 'Oropharynx NOS', 'Lower limb NOS', 'Overlapping lesion of brain', 'Overlapping lesion of larynx', 'Cornea NOS', 'Corpus uteri', 'External ear', 'Commissure of lip', 'unknown', 'Cheek mucosa', 'Overlapping lesion of hypopharynx', 'Pituitary gland', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Ascending colon', 'Epididymis', 'Esophagus NOS', 'Overlapping lesion of other and unspecified parts of mouth', 'Laryngeal cartilage', 'Skin of trunk', 'Transverse colon', 'Penis NOS', 'Ovary', 'Anterior wall of bladder', 'Carotid body', 'Colon NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Jejunum', 'Spermatic cord', 'Long bones of lower limb and associated joints', 'Undescended testis', 'Head of pancreas', 'Vestibule of mouth', 'Middle lobe lung', 'Posterior wall of bladder', 'Overlapping lesion of eye and adnexa', 'Overlapping lesion of palate', 'Overlapping lesion of lip oral cavity and pharynx', 'Cerebral meninges', 'Sphenoid sinus', 'Gastrointestinal tract NOS', 'Uvula', 'Other specified parts of pancreas', 'Uterus NOS', 'Tail of pancreas', 'Acoustic nerve', 'Lacrimal gland', 'Cortex of adrenal gland', 'Palate NOS', 'Extrahepatic bile duct', 'Vallecula', 'Ciliary body', 'Hypopharyngeal aspect of aryepiglottic fold', 'Greater curvature of stomach NOS', 'Overlapping lesion of female genital organs', 'Retina', 'Other ill-defined sites', 'Posterior wall of hypopharynx', 'Urethra', 'Overlapping lesion of small intestine', 'Peripheral nerves and autonomic nervous system of pelvis', 'Overlapping lesion of retroperitoneum and peritoneum', 'Postcricoid region', 'Lower lobe lung', 'Skin of other and unspecified parts of face', 'Mucosa of lip NOS', 'Eyelid', 'Mucosa of upper lip', 'Paraurethral gland', 'Connective subcutaneous and other soft tissues of pelvis', 'Placenta', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen +Site of Resection or Biopsy,Site of Resection or Biopsy,SiteofResectionorBiopsy,"The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).",False,True,"['Appendix', 'Parametrium', 'Aortic body and other paraganglia', 'Trachea', 'Transverse colon', 'Lateral floor of mouth', 'Paraspinal', 'Cerebellum NOS', 'Paraurethral gland', 'Overlapping lesion of bones joints and articular cartilage of limbs', 'Overlapping lesion of female genital organs', 'Cloacogenic zone', 'Peripheral nerves and autonomic nervous system of trunk NOS', 'Overlapping lesion of bladder', 'Overlapping lesion of retroperitoneum and peritoneum', 'Uterine adnexa', 'Vertebral column', 'Upper lobe lung', 'Overlapping lesion of floor of mouth', 'Spinal meninges', 'Labium minus', 'Hard palate', 'Spleen', 'Breast NOS', 'Middle third of esophagus', 'Overlapping lesion of respiratory system and intrathoracic organs', 'Duodenum', 'Spinal cord', 'Anterior wall of nasopharynx', 'Body of pancreas', 'Fundus uteri', 'Upper third of esophagus', 'Short bones of upper limb and associated joints', 'Overlapping lesion of cervix uteri', 'Lateral wall of bladder', 'Nervous system NOS', 'Upper-outer quadrant of breast', 'Nipple', 'Labium majus', 'Exocervix', 'Vulva NOS', 'Gum NOS', 'Mediastinum NOS', 'Urinary system NOS', 'Medulla of adrenal gland', 'Tongue NOS', 'Overlapping lesion of eye and adnexa', 'Bone marrow', 'Reticuloendothelial system NOS', 'Renal pelvis', 'Brain stem', 'Ureter', 'Overlapping lesion of small intestine', 'unknown primary site', 'Intestinal tract NOS', 'Laryngeal cartilage', 'Scrotum NOS', 'Upper respiratory tract NOS', 'Rectosigmoid junction', 'Overlapping lesion of stomach', 'Sphenoid sinus', 'Lymph nodes of inguinal region or leg', 'Pancreas NOS', 'Kidney NOS', 'Branchial cleft', 'Pharynx NOS', 'Tonsillar pillar', 'Islets of Langerhans', 'Optic nerve', 'Lymph nodes of multiple regions', 'Overlapping lesion of tonsil', 'Posterior wall of hypopharynx', 'Intrahepatic bile duct', 'Lacrimal gland', 'Orbit NOS', 'Bone NOS', 'Submandibular gland', 'Endocervix', 'Corpus uteri', 'Skin of trunk', 'Retina', 'Overlapping lesion of endocrine glands and related structures', 'Ciliary body', 'Overlapping lesion of larynx', 'Anterior mediastinum', 'Lower limb NOS', 'Frontal sinus', 'Superior wall of nasopharynx', 'Prepuce', 'Major salivary gland NOS', 'Stomach NOS', 'Overlapping lesion of rectum anus and anal canal', 'Olfactory nerve', 'Peripheral nerves and autonomic nervous system of thorax', 'Testis NOS', 'Cheek mucosa', 'Abdomen NOS', 'Waldeyer ring', 'Bone of limb NOS', 'Cervical esophagus', 'Intrathoracic lymph nodes', 'Overlapping lesion of digestive system', 'Axillary tail of breast', 'Lower-outer quadrant of breast', 'Overlapping lesion of brain and central nervous system', 'Lymph node NOS', 'Adrenal gland NOS', 'Soft palate NOS', 'Overlapping lesion of pancreas', 'Autonomic nervous system NOS', 'Border of tongue', 'Posterior wall of oropharynx', 'Meninges NOS', 'Colon NOS', 'Lateral wall of oropharynx', 'Supraglottis', 'Overlapping lesion of vulva', 'Fallopian tube', 'Extrahepatic bile duct', 'Posterior wall of nasopharynx', 'External ear', 'skin of upper limb and shoulder', 'Craniopharyngeal duct', 'Specified parts of peritoneum', 'Lingual tonsil', 'Maxillary sinus', 'Lower gum', 'Female genital tract NOS', 'Central portion of breast', 'Overlapping lesion of male genital organs', 'Overlapping lesion of colon', 'Connective subcutaneous and other soft tissues of upper limb and shoulder', 'Mucosa of lower lip', 'Tonsillar fossa', 'Other specified parts of pancreas', 'Anterior wall of bladder', 'Overlapping lesion of esophagus', 'Overlapping lesion of other and unspecified parts of mouth', 'Connective subcutaneous and other soft tissues of thorax', 'Conjunctiva', 'Nasopharynx NOS', 'Mandible', 'Lung NOS', 'Overlapping lesions of oropharynx', 'External upper lip', 'Vagina NOS', 'Short bones of lower limb and associated joints', 'Placenta', 'Ileum', 'Overlapping lesion of lung', 'Broad ligament', 'Lower third of esophagus', 'Abdominal esophagus', 'External lip NOS', 'Other specified parts of male genital organs', 'Lateral wall of nasopharynx', 'Other specified parts of female genital organs', 'Bones of skull and face and associated joints', 'Palate NOS', 'Retromolar area', 'Connective subcutaneous and other soft tissues of head face and neck', 'Overlapping lesion of heart mediastinum and pleura', 'Oropharynx NOS', 'Bladder neck', 'Anal canal', 'Lymph nodes of head face and neck', 'Middle ear', 'Brain NOS', 'Ascending colon', 'Isthmus uteri', 'Ill-defined sites within respiratory system', 'Eye NOS', 'Hematopoietic system NOS', 'Accessory sinus NOS', 'Gastric antrum', 'Trigone of bladder', 'Head face or neck NOS', 'Pylorus', 'Cornea NOS', 'Pelvic lymph nodes', 'Occipital lobe', 'Meckel diverticulum', 'Peripheral nerves and autonomic nervous system of upper limb and shoulder', 'Base of tongue NOS', 'Cranial nerve NOS', 'Overlapping lesion of hypopharynx', 'Greater curvature of stomach NOS', 'Overlapping lesion of lip oral cavity and pharynx', 'Commissure of lip', 'Overlapping lesion of penis', 'Ovary', 'Cervix uteri', 'Vestibule of mouth', 'Hypopharyngeal aspect of aryepiglottic fold', 'Prostate gland', 'Dome of bladder', 'Parotid gland', 'Pelvis NOS', 'Lower-inner quadrant of breast', 'Connective subcutaneous and other soft tissues of abdomen', 'Pineal gland', 'Fundus of stomach', 'Endocrine gland NOS', 'Cerebrum', 'Splenic flexure of colon', 'Floor of mouth NOS', 'External lower lip', 'Eyelid', 'Carotid body', 'Choroid', 'Overlapping lesion of major salivary glands', 'Mucosa of lip NOS', 'Not Reported', 'Urachus', 'Liver', 'skin of lower limb and hip', 'Overlapping lesion of brain', 'Overlapping lesion of peripheral nerves and autonomic nervous system', 'Connective subcutaneous and other soft tissues of trunk NOS', 'Thyroid gland', 'Thoracic esophagus', 'Biliary tract NOS', 'Other ill-defined sites', 'Overlapping lesion of palate', 'Heart', 'Larynx NOS', 'Clitoris', 'Middle lobe lung', 'Peripheral nerves and autonomic nervous system of abdomen', 'Upper gum', 'Peripheral nerves and autonomic nervous system of head face and neck', 'Parathyroid gland', 'Peripheral nerves and autonomic nervous system of pelvis', 'Lesser curvature of stomach NOS', 'Anterior 2/3 of tongue NOS', 'Thymus', 'Frontal lobe', 'Blood', 'Descending colon', 'Gallbladder', 'Pelvic bones sacrum coccyx and associated joints', 'Lymph nodes of axilla or arm', 'Male genital organs NOS', 'Acoustic nerve', 'Thorax NOS', 'Connective subcutaneous and other soft tissues of pelvis', 'Urethra', 'Body of penis', 'Peripheral nerves and autonomic nervous system of lower limb and hip', 'Rib sternum clavicle and associated joints', 'Cortex of adrenal gland', 'Jejunum', 'Temporal lobe', 'Overlapping lesion of skin', 'Upper-inner quadrant of breast', 'Bladder NOS', 'Ventral surface of tongue NOS', 'Uterus NOS', 'Anus NOS', 'Overlapping lesion of accessory sinuses', 'Rectum NOS', 'Overlapping lesion of bones joints and articular cartilage', 'Cardia NOS', 'Anterior surface of epiglottis', 'Overlapping lesion of urinary organs', 'Skin of other and unspecified parts of face', 'Skin of scalp and neck', 'Overlapping lesion of connective subcutaneous and other soft tissues', 'Lip NOS', 'Posterior mediastinum', 'Sigmoid colon', 'Main bronchus', 'Anterior floor of mouth', 'Overlapping lesion of ill-defined sites', 'Hepatic flexure of colon', 'Overlapping lesion of biliary tract', 'Connective subcutaneous and other soft tissues NOS', 'Tonsil NOS', 'Long bones of upper limb scapula and associated joints', 'Lower lobe lung', 'Myometrium', 'Posterior wall of bladder', 'Hypopharynx NOS', 'Skin of lip NOS', 'Cauda equina', 'Pleura NOS', 'Esophagus NOS', 'Overlapping lesion of breast', 'Cerebral meninges', 'Sublingual gland', 'Penis NOS', 'Overlapping lesion of lip', 'Descended testis', 'Glottis', 'Upper limb NOS', 'Nasal cavity', 'Ethmoid sinus', 'Ampulla of Vater', 'Vallecula', 'Overlapping lesion of tongue', 'skin NOS', 'Epididymis', 'Undescended testis', 'Ventricle NOS', 'Pancreatic duct', 'Body of stomach', 'Endometrium', 'Long bones of lower limb and associated joints', 'Dorsal surface of tongue NOS', 'unknown', 'Overlapping lesion of nasopharynx', 'Pituitary gland', 'Head of pancreas', 'Gastrointestinal tract NOS', 'Glans penis', 'Postcricoid region', 'Mucosa of upper lip', 'Intra-abdominal lymph nodes', 'Pyriform sinus', 'Round ligament', 'Ureteric orifice', 'Cecum', 'Peritoneum NOS', 'Parietal lobe', 'Subglottis', 'Mouth NOS', 'Small intestine NOS', 'Connective subcutaneous and other soft tissues of lower limb and hip', 'Overlapping lesion of corpus uteri', 'Uvula', 'Spermatic cord', 'Retroperitoneum', 'Tail of pancreas', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen Portion Weight,Portion Weight,PortionWeight,"Numeric value that represents the sample portion weight, measured in milligrams.",False,True,,"['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen +Specimen Laterality,Specimen Laterality,SpecimenLaterality,"For tumors in paired organs, designates the side on which the specimen was obtained.",False,True,"['Right', 'unknown', 'Bilateral', 'Not Applicable', 'Not Reported', 'Left', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen +Tumor Tissue Type,Tumor Tissue Type,TumorTissueType,Text that describes the kind of disease present in the tumor specimen as related to a specific timepoint (add rows to select multiple values along with timepoints),False,True,"['Normal', 'Metastatic', 'Post therapy neoadjuvant', 'Premalignant - in situ', 'Post therapy adjuvant', 'Atypia - hyperplasia', 'Not analyzed', 'Normal adjacent', 'Recurrent', 'Additional Primary', 'Not Otherwise Specified', 'Post therapy', 'Local recurrence', 'Primary', 'Premalignant', 'Normal distant', '']","['Biospecimen is ""Urine""', 'Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen +Section Thickness Value,Section Thickness Value,SectionThicknessValue,"Numeric value to describe the thickness of a slice to tissue taken from a biospecimen, measured in microns (um).",False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen +Sectioning Days from Index,Sectioning Days from Index,SectioningDaysfromIndex,Number of days from the research participant's index date that the biospecimen was sectioned after collection. If not applicable please enter 'Not Applicable',False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen +Slide Charge Type,Slide Charge Type,SlideChargeType,A description of the charge on the glass slide.,False,True,"['Uncharged', 'Charged', 'Coverslip', 'Other', 'Not applicable', '']","['Biospecimen is ""Analyte""']",SRRSBiospecimen +Shipping Condition Type,Shipping Condition Type,ShippingConditionType,Text descriptor of the shipping environment of a biospecimen.,False,True,"['Ambient Pack', 'Specimen at Room Temperature', 'Other Shipping Environment', 'Liquid Nitrogen', 'Not Shipped', 'Ice Pack', 'Dry Ice', 'Cold Pack', '']","['Biospecimen is ""Analyte""', 'Biospecimen is ""Blood""']",SRRSBiospecimen +Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,False,True,"['lipid', 'Tissue Section Analyte', 'PBMCs or Plasma or Serum Analyte', 'metabolite', 'RNA Analyte', 'cfDNA Analyte', 'Total RNA Analyte', 'Tissue Block Analyte', 'DNA Analyte', 'cDNA Libraries Analyte', 'PBMCs', 'protein', 'Plasma', 'Serum Analyte', '']","['Biospecimen is ""Analyte""']",SRRSBiospecimen +Fixation Duration,Fixation Duration,FixationDuration,"The length of time, from beginning to end, required to process or preserve biospecimens in fixative (measured in minutes)",False,True,,"['Biospecimen is ""Analyte""']",SRRSBiospecimen +Biospecimen Dimension 3,Biospecimen Dimension 3,BiospecimenDimension3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen Biospecimen Dimension 2,Biospecimen Dimension 2,BiospecimenDimension2,"Second dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen Section Number in Sequence,Section Number in Sequence,SectionNumberinSequence,"Numeric value (integer, including ranges) provided to a sample in a series of sections (list all adjacent sections in the Adjacent Biospecimen IDs field)",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen -Biospecimen Dimension 3,Biospecimen Dimension 3,BiospecimenDimension3,"Third dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen Biospecimen Dimension 1,Biospecimen Dimension 1,BiospecimenDimension1,"First dimension of tissue fragment (number, up to one decimal place) measured in units as defined by the ""dimensions_unit"" CDE",False,True,,"['Biospecimen is ""Bone""', 'Biospecimen is ""Tissue""']",SRRSBiospecimen Acquisition Method Other Specify,Acquisition Method Other Specify,AcquisitionMethodOtherSpecify,A custom acquisition method [Text - max length 100 characters],False,True,,"['Acquisition is ""Other Acquisition Method""']",SRRSBiospecimen -Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['square centimeter', 'cubic millimeter', 'mL', '']",,SRRSBiospecimen +Total Volume Unit,Total Volume Unit,TotalVolumeUnit,Unit of measurement used for the total amount of sample or specimen,False,,"['cubic millimeter', 'mL', 'square centimeter', '']",,SRRSBiospecimen Dimensions Unit,Dimensions Unit,DimensionsUnit,"Unit of measurement used for dimension CDEs in metric system (i.e. cm, mm, etc)",False,,"['mm', 'cm', '']",,SRRSBiospecimen HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,OtherAssay -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,OtherAssay -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,OtherAssay -Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,OtherAssay Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,OtherAssay Filename,Filename,Filename,Name of a file,True,,,,OtherAssay +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,OtherAssay +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,OtherAssay +Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,OtherAssay HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ExSeqMinimal -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ExSeqMinimal -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ExSeqMinimal -Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,ExSeqMinimal Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ExSeqMinimal Filename,Filename,Filename,Name of a file,True,,,,ExSeqMinimal -Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Random', 'Oligo-dT', 'Feature barcoding', 'Poly-dT']",,ScRNA-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,ScRNA-seqLevel1 -Input Cells and Nuclei,Input Cells and Nuclei,InputCellsandNuclei,"Number of cells and number of nuclei input; entry format: number, number",True,,,,ScRNA-seqLevel1 -Read1,Read1,Read1,Read 1 content description,True,,"['cDNA', 'Cell Barcode and UMI']",,ScRNA-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer IIx', 'Illumina HiSeq 2500', 'GridION', '454 GS FLX Titanium', 'Illumina NovaSeq 6000', 'NovaSeqS4', 'Illumina HiSeq X Five', 'Illumina MiSeq', 'Ion Torrent Proton', 'Other', 'PromethION', 'Illumina NextSeq', 'Revio', 'AB SOLiD 4', 'NovaSeq 6000', 'unknown', 'Ultima Genomics UG100', 'Ion Torrent PGM', 'Illumina HiSeq X Ten', 'Oxford Nanopore minION', 'Illumina NextSeq 1000', 'Illumina Next Seq 2500', 'PacBio RS', 'Illumina NextSeq 2000', 'Illumina Next Seq 500', 'AB SOLiD 2', 'Ion Torrent S5', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Complete Genomics', 'Illumina HiSeq 2000', 'AB SOLiD 3', 'Not Reported', 'Illumina Genome Analyzer II', 'Illumina HiSeq 4000']",,ScRNA-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ExSeqMinimal +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ExSeqMinimal +Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,ExSeqMinimal +Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Enzymatic Digestion', 'Not Applicable', 'Dounce', 'gentleMACS']",,ScRNA-seqLevel1 Total Number of Input Cells,Total Number of Input Cells,TotalNumberofInputCells,Number of cells loaded/placed on plates,True,,,,ScRNA-seqLevel1 -Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['gentleMACS', 'Not Applicable', 'Dounce', 'Enzymatic Digestion']",,ScRNA-seqLevel1 -Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['inDropsV3', 'Smart-seq2', 'inDropsV2', 'Nextera XT', 'sci-ATAC-seq', '10xV3', 'CEL-seq2', '10x Multiome', '10xV1.1', 'Drop-seq', '10xV2', '10x FLEX', '10xV3.1', 'Smart-SeqV4', 'TruDrop', ""10x GEM 3'"", '10xV1.0', ""10x GEM 5'""]",,ScRNA-seqLevel1 Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,ScRNA-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Single Nucleus', 'Micro-region', 'Bulk Nuclei', 'Single Cell']",,ScRNA-seqLevel1 -Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['no', 'yes']",,ScRNA-seqLevel1 -Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScRNA-seqLevel1 -Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['10x', 'Droplets', 'Nuclei Isolation', 'Plates', 'FACS', 'Microfluidics Chip']",,ScRNA-seqLevel1 -Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,ScRNA-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,ScRNA-seqLevel1 +Input Cells and Nuclei,Input Cells and Nuclei,InputCellsandNuclei,"Number of cells and number of nuclei input; entry format: number, number",True,,,,ScRNA-seqLevel1 Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable',True,,,,ScRNA-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel1 -Read2,Read2,Read2,Read 2 content description,True,,"['cDNA', 'Cell Barcode and UMI']",,ScRNA-seqLevel1 -End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,ScRNA-seqLevel1 -Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'Other Spike In', 'PhiX', 'ERCC']",,ScRNA-seqLevel1 +Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScRNA-seqLevel1 Single Cell Dissociation Days from Index,Single Cell Dissociation Days from Index,SingleCellDissociationDaysfromIndex,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable',True,,,,ScRNA-seqLevel1 -Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel1 +Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,ScRNA-seqLevel1 Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScRNA-seqLevel1 +Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['yes', 'no']",,ScRNA-seqLevel1 +Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,ScRNA-seqLevel1 +End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,ScRNA-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['I1', 'R2', 'R1', 'Other', 'R1&R2']",,ScRNA-seqLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScRNA-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ScRNA-seqLevel1 +Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Plates', 'Nuclei Isolation', '10x', 'Droplets', 'Microfluidics Chip', 'FACS']",,ScRNA-seqLevel1 +Read1,Read1,Read1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScRNA-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel1 -Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",ScRNA-seqLevel1 -cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Read2 is ""cDNA""']",ScRNA-seqLevel1 -cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Read2 is ""cDNA""']",ScRNA-seqLevel1 -UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 +Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV3.1', '10x FLEX', ""10x GEM 5'"", 'inDropsV3', 'Nextera XT', 'Smart-SeqV4', '10xV3', 'CEL-seq2', '10xV2', '10xV1.1', ""10x GEM 3'"", 'sci-ATAC-seq', 'Smart-seq2', 'inDropsV2', '10x Multiome', '10xV1.0', 'TruDrop', 'Drop-seq']",,ScRNA-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel1 +Read2,Read2,Read2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScRNA-seqLevel1 +Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['Other Spike In', 'No Spike In', 'ERCC', 'PhiX']",,ScRNA-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScRNA-seqLevel1 +Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Feature barcoding', 'Poly-dT', 'Random', 'Oligo-dT']",,ScRNA-seqLevel1 +Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 +UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 +UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 -Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 -UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",ScRNA-seqLevel1 -Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,True,"['no', 'yes', '']","['Library Construction Method is ""CEL-seq2""']",ScRNA-seqLevel1 +cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Read2 is ""cDNA""']",ScRNA-seqLevel1 +cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Read2 is ""cDNA""']",ScRNA-seqLevel1 Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,False,True,,"['Library Construction Method is ""CEL-seq2""']",ScRNA-seqLevel1 +Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,True,"['yes', 'no', '']","['Library Construction Method is ""CEL-seq2""']",ScRNA-seqLevel1 Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,,"['Spike In is ""ERCC""']",ScRNA-seqLevel1 +Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",ScRNA-seqLevel1 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cufflinks', 'HCA Optimus', 'DEXSeq', 'HTSeq - FPKM', 'STARsolo', 'Other', 'Differentiation trajectory analysis', 'dropEST', 'SEQC', 'CellRanger', 'Cell annotation']",,ScRNA-seqLevel2 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScRNA-seqLevel2 -UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,ScRNA-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ScRNA-seqLevel2 -Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,ScRNA-seqLevel2 Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel2 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Other', 'HTSeq - FPKM', 'DEXSeq', 'Differentiation trajectory analysis', 'SEQC', 'HCA Optimus', 'CellRanger', 'Cufflinks', 'STARsolo', 'Cell annotation', 'dropEST']",,ScRNA-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel2 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel2 -Cell Barcode Tag,Cell Barcode Tag,CellBarcodeTag,SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z),True,,,,ScRNA-seqLevel2 Whitelist Cell Barcode File Link,Whitelist Cell Barcode File Link,WhitelistCellBarcodeFileLink,Link to file listing all possible cell barcodes. URL,True,,,,ScRNA-seqLevel2 -Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,ScRNA-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel2 Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel2 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel2 +Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,ScRNA-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel2 +Cell Barcode Tag,Cell Barcode Tag,CellBarcodeTag,SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z),True,,,,ScRNA-seqLevel2 scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel2 +Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,ScRNA-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScRNA-seqLevel2 +Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,ScRNA-seqLevel2 Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScRNA-seqLevel2 -Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['no', 'Yes - Applied Hard Trimming']",,ScRNA-seqLevel2 +UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,ScRNA-seqLevel2 Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,,"['Applied Hard Trimming is ""Yes - Applied Hard Trimming""']",ScRNA-seqLevel2 Cell Total,Cell Total,CellTotal,Number of sequenced cells. Applies to raw counts matrix only.,True,,,,ScRNA-seqLevel3 -Cell Median Number Genes,Cell Median Number Genes,CellMedianNumberGenes,Median number of genes detected per cell. Number,True,,,,ScRNA-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ScRNA-seqLevel3 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cufflinks', 'HCA Optimus', 'DEXSeq', 'HTSeq - FPKM', 'STARsolo', 'Other', 'Differentiation trajectory analysis', 'dropEST', 'SEQC', 'CellRanger', 'Cell annotation']",,ScRNA-seqLevel3 +Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Normalized Counts', 'Batch Corrected Counts']",,ScRNA-seqLevel3 Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel3 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel3 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Other', 'HTSeq - FPKM', 'DEXSeq', 'Differentiation trajectory analysis', 'SEQC', 'HCA Optimus', 'CellRanger', 'Cufflinks', 'STARsolo', 'Cell annotation', 'dropEST']",,ScRNA-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel3 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel3 -Cell Median Number Reads,Cell Median Number Reads,CellMedianNumberReads,Median number of reads per cell. Number,True,,,,ScRNA-seqLevel3 -Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Other', 'Transcript Expression', 'Isoform Expression Quantification', 'Gene Expression', 'Splice Junction Quantification', 'Gene Expression Quantification', 'Exon Expression Quantification']",,ScRNA-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel3 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel3 +Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification', 'Gene Expression Quantification', 'Other', 'Exon Expression Quantification']",,ScRNA-seqLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel3 scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel3 -Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Batch Corrected Counts', 'Raw Counts', 'Normalized Counts', 'Scaled Counts']",,ScRNA-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScRNA-seqLevel3 +Cell Median Number Genes,Cell Median Number Genes,CellMedianNumberGenes,Median number of genes detected per cell. Number,True,,,,ScRNA-seqLevel3 +Cell Median Number Reads,Cell Median Number Reads,CellMedianNumberReads,Median number of reads per cell. Number,True,,,,ScRNA-seqLevel3 Linked Matrices,Linked Matrices,LinkedMatrices,All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames,False,,,,ScRNA-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ScRNA-seqLevel4 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cufflinks', 'HCA Optimus', 'DEXSeq', 'HTSeq - FPKM', 'STARsolo', 'Other', 'Differentiation trajectory analysis', 'dropEST', 'SEQC', 'CellRanger', 'Cell annotation']",,ScRNA-seqLevel4 Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScRNA-seqLevel4 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel4 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Other', 'HTSeq - FPKM', 'DEXSeq', 'Differentiation trajectory analysis', 'SEQC', 'HCA Optimus', 'CellRanger', 'Cufflinks', 'STARsolo', 'Cell annotation', 'dropEST']",,ScRNA-seqLevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel4 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScRNA-seqLevel4 Filename,Filename,Filename,Name of a file,True,,,,ScRNA-seqLevel4 -scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel4 -Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Random', 'Oligo-dT', 'Feature barcoding', 'Poly-dT']",,Slide-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,Slide-seqLevel1 -Spatial Library Construction Method,Spatial Library Construction Method,SpatialLibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['inDropsV3', 'Smart-seq2', 'inDropsV2', 'Nextera XT', '10xV3', '10xV1.1', 'Drop-seq', '10xV2', '10xV3.1', 'Smart-SeqV4', 'TruDrop', '10xV1.0']",,Slide-seqLevel1 -Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,,"['cDNA', 'Spatial Barcode and UMI']",,Slide-seqLevel1 -Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,,"['cDNA', 'Spatial Barcode and UMI']",,Slide-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer IIx', 'Illumina HiSeq 2500', 'GridION', '454 GS FLX Titanium', 'Illumina NovaSeq 6000', 'NovaSeqS4', 'Illumina HiSeq X Five', 'Illumina MiSeq', 'Ion Torrent Proton', 'Other', 'PromethION', 'Illumina NextSeq', 'Revio', 'AB SOLiD 4', 'NovaSeq 6000', 'unknown', 'Ultima Genomics UG100', 'Ion Torrent PGM', 'Illumina HiSeq X Ten', 'Oxford Nanopore minION', 'Illumina NextSeq 1000', 'Illumina Next Seq 2500', 'PacBio RS', 'Illumina NextSeq 2000', 'Illumina Next Seq 500', 'AB SOLiD 2', 'Ion Torrent S5', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Complete Genomics', 'Illumina HiSeq 2000', 'AB SOLiD 3', 'Not Reported', 'Illumina Genome Analyzer II', 'Illumina HiSeq 4000']",,Slide-seqLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,Slide-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Single Nucleus', 'Micro-region', 'Bulk Nuclei', 'Single Cell']",,Slide-seqLevel1 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScRNA-seqLevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScRNA-seqLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScRNA-seqLevel4 +scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,ScRNA-seqLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScRNA-seqLevel4 Spatial Barcode and UMI,Spatial Barcode and UMI,SpatialBarcodeandUMI,Spot and transcript identifiers,True,,,,Slide-seqLevel1 -Spatial Barcode Offset,Spatial Barcode Offset,SpatialBarcodeOffset,Offset in sequence for spot barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1 +Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,,"['Spatial Barcode and UMI', 'cDNA']",,Slide-seqLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,Slide-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,Slide-seqLevel1 +Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable',True,,,,Slide-seqLevel1 Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,Slide-seqLevel1 Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,Slide-seqLevel1 -Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable',True,,,,Slide-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Slide-seqLevel1 -End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,Slide-seqLevel1 -Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'Other Spike In', 'PhiX', 'ERCC']",,Slide-seqLevel1 -Filename,Filename,Filename,Name of a file,True,,,,Slide-seqLevel1 Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,Slide-seqLevel1 +Spatial Barcode Offset,Spatial Barcode Offset,SpatialBarcodeOffset,Offset in sequence for spot barcode read (in bp): number,False,True,,"['Spatial Read1 is ""Spatial Barcode and UMI""']",Slide-seqLevel1 +Filename,Filename,Filename,Name of a file,True,,,,Slide-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,Slide-seqLevel1 +End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,Slide-seqLevel1 +Spatial Library Construction Method,Spatial Library Construction Method,SpatialLibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV3.1', 'inDropsV3', 'Nextera XT', 'Smart-SeqV4', '10xV3', '10xV2', '10xV1.1', 'Smart-seq2', 'inDropsV2', '10xV1.0', 'TruDrop', 'Drop-seq']",,Slide-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['I1', 'R2', 'R1', 'Other', 'R1&R2']",,Slide-seqLevel1 +Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,,"['Spatial Barcode and UMI', 'cDNA']",,Slide-seqLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,Slide-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,Slide-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Slide-seqLevel1 -UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Slide-seqLevel1 +Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['Other Spike In', 'No Spike In', 'ERCC', 'PhiX']",,Slide-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,Slide-seqLevel1 +Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Feature barcoding', 'Poly-dT', 'Random', 'Oligo-dT']",,Slide-seqLevel1 UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1 +UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1 Spatial Barcode Length,Spatial Barcode Length,SpatialBarcodeLength,Length of spot barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",Slide-seqLevel1 -Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",Slide-seqLevel1 -cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",Slide-seqLevel1 cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",Slide-seqLevel1 +cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",Slide-seqLevel1 Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,,"['Spike In is ""ERCC""']",Slide-seqLevel1 +Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",Slide-seqLevel1 +Slide-seq Workflow Parameter Description,Slide-seq Workflow Parameter Description,Slide-seqWorkflowParameterDescription,Parameters used to run the Slide-seq workflow. String,True,,,,Slide-seqLevel2 Spatial Barcode Tag,Spatial Barcode Tag,SpatialBarcodeTag,SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z),True,,,,Slide-seqLevel2 -Slide-seq Workflow Type,Slide-seq Workflow Type,Slide-seqWorkflowType,Generic name for the workflow used to analyze the Slide-seq data set. String,True,,,,Slide-seqLevel2 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,Slide-seqLevel2 -UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,Slide-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Slide-seqLevel2 -Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,Slide-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,Slide-seqLevel2 Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,Slide-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,Slide-seqLevel2 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,Slide-seqLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Slide-seqLevel2 -Matched Spatial Barcode Tag,Matched Spatial Barcode Tag,MatchedSpatialBarcodeTag,SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific),True,,,,Slide-seqLevel2 -Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,Slide-seqLevel2 Filename,Filename,Filename,Name of a file,True,,,,Slide-seqLevel2 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,Slide-seqLevel2 +Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,Slide-seqLevel2 +Slide-seq Workflow Type,Slide-seq Workflow Type,Slide-seqWorkflowType,Generic name for the workflow used to analyze the Slide-seq data set. String,True,,,,Slide-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,Slide-seqLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Slide-seqLevel2 +Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,Slide-seqLevel2 +Matched Spatial Barcode Tag,Matched Spatial Barcode Tag,MatchedSpatialBarcodeTag,SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific),True,,,,Slide-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,Slide-seqLevel2 +Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,Slide-seqLevel2 Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,Slide-seqLevel2 -Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['no', 'Yes - Applied Hard Trimming']",,Slide-seqLevel2 -Slide-seq Workflow Parameter Description,Slide-seq Workflow Parameter Description,Slide-seqWorkflowParameterDescription,Parameters used to run the Slide-seq workflow. String,True,,,,Slide-seqLevel2 +UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,Slide-seqLevel2 Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,,"['Applied Hard Trimming is ""Yes - Applied Hard Trimming""']",Slide-seqLevel2 -Slide-seq Workflow Type,Slide-seq Workflow Type,Slide-seqWorkflowType,Generic name for the workflow used to analyze the Slide-seq data set. String,True,,,,Slide-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Slide-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,Slide-seqLevel3 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,Slide-seqLevel3 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,Slide-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,Slide-seqLevel3 Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,Slide-seqLevel3 -Beads Total,Beads Total,BeadsTotal,Number of sequenced beads. Applies to raw counts matrix only. Integer,False,,,,Slide-seqLevel3 +Slide-seq Workflow Parameter Description,Slide-seq Workflow Parameter Description,Slide-seqWorkflowParameterDescription,Parameters used to run the Slide-seq workflow. String,True,,,,Slide-seqLevel3 +Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Normalized Counts', 'Batch Corrected Counts']",,Slide-seqLevel3 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,Slide-seqLevel3 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,Slide-seqLevel3 -Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,,,Slide-seqLevel3 -Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Other', 'Transcript Expression', 'Isoform Expression Quantification', 'Gene Expression', 'Splice Junction Quantification', 'Gene Expression Quantification', 'Exon Expression Quantification']",,Slide-seqLevel3 Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,Slide-seqLevel3 -Slide-seq Bead File Type,Slide-seq Bead File Type,Slide-seqBeadFileType,The type of Level 3 file submitted as part of the Slide-seq workflow.,True,,"['All Bead Locations', 'Matrix Barcodes', 'Not Applicable', 'Matched Bead Barcodes', 'All Bead Barcodes', 'Matrix Features', 'Matched Bead Locations']",,Slide-seqLevel3 -Slide-seq Fragment Size,Slide-seq Fragment Size,Slide-seqFragmentSize,Average cDNA length associated with the experiemtn. Integer,False,,,,Slide-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,Slide-seqLevel3 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,Slide-seqLevel3 +Slide-seq Workflow Type,Slide-seq Workflow Type,Slide-seqWorkflowType,Generic name for the workflow used to analyze the Slide-seq data set. String,True,,,,Slide-seqLevel3 +Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,,,Slide-seqLevel3 +Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification', 'Gene Expression Quantification', 'Other', 'Exon Expression Quantification']",,Slide-seqLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,Slide-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,Slide-seqLevel3 +Slide-seq Fragment Size,Slide-seq Fragment Size,Slide-seqFragmentSize,Average cDNA length associated with the experiemtn. Integer,False,,,,Slide-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,Slide-seqLevel3 +Beads Total,Beads Total,BeadsTotal,Number of sequenced beads. Applies to raw counts matrix only. Integer,False,,,,Slide-seqLevel3 +Slide-seq Bead File Type,Slide-seq Bead File Type,Slide-seqBeadFileType,The type of Level 3 file submitted as part of the Slide-seq workflow.,True,,"['Matched Bead Barcodes', 'All Bead Locations', 'Matrix Features', 'Matched Bead Locations', 'Not Applicable', 'All Bead Barcodes', 'Matrix Barcodes']",,Slide-seqLevel3 Median UMI Counts per Spot,Median UMI Counts per Spot,MedianUMICountsperSpot,The median number of UMI counts per tissue covered spot.,True,,,,Slide-seqLevel3 -Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Batch Corrected Counts', 'Raw Counts', 'Normalized Counts', 'Scaled Counts']",,Slide-seqLevel3 -Slide-seq Workflow Parameter Description,Slide-seq Workflow Parameter Description,Slide-seqWorkflowParameterDescription,Parameters used to run the Slide-seq workflow. String,True,,,,Slide-seqLevel3 -Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,BulkRNA-seqLevel1 -QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkRNA-seqLevel1 -Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1 Transcript Integrity Number,Transcript Integrity Number,TranscriptIntegrityNumber,"Used to describe the quality of the starting material, esp. in regards to FFPE samples. Number",False,,,,BulkRNA-seqLevel1 -Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 -Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkRNA-seqLevel1 -QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkRNA-seqLevel1 -Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 -Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1 +Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkRNA-seqLevel1 -Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 -Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 -Kmer Content,Kmer Content,KmerContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer IIx', 'Illumina HiSeq 2500', 'GridION', '454 GS FLX Titanium', 'Illumina NovaSeq 6000', 'NovaSeqS4', 'Illumina HiSeq X Five', 'Illumina MiSeq', 'Ion Torrent Proton', 'Other', 'PromethION', 'Illumina NextSeq', 'Revio', 'AB SOLiD 4', 'NovaSeq 6000', 'unknown', 'Ultima Genomics UG100', 'Ion Torrent PGM', 'Illumina HiSeq X Ten', 'Oxford Nanopore minION', 'Illumina NextSeq 1000', 'Illumina Next Seq 2500', 'PacBio RS', 'Illumina NextSeq 2000', 'Illumina Next Seq 500', 'AB SOLiD 2', 'Ion Torrent S5', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Complete Genomics', 'Illumina HiSeq 2000', 'AB SOLiD 3', 'Not Reported', 'Illumina Genome Analyzer II', 'Illumina HiSeq 4000']",,BulkRNA-seqLevel1 Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,BulkRNA-seqLevel1 -Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkRNA-seqLevel1 -Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 -Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['Other', 'Random', 'miRNA Size Fractionation', 'rRNA Depletion', 'Poly-T Enrichment', 'PCR', 'Affinity Enrichment', 'Hybrid Selection']",,BulkRNA-seqLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,BulkRNA-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Single Nucleus', 'Micro-region', 'Bulk Nuclei', 'Single Cell']",,BulkRNA-seqLevel1 -Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 -Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkRNA-seqLevel1 -Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkRNA-seqLevel1 Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,BulkRNA-seqLevel1 +Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,BulkRNA-seqLevel1 +Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkRNA-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,BulkRNA-seqLevel1 Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 +Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 +Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1 Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkRNA-seqLevel1 +Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Long Read', 'Single Read', 'Paired End', 'Mid-length']",,BulkRNA-seqLevel1 +Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkRNA-seqLevel1 +Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 +Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 +Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkRNA-seqLevel1 +Micro-region Seq Platform,Micro-region Seq Platform,Micro-regionSeqPlatform,The platform used for micro-regional RNA sequencing (if applicable),False,,"['Laser Capture Microdissection', 'Rarecyte Pick-Seq', '']",,BulkRNA-seqLevel1 +RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,,,BulkRNA-seqLevel1 ROI Tag,ROI Tag,ROITag,The tag or grouping used to identify the ROI in micro-regional RNA sequencing (if applicable). Must match the ROI tag within the count matrix in level 3.,False,,,,BulkRNA-seqLevel1 -Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1 -Micro-region Seq Platform,Micro-region Seq Platform,Micro-regionSeqPlatform,The platform used for micro-regional RNA sequencing (if applicable),False,,"['Rarecyte Pick-Seq', 'Laser Capture Microdissection', '']",,BulkRNA-seqLevel1 -Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1 -Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 -Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkRNA-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel1 -Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 -QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkRNA-seqLevel1 -Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'Other Spike In', 'PhiX', 'ERCC']",,BulkRNA-seqLevel1 -Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel1 -DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,BulkRNA-seqLevel1 -RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,,,BulkRNA-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkRNA-seqLevel1 -Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,BulkRNA-seqLevel1 -Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Mid-length', 'Long Read', 'Paired End', 'Single Read']",,BulkRNA-seqLevel1 +Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkRNA-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,BulkRNA-seqLevel1 +Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkRNA-seqLevel1 +QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkRNA-seqLevel1 +Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['Random', 'miRNA Size Fractionation', 'Poly-T Enrichment', 'Affinity Enrichment', 'Other', 'rRNA Depletion', 'Hybrid Selection', 'PCR']",,BulkRNA-seqLevel1 +Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1 +Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkRNA-seqLevel1 +Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Unstranded', 'Not Applicable', 'First Stranded', 'Second Stranded', '']",,BulkRNA-seqLevel1 +Kmer Content,Kmer Content,KmerContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 +Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['I1', 'R2', 'R1', 'Other', 'R1&R2']",,BulkRNA-seqLevel1 +To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['no', 'Yes - Trim Adapter Sequence', '']",,BulkRNA-seqLevel1 +Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkRNA-seqLevel1 Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,BulkRNA-seqLevel1 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkRNA-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkRNA-seqLevel1 +DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,BulkRNA-seqLevel1 +QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkRNA-seqLevel1 +QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkRNA-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel1 -Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Not Applicable', 'Unstranded', 'Second Stranded', 'First Stranded', '']",,BulkRNA-seqLevel1 -Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkRNA-seqLevel1 -To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['no', 'Yes - Trim Adapter Sequence', '']",,BulkRNA-seqLevel1 -Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,BulkRNA-seqLevel1 -Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 +Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkRNA-seqLevel1 Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,BulkRNA-seqLevel1 -Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 +Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1 +Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkRNA-seqLevel1 +Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel1 +Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkRNA-seqLevel1 +Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 +Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['Other Spike In', 'No Spike In', 'ERCC', 'PhiX']",,BulkRNA-seqLevel1 +Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkRNA-seqLevel1 +Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 +Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkRNA-seqLevel1 Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],False,True,,"['Spike In is ""ERCC""']",BulkRNA-seqLevel1 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2 +MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI-low', 'MSI-high', 'MSS', 'MSI', '']",,BulkRNA-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkRNA-seqLevel2 +Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2 Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 -Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkRNA-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel2 -MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI-low', 'MSS', 'MSI', 'MSI-high', '']",,BulkRNA-seqLevel2 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkRNA-seqLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 +Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,BulkRNA-seqLevel2 Is lowest level,Is lowest level,Islowestlevel,Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing,False,,"['Yes - Is lowest level', 'no', '']",,BulkRNA-seqLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkRNA-seqLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BatMeth', 'MethylCoder', 'BRAT-BW', 'BSMAP', 'Bowtie', 'ERNE-BS5', 'STAR 2-Pass Genome', 'BS-Seeker2', 'STAR 2-Pass', 'BWA with Mark Duplicates and BQSR', 'BWA-aln', 'BWA-mem', 'STAR 2-Pass Transcriptome', 'BWA', 'STAR 2-Pass Chimeric', 'Segemehl', 'BSmooth', 'Other Alignment Workflow', 'None', 'GSNAP', 'Pash', 'BS-Seeker', 'Bisulfighter', 'BWA with BQSR', 'Bismark', 'RMAP', 'B-SOLANA', 'SOCS-B', 'BWA-meth', 'LAST']",,BulkRNA-seqLevel2 -MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkRNA-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel2 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkRNA-seqLevel2 +Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkRNA-seqLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkRNA-seqLevel2 Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkRNA-seqLevel2 Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,BulkRNA-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2 -Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,BulkRNA-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel2 -Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkRNA-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkRNA-seqLevel2 Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkRNA-seqLevel2 -MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkRNA-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,BulkRNA-seqLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkRNA-seqLevel2 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkRNA-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkRNA-seqLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkRNA-seqLevel2 +MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkRNA-seqLevel2 Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkRNA-seqLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkRNA-seqLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BWA-meth', 'Bismark', 'BSMAP', 'STAR 2-Pass Transcriptome', 'STAR 2-Pass Chimeric', 'BWA-mem', 'MethylCoder', 'B-SOLANA', 'Pash', 'BWA', 'SOCS-B', 'BWA with Mark Duplicates and BQSR', 'BS-Seeker2', 'None', 'LAST', 'BatMeth', 'ERNE-BS5', 'BRAT-BW', 'Segemehl', 'STAR 2-Pass Genome', 'GSNAP', 'BWA with BQSR', 'RMAP', 'STAR 2-Pass', 'Bowtie', 'BSmooth', 'Other Alignment Workflow', 'Bisulfighter', 'BWA-aln', 'BS-Seeker']",,BulkRNA-seqLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkRNA-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkRNA-seqLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkRNA-seqLevel2 +MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkRNA-seqLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkRNA-seqLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkRNA-seqLevel2 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,False,True,,"['Is lowest level is ""Yes - Is lowest level""']",BulkRNA-seqLevel2 Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",BulkRNA-seqLevel2 -Pseudo Alignment Used,Pseudo Alignment Used,PseudoAlignmentUsed,Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.,True,,"['no', 'Yes - Pseudo Alignment Used']",,BulkRNA-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,BulkRNA-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel3 -Fusion Gene Detected,Fusion Gene Detected,FusionGeneDetected,Was a fusion gene identified?,False,,"['no', 'Yes - Fusion Gene Detected', 'unknown', '']",,BulkRNA-seqLevel3 +Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Normalized Counts', 'Batch Corrected Counts']",,BulkRNA-seqLevel3 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkRNA-seqLevel3 -Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Other', 'Transcript Expression', 'Isoform Expression Quantification', 'Gene Expression', 'Splice Junction Quantification', 'Gene Expression Quantification', 'Exon Expression Quantification']",,BulkRNA-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,BulkRNA-seqLevel3 -Expression Units,Expression Units,ExpressionUnits,How quantities are corrected for gene length,True,,"['Other', 'FPKM', 'NA', 'Counts', 'TPM', 'RPKM']",,BulkRNA-seqLevel3 -Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Batch Corrected Counts', 'Raw Counts', 'Normalized Counts', 'Scaled Counts']",,BulkRNA-seqLevel3 +Pseudo Alignment Used,Pseudo Alignment Used,PseudoAlignmentUsed,Pseudo aligners such as Kallisto or Salmon do not produce aligned reads BAM files. True indicates pseudoalignment was used.,True,,"['Yes - Pseudo Alignment Used', 'no']",,BulkRNA-seqLevel3 Fusion Gene Identity,Fusion Gene Identity,FusionGeneIdentity,The gene symbols of fused genes.,False,,,,BulkRNA-seqLevel3 +Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification', 'Gene Expression Quantification', 'Other', 'Exon Expression Quantification']",,BulkRNA-seqLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkRNA-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkRNA-seqLevel3 +Expression Units,Expression Units,ExpressionUnits,How quantities are corrected for gene length,True,,"['Counts', 'NA', 'TPM', 'RPKM', 'Other', 'FPKM']",,BulkRNA-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkRNA-seqLevel3 +Fusion Gene Detected,Fusion Gene Detected,FusionGeneDetected,Was a fusion gene identified?,False,,"['Yes - Fusion Gene Detected', 'no', 'unknown', '']",,BulkRNA-seqLevel3 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3 -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3 +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,False,True,,"['Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""']",BulkRNA-seqLevel3 Specify Other Fusion Gene,Specify Other Fusion Gene,SpecifyOtherFusionGene,"Specify fusion gene detected, if not in list",False,True,,"['Fusion Gene Identity is ""Other Fusion Gene""']",BulkRNA-seqLevel3 -Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,BulkWESLevel1 -Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1 -Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkWESLevel1 -Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1 Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkWESLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer IIx', 'Illumina HiSeq 2500', 'GridION', '454 GS FLX Titanium', 'Illumina NovaSeq 6000', 'NovaSeqS4', 'Illumina HiSeq X Five', 'Illumina MiSeq', 'Ion Torrent Proton', 'Other', 'PromethION', 'Illumina NextSeq', 'Revio', 'AB SOLiD 4', 'NovaSeq 6000', 'unknown', 'Ultima Genomics UG100', 'Ion Torrent PGM', 'Illumina HiSeq X Ten', 'Oxford Nanopore minION', 'Illumina NextSeq 1000', 'Illumina Next Seq 2500', 'PacBio RS', 'Illumina NextSeq 2000', 'Illumina Next Seq 500', 'AB SOLiD 2', 'Ion Torrent S5', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Complete Genomics', 'Illumina HiSeq 2000', 'AB SOLiD 3', 'Not Reported', 'Illumina Genome Analyzer II', 'Illumina HiSeq 4000']",,BulkWESLevel1 Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,BulkWESLevel1 -Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['Other', 'Random', 'miRNA Size Fractionation', 'rRNA Depletion', 'Poly-T Enrichment', 'PCR', 'Affinity Enrichment', 'Hybrid Selection']",,BulkWESLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,BulkWESLevel1 -Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkWESLevel1 -Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkWESLevel1 -Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkWESLevel1 Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,BulkWESLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,BulkWESLevel1 +Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,BulkWESLevel1 +Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkWESLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,BulkWESLevel1 Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,BulkWESLevel1 -Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1 Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,BulkWESLevel1 -Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkWESLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel1 +Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Long Read', 'Single Read', 'Paired End', 'Mid-length']",,BulkWESLevel1 +Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,BulkWESLevel1 Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkWESLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,BulkWESLevel1 -Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Mid-length', 'Long Read', 'Paired End', 'Single Read']",,BulkWESLevel1 -Target Capture Kit,Target Capture Kit,TargetCaptureKit,"Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.",True,,"['Custom Twist Broad Exome v1.0 - 35.0 Mb', 'TruSight Myeloid Sequencing Panel', 'Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb', 'Ion AmpliSeq Comprehensive Cancer Panel', 'SeqCap EZ Human Exome v2.0', 'SureSelect Human All Exon v5 + UTR', 'xGen Universal Blocking Oligo – TS HT-i5 - 25 rxn', 'Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes', 'Custom Twist Broad PanCancer Panel - 396 Genes', 'Custom HaloPlex DLBCL Panel - 370 Genes', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2', 'SureSelect Human All Exon v6', 'Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb', 'Custom Large Construct Capture TARGET-OS Panel - 8 Genes', 'Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb', 'SureSelect Human All Exon v5', 'xGen Exome Research Panel v1.0', 'Custom Myeloid GENIE-VICC Panel - 37 Genes', 'SureSelect Human All Exon v3', 'unknown', 'TruSeq Amplicon Cancer Panel', 'Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb', 'SeqCap EZ HGSC VCRome v2.1', 'TruSeq RNA Exome', 'Custom GENIE-DFCI OncoPanel - 275 Genes', 'SureSelect Human All Exon v4', 'Nextera Rapid Capture Exome v1.2', 'Custom Personalis ACEcp VAREPOP-APOLLO Panel v2', 'Custom MSK IMPACT Panel - 410 Genes', 'Custom SureSelect Human All Exon v1.1 Plus 3 Boosters', '25 rxn xGen Universal Blocking Oligo – TS HT-i7', 'Ion AmpliSeq Cancer Hotspot Panel v2', 'Foundation Medicine T5a Panel - 322 Genes', 'SeqCap EZ Human Exome v3.0', 'Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes', 'TruSeq Exome Enrichment - 62 Mb', 'Custom Solid Tumor GENIE-VICC Panel - 34 Genes', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes', 'Custom MSK IMPACT Panel - 341 Genes', 'Custom GENIE-DFCI Oncopanel - 300 Genes', 'Custom MSK IMPACT Panel - 468 Genes', 'Custom Targets File Provided', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1', 'Foundation Medicine T7 Panel - 429 Genes', 'Not Applicable', 'Nextera DNA Exome', 'Custom SureSelect GENIE-UHN Panel - 555 Genes', 'Custom GENIE-DFCI Oncopanel - 447 Genes', 'Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb']",,BulkWESLevel1 +Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,BulkWESLevel1 +Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,BulkWESLevel1 +Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['Random', 'miRNA Size Fractionation', 'Poly-T Enrichment', 'Affinity Enrichment', 'Other', 'rRNA Depletion', 'Hybrid Selection', 'PCR']",,BulkWESLevel1 +Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['I1', 'R2', 'R1', 'Other', 'R1&R2']",,BulkWESLevel1 +To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['no', 'Yes - Trim Adapter Sequence', '']",,BulkWESLevel1 +Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,BulkWESLevel1 Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,BulkWESLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkWESLevel1 +Target Capture Kit,Target Capture Kit,TargetCaptureKit,"Description that can uniquely identify a target capture kit. Suggested value is a combination of vendor, kit name, and kit version.",True,,"['Custom SureSelect GENIE-UHN Panel - 555 Genes', 'Custom AmpliSeq Cancer Hotspot GENIE-MDA Augmented Panel v1 - 46 Genes', 'Custom GENIE-DFCI Oncopanel - 447 Genes', 'Custom MSK IMPACT Panel - 341 Genes', 'Custom SureSelect TARGET-AML_NBL_WT Panel - 2.8 Mb', 'Custom Large Construct Capture TARGET-OS Panel - 8 Genes', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 203 Genes', 'SeqCap EZ HGSC VCRome v2.1', 'Custom SureSelect Human All Exon v1.1 Plus 3 Boosters', 'Foundation Medicine T7 Panel - 429 Genes', 'Custom SureSelect CGCI-HTMCP-CC Panel - 19.7 Mb', 'SureSelect Human All Exon v5 + UTR', 'Custom MSK IMPACT Panel - 468 Genes', 'SureSelect Human All Exon v6', 'Ion AmpliSeq Comprehensive Cancer Panel', 'SeqCap EZ Human Exome v3.0', 'xGen Exome Research Panel v1.0', 'Custom GENIE-DFCI OncoPanel - 275 Genes', '25 rxn xGen Universal Blocking Oligo – TS HT-i7', 'Custom HaloPlex DLBCL Panel - 370 Genes', 'Custom SureSelect CGCI-BLGSP Panel - 4.6 Mb', 'Not Applicable', 'Custom Targets File Provided', 'SureSelect Human All Exon v3', 'Custom Myeloid GENIE-VICC Panel - 37 Genes', 'Custom Personalis ACEcp VAREPOP-APOLLO Panel v2', 'SureSelect Human All Exon v4', 'SureSelect Human All Exon v5', 'TruSight Myeloid Sequencing Panel', 'TruSeq Amplicon Cancer Panel', 'Custom SeqCap EZ TARGET-OS Panel - 7.0 Mb', 'unknown', 'Ion AmpliSeq Cancer Hotspot Panel v2', 'Custom SureSelect CGCI-HTMCP-CC KMT2D And Hotspot Panel - 37.0 Kb', 'Custom MSK IMPACT Panel - 410 Genes', 'Custom GENIE-DFCI Oncopanel - 300 Genes', 'Nextera Rapid Capture Exome v1.2', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v1', 'Custom Twist Broad PanCancer Panel - 396 Genes', 'xGen Universal Blocking Oligo – TS HT-i5 - 25 rxn', 'SeqCap EZ Human Exome v2.0', 'Custom Ion AmpliSeq Hotspot GENIE-MOSC3 Augmented Panel - 74 Genes', 'Custom Twist Broad Exome v1.0 - 35.0 Mb', 'TruSeq RNA Exome', 'Custom SeqCap EZ HGSC VCRome v2.1 ER Augmented v2', 'Nextera DNA Exome', 'TruSeq Exome Enrichment - 62 Mb', 'Custom PGDX SureSelect CancerSelect VAREPOP-APOLLO Panel - 88 Genes', 'Foundation Medicine T5a Panel - 322 Genes', 'Custom Solid Tumor GENIE-VICC Panel - 34 Genes']",,BulkWESLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel1 -To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['no', 'Yes - Trim Adapter Sequence', '']",,BulkWESLevel1 -Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,BulkWESLevel1 -Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,BulkWESLevel1 +Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,BulkWESLevel1 Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,BulkWESLevel1 -QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkWESLevel2 +Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1 +Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,BulkWESLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel1 +Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,BulkWESLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkWESLevel1 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2 +Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkWESLevel2 +MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI-low', 'MSI-high', 'MSS', 'MSI', '']",,BulkWESLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkWESLevel2 +Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2 +Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,BulkWESLevel2 Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkWESLevel2 -Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkWESLevel2 -Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel2 -QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkWESLevel2 -Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 -MSI Status,MSI Status,MSIStatus,MSIsensor determination of either microsatellite stability or instability.,False,,"['MSI-low', 'MSS', 'MSI', 'MSI-high', '']",,BulkWESLevel2 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkWESLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkWESLevel2 -Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 -Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 Is lowest level,Is lowest level,Islowestlevel,Denotes that the manifest represents the lowest data level submitted. Use when L1 data is missing,False,,"['Yes - Is lowest level', 'no', '']",,BulkWESLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkWESLevel2 -Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkWESLevel2 -Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkWESLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkWESLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BatMeth', 'MethylCoder', 'BRAT-BW', 'BSMAP', 'Bowtie', 'ERNE-BS5', 'STAR 2-Pass Genome', 'BS-Seeker2', 'STAR 2-Pass', 'BWA with Mark Duplicates and BQSR', 'BWA-aln', 'BWA-mem', 'STAR 2-Pass Transcriptome', 'BWA', 'STAR 2-Pass Chimeric', 'Segemehl', 'BSmooth', 'Other Alignment Workflow', 'None', 'GSNAP', 'Pash', 'BS-Seeker', 'Bisulfighter', 'BWA with BQSR', 'Bismark', 'RMAP', 'B-SOLANA', 'SOCS-B', 'BWA-meth', 'LAST']",,BulkWESLevel2 -MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkWESLevel2 +Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel2 Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,BulkWESLevel2 +Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkWESLevel2 +Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 +Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 +Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkWESLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkWESLevel2 Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkWESLevel2 -Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,BulkWESLevel2 -Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,BulkWESLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2 -Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,BulkWESLevel2 -Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 -QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkWESLevel2 -Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 -Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel2 -Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkWESLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkWESLevel2 Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkWESLevel2 -MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkWESLevel2 -Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,BulkWESLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkWESLevel2 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkWESLevel2 +Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkWESLevel2 +QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,BulkWESLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkWESLevel2 +MSI Workflow Link,MSI Workflow Link,MSIWorkflowLink,Link to method workflow (or command) used in estimating the MSI. URL,False,,,,BulkWESLevel2 +Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,BulkWESLevel2 +Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkWESLevel2 +QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,BulkWESLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkWESLevel2 +QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,BulkWESLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkWESLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BWA-meth', 'Bismark', 'BSMAP', 'STAR 2-Pass Transcriptome', 'STAR 2-Pass Chimeric', 'BWA-mem', 'MethylCoder', 'B-SOLANA', 'Pash', 'BWA', 'SOCS-B', 'BWA with Mark Duplicates and BQSR', 'BS-Seeker2', 'None', 'LAST', 'BatMeth', 'ERNE-BS5', 'BRAT-BW', 'Segemehl', 'STAR 2-Pass Genome', 'GSNAP', 'BWA with BQSR', 'RMAP', 'STAR 2-Pass', 'Bowtie', 'BSmooth', 'Other Alignment Workflow', 'Bisulfighter', 'BWA-aln', 'BS-Seeker']",,BulkWESLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkWESLevel2 -Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 -Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkWESLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkWESLevel2 +Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 +MSI Score,MSI Score,MSIScore,Numeric score denoting the aligned reads file's MSI score from MSIsensor. Number,False,,,,BulkWESLevel2 +Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,BulkWESLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel2 +Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 +Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkWESLevel2 +Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkWESLevel2 +Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,BulkWESLevel2 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,False,True,,"['Is lowest level is ""Yes - Is lowest level""']",BulkWESLevel2 Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",BulkWESLevel2 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,BulkWESLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,BulkWESLevel3 -Structural Variant Workflow Type,Structural Variant Workflow Type,StructuralVariantWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['CNV', 'None', 'GATK4', 'Other Structural Variant Workflow Type', 'CNVkit', 'BRASS', '']",,BulkWESLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel3 -Structural Variant Workflow URL,Structural Variant Workflow URL,StructuralVariantWorkflowURL,Link to workflow document. DockStore.org recommended. URL,True,,,,BulkWESLevel3 -Somatic Variants Workflow URL,Somatic Variants Workflow URL,SomaticVariantsWorkflowURL,Generic name for the workflow used to analyze a data set.,True,,,,BulkWESLevel3 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkWESLevel3 -Somatic Variants Workflow Type,Somatic Variants Workflow Type,SomaticVariantsWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['SomaticSniper', 'None', 'Other Somatic Variants Workflow Type', 'MuTect2', 'GATK4', 'MuSE', 'Pindel', 'VarScan2', 'CaVEMan', '']",,BulkWESLevel3 +Somatic Variants Sample Type,Somatic Variants Sample Type,SomaticVariantsSampleType,Is the sample case or control in somatic variant analysis,True,,"['Not Applicable', 'Case Sample', 'Control Sample']",,BulkWESLevel3 Filename,Filename,Filename,Name of a file,True,,,,BulkWESLevel3 -Somatic Variants Sample Type,Somatic Variants Sample Type,SomaticVariantsSampleType,Is the sample case or control in somatic variant analysis,True,,"['Control Sample', 'Not Applicable', 'Case Sample']",,BulkWESLevel3 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkWESLevel3 -Germline Variants Workflow Type,Germline Variants Workflow Type,GermlineVariantsWorkflowType,Generic name for the workflow used to analyze a data set,False,,"['None', 'Other Germline Variants Workflow Type', 'GATK4', '']",,BulkWESLevel3 +Somatic Variants Workflow URL,Somatic Variants Workflow URL,SomaticVariantsWorkflowURL,Generic name for the workflow used to analyze a data set.,True,,,,BulkWESLevel3 +Structural Variant Workflow Type,Structural Variant Workflow Type,StructuralVariantWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['None', 'BRASS', 'CNV', 'Other Structural Variant Workflow Type', 'GATK4', 'CNVkit', '']",,BulkWESLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkWESLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkWESLevel3 +Germline Variants Workflow Type,Germline Variants Workflow Type,GermlineVariantsWorkflowType,Generic name for the workflow used to analyze a data set,False,,"['Other Germline Variants Workflow Type', 'GATK4', 'None', '']",,BulkWESLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkWESLevel3 +Somatic Variants Workflow Type,Somatic Variants Workflow Type,SomaticVariantsWorkflowType,Generic name for the workflow used to analyze a data set.,False,,"['CaVEMan', 'MuTect2', 'Pindel', 'None', 'SomaticSniper', 'MuSE', 'Other Somatic Variants Workflow Type', 'VarScan2', 'GATK4', '']",,BulkWESLevel3 Germline Variants Workflow URL,Germline Variants Workflow URL,GermlineVariantsWorkflowURL,"Link to workflow document, e.g. Github, DockStore.org recommended",True,,,,BulkWESLevel3 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkWESLevel3 +Structural Variant Workflow URL,Structural Variant Workflow URL,StructuralVariantWorkflowURL,Link to workflow document. DockStore.org recommended. URL,True,,,,BulkWESLevel3 Custom Structural Variant Workflow Type,Custom Structural Variant Workflow Type,CustomStructuralVariantWorkflowType,Specify the name of a custom workflow name,False,True,,"['Structural is ""Other""']",BulkWESLevel3 -Custom Somatic Variants Workflow Type,Custom Somatic Variants Workflow Type,CustomSomaticVariantsWorkflowType,Specify the name of a custom workflow name,False,True,,"['Somatic is ""Other""']",BulkWESLevel3 Custom Germline Variants Workflow Type,Custom Germline Variants Workflow Type,CustomGermlineVariantsWorkflowType,Specify the name of a custom alignment workflow,False,True,,"['Germline is ""Other""']",BulkWESLevel3 -Microarray Platform ID,Microarray Platform ID,MicroarrayPlatformID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,True,,,,MicroarrayLevel1 -Microarray Value Definition,Microarray Value Definition,MicroarrayValueDefinition,What the provided value signifies,True,,,,MicroarrayLevel1 -Microarray Protocol Auxiliary File,Microarray Protocol Auxiliary File,MicroarrayProtocolAuxiliaryFile,"Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).",True,,,,MicroarrayLevel1 +Custom Somatic Variants Workflow Type,Custom Somatic Variants Workflow Type,CustomSomaticVariantsWorkflowType,Specify the name of a custom workflow name,False,True,,"['Somatic is ""Other""']",BulkWESLevel3 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MicroarrayLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MicroarrayLevel1 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MicroarrayLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,MicroarrayLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Single Nucleus', 'Micro-region', 'Bulk Nuclei', 'Single Cell']",,MicroarrayLevel1 -Microarray Label,Microarray Label,MicroarrayLabel,Microarray used this kind of label,True,,,,MicroarrayLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MicroarrayLevel1 -Microarray Molecule,Microarray Molecule,MicroarrayMolecule,Microarray is measuring this kind of molecule,True,,"['DNA', 'RNA']",,MicroarrayLevel1 +Microarray Value Definition,Microarray Value Definition,MicroarrayValueDefinition,What the provided value signifies,True,,,,MicroarrayLevel1 Filename,Filename,Filename,Name of a file,True,,,,MicroarrayLevel1 -Microarray Platform ID,Microarray Platform ID,MicroarrayPlatformID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,True,,,,MicroarrayLevel2 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,MicroarrayLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MicroarrayLevel1 +Microarray Platform ID,Microarray Platform ID,MicroarrayPlatformID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,True,,,,MicroarrayLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MicroarrayLevel1 +Microarray Label,Microarray Label,MicroarrayLabel,Microarray used this kind of label,True,,,,MicroarrayLevel1 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MicroarrayLevel1 +Microarray Molecule,Microarray Molecule,MicroarrayMolecule,Microarray is measuring this kind of molecule,True,,"['RNA', 'DNA']",,MicroarrayLevel1 +Microarray Protocol Auxiliary File,Microarray Protocol Auxiliary File,MicroarrayProtocolAuxiliaryFile,"Auxiliary file describing the experimental protocols used, as described in the NCBI GEO microarray template, recorded as synapse ID (syn12345).",True,,,,MicroarrayLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MicroarrayLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MicroarrayLevel2 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MicroarrayLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,MicroarrayLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MicroarrayLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MicroarrayLevel2 -Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,MicroarrayLevel2 Filename,Filename,Filename,Name of a file,True,,,,MicroarrayLevel2 -HTAN RPPA Antibody Table,HTAN RPPA Antibody Table,HTANRPPAAntibodyTable,A table containing antibody level metadata for RPPA,True,,,,RPPALevel2 +Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,MicroarrayLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MicroarrayLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MicroarrayLevel2 +Microarray Platform ID,Microarray Platform ID,MicroarrayPlatformID,The NCBI GEO Microarray Platform ID that links to the table containing the array definition,True,,,,MicroarrayLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MicroarrayLevel2 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,MicroarrayLevel2 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,RPPALevel2 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,RPPALevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel2 +Filename,Filename,Filename,Name of a file,True,,,,RPPALevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel2 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,RPPALevel2 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf', '']",,RPPALevel2 +HTAN RPPA Antibody Table,HTAN RPPA Antibody Table,HTANRPPAAntibodyTable,A table containing antibody level metadata for RPPA,True,,,,RPPALevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf', '']",,RPPALevel2 Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel2 -Filename,Filename,Filename,Name of a file,False,,,,RPPALevel2 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,RPPALevel2 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel2 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,RPPALevel2 -Antibody Notes,Antibody Notes,AntibodyNotes,Notes on antibodies replacements and antibody recognition observations.,False,,,,RPPALevel2 +Ab Name Reported on Dataset,Ab Name Reported on Dataset,AbNameReportedonDataset,The antibody name.,False,,,,RPPALevel2 +Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Clonal', 'Non-clonal', '']",,RPPALevel2 +Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,RPPALevel2 +RPPA Dilution,RPPA Dilution,RPPADilution,The dilution ratio.,False,,,,RPPALevel2 +Species,Species,Species,Host animal.,False,,"['Goat', 'Rabbit', 'Mouse', '']",,RPPALevel2 Internal Ab ID,Internal Ab ID,InternalAbID,Internal lab ID for an antibody.,False,,,,RPPALevel2 -Vendor,Vendor,Vendor,Vendor,False,,,,RPPALevel2 +Antibody Notes,Antibody Notes,AntibodyNotes,Notes on antibodies replacements and antibody recognition observations.,False,,,,RPPALevel2 Phospho Site,Phospho Site,PhosphoSite,The protein site for a phosphoprotein targeting antibody. Report AA and site (i.e. S442),False,,,,RPPALevel2 -Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,RPPALevel2 +RPPA Validation Status,RPPA Validation Status,RPPAValidationStatus,Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC),False,,"['Valid', 'Use with Caution', 'Under Evaluation', 'Used for QC', '']",,RPPALevel2 HTAN RPPA Antibody Table ID,HTAN RPPA Antibody Table ID,HTANRPPAAntibodyTableID,HTAN identifier associated with RPPA antibody level metadata. Identical for every row of the table.,False,,,,RPPALevel2 -Ab Name Reported on Dataset,Ab Name Reported on Dataset,AbNameReportedonDataset,The antibody name.,False,,,,RPPALevel2 +GENCODE Gene Symbol Target,GENCODE Gene Symbol Target,GENCODEGeneSymbolTarget,The comma separated list of gene symbols targeted by the antibody.,False,,,,RPPALevel2 +Vendor,Vendor,Vendor,Vendor,False,,,,RPPALevel2 +Phosphoprotein Flag,Phosphoprotein Flag,PhosphoproteinFlag,A flag the denotes if an antibody targets a phosphoprotein.,False,,"['false', 'true', '']",,RPPALevel2 UNIPROT Protein ID Target,UNIPROT Protein ID Target,UNIPROTProteinIDTarget,The comma separated list of UNIPROT IDs targeted by the antibody.,False,,,,RPPALevel2 -Phosphoprotein Flag,Phosphoprotein Flag,PhosphoproteinFlag,A flag the denotes if an antibody targets a phosphoprotein.,False,,"['true', 'false', '']",,RPPALevel2 -RPPA Dilution,RPPA Dilution,RPPADilution,The dilution ratio.,False,,,,RPPALevel2 Clone,Clone,Clone,Clone,False,,,,RPPALevel2 -Species,Species,Species,Host animal.,False,,"['Goat', 'Mouse', 'Rabbit', '']",,RPPALevel2 -Clonality,Clonality,Clonality,The text term used to describe whether a genomic variant is related by descent from a single progenitor cell. Note: This node is meant to capture molecular tests that were completed clinically for the participant and only includes data from diagnostic array that was completed prior to research sequencing was done. Do not include data related to research assay outputs here.,False,,"['Non-clonal', 'Clonal', '']",,RPPALevel2 -RPPA Validation Status,RPPA Validation Status,RPPAValidationStatus,Valid = RPPA and WB correlation > 0.7; Use with Caution = RPPA and WB correlation < 0.7; Under Evaluation = Antibody has given mixed results and/or evaluated by another lab; We are in the process of (re)validating; Used for QC = These antibodies are used for tissue sample quality control (QC),False,,"['Used for QC', 'Under Evaluation', 'Use with Caution', 'Valid', '']",,RPPALevel2 -GENCODE Gene Symbol Target,GENCODE Gene Symbol Target,GENCODEGeneSymbolTarget,The comma separated list of gene symbols targeted by the antibody.,False,,,,RPPALevel2 -Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScATAC-seqLevel1 -scATACseq Read1,scATACseq Read1,ScATACseqRead1,Read 1 content description,True,,"['Cell Barcode', 'DNA Insert', 'Sample Index', 'Sample Index and DNA Insert', 'Cell Barcode and DNA Insert']",,ScATAC-seqLevel1 -Median Passing Read Percentage,Median Passing Read Percentage,MedianPassingReadPercentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,True,,,,ScATAC-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer IIx', 'Illumina HiSeq 2500', 'GridION', '454 GS FLX Titanium', 'Illumina NovaSeq 6000', 'NovaSeqS4', 'Illumina HiSeq X Five', 'Illumina MiSeq', 'Ion Torrent Proton', 'Other', 'PromethION', 'Illumina NextSeq', 'Revio', 'AB SOLiD 4', 'NovaSeq 6000', 'unknown', 'Ultima Genomics UG100', 'Ion Torrent PGM', 'Illumina HiSeq X Ten', 'Oxford Nanopore minION', 'Illumina NextSeq 1000', 'Illumina Next Seq 2500', 'PacBio RS', 'Illumina NextSeq 2000', 'Illumina Next Seq 500', 'AB SOLiD 2', 'Ion Torrent S5', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Complete Genomics', 'Illumina HiSeq 2000', 'AB SOLiD 3', 'Not Reported', 'Illumina Genome Analyzer II', 'Illumina HiSeq 4000']",,ScATAC-seqLevel1 -Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['gentleMACS', 'Not Applicable', 'Dounce', 'Enzymatic Digestion']",,ScATAC-seqLevel1 -Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['inDropsV3', 'Smart-seq2', 'inDropsV2', 'Nextera XT', 'sci-ATAC-seq', '10xV3', 'CEL-seq2', '10x Multiome', '10xV1.1', 'Drop-seq', '10xV2', '10x FLEX', '10xV3.1', 'Smart-SeqV4', 'TruDrop', ""10x GEM 3'"", '10xV1.0', ""10x GEM 5'""]",,ScATAC-seqLevel1 +Median Fraction of Reads in Peaks,Median Fraction of Reads in Peaks,MedianFractionofReadsinPeaks,Median fraction of reads in peaks (FRIP),True,,,,ScATAC-seqLevel1 +scATACseq Read2,scATACseq Read2,ScATACseqRead2,Read 2 content description,True,,"['DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', 'Sample Index', 'Cell Barcode and DNA Insert']",,ScATAC-seqLevel1 +Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Enzymatic Digestion', 'Not Applicable', 'Dounce', 'gentleMACS']",,ScATAC-seqLevel1 +scATACseq Read1,scATACseq Read1,ScATACseqRead1,Read 1 content description,True,,"['DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', 'Sample Index', 'Cell Barcode and DNA Insert']",,ScATAC-seqLevel1 +Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,True,,,,ScATAC-seqLevel1 Nuclei Barcode Length,Nuclei Barcode Length,NucleiBarcodeLength,Nuclei Barcode Length,True,,,,ScATAC-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Single Nucleus', 'Micro-region', 'Bulk Nuclei', 'Single Cell']",,ScATAC-seqLevel1 +Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScATAC-seqLevel1 +Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScATAC-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,ScATAC-seqLevel1 Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScATAC-seqLevel1 -Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['10x', 'Droplets', 'Nuclei Isolation', 'Plates', 'FACS', 'Microfluidics Chip']",,ScATAC-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel1 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel1 +Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['10x', 'NIB', 'TST', 'Omni']",,ScATAC-seqLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScATAC-seqLevel1 Threshold for Minimum Passing Reads,Threshold for Minimum Passing Reads,ThresholdforMinimumPassingReads,Threshold for calling cells,True,,,,ScATAC-seqLevel1 -Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScATAC-seqLevel1 Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel1 +Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['Tn5', 'Diagenode-loaded Apex-Bio', 'Diagenode-unloaded Apex-Bio', 'Tn5-059', 'EZ-Tn5', 'In-House', 'Nextera Tn5']",,ScATAC-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,ScATAC-seqLevel1 Nucleus Identifier,Nucleus Identifier,NucleusIdentifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,True,,['Nuclei Barcode'],,ScATAC-seqLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ScATAC-seqLevel1 -scATACseq Read2,scATACseq Read2,ScATACseqRead2,Read 2 content description,True,,"['Cell Barcode', 'DNA Insert', 'Sample Index', 'Sample Index and DNA Insert', 'Cell Barcode and DNA Insert']",,ScATAC-seqLevel1 -scATACseq Library Layout,scATACseq Library Layout,ScATACseqLibraryLayout,Sequencing read type,True,,['scATACseq Paired End'],,ScATAC-seqLevel1 -Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['10x', 'NIB', 'TST', 'Omni']",,ScATAC-seqLevel1 -scATACseq Read3,scATACseq Read3,ScATACseqRead3,Read 3 content description,False,,"['Cell Barcode', 'DNA Insert', 'Sample Index', 'Sample Index and DNA Insert', 'Cell Barcode and DNA Insert', '']",,ScATAC-seqLevel1 -Median Fraction of Reads in Peaks,Median Fraction of Reads in Peaks,MedianFractionofReadsinPeaks,Median fraction of reads in peaks (FRIP),True,,,,ScATAC-seqLevel1 +scATACseq Read3,scATACseq Read3,ScATACseqRead3,Read 3 content description,False,,"['DNA Insert', 'Sample Index and DNA Insert', 'Cell Barcode', 'Sample Index', 'Cell Barcode and DNA Insert', '']",,ScATAC-seqLevel1 +Median Passing Read Percentage,Median Passing Read Percentage,MedianPassingReadPercentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,True,,,,ScATAC-seqLevel1 +Median Fraction of Reads in Annotated cis DNA Elements,Median Fraction of Reads in Annotated cis DNA Elements,MedianFractionofReadsinAnnotatedcisDNAElements,Median fraction of reads in annotated cis-DNA elements (FRIADE),True,,,,ScATAC-seqLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScATAC-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ScATAC-seqLevel1 -Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,True,,,,ScATAC-seqLevel1 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel1 +Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Plates', 'Nuclei Isolation', '10x', 'Droplets', 'Microfluidics Chip', 'FACS']",,ScATAC-seqLevel1 +scATACseq Library Layout,scATACseq Library Layout,ScATACseqLibraryLayout,Sequencing read type,True,,['scATACseq Paired End'],,ScATAC-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel1 -Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['EZ-Tn5', 'Diagenode-unloaded Apex-Bio', 'Tn5', 'Tn5-059', 'In-House', 'Nextera Tn5', 'Diagenode-loaded Apex-Bio']",,ScATAC-seqLevel1 -Median Fraction of Reads in Annotated cis DNA Elements,Median Fraction of Reads in Annotated cis DNA Elements,MedianFractionofReadsinAnnotatedcisDNAElements,Median fraction of reads in annotated cis-DNA elements (FRIADE),True,,,,ScATAC-seqLevel1 +Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV3.1', '10x FLEX', ""10x GEM 5'"", 'inDropsV3', 'Nextera XT', 'Smart-SeqV4', '10xV3', 'CEL-seq2', '10xV2', '10xV1.1', ""10x GEM 3'"", 'sci-ATAC-seq', 'Smart-seq2', 'inDropsV2', '10x Multiome', '10xV1.0', 'TruDrop', 'Drop-seq']",,ScATAC-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScATAC-seqLevel1 Peaks Calling Software,Peaks Calling Software,PeaksCallingSoftware,Generic name of peaks calling tool,False,,,,ScATAC-seqLevel1 -Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,True,"['no', 'yes', '']","['Library Construction Method is ""CEL-seq2""']",ScATAC-seqLevel1 Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,False,True,,"['Library Construction Method is ""CEL-seq2""']",ScATAC-seqLevel1 -Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScATAC-seqLevel2 -Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScATAC-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel2 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScATAC-seqLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScATAC-seqLevel2 -MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScATAC-seqLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScATAC-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScATAC-seqLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScATAC-seqLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BatMeth', 'MethylCoder', 'BRAT-BW', 'BSMAP', 'Bowtie', 'ERNE-BS5', 'STAR 2-Pass Genome', 'BS-Seeker2', 'STAR 2-Pass', 'BWA with Mark Duplicates and BQSR', 'BWA-aln', 'BWA-mem', 'STAR 2-Pass Transcriptome', 'BWA', 'STAR 2-Pass Chimeric', 'Segemehl', 'BSmooth', 'Other Alignment Workflow', 'None', 'GSNAP', 'Pash', 'BS-Seeker', 'Bisulfighter', 'BWA with BQSR', 'Bismark', 'RMAP', 'B-SOLANA', 'SOCS-B', 'BWA-meth', 'LAST']",,ScATAC-seqLevel2 -Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScATAC-seqLevel2 -Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,ScATAC-seqLevel2 -Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,ScATAC-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel2 +Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,True,"['yes', 'no', '']","['Library Construction Method is ""CEL-seq2""']",ScATAC-seqLevel1 Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScATAC-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScATAC-seqLevel2 +Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2 Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,ScATAC-seqLevel2 +Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScATAC-seqLevel2 Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScATAC-seqLevel2 Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScATAC-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel2 -Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScATAC-seqLevel2 -Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScATAC-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ScATAC-seqLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScATAC-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel2 Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScATAC-seqLevel2 +Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScATAC-seqLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScATAC-seqLevel2 +Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScATAC-seqLevel2 +Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,ScATAC-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScATAC-seqLevel2 +Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScATAC-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScATAC-seqLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScATAC-seqLevel2 Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScATAC-seqLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScATAC-seqLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScATAC-seqLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BWA-meth', 'Bismark', 'BSMAP', 'STAR 2-Pass Transcriptome', 'STAR 2-Pass Chimeric', 'BWA-mem', 'MethylCoder', 'B-SOLANA', 'Pash', 'BWA', 'SOCS-B', 'BWA with Mark Duplicates and BQSR', 'BS-Seeker2', 'None', 'LAST', 'BatMeth', 'ERNE-BS5', 'BRAT-BW', 'Segemehl', 'STAR 2-Pass Genome', 'GSNAP', 'BWA with BQSR', 'RMAP', 'STAR 2-Pass', 'Bowtie', 'BSmooth', 'Other Alignment Workflow', 'Bisulfighter', 'BWA-aln', 'BS-Seeker']",,ScATAC-seqLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScATAC-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScATAC-seqLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScATAC-seqLevel2 +Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,ScATAC-seqLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel2 +MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScATAC-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScATAC-seqLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScATAC-seqLevel2 Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",ScATAC-seqLevel2 -TSS Percentile,TSS Percentile,TSSPercentile,Percentile rank of TSS score,False,,,,ScATAC-seqLevel3 -Promoter Region Fragments,Promoter Region Fragments,PromoterRegionFragments,Number of fragments overlapping promoter regions,False,,,,ScATAC-seqLevel3 +Mitochondrial Read-Pairs,Mitochondrial Read-Pairs,MitochondrialRead-Pairs,Number of read-pairs mapping to mitochondria and non-nuclear contigs,False,,,,ScATAC-seqLevel3 +Passed Filters,Passed Filters,PassedFilters,"Number of non-duplicate, usable read-pairs i.e. fragments",False,,,,ScATAC-seqLevel3 MACS2 Start,MACS2 Start,MACS2Start,Genomic starting position in MACS2,False,,,,ScATAC-seqLevel3 -Nucleosome Percentile,Nucleosome Percentile,NucleosomePercentile,Percentile rank of nucleosome score,False,,,,ScATAC-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel3 -nCount Peaks,nCount Peaks,NCountPeaks,Total number of fragments in peaks,False,,,,ScATAC-seqLevel3 -On Target Fragments,On Target Fragments,OnTargetFragments,"Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)",False,,,,ScATAC-seqLevel3 -Blacklist Region Fragments,Blacklist Region Fragments,BlacklistRegionFragments,Number of fragments overlapping blacklisted regions,False,,,,ScATAC-seqLevel3 -nFeature RNA,nFeature RNA,NFeatureRNA,Number of genes detected in cell,False,,,,ScATAC-seqLevel3 scATAC-seq Object ID,scATAC-seq Object ID,ScATAC-seqObjectID,Orig.Ident or scATAC-seq Object ID,False,,,,ScATAC-seqLevel3 +MACS2 Width,MACS2 Width,MACS2Width,Width of the peak in bases in MACS2,False,,,,ScATAC-seqLevel3 +nFeature RNA,nFeature RNA,NFeatureRNA,Number of genes detected in cell,False,,,,ScATAC-seqLevel3 Blacklist Ratio,Blacklist Ratio,BlacklistRatio,Ratio of reads in blacklist regions,False,,,,ScATAC-seqLevel3 -MACS2 Relative Summit Position,MACS2 Relative Summit Position,MACS2RelativeSummitPosition,Position of the peak summit related to the start position in MACS2,False,,,,ScATAC-seqLevel3 -Passed Filters,Passed Filters,PassedFilters,"Number of non-duplicate, usable read-pairs i.e. fragments",False,,,,ScATAC-seqLevel3 +Peak Region Cutsites,Peak Region Cutsites,PeakRegionCutsites,Number of ends of fragments in peak regions,False,,,,ScATAC-seqLevel3 +MACS2 Fold Change,MACS2 Fold Change,MACS2FoldChange,Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2,False,,,,ScATAC-seqLevel3 +Nucleosome Percentile,Nucleosome Percentile,NucleosomePercentile,Percentile rank of nucleosome score,False,,,,ScATAC-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel3 TSS Enrichment,TSS Enrichment,TSSEnrichment,Transcription start site (TSS) enrichment score,False,,,,ScATAC-seqLevel3 -Chimeric Read-Pairs,Chimeric Read-Pairs,ChimericRead-Pairs,Number of chimerically mapped read-pairs,False,,,,ScATAC-seqLevel3 -MACS2 Width,MACS2 Width,MACS2Width,Width of the peak in bases in MACS2,False,,,,ScATAC-seqLevel3 -Seurat Clusters,Seurat Clusters,SeuratClusters,Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm,False,,,,ScATAC-seqLevel3 +Promoter Region Fragments,Promoter Region Fragments,PromoterRegionFragments,Number of fragments overlapping promoter regions,False,,,,ScATAC-seqLevel3 +Duplicate Read-Pairs,Duplicate Read-Pairs,DuplicateRead-Pairs,Number of duplicate read-pairs,False,,,,ScATAC-seqLevel3 +MACS2 Relative Summit Position,MACS2 Relative Summit Position,MACS2RelativeSummitPosition,Position of the peak summit related to the start position in MACS2,False,,,,ScATAC-seqLevel3 +MACS2 Name,MACS2 Name,MACS2Name,Name of the peak in MACS2,False,,,,ScATAC-seqLevel3 nCount RNA,nCount RNA,NCountRNA,Total number of fragments in genes,False,,,,ScATAC-seqLevel3 -MACS2 End,MACS2 End,MACS2End,Genomic ending position in MACS2,False,,,,ScATAC-seqLevel3 -MACS2 Strand,MACS2 Strand,MACS2Strand,DNA stand aligned with in MACS2,False,,,,ScATAC-seqLevel3 +Total Read-Pairs,Total Read-Pairs,TotalRead-Pairs,Total read-pairs,False,,,,ScATAC-seqLevel3 +Enhancer Region Fragments,Enhancer Region Fragments,EnhancerRegionFragments,Number of fragments overlapping enhancer regions,False,,,,ScATAC-seqLevel3 +Seurat Clusters,Seurat Clusters,SeuratClusters,Clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm,False,,,,ScATAC-seqLevel3 +Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel3 +TSS Percentile,TSS Percentile,TSSPercentile,Percentile rank of TSS score,False,,,,ScATAC-seqLevel3 +nCount Peaks,nCount Peaks,NCountPeaks,Total number of fragments in peaks,False,,,,ScATAC-seqLevel3 +TSS Fragments,TSS Fragments,TSSFragments,Number of fragments overlapping with TSS regions,False,,,,ScATAC-seqLevel3 +Unmapped Read-Pairs,Unmapped Read-Pairs,UnmappedRead-Pairs,Number of read-pairs with at least one end not mapped,False,,,,ScATAC-seqLevel3 +LowMapQ,LowMapQ,LowMapQ,Number of read-pairs with <30 mapq on at least one end,False,,,,ScATAC-seqLevel3 DNase Sensitive Region Fragments,DNase Sensitive Region Fragments,DNaseSensitiveRegionFragments,Number of fragments overlapping with DNase sensitive regions,False,,,,ScATAC-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel3 Peak Region Fragments,Peak Region Fragments,PeakRegionFragments,Number of fragments overlapping peaks,False,,,,ScATAC-seqLevel3 -Pct Reads in Peaks,Pct Reads in Peaks,PctReadsinPeaks,Percentage of reads in peaks,False,,,,ScATAC-seqLevel3 MACS2 Score,MACS2 Score,MACS2Score,Peak score (proportional to q-value) in MACS2,False,,,,ScATAC-seqLevel3 -MACS2 Fold Change,MACS2 Fold Change,MACS2FoldChange,Fold enrichment for this peak summit against random Poisson distribution with local lambda in MACS2,False,,,,ScATAC-seqLevel3 +MACS2 Neg Log10 pvalue Summit,MACS2 Neg Log10 pvalue Summit,MACS2NegLog10pvalueSummit,Negative log10 p-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3 +Blacklist Region Fragments,Blacklist Region Fragments,BlacklistRegionFragments,Number of fragments overlapping blacklisted regions,False,,,,ScATAC-seqLevel3 +MACS2 Seqnames,MACS2 Seqnames,MACS2Seqnames,Chromosome id,False,,,,ScATAC-seqLevel3 +MACS2 Strand,MACS2 Strand,MACS2Strand,DNA stand aligned with in MACS2,False,,,,ScATAC-seqLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel3 MACS2 Neg Log10 qvalue Summit,MACS2 Neg Log10 qvalue Summit,MACS2NegLog10qvalueSummit,Negative log10 q-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3 -Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel3 -Enhancer Region Fragments,Enhancer Region Fragments,EnhancerRegionFragments,Number of fragments overlapping enhancer regions,False,,,,ScATAC-seqLevel3 +MACS2 End,MACS2 End,MACS2End,Genomic ending position in MACS2,False,,,,ScATAC-seqLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel3 +Chimeric Read-Pairs,Chimeric Read-Pairs,ChimericRead-Pairs,Number of chimerically mapped read-pairs,False,,,,ScATAC-seqLevel3 Nucleosome Signal,Nucleosome Signal,NucleosomeSignal,"Nucleosome signal score (strength of the nucleosome signal per cell, computed as the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free))",False,,,,ScATAC-seqLevel3 -MACS2 Neg Log10 pvalue Summit,MACS2 Neg Log10 pvalue Summit,MACS2NegLog10pvalueSummit,Negative log10 p-value for the peak summit in MACS2,False,,,,ScATAC-seqLevel3 -Mitochondrial Read-Pairs,Mitochondrial Read-Pairs,MitochondrialRead-Pairs,Number of read-pairs mapping to mitochondria and non-nuclear contigs,False,,,,ScATAC-seqLevel3 -MACS2 Seqnames,MACS2 Seqnames,MACS2Seqnames,Chromosome id,False,,,,ScATAC-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScATAC-seqLevel3 +On Target Fragments,On Target Fragments,OnTargetFragments,"Number of fragments overlapping any of TSS, enhancer, promoter and DNase hypersensitivity sites (counted with multiplicity)",False,,,,ScATAC-seqLevel3 +Pct Reads in Peaks,Pct Reads in Peaks,PctReadsinPeaks,Percentage of reads in peaks,False,,,,ScATAC-seqLevel3 nFeature Peaks,nFeature Peaks,NFeaturePeaks,Number of peaks with at least one read,False,,,,ScATAC-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ScATAC-seqLevel3 -Unmapped Read-Pairs,Unmapped Read-Pairs,UnmappedRead-Pairs,Number of read-pairs with at least one end not mapped,False,,,,ScATAC-seqLevel3 -LowMapQ,LowMapQ,LowMapQ,Number of read-pairs with <30 mapq on at least one end,False,,,,ScATAC-seqLevel3 -MACS2 Name,MACS2 Name,MACS2Name,Name of the peak in MACS2,False,,,,ScATAC-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel3 -Total Read-Pairs,Total Read-Pairs,TotalRead-Pairs,Total read-pairs,False,,,,ScATAC-seqLevel3 -TSS Fragments,TSS Fragments,TSSFragments,Number of fragments overlapping with TSS regions,False,,,,ScATAC-seqLevel3 -Duplicate Read-Pairs,Duplicate Read-Pairs,DuplicateRead-Pairs,Number of duplicate read-pairs,False,,,,ScATAC-seqLevel3 -Peak Region Cutsites,Peak Region Cutsites,PeakRegionCutsites,Number of ends of fragments in peak regions,False,,,,ScATAC-seqLevel3 -Median Passing Read Percentage,Median Passing Read Percentage,MedianPassingReadPercentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,True,,,,ScmC-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer IIx', 'Illumina HiSeq 2500', 'GridION', '454 GS FLX Titanium', 'Illumina NovaSeq 6000', 'NovaSeqS4', 'Illumina HiSeq X Five', 'Illumina MiSeq', 'Ion Torrent Proton', 'Other', 'PromethION', 'Illumina NextSeq', 'Revio', 'AB SOLiD 4', 'NovaSeq 6000', 'unknown', 'Ultima Genomics UG100', 'Ion Torrent PGM', 'Illumina HiSeq X Ten', 'Oxford Nanopore minION', 'Illumina NextSeq 1000', 'Illumina Next Seq 2500', 'PacBio RS', 'Illumina NextSeq 2000', 'Illumina Next Seq 500', 'AB SOLiD 2', 'Ion Torrent S5', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Complete Genomics', 'Illumina HiSeq 2000', 'AB SOLiD 3', 'Not Reported', 'Illumina Genome Analyzer II', 'Illumina HiSeq 4000']",,ScmC-seqLevel1 -scmCseq Read2,scmCseq Read2,ScmCseqRead2,Read 2 content description,True,,"['cDNA', 'Cell Barcode and UMI']",,ScmC-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Single Nucleus', 'Micro-region', 'Bulk Nuclei', 'Single Cell']",,ScmC-seqLevel1 +Peaks Calling Software,Peaks Calling Software,PeaksCallingSoftware,Generic name of peaks calling tool,True,,,,ScmC-seqLevel1 +Median Fraction of Reads in Peaks,Median Fraction of Reads in Peaks,MedianFractionofReadsinPeaks,Median fraction of reads in peaks (FRIP),True,,,,ScmC-seqLevel1 +Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,True,,,,ScmC-seqLevel1 +Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScmC-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,ScmC-seqLevel1 +Bisulfite Conversion,Bisulfite Conversion,BisulfiteConversion,Name of the kit used in bisulfite conversion.,True,,"['Agilent SureSelectXT Methyl-Seq', 'Zimo EZ-96 DNA Methylation Deep Kit', 'Zimo EZ-96 DNA Methylation Shallow Kit', 'Zimo EZ DNA Methylation Kit', 'NEBNext Enzymatic Methyl-seq Kit']",,ScmC-seqLevel1 Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,ScmC-seqLevel1 -scmCseq Read1,scmCseq Read1,ScmCseqRead1,Read 1 content description,True,,"['cDNA', 'Cell Barcode and UMI']",,ScmC-seqLevel1 -Bisulfite Conversion,Bisulfite Conversion,BisulfiteConversion,Name of the kit used in bisulfite conversion.,True,,"['Zimo EZ DNA Methylation Kit', 'Zimo EZ-96 DNA Methylation Deep Kit', 'Agilent SureSelectXT Methyl-Seq', 'Zimo EZ-96 DNA Methylation Shallow Kit', 'NEBNext Enzymatic Methyl-seq Kit']",,ScmC-seqLevel1 -Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['10x', 'Droplets', 'Nuclei Isolation', 'Plates', 'FACS', 'Microfluidics Chip']",,ScmC-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScmC-seqLevel1 +scmCseq Read2,scmCseq Read2,ScmCseqRead2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1 +Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Long Read', 'Single Read', 'Paired End', 'Mid-length']",,ScmC-seqLevel1 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScmC-seqLevel1 +Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['10x', 'NIB', 'TST', 'Omni']",,ScmC-seqLevel1 Threshold for Minimum Passing Reads,Threshold for Minimum Passing Reads,ThresholdforMinimumPassingReads,Threshold for calling cells,True,,,,ScmC-seqLevel1 -Median Percentage of Mitochondrial Reads per Nucleus,Median Percentage of Mitochondrial Reads per Nucleus,MedianPercentageofMitochondrialReadsperNucleus,Contamination from mitochondrial sequences,True,,,,ScmC-seqLevel1 Filename,Filename,Filename,Name of a file,True,,,,ScmC-seqLevel1 +scmCseq Read3,scmCseq Read3,ScmCseqRead3,Read 3 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,ScmC-seqLevel1 +Single Nucleus Capture,Single Nucleus Capture,SingleNucleusCapture,Nuclei isolation method,False,,"['Plates', '10x', 'droplet', '']",,ScmC-seqLevel1 Nucleus Identifier,Nucleus Identifier,NucleusIdentifier,Unique nuclei barcode; added at transposition step. Determines which nucleus the reads originated from,True,,['Nuclei Barcode'],,ScmC-seqLevel1 -Single Nucleus Buffer,Single Nucleus Buffer,SingleNucleusBuffer,Nuclei isolation buffer,True,,"['10x', 'NIB', 'TST', 'Omni']",,ScmC-seqLevel1 -Median Fraction of Reads in Peaks,Median Fraction of Reads in Peaks,MedianFractionofReadsinPeaks,Median fraction of reads in peaks (FRIP),True,,,,ScmC-seqLevel1 +Median Passing Read Percentage,Median Passing Read Percentage,MedianPassingReadPercentage,Non-PCR duplicate nuclear genomic sequence reads not aligning to unanchored contigs out of total reads assigned to the nucleus barcode,True,,,,ScmC-seqLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScmC-seqLevel1 -scmCseq Read3,scmCseq Read3,ScmCseqRead3,Read 3 content description,True,,"['cDNA', 'Cell Barcode and UMI']",,ScmC-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ScmC-seqLevel1 -Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Mid-length', 'Long Read', 'Paired End', 'Single Read']",,ScmC-seqLevel1 -Total Number of Passing Nuclei,Total Number of Passing Nuclei,TotalNumberofPassingNuclei,Number of nuclei sequenced,True,,,,ScmC-seqLevel1 -Peaks Calling Software,Peaks Calling Software,PeaksCallingSoftware,Generic name of peaks calling tool,False,,,,ScmC-seqLevel1 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScmC-seqLevel1 +Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Plates', 'Nuclei Isolation', '10x', 'Droplets', 'Microfluidics Chip', 'FACS']",,ScmC-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScmC-seqLevel1 -Single Nucleus Capture,Single Nucleus Capture,SingleNucleusCapture,Nuclei isolation method,False,,"['Plates', '10x', 'droplet', '']",,ScmC-seqLevel1 -cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Scmcseq read3 is ""cDNA""']",ScmC-seqLevel1 -cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Scmcseq read3 is ""cDNA""']",ScmC-seqLevel1 -UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Scmcseq read3 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 -Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Scmcseq read3 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 -Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Scmcseq read3 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 -Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Scmcseq read3 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 -Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Scmcseq read3 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 -UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Scmcseq read3 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 -Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScmC-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScmC-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScmC-seqLevel1 +scmCseq Read1,scmCseq Read1,ScmCseqRead1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,ScmC-seqLevel1 +Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 +UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 +Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 +Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 +UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 +Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Scmcseq read1 is ""Cell Barcode and UMI""']",ScmC-seqLevel1 +cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Scmcseq read1 is ""cDNA""']",ScmC-seqLevel1 +cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Scmcseq read1 is ""cDNA""']",ScmC-seqLevel1 Nuclei Barcode Length,Nuclei Barcode Length,NucleiBarcodeLength,Nuclei Barcode Length,True,,,,ScmC-seqLevel1 +Nuclei Barcode Read,Nuclei Barcode Read,NucleiBarcodeRead,Nuclei Barcode Read,True,,,,ScmC-seqLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,BulkMethylation-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkMethylation-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,BulkMethylation-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Single Nucleus', 'Micro-region', 'Bulk Nuclei', 'Single Cell']",,BulkMethylation-seqLevel1 -Replicate Type,Replicate Type,ReplicateType,A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.,True,,"['Not Applicable', 'Technical replicate', 'Biological replicate']",,BulkMethylation-seqLevel1 +Bulk Methylation Assay Type,Bulk Methylation Assay Type,BulkMethylationAssayType,Assay types normally determine genomic coverage,True,,"['Beadchip Array', 'Targeted Genome', 'Whole genome']",,BulkMethylation-seqLevel1 Total DNA Input,Total DNA Input,TotalDNAInput,"Overall number of reads for a given sample in digits (microgram, nanogram).",False,,,,BulkMethylation-seqLevel1 -Bulk Methylation Assay Type,Bulk Methylation Assay Type,BulkMethylationAssayType,Assay types normally determine genomic coverage,True,,"['Targeted Genome', 'Beadchip Array', 'Whole genome']",,BulkMethylation-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel1 Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer IIx', 'Illumina HiSeq 2500', 'GridION', '454 GS FLX Titanium', 'Illumina NovaSeq 6000', 'NovaSeqS4', 'Illumina HiSeq X Five', 'Illumina MiSeq', 'Ion Torrent Proton', 'Other', 'PromethION', 'Illumina NextSeq', 'Revio', 'AB SOLiD 4', 'NovaSeq 6000', 'unknown', 'Ultima Genomics UG100', 'Ion Torrent PGM', 'Illumina HiSeq X Ten', 'Oxford Nanopore minION', 'Illumina NextSeq 1000', 'Illumina Next Seq 2500', 'PacBio RS', 'Illumina NextSeq 2000', 'Illumina Next Seq 500', 'AB SOLiD 2', 'Ion Torrent S5', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Complete Genomics', 'Illumina HiSeq 2000', 'AB SOLiD 3', 'Not Reported', 'Illumina Genome Analyzer II', 'Illumina HiSeq 4000']",,BulkMethylation-seqLevel1 -Bisulfite Conversion,Bisulfite Conversion,BisulfiteConversion,Name of the kit used in bisulfite conversion.,True,,"['Zimo EZ DNA Methylation Kit', 'Zimo EZ-96 DNA Methylation Deep Kit', 'Agilent SureSelectXT Methyl-Seq', 'Zimo EZ-96 DNA Methylation Shallow Kit', 'NEBNext Enzymatic Methyl-seq Kit']",,BulkMethylation-seqLevel1 -Targeted Genome,Targeted Genome,TargetedGenome,Assay for analyzing specific mutations in a given sample,False,,"['RRBS', 'MeDIP', '']",,BulkMethylation-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,BulkMethylation-seqLevel1 +Bisulfite Conversion,Bisulfite Conversion,BisulfiteConversion,Name of the kit used in bisulfite conversion.,True,,"['Agilent SureSelectXT Methyl-Seq', 'Zimo EZ-96 DNA Methylation Deep Kit', 'Zimo EZ-96 DNA Methylation Shallow Kit', 'Zimo EZ DNA Methylation Kit', 'NEBNext Enzymatic Methyl-seq Kit']",,BulkMethylation-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,BulkMethylation-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkMethylation-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkMethylation-seqLevel1 +Replicate Type,Replicate Type,ReplicateType,A common term for all files belonging to the same sample. We suggest using a stable sample accession from a biosample archive like BioSamples.,True,,"['Not Applicable', 'Technical replicate', 'Biological replicate']",,BulkMethylation-seqLevel1 Beadchip Array,Beadchip Array,BeadchipArray,Assay that uses beads to target a specific locus on the genome.,False,,"['HM27K', 'HM450K', '']",,BulkMethylation-seqLevel1 +Targeted Genome,Targeted Genome,TargetedGenome,Assay for analyzing specific mutations in a given sample,False,,"['MeDIP', 'RRBS', '']",,BulkMethylation-seqLevel1 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScmC-seqLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScmC-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScmC-seqLevel2 +Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScmC-seqLevel2 Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScmC-seqLevel2 -Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScmC-seqLevel2 +Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScmC-seqLevel2 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScmC-seqLevel2 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScmC-seqLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScmC-seqLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScmC-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScmC-seqLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScmC-seqLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BatMeth', 'MethylCoder', 'BRAT-BW', 'BSMAP', 'Bowtie', 'ERNE-BS5', 'STAR 2-Pass Genome', 'BS-Seeker2', 'STAR 2-Pass', 'BWA with Mark Duplicates and BQSR', 'BWA-aln', 'BWA-mem', 'STAR 2-Pass Transcriptome', 'BWA', 'STAR 2-Pass Chimeric', 'Segemehl', 'BSmooth', 'Other Alignment Workflow', 'None', 'GSNAP', 'Pash', 'BS-Seeker', 'Bisulfighter', 'BWA with BQSR', 'Bismark', 'RMAP', 'B-SOLANA', 'SOCS-B', 'BWA-meth', 'LAST']",,ScmC-seqLevel2 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScmC-seqLevel2 +Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScmC-seqLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScmC-seqLevel2 Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScmC-seqLevel2 Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,ScmC-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScmC-seqLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScmC-seqLevel2 -Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScmC-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,,,ScmC-seqLevel2 -Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScmC-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScmC-seqLevel2 Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScmC-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ScmC-seqLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScmC-seqLevel2 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScmC-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,,,ScmC-seqLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScmC-seqLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScmC-seqLevel2 Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScmC-seqLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScmC-seqLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScmC-seqLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BWA-meth', 'Bismark', 'BSMAP', 'STAR 2-Pass Transcriptome', 'STAR 2-Pass Chimeric', 'BWA-mem', 'MethylCoder', 'B-SOLANA', 'Pash', 'BWA', 'SOCS-B', 'BWA with Mark Duplicates and BQSR', 'BS-Seeker2', 'None', 'LAST', 'BatMeth', 'ERNE-BS5', 'BRAT-BW', 'Segemehl', 'STAR 2-Pass Genome', 'GSNAP', 'BWA with BQSR', 'RMAP', 'STAR 2-Pass', 'Bowtie', 'BSmooth', 'Other Alignment Workflow', 'Bisulfighter', 'BWA-aln', 'BS-Seeker']",,ScmC-seqLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScmC-seqLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScmC-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScmC-seqLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScmC-seqLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScmC-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScmC-seqLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScmC-seqLevel2 Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",ScmC-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ScATAC-seqLevel4 Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,ScATAC-seqLevel4 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScATAC-seqLevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel4 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScATAC-seqLevel4 -scATACseq Workflow Type,scATACseq Workflow Type,ScATACseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,,,ScATAC-seqLevel4 Filename,Filename,Filename,Name of a file,True,,,,ScATAC-seqLevel4 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,ScATAC-seqLevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScATAC-seqLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScATAC-seqLevel4 scATACseq Workflow Parameters Description,scATACseq Workflow Parameters Description,ScATACseqWorkflowParametersDescription,Parameters used to run the scATAC-seq workflow.,True,,,,ScATAC-seqLevel4 -Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,ScDNA-seqLevel1 -QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,ScDNA-seqLevel1 -Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,ScDNA-seqLevel1 -Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 -Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,ScDNA-seqLevel1 -QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,ScDNA-seqLevel1 -Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 -Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,ScDNA-seqLevel1 +scATACseq Workflow Type,scATACseq Workflow Type,ScATACseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,,,ScATAC-seqLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScATAC-seqLevel4 +Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 Fragment Standard Deviation Length,Fragment Standard Deviation Length,FragmentStandardDeviationLength,"Standard deviation of the sequenced fragments length (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,ScDNA-seqLevel1 -Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 -Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 -Kmer Content,Kmer Content,KmerContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 Base Caller Version,Base Caller Version,BaseCallerVersion,Version of the base caller. String,False,,,,ScDNA-seqLevel1 -Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,ScDNA-seqLevel1 -Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 -Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['Other', 'Random', 'miRNA Size Fractionation', 'rRNA Depletion', 'Poly-T Enrichment', 'PCR', 'Affinity Enrichment', 'Hybrid Selection']",,ScDNA-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Single Nucleus', 'Micro-region', 'Bulk Nuclei', 'Single Cell']",,ScDNA-seqLevel1 -Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1 -Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,ScDNA-seqLevel1 -Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,ScDNA-seqLevel1 Library Preparation Kit Vendor,Library Preparation Kit Vendor,LibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1 +Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,ScDNA-seqLevel1 +Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,ScDNA-seqLevel1 Library Preparation Kit Name,Library Preparation Kit Name,LibraryPreparationKitName,Name of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1 -Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,ScDNA-seqLevel1 -Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,ScDNA-seqLevel1 +Adapter Content,Adapter Content,AdapterContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 Adapter Name,Adapter Name,AdapterName,Name of the sequencing adapter. String,False,,,,ScDNA-seqLevel1 -Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 -Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,ScDNA-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScDNA-seqLevel1 -Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 -QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,ScDNA-seqLevel1 -Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +Percent GC Content,Percent GC Content,PercentGCContent,The overall %GC of all bases in all sequences. Integer,False,,,,ScDNA-seqLevel1 +Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Long Read', 'Single Read', 'Paired End', 'Mid-length']",,ScDNA-seqLevel1 +Overrepresented Sequences,Overrepresented Sequences,OverrepresentedSequences,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScDNA-seqLevel1 +Sequence Length Distribution,Sequence Length Distribution,SequenceLengthDistribution,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +Library Preparation Kit Version,Library Preparation Kit Version,LibraryPreparationKitVersion,Version of Library Preparation Kit. String,True,,,,ScDNA-seqLevel1 Filename,Filename,Filename,Name of a file,True,,,,ScDNA-seqLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScDNA-seqLevel1 -Per Sequence Quality Score,Per Sequence Quality Score,PerSequenceQualityScore,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ScDNA-seqLevel1 -Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Mid-length', 'Long Read', 'Paired End', 'Single Read']",,ScDNA-seqLevel1 +Base Caller Name,Base Caller Name,BaseCallerName,Name of the base caller. String,False,,,,ScDNA-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,ScDNA-seqLevel1 +Target Depth,Target Depth,TargetDepth,The targeted read depth prior to sequencing. Integer,False,,,,ScDNA-seqLevel1 +QC Workflow Version,QC Workflow Version,QCWorkflowVersion,Major version for a workflow. String,False,,,,ScDNA-seqLevel1 +Library Selection Method,Library Selection Method,LibrarySelectionMethod,How RNA molecules are isolated.,True,,"['Random', 'miRNA Size Fractionation', 'Poly-T Enrichment', 'Affinity Enrichment', 'Other', 'rRNA Depletion', 'Hybrid Selection', 'PCR']",,ScDNA-seqLevel1 +Fragment Maximum Length,Fragment Maximum Length,FragmentMaximumLength,"Maximum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,ScDNA-seqLevel1 +Encoding,Encoding,Encoding,Version of ASCII encoding of quality values found in the file. String,False,,,,ScDNA-seqLevel1 +Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Unstranded', 'Not Applicable', 'First Stranded', 'Second Stranded', '']",,ScDNA-seqLevel1 +Kmer Content,Kmer Content,KmerContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +Per Base Sequence Quality,Per Base Sequence Quality,PerBaseSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['no', 'Yes - Trim Adapter Sequence', '']",,ScDNA-seqLevel1 +Fragment Mean Length,Fragment Mean Length,FragmentMeanLength,"Mean length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Number",False,,,,ScDNA-seqLevel1 Adapter Sequence,Adapter Sequence,AdapterSequence,Base sequence of the sequencing adapter. String,False,,,,ScDNA-seqLevel1 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScDNA-seqLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ScDNA-seqLevel1 +QC Workflow Type,QC Workflow Type,QCWorkflowType,Generic name for the workflow used to analyze a data set. String,False,,,,ScDNA-seqLevel1 +QC Workflow Link,QC Workflow Link,QCWorkflowLink,Link to workflow used. String,False,,,,ScDNA-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScDNA-seqLevel1 -Library Strand,Library Strand,LibraryStrand,Library stranded-ness.,False,,"['Not Applicable', 'Unstranded', 'Second Stranded', 'First Stranded', '']",,ScDNA-seqLevel1 -Sequencing Batch ID,Sequencing Batch ID,SequencingBatchID,Links samples to a specific local sequencer run. Can be string or 'null',True,,,,ScDNA-seqLevel1 -To Trim Adapter Sequence,To Trim Adapter Sequence,ToTrimAdapterSequence,Does the user suggest adapter trimming?,False,,"['no', 'Yes - Trim Adapter Sequence', '']",,ScDNA-seqLevel1 -Lane Number,Lane Number,LaneNumber,"The basic machine unit for sequencing. For Illumina machines, this reflects the physical lane number. Wrong or missing information may affect analysis results. Integer",False,,,,ScDNA-seqLevel1 -Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +Read Length,Read Length,ReadLength,"The length of the sequencing reads. Can be integer, null",True,,,,ScDNA-seqLevel1 Size Selection Range,Size Selection Range,SizeSelectionRange,Range of size selection. String,False,,,,ScDNA-seqLevel1 -Per Base N Content,Per Base N Content,PerBaseNContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['FAIL', 'unknown', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +Multiplex Barcode,Multiplex Barcode,MultiplexBarcode,The barcode/index sequence used. Wrong or missing information may affect analysis results. String,False,,,,ScDNA-seqLevel1 +Fragment Minimum Length,Fragment Minimum Length,FragmentMinimumLength,"Minimum length of the sequenced fragments (e.g., as predicted by Agilent Bioanalyzer). Integer",False,,,,ScDNA-seqLevel1 +Basic Statistics,Basic Statistics,BasicStatistics,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScDNA-seqLevel1 +Flow Cell Barcode,Flow Cell Barcode,FlowCellBarcode,Flow cell barcode. Wrong or missing information may affect analysis results. String,False,,,,ScDNA-seqLevel1 +Per Tile Sequence Quality,Per Tile Sequence Quality,PerTileSequenceQuality,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +Sequence Duplication Levels,Sequence Duplication Levels,SequenceDuplicationLevels,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScDNA-seqLevel1 +Per Sequence GC Content,Per Sequence GC Content,PerSequenceGCContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +Per Base Sequence Content,Per Base Sequence Content,PerBaseSequenceContent,State classification given by FASTQC for the metric. Metric specific details about the states are available on their website.,False,,"['unknown', 'FAIL', 'PASS', 'Not Reported', 'WARN', '']",,ScDNA-seqLevel1 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScDNA-seqLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScDNA-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScDNA-seqLevel2 +Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScDNA-seqLevel2 +Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,ScDNA-seqLevel2 Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,ScDNA-seqLevel2 -Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScDNA-seqLevel2 +Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScDNA-seqLevel2 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ScDNA-seqLevel2 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScDNA-seqLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScDNA-seqLevel2 -MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScDNA-seqLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,ScDNA-seqLevel2 -Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScDNA-seqLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScDNA-seqLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BatMeth', 'MethylCoder', 'BRAT-BW', 'BSMAP', 'Bowtie', 'ERNE-BS5', 'STAR 2-Pass Genome', 'BS-Seeker2', 'STAR 2-Pass', 'BWA with Mark Duplicates and BQSR', 'BWA-aln', 'BWA-mem', 'STAR 2-Pass Transcriptome', 'BWA', 'STAR 2-Pass Chimeric', 'Segemehl', 'BSmooth', 'Other Alignment Workflow', 'None', 'GSNAP', 'Pash', 'BS-Seeker', 'Bisulfighter', 'BWA with BQSR', 'Bismark', 'RMAP', 'B-SOLANA', 'SOCS-B', 'BWA-meth', 'LAST']",,ScDNA-seqLevel2 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScDNA-seqLevel2 +Proportion Mitochondrial Reads,Proportion Mitochondrial Reads,ProportionMitochondrialReads,Proportion of reads mapping to mitochondria.,False,,,,ScDNA-seqLevel2 +Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,ScDNA-seqLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScDNA-seqLevel2 Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,ScDNA-seqLevel2 -Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,ScDNA-seqLevel2 Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,ScDNA-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScDNA-seqLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,ScDNA-seqLevel2 -Proportion Coverage 10x,Proportion Coverage 10x,ProportionCoverage10x,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 10X or greater coverage from Picard Tools.",False,,,,ScDNA-seqLevel2 -Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,ScDNA-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,,,ScDNA-seqLevel2 -Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,ScDNA-seqLevel2 +Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,ScDNA-seqLevel2 Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,ScDNA-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ScDNA-seqLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,ScDNA-seqLevel2 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,ScDNA-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,,,ScDNA-seqLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScDNA-seqLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScDNA-seqLevel2 Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,ScDNA-seqLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,ScDNA-seqLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,ScDNA-seqLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BWA-meth', 'Bismark', 'BSMAP', 'STAR 2-Pass Transcriptome', 'STAR 2-Pass Chimeric', 'BWA-mem', 'MethylCoder', 'B-SOLANA', 'Pash', 'BWA', 'SOCS-B', 'BWA with Mark Duplicates and BQSR', 'BS-Seeker2', 'None', 'LAST', 'BatMeth', 'ERNE-BS5', 'BRAT-BW', 'Segemehl', 'STAR 2-Pass Genome', 'GSNAP', 'BWA with BQSR', 'RMAP', 'STAR 2-Pass', 'Bowtie', 'BSmooth', 'Other Alignment Workflow', 'Bisulfighter', 'BWA-aln', 'BS-Seeker']",,ScDNA-seqLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ScDNA-seqLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,ScDNA-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,ScDNA-seqLevel2 -Proportion Mitochondrial Reads,Proportion Mitochondrial Reads,ProportionMitochondrialReads,Proportion of reads mapping to mitochondria.,False,,,,ScDNA-seqLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,ScDNA-seqLevel2 +Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,ScDNA-seqLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ScDNA-seqLevel2 +MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,ScDNA-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ScDNA-seqLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,ScDNA-seqLevel2 Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",ScDNA-seqLevel2 -Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Random', 'Oligo-dT', 'Feature barcoding', 'Poly-dT']",,MultiplexedCITE-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,MultiplexedCITE-seqLevel1 -Input Cells and Nuclei,Input Cells and Nuclei,InputCellsandNuclei,"Number of cells and number of nuclei input; entry format: number, number",True,,,,MultiplexedCITE-seqLevel1 -Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],True,,,,MultiplexedCITE-seqLevel1 -Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,True,,,,MultiplexedCITE-seqLevel1 -Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,,"['no', 'yes', '']",,MultiplexedCITE-seqLevel1 -Read1,Read1,Read1,Read 1 content description,True,,"['cDNA', 'Cell Barcode and UMI']",,MultiplexedCITE-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer IIx', 'Illumina HiSeq 2500', 'GridION', '454 GS FLX Titanium', 'Illumina NovaSeq 6000', 'NovaSeqS4', 'Illumina HiSeq X Five', 'Illumina MiSeq', 'Ion Torrent Proton', 'Other', 'PromethION', 'Illumina NextSeq', 'Revio', 'AB SOLiD 4', 'NovaSeq 6000', 'unknown', 'Ultima Genomics UG100', 'Ion Torrent PGM', 'Illumina HiSeq X Ten', 'Oxford Nanopore minION', 'Illumina NextSeq 1000', 'Illumina Next Seq 2500', 'PacBio RS', 'Illumina NextSeq 2000', 'Illumina Next Seq 500', 'AB SOLiD 2', 'Ion Torrent S5', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Complete Genomics', 'Illumina HiSeq 2000', 'AB SOLiD 3', 'Not Reported', 'Illumina Genome Analyzer II', 'Illumina HiSeq 4000']",,MultiplexedCITE-seqLevel1 +Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['Enzymatic Digestion', 'Not Applicable', 'Dounce', 'gentleMACS']",,MultiplexedCITE-seqLevel1 +Barcode Folder Synapse ID,Barcode Folder Synapse ID,BarcodeFolderSynapseID,Synapse ID of the folder containing the barcode lists,True,,,,MultiplexedCITE-seqLevel1 Total Number of Input Cells,Total Number of Input Cells,TotalNumberofInputCells,Number of cells loaded/placed on plates,True,,,,MultiplexedCITE-seqLevel1 +Spike In Concentration,Spike In Concentration,SpikeInConcentration,The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910],True,,,,MultiplexedCITE-seqLevel1 +Feature Barcode Library Type,Feature Barcode Library Type,FeatureBarcodeLibraryType,The library construction methods for the feature barcode library,True,,"['10x BCR', '10x TCR', '10x ADT – citeseq/hashing']",,MultiplexedCITE-seqLevel1 Barcode Folder File List,Barcode Folder File List,BarcodeFolderFileList,A comma separated list of filenames in the gzipped folder detailing what barcodes are specific to demultiplexing samples versus providing surface protein data,True,,,,MultiplexedCITE-seqLevel1 -Dissociation Method,Dissociation Method,DissociationMethod,The tissue dissociation method used for scRNASeq or scATAC-seq assays,True,,"['gentleMACS', 'Not Applicable', 'Dounce', 'Enzymatic Digestion']",,MultiplexedCITE-seqLevel1 -Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel1 -Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['inDropsV3', 'Smart-seq2', 'inDropsV2', 'Nextera XT', 'sci-ATAC-seq', '10xV3', 'CEL-seq2', '10x Multiome', '10xV1.1', 'Drop-seq', '10xV2', '10x FLEX', '10xV3.1', 'Smart-SeqV4', 'TruDrop', ""10x GEM 3'"", '10xV1.0', ""10x GEM 5'""]",,MultiplexedCITE-seqLevel1 Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,MultiplexedCITE-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Single Nucleus', 'Micro-region', 'Bulk Nuclei', 'Single Cell']",,MultiplexedCITE-seqLevel1 -Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['no', 'yes']",,MultiplexedCITE-seqLevel1 -cDNA,cDNA,CDNA,"Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase",False,,,,MultiplexedCITE-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,MultiplexedCITE-seqLevel1 +Input Cells and Nuclei,Input Cells and Nuclei,InputCellsandNuclei,"Number of cells and number of nuclei input; entry format: number, number",True,,,,MultiplexedCITE-seqLevel1 +Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable',True,,,,MultiplexedCITE-seqLevel1 +Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel1 Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,MultiplexedCITE-seqLevel1 -Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['10x', 'Droplets', 'Nuclei Isolation', 'Plates', 'FACS', 'Microfluidics Chip']",,MultiplexedCITE-seqLevel1 +Single Cell Dissociation Days from Index,Single Cell Dissociation Days from Index,SingleCellDissociationDaysfromIndex,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable',True,,,,MultiplexedCITE-seqLevel1 Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,MultiplexedCITE-seqLevel1 -Nucleic Acid Capture Days from Index,Nucleic Acid Capture Days from Index,NucleicAcidCaptureDaysfromIndex,Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable',True,,,,MultiplexedCITE-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel1 +Well Index,Well Index,WellIndex,Indicate if protein expression (EPCAM/CD45) positive/negative data is available for each cell in CEL-seq2 assays,False,,"['yes', 'no', '']",,MultiplexedCITE-seqLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,MultiplexedCITE-seqLevel1 Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",True,,,,MultiplexedCITE-seqLevel1 -Read2,Read2,Read2,Read 2 content description,True,,"['cDNA', 'Cell Barcode and UMI']",,MultiplexedCITE-seqLevel1 -End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,MultiplexedCITE-seqLevel1 -Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['No Spike In', 'Other Spike In', 'PhiX', 'ERCC']",,MultiplexedCITE-seqLevel1 -Single Cell Dissociation Days from Index,Single Cell Dissociation Days from Index,SingleCellDissociationDaysfromIndex,Number of days between sample for single cell assay was received in lab and when the sample was dissociated and cells were isolated [number]. If not applicable please enter 'Not Applicable',True,,,,MultiplexedCITE-seqLevel1 +Cryopreserved Cells in Sample,Cryopreserved Cells in Sample,CryopreservedCellsinSample,Indicate if library preparation was based on revived frozen cells.,True,,"['yes', 'no']",,MultiplexedCITE-seqLevel1 Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,MultiplexedCITE-seqLevel1 -Feature Barcode Library Type,Feature Barcode Library Type,FeatureBarcodeLibraryType,The library construction methods for the feature barcode library,True,,"['10x ADT – citeseq/hashing', '10x TCR', '10x BCR']",,MultiplexedCITE-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,MultiplexedCITE-seqLevel1 +Single Cell Barcode Method Applied,Single Cell Barcode Method Applied,SingleCellBarcodeMethodApplied,The method by which cells are multiplex or labeled with cell surface markers or probes,True,,"['Biolegend Total seq B Human Universal cocktail V1.0', 'Biolegend Total seq C Human Universal cocktail V1.0', 'Biolegend Total seq B Custom', 'Biolegend Total seq C Custom', 'Cell', 'Other', 'Hashtag- multiplex', 'Nuclear Hashtag- multiplex', 'Universal cocktail V1.0', 'Cite-seq custom panel', 'Biolegend Total seq A Custom', 'Biolegend Total seq A Human']",,MultiplexedCITE-seqLevel1 +End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,MultiplexedCITE-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['I1', 'R2', 'R1', 'Other', 'R1&R2']",,MultiplexedCITE-seqLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MultiplexedCITE-seqLevel1 -Single Cell Barcode Method Applied,Single Cell Barcode Method Applied,SingleCellBarcodeMethodApplied,The method by which cells are multiplex or labeled with cell surface markers or probes,True,,"['Other', 'Cite-seq custom panel', 'Biolegend Total seq B Human Universal cocktail V1.0', 'Nuclear Hashtag- multiplex', 'Biolegend Total seq C Human Universal cocktail V1.0', 'Biolegend Total seq A Human', 'Biolegend Total seq C Custom', 'Hashtag- multiplex', 'Cell', 'Biolegend Total seq B Custom', 'Biolegend Total seq A Custom', 'Universal cocktail V1.0']",,MultiplexedCITE-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,MultiplexedCITE-seqLevel1 +Single Cell Isolation Method,Single Cell Isolation Method,SingleCellIsolationMethod,"The method by which cells are isolated into individual reaction containers at a single cell resolution (e.g. wells, micro-droplets)",True,,"['Plates', 'Nuclei Isolation', '10x', 'Droplets', 'Microfluidics Chip', 'FACS']",,MultiplexedCITE-seqLevel1 +Empty Well Barcode,Empty Well Barcode,EmptyWellBarcode,Unique cell barcode assigned to empty cells used as controls in CEL-seq2 assays.,True,,,,MultiplexedCITE-seqLevel1 +Read1,Read1,Read1,Read 1 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,MultiplexedCITE-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel1 -Barcode Folder Synapse ID,Barcode Folder Synapse ID,BarcodeFolderSynapseID,Synapse ID of the folder containing the barcode lists,True,,,,MultiplexedCITE-seqLevel1 -cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Read2 is ""cDNA""']",MultiplexedCITE-seqLevel1 -cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Read2 is ""cDNA""']",MultiplexedCITE-seqLevel1 -UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 +Library Construction Method,Library Construction Method,LibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV3.1', '10x FLEX', ""10x GEM 5'"", 'inDropsV3', 'Nextera XT', 'Smart-SeqV4', '10xV3', 'CEL-seq2', '10xV2', '10xV1.1', ""10x GEM 3'"", 'sci-ATAC-seq', 'Smart-seq2', 'inDropsV2', '10x Multiome', '10xV1.0', 'TruDrop', 'Drop-seq']",,MultiplexedCITE-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel1 +Read2,Read2,Read2,Read 2 content description,True,,"['Cell Barcode and UMI', 'cDNA']",,MultiplexedCITE-seqLevel1 +Spike In,Spike In,SpikeIn,A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix,True,,"['Other Spike In', 'No Spike In', 'ERCC', 'PhiX']",,MultiplexedCITE-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MultiplexedCITE-seqLevel1 +Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Feature barcoding', 'Poly-dT', 'Random', 'Oligo-dT']",,MultiplexedCITE-seqLevel1 +Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 +UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 Cell Barcode Offset,Cell Barcode Offset,CellBarcodeOffset,Offset in sequence for cell barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 Valid Barcodes Cell Number,Valid Barcodes Cell Number,ValidBarcodesCellNumber,Number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 +UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 Cell Barcode Length,Cell Barcode Length,CellBarcodeLength,Length of cell barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 -Median UMIs per Cell Number,Median UMIs per Cell Number,MedianUMIsperCellNumber,Number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 -UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Read2 is ""Cell Barcode and UMI""']",MultiplexedCITE-seqLevel1 +cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Read2 is ""cDNA""']",MultiplexedCITE-seqLevel1 +cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Read2 is ""cDNA""']",MultiplexedCITE-seqLevel1 +Whitelist Cell Barcode File Link,Whitelist Cell Barcode File Link,WhitelistCellBarcodeFileLink,Link to file listing all possible cell barcodes. URL,True,,,,MultiplexedCITE-seqLevel2 Cell Barcode Tag,Cell Barcode Tag,CellBarcodeTag,SAM tag for cell barcode field; please provide a valid cell barcode tag (e.g. CB:Z),True,,,,MultiplexedCITE-seqLevel2 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Other', 'HTSeq - FPKM', 'DEXSeq', 'Differentiation trajectory analysis', 'SEQC', 'HCA Optimus', 'CellRanger', 'Cufflinks', 'STARsolo', 'Cell annotation', 'dropEST']",,MultiplexedCITE-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel2 +Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,MultiplexedCITE-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,MultiplexedCITE-seqLevel2 +UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,MultiplexedCITE-seqLevel2 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cufflinks', 'HCA Optimus', 'DEXSeq', 'HTSeq - FPKM', 'STARsolo', 'Other', 'Differentiation trajectory analysis', 'dropEST', 'SEQC', 'CellRanger', 'Cell annotation']",,MultiplexedCITE-seqLevel2 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel2 Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel2 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,MultiplexedCITE-seqLevel2 -Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,MultiplexedCITE-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel2 -Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel2 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel2 Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel2 +Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,MultiplexedCITE-seqLevel2 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MultiplexedCITE-seqLevel2 -UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,MultiplexedCITE-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,MultiplexedCITE-seqLevel2 -Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,MultiplexedCITE-seqLevel2 +Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel2 -Whitelist Cell Barcode File Link,Whitelist Cell Barcode File Link,WhitelistCellBarcodeFileLink,Link to file listing all possible cell barcodes. URL,True,,,,MultiplexedCITE-seqLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel2 scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,MultiplexedCITE-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,MultiplexedCITE-seqLevel2 -Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['no', 'Yes - Applied Hard Trimming']",,MultiplexedCITE-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MultiplexedCITE-seqLevel2 +Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,MultiplexedCITE-seqLevel2 Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,,"['Applied Hard Trimming is ""Yes - Applied Hard Trimming""']",MultiplexedCITE-seqLevel2 -Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel3 +Cell Total,Cell Total,CellTotal,Number of sequenced cells. Applies to raw counts matrix only.,True,,,,MultiplexedCITE-seqLevel3 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MultiplexedCITE-seqLevel3 -Cell Median Number Genes,Cell Median Number Genes,CellMedianNumberGenes,Median number of genes detected per cell. Number,True,,,,MultiplexedCITE-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,MultiplexedCITE-seqLevel3 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cufflinks', 'HCA Optimus', 'DEXSeq', 'HTSeq - FPKM', 'STARsolo', 'Other', 'Differentiation trajectory analysis', 'dropEST', 'SEQC', 'CellRanger', 'Cell annotation']",,MultiplexedCITE-seqLevel3 +Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Normalized Counts', 'Batch Corrected Counts']",,MultiplexedCITE-seqLevel3 Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel3 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel3 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Other', 'HTSeq - FPKM', 'DEXSeq', 'Differentiation trajectory analysis', 'SEQC', 'HCA Optimus', 'CellRanger', 'Cufflinks', 'STARsolo', 'Cell annotation', 'dropEST']",,MultiplexedCITE-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel3 -Cell Total,Cell Total,CellTotal,Number of sequenced cells. Applies to raw counts matrix only.,True,,,,MultiplexedCITE-seqLevel3 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel3 -Cell Median Number Reads,Cell Median Number Reads,CellMedianNumberReads,Median number of reads per cell. Number,True,,,,MultiplexedCITE-seqLevel3 -Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Other', 'Transcript Expression', 'Isoform Expression Quantification', 'Gene Expression', 'Splice Junction Quantification', 'Gene Expression Quantification', 'Exon Expression Quantification']",,MultiplexedCITE-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel3 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel3 +Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel3 +Data Category,Data Category,DataCategory,Specific content type of the data file.,True,,"['Gene Expression', 'Transcript Expression', 'Isoform Expression Quantification', 'Splice Junction Quantification', 'Gene Expression Quantification', 'Other', 'Exon Expression Quantification']",,MultiplexedCITE-seqLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel3 scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,MultiplexedCITE-seqLevel3 -Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Batch Corrected Counts', 'Raw Counts', 'Normalized Counts', 'Scaled Counts']",,MultiplexedCITE-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MultiplexedCITE-seqLevel3 +Cell Median Number Genes,Cell Median Number Genes,CellMedianNumberGenes,Median number of genes detected per cell. Number,True,,,,MultiplexedCITE-seqLevel3 +Cell Median Number Reads,Cell Median Number Reads,CellMedianNumberReads,Median number of reads per cell. Number,True,,,,MultiplexedCITE-seqLevel3 Linked Matrices,Linked Matrices,LinkedMatrices,All matrices associated with every part of a SingleCellExperiment object. Comma-delimited list of filenames,False,,,,MultiplexedCITE-seqLevel3 -Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel4 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MultiplexedCITE-seqLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,MultiplexedCITE-seqLevel4 +scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Cufflinks', 'HCA Optimus', 'DEXSeq', 'HTSeq - FPKM', 'STARsolo', 'Other', 'Differentiation trajectory analysis', 'dropEST', 'SEQC', 'CellRanger', 'Cell annotation']",,MultiplexedCITE-seqLevel4 Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,MultiplexedCITE-seqLevel4 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel4 -scRNAseq Workflow Type,scRNAseq Workflow Type,ScRNAseqWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['Other', 'HTSeq - FPKM', 'DEXSeq', 'Differentiation trajectory analysis', 'SEQC', 'HCA Optimus', 'CellRanger', 'Cufflinks', 'STARsolo', 'Cell annotation', 'dropEST']",,MultiplexedCITE-seqLevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel4 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MultiplexedCITE-seqLevel4 Filename,Filename,Filename,Name of a file,True,,,,MultiplexedCITE-seqLevel4 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,MultiplexedCITE-seqLevel4 +Associated mRNA Library Data File ID,Associated mRNA Library Data File ID,AssociatedmRNALibraryDataFileID,Sample Level HTAN Data File ID for the associated level - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MultiplexedCITE-seqLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MultiplexedCITE-seqLevel4 scRNAseq Workflow Parameters Description,scRNAseq Workflow Parameters Description,ScRNAseqWorkflowParametersDescription,"Parameters used to run the workflow. scRNA-seq level 3: e.g. Normalization and log transformation, ran empty drops or doublet detection, used filter on # genes/cell, etc. scRNA-seq Level 4: dimensionality reduction with PCA and 50 components, nearest-neighbor graph with k = 20 and Leiden clustering with resolution = 1, UMAP visualization using 50 PCA components, marker genes used to annotate cell types, information about droplet matrix (all barcodes) to cell matrix (only informative barcodes representing real cells) conversion",True,,,,MultiplexedCITE-seqLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MultiplexedCITE-seqLevel4 +Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkMethylation-seqLevel2 +Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 +Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkMethylation-seqLevel2 +Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkMethylation-seqLevel2 +Duplicate Removal Software,Duplicate Removal Software,DuplicateRemovalSoftware,Software used for remove duplicate reads,True,,"['picard MarkDuplicates', 'Samtools sort']",,BulkMethylation-seqLevel2 Pairs On Diff CHR,Pairs On Diff CHR,PairsOnDiffCHR,Pairs on different chromosomes collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2 -Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 +Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,BulkMethylation-seqLevel2 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkMethylation-seqLevel2 -Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkMethylation-seqLevel2 -Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2 -Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 -Trimmer,Trimmer,Trimmer,Software used for trimming,True,,"['Adapter removal', 'Trim Galore!', 'Kraken', 'ConDeTri', 'SolexaQA', 'PRINSEQ', 'ERNE-FILTER', 'Btrim', 'FASTX toolkit', 'Cutadapt', 'Trimmo-matic']",,BulkMethylation-seqLevel2 -Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2 -Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BatMeth', 'MethylCoder', 'BRAT-BW', 'BSMAP', 'Bowtie', 'ERNE-BS5', 'STAR 2-Pass Genome', 'BS-Seeker2', 'STAR 2-Pass', 'BWA with Mark Duplicates and BQSR', 'BWA-aln', 'BWA-mem', 'STAR 2-Pass Transcriptome', 'BWA', 'STAR 2-Pass Chimeric', 'Segemehl', 'BSmooth', 'Other Alignment Workflow', 'None', 'GSNAP', 'Pash', 'BS-Seeker', 'Bisulfighter', 'BWA with BQSR', 'Bismark', 'RMAP', 'B-SOLANA', 'SOCS-B', 'BWA-meth', 'LAST']",,BulkMethylation-seqLevel2 +Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Long Read', 'Single Read', 'Paired End', 'Mid-length']",,BulkMethylation-seqLevel2 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkMethylation-seqLevel2 +Bulk Methylation Genomic Reference,Bulk Methylation Genomic Reference,BulkMethylationGenomicReference,The human genome reference used in the alignment of reads,True,,"['T2T CHM13', 'HG38', 'HG19']",,BulkMethylation-seqLevel2 +Proportion Base Mismatch,Proportion Base Mismatch,ProportionBaseMismatch,Proportion of mismatched bases collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 +Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 Short Reads,Short Reads,ShortReads,Number of reads that were too short. Integer,False,,,,BulkMethylation-seqLevel2 -Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,BulkMethylation-seqLevel2 -Bulk Methylation Genomic Reference,Bulk Methylation Genomic Reference,BulkMethylationGenomicReference,The human genome reference used in the alignment of reads,True,,"['HG19', 'HG38', 'T2T CHM13']",,BulkMethylation-seqLevel2 +Trimmer,Trimmer,Trimmer,Software used for trimming,True,,"['Btrim', 'FASTX toolkit', 'ERNE-FILTER', 'Trim Galore!', 'Trimmo-matic', 'Cutadapt', 'ConDeTri', 'Adapter removal', 'SolexaQA', 'PRINSEQ', 'Kraken']",,BulkMethylation-seqLevel2 Proportion Targets No Coverage,Proportion Targets No Coverage,ProportionTargetsNoCoverage,Proportion of targets that did not reach 1X coverage over any base from Picard Tools. Number,False,,,,BulkMethylation-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkMethylation-seqLevel2 -Contamination,Contamination,Contamination,Fraction of reads coming from cross-sample contamination collected from GATK4. Number,False,,,,BulkMethylation-seqLevel2 -Alignment Workflow Url,Alignment Workflow Url,AlignmentWorkflowUrl,Link to workflow used for read alignment. DockStore.org recommended. String,True,,,,BulkMethylation-seqLevel2 -Duplicate Removal Software,Duplicate Removal Software,DuplicateRemovalSoftware,Software used for remove duplicate reads,True,,"['picard MarkDuplicates', 'Samtools sort']",,BulkMethylation-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel2 -Proportion of Minimum CpG Coverage 10X,Proportion of Minimum CpG Coverage 10X,ProportionofMinimumCpGCoverage10X,"Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.",False,,,,BulkMethylation-seqLevel2 -Contamination Error,Contamination Error,ContaminationError,Estimation error of cross-sample contamination collected from GATK4. Number,False,,,,BulkMethylation-seqLevel2 Total Unmapped reads,Total Unmapped reads,TotalUnmappedreads,Number of reads that did not map to genome. Integer,False,,,,BulkMethylation-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,BulkMethylation-seqLevel2 -Library Layout,Library Layout,LibraryLayout,Sequencing read type,True,,"['Mid-length', 'Long Read', 'Paired End', 'Single Read']",,BulkMethylation-seqLevel2 -Average Base Quality,Average Base Quality,AverageBaseQuality,Average base quality collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,BulkMethylation-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel2 +Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkMethylation-seqLevel2 +Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkMethylation-seqLevel2 Proportion Reads Duplicated,Proportion Reads Duplicated,ProportionReadsDuplicated,Proportion of duplicated reads collected from samtools. Number,False,,,,BulkMethylation-seqLevel2 +Average Insert Size,Average Insert Size,AverageInsertSize,Average insert size collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2 +Average Read Length,Average Read Length,AverageReadLength,Average read length collected from samtools. Integer,False,,,,BulkMethylation-seqLevel2 +Alignment Workflow Type,Alignment Workflow Type,AlignmentWorkflowType,Generic name for the workflow used to analyze a data set.,True,,"['BWA-meth', 'Bismark', 'BSMAP', 'STAR 2-Pass Transcriptome', 'STAR 2-Pass Chimeric', 'BWA-mem', 'MethylCoder', 'B-SOLANA', 'Pash', 'BWA', 'SOCS-B', 'BWA with Mark Duplicates and BQSR', 'BS-Seeker2', 'None', 'LAST', 'BatMeth', 'ERNE-BS5', 'BRAT-BW', 'Segemehl', 'STAR 2-Pass Genome', 'GSNAP', 'BWA with BQSR', 'RMAP', 'STAR 2-Pass', 'Bowtie', 'BSmooth', 'Other Alignment Workflow', 'Bisulfighter', 'BWA-aln', 'BS-Seeker']",,BulkMethylation-seqLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel2 -Index File Name,Index File Name,IndexFileName,The name (or part of a name) of a file (of any type). String,True,,,,BulkMethylation-seqLevel2 -Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,BulkMethylation-seqLevel2 -Total Uniquely Mapped,Total Uniquely Mapped,TotalUniquelyMapped,Number of reads that map to genome. Integer,False,,,,BulkMethylation-seqLevel2 +Proportion Coverage 30X,Proportion Coverage 30X,ProportionCoverage30X,"Proportion of all reference bases for whole genome sequencing, or targeted bases for whole exome and targeted sequencing, that achieves 30X or greater coverage from Picard Tools.",False,,,,BulkMethylation-seqLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkMethylation-seqLevel2 +Proportion of Minimum CpG Coverage 10X,Proportion of Minimum CpG Coverage 10X,ProportionofMinimumCpGCoverage10X,"Proportion of all reference bases for whole genome sequencing, or targeted sequencing, that achieves 10X or greater coverage per CpG.",False,,,,BulkMethylation-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkMethylation-seqLevel2 +Mean Coverage,Mean Coverage,MeanCoverage,"Mean coverage for whole genome sequencing, or mean target coverage for whole exome and targeted sequencing, collected from Picard. Number",False,,,,BulkMethylation-seqLevel2 Custom Alignment Workflow,Custom Alignment Workflow,CustomAlignmentWorkflow,Specify the name of a custom alignment workflow,False,True,,"['Alignment is ""Other Alignment Workflow""']",BulkMethylation-seqLevel2 -DMC Calling Tool,DMC Calling Tool,DMCCallingTool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),True,,"['metilene', 'BSmooth', 'MethylKit', 'MOABS', 'DSS-single', 'MACAU', 'MethylSig', 'MethylDackel', 'BiSeq', 'DSS']",,BulkMethylation-seqLevel3 -DMC Calling Workflow URL,DMC Calling Workflow URL,DMCCallingWorkflowURL,Generic name for the workflow used to analyze a data set,True,,,,BulkMethylation-seqLevel3 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel3 Lambda methylation ratio,Lambda methylation ratio,Lambdamethylationratio,"Methylation ratio of mostly unmethylated lambda control, as a percentage",True,,,,BulkMethylation-seqLevel3 +Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkMethylation-seqLevel3 HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,BulkMethylation-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,BulkMethylation-seqLevel3 DMC data file format,DMC data file format,DMCdatafileformat,Format of the data files,True,,"['BED', 'bedGraph']",,BulkMethylation-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,BulkMethylation-seqLevel3 -DMR data file Format,DMR data file Format,DMRdatafileFormat,Format of the data files.,True,,"['BED', 'bedGraph']",,BulkMethylation-seqLevel3 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,BulkMethylation-seqLevel3 -DMR Calling Tool,DMR Calling Tool,DMRCallingTool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),True,,"['metilene', 'BSmooth', 'MethylKit', 'MOABS', 'DSS-single', 'MACAU', 'MethylSig', 'BiSeq', 'DSS']",,BulkMethylation-seqLevel3 DMR Calling Workflow URL,DMR Calling Workflow URL,DMRCallingWorkflowURL,Generic name for the workflow used to analyze a data set,True,,,,BulkMethylation-seqLevel3 -Filename,Filename,Filename,Name of a file,True,,,,BulkMethylation-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,BulkMethylation-seqLevel3 +DMC Calling Tool,DMC Calling Tool,DMCCallingTool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),True,,"['MOABS', 'DSS-single', 'BSmooth', 'BiSeq', 'MethylSig', 'DSS', 'metilene', 'MACAU', 'MethylKit', 'MethylDackel']",,BulkMethylation-seqLevel3 +DMC Calling Workflow URL,DMC Calling Workflow URL,DMCCallingWorkflowURL,Generic name for the workflow used to analyze a data set,True,,,,BulkMethylation-seqLevel3 +DMR data file Format,DMR data file Format,DMRdatafileFormat,Format of the data files.,True,,"['BED', 'bedGraph']",,BulkMethylation-seqLevel3 +DMR Calling Tool,DMR Calling Tool,DMRCallingTool,Software used for calling differentially methylated CpG (DMC) and differentially methylated region (DMR),True,,"['MOABS', 'DSS-single', 'BSmooth', 'BiSeq', 'MethylSig', 'DSS', 'metilene', 'MACAU', 'MethylKit']",,BulkMethylation-seqLevel3 pUC19 methylation ratio,pUC19 methylation ratio,PUC19methylationratio,"Methylation ratio of mostly methylated pUC19 control, as a percentage",True,,,,BulkMethylation-seqLevel3 -Pre-processing Completed,Pre-processing Completed,Pre-processingCompleted,Pre-processing steps completed to convert level 1 raw data to a single level 2 image,True,,"['Other', 'None', 'TMA de-arraying', 'Illumination correction', 'Channel/Cycle Registration', 'Tile Stitching']",,ImagingLevel1 -Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel1 -Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['mIHC', 'IMC', 'IHC', 'Not Applicable', 'CyCIF', 'ExSeq', 't-CyCIF', 'H&E', 'GeoMX-DSP', 'CODEX', 'MERFISH', 'MxIF', 'RareCyte Orion', 'MIBI', 'SABER']",,ImagingLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ImagingLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel1 Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel1 -Pre-processing Required,Pre-processing Required,Pre-processingRequired,Pre-processing steps required to convert level 1 raw data to a single level 2 image,True,,"['Other', 'None', 'TMA de-arraying', 'Illumination correction', 'Channel/Cycle Registration', 'Tile Stitching']",,ImagingLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel1 +Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel1 +Pre-processing Completed,Pre-processing Completed,Pre-processingCompleted,Pre-processing steps completed to convert level 1 raw data to a single level 2 image,True,,"['None', 'Tile Stitching', 'Other', 'TMA de-arraying', 'Illumination correction', 'Channel/Cycle Registration']",,ImagingLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel1 +Pre-processing Required,Pre-processing Required,Pre-processingRequired,Pre-processing steps required to convert level 1 raw data to a single level 2 image,True,,"['None', 'Tile Stitching', 'Other', 'TMA de-arraying', 'Illumination correction', 'Channel/Cycle Registration']",,ImagingLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ImagingLevel1 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel1 +Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['MxIF', 'mIHC', 'CODEX', 'SABER', 'IHC', 'H&E', 'MIBI', 'RareCyte Orion', 'IMC', 'GeoMX-DSP', 't-CyCIF', 'Not Applicable', 'ExSeq', 'CyCIF', 'MERFISH']",,ImagingLevel1 Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel1 -SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 -Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['mIHC', 'IMC', 'IHC', 'Not Applicable', 'CyCIF', 'ExSeq', 't-CyCIF', 'H&E', 'GeoMX-DSP', 'CODEX', 'MERFISH', 'MxIF', 'RareCyte Orion', 'MIBI', 'SABER']",,ImagingLevel2 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ImagingLevel2 -WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel2 -PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,ImagingLevel2 -Immersion,Immersion,Immersion,Immersion medium,False,,"['Other', 'Oil', 'Air', 'Water', '']",,ImagingLevel2 -Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,ImagingLevel2 FOVY,FOVY,FOVY,Field of view Y dimension. Floating point value,False,,,,ImagingLevel2 -PhysicalSizeZUnit,PhysicalSizeZUnit,PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,ImagingLevel2 -PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['double', 'int16', 'int32', 'uint8', 'bit', 'int8', 'uint16', 'float', 'uint32']",,ImagingLevel2 -PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,ImagingLevel2 +FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel2 +LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel2 +WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel2 +Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['yes', 'no']",,ImagingLevel2 +PhysicalSizeZUnit,PhysicalSizeZUnit,PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['mm', 'Å', 'nm', 'cm', 'µm']",,ImagingLevel2 SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,ImagingLevel2 -MERFISH Codebook File,MERFISH Codebook File,MERFISHCodebookFile,The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.,False,,,,ImagingLevel2 -FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,ImagingLevel2 -Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,ImagingLevel2 -Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel2 +Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['false', 'true']",,ImagingLevel2 +SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,ImagingLevel2 +MERFISH Positions File,MERFISH Positions File,MERFISHPositionsFile,The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.,False,,,,ImagingLevel2 +Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,ImagingLevel2 +SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 +NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel2 +PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,ImagingLevel2 +FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel2 +Immersion,Immersion,Immersion,Immersion medium,False,,"['Air', 'Other', 'Water', 'Oil', '']",,ImagingLevel2 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,ImagingLevel2 +Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['MxIF', 'mIHC', 'CODEX', 'SABER', 'IHC', 'H&E', 'MIBI', 'RareCyte Orion', 'IMC', 'GeoMX-DSP', 't-CyCIF', 'Not Applicable', 'ExSeq', 'CyCIF', 'MERFISH']",,ImagingLevel2 Objective,Objective,Objective,Objective,False,,,,ImagingLevel2 -Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel2 +Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['yes', 'no']",,ImagingLevel2 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel2 +FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel2 +DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['XYTZC', 'XYZTC', 'ZYX', 'XYCTZ', 'XYCZT', 'XYZCT']",,ImagingLevel2 +Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel2 +SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 +SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 +PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['bit', 'double', 'uint8', 'float', 'int8', 'uint32', 'uint16', 'int32', 'int16']",,ImagingLevel2 Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,ImagingLevel2 -PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,ImagingLevel2 -LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel2 -MERFISH Positions File,MERFISH Positions File,MERFISHPositionsFile,The positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.,False,,,,ImagingLevel2 +MERFISH Codebook File,MERFISH Codebook File,MERFISHCodebookFile,The codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.,False,,,,ImagingLevel2 +Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['yes', 'no']",,ImagingLevel2 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel2 -PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,ImagingLevel2 +PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,ImagingLevel2 +PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['mm', 'Å', 'nm', 'cm', 'µm']",,ImagingLevel2 FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel2 -PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,ImagingLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel2 -SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 -DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['ZYX', 'XYTZC', 'XYCTZ', 'XYCZT', 'XYZTC', 'XYZCT']",,ImagingLevel2 -Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel2 -SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,ImagingLevel2 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel2 -Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['true', 'false']",,ImagingLevel2 -NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel2 -Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,ImagingLevel2 -Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['no', 'yes']",,ImagingLevel2 +Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,ImagingLevel2 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ImagingLevel2 -SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,ImagingLevel2 -WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,ImagingLevel2 -Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['no', 'yes']",,ImagingLevel2 +Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel2 -FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,ImagingLevel2 -FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel2 -PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,ImagingLevel2 -Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['no', 'yes']",,ImagingLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Segmentation -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ImagingLevel3Segmentation -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Segmentation -Imaging Segmentation Data Type,Imaging Segmentation Data Type,ImagingSegmentationDataType,Specifies how the segmentation is stored,True,,"['Probability Map', 'Polygon', 'Outline', 'Point', 'Mask']",,ImagingLevel3Segmentation -Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,ImagingLevel3Segmentation +PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,ImagingLevel2 +Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel2 +WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ImagingLevel2 +Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,ImagingLevel2 +PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,ImagingLevel2 +PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel3Segmentation -Number of Objects,Number of Objects,NumberofObjects,The number of objects (eg cells) described,True,,,,ImagingLevel3Segmentation +Imaging Segmentation Data Type,Imaging Segmentation Data Type,ImagingSegmentationDataType,Specifies how the segmentation is stored,True,,"['Polygon', 'Mask', 'Probability Map', 'Outline', 'Point']",,ImagingLevel3Segmentation Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel3Segmentation +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Segmentation +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Segmentation +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ImagingLevel3Segmentation Parameter file,Parameter file,Parameterfile,Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis,False,,,,ImagingLevel3Segmentation +Number of Objects,Number of Objects,NumberofObjects,The number of objects (eg cells) described,True,,,,ImagingLevel3Segmentation Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel3Segmentation +Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,ImagingLevel3Segmentation Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel3Segmentation Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,,"['Imaging Object Class is ""Imaging Object Class Other""']",ImagingLevel3Segmentation -Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['mIHC', 'IMC', 'IHC', 'Not Applicable', 'CyCIF', 'ExSeq', 't-CyCIF', 'H&E', 'GeoMX-DSP', 'CODEX', 'MERFISH', 'MxIF', 'RareCyte Orion', 'MIBI', 'SABER']",,ImagingLevel3Image +FOVY,FOVY,FOVY,Field of view Y dimension. Floating point value,False,,,,ImagingLevel3Image +FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel3Image +LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel3Image WorkingDistance,WorkingDistance,WorkingDistance,"The working distance of the lens, expressed as a floating point number. Floating point > 0.",False,,,,ImagingLevel3Image +Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['yes', 'no']",,ImagingLevel3Image +HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,HTAN ID for a level 3 channels table.,True,,,,ImagingLevel3Image HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel3Image -Immersion,Immersion,Immersion,Immersion medium,False,,"['Other', 'Oil', 'Air', 'Water', '']",,ImagingLevel3Image -Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,ImagingLevel3Image -FOVY,FOVY,FOVY,Field of view Y dimension. Floating point value,False,,,,ImagingLevel3Image -Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel3Image +NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel3Image +Immersion,Immersion,Immersion,Immersion medium,False,,"['Air', 'Other', 'Water', 'Oil', '']",,ImagingLevel3Image +Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['yes', 'no']",,ImagingLevel3Image +Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['MxIF', 'mIHC', 'CODEX', 'SABER', 'IHC', 'H&E', 'MIBI', 'RareCyte Orion', 'IMC', 'GeoMX-DSP', 't-CyCIF', 'Not Applicable', 'ExSeq', 'CyCIF', 'MERFISH']",,ImagingLevel3Image Objective,Objective,Objective,Objective,False,,,,ImagingLevel3Image -Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel3Image +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel3Image +Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel3Image Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,ImagingLevel3Image -LensNA,LensNA,LensNA,The numerical aperture of the lens. Floating point value > 0.,False,,,,ImagingLevel3Image +Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['yes', 'no']",,ImagingLevel3Image Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel3Image FOV number,FOV number,FOVnumber,Index of FOV (as it pertains to its sequence order). Integer >= 1,False,,,,ImagingLevel3Image -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Image -HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,HTAN ID for a level 3 channels table.,True,,,,ImagingLevel3Image -Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel3Image -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ImagingLevel3Image -NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,ImagingLevel3Image -Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['no', 'yes']",,ImagingLevel3Image HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ImagingLevel3Image -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ImagingLevel3Image -Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['no', 'yes']",,ImagingLevel3Image +Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,ImagingLevel3Image Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel3Image -FOVX,FOVX,FOVX,Field of view X dimension. Floating point,False,,,,ImagingLevel3Image -Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['no', 'yes']",,ImagingLevel3Image -WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,ImagingLevel3Image -FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,ImagingLevel3Image -FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,ImagingLevel3Image -Dilution,Dilution,Dilution,Dilution (eg 1:1000),False,,,,ImagingLevel3Channels -Lot,Lot,Lot,Lot number from vendor,False,,,,ImagingLevel3Channels -Channel Name,Channel Name,ChannelName,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin'),True,,,,ImagingLevel3Channels -Channel Passed QC,Channel Passed QC,ChannelPassedQC,Identify stains that did not pass QC but are included in the dataset.,True,,"['No - Channel Failed QC', 'yes']",,ImagingLevel3Channels -Oligo Barcode Upper Strand,Oligo Barcode Upper Strand,OligoBarcodeUpperStrand,Oligo Barcode - Upper Strand,False,,,,ImagingLevel3Channels -Emission Wavelength,Emission Wavelength,EmissionWavelength,Center/peak of the emission spectrum (nm),False,,,,ImagingLevel3Channels -Fluorophore,Fluorophore,Fluorophore,Fluorescent dye label (eg Alexa Fluor 488),False,,,,ImagingLevel3Channels -Concentration,Concentration,Concentration,Concentration (eg 10ug/mL),False,,,,ImagingLevel3Channels +Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ImagingLevel3Image +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel3Image +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ImagingLevel3Image +Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,ImagingLevel3Image +FOVYUnit,FOVYUnit,FOVYUnit,Field of view Y dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel3Image +FOVXUnit,FOVXUnit,FOVXUnit,Field of view X dimension units. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel3Image +WorkingDistanceUnit,WorkingDistanceUnit,WorkingDistanceUnit,The units of the working distance. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ImagingLevel3Image +Cycle Number,Cycle Number,CycleNumber,The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles),False,,,,ImagingLevel3Channels Sub Cycle Number,Sub Cycle Number,SubCycleNumber,Sub cycle number,False,,,,ImagingLevel3Channels -Channel ID,Channel ID,ChannelID,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1'),True,,,,ImagingLevel3Channels Antibody Name,Antibody Name,AntibodyName,"Antibody Name (free text (eg “Keratin”, “CD163”, “DNA”))",True,,,,ImagingLevel3Channels HTAN Channel Metadata ID,HTAN Channel Metadata ID,HTANChannelMetadataID,HTAN ID for this channel metadata table (same for all rows),True,,,,ImagingLevel3Channels +Emission Wavelength,Emission Wavelength,EmissionWavelength,Center/peak of the emission spectrum (nm),False,,,,ImagingLevel3Channels +Emission Bandwidth,Emission Bandwidth,EmissionBandwidth,Nominal width of emission spectrum (nm),False,,,,ImagingLevel3Channels Metal Isotope Mass,Metal Isotope Mass,MetalIsotopeMass,Element mass number,False,,,,ImagingLevel3Channels -Vendor,Vendor,Vendor,Vendor,False,,,,ImagingLevel3Channels +Oligo Barcode Upper Strand,Oligo Barcode Upper Strand,OligoBarcodeUpperStrand,Oligo Barcode - Upper Strand,False,,,,ImagingLevel3Channels +Concentration,Concentration,Concentration,Concentration (eg 10ug/mL),False,,,,ImagingLevel3Channels Target Name,Target Name,TargetName,Short descriptive name (abbreviation) for this target (antigen),True,,,,ImagingLevel3Channels -Clone,Clone,Clone,Clone,False,,,,ImagingLevel3Channels -Oligo Barcode Lower Strand,Oligo Barcode Lower Strand,OligoBarcodeLowerStrand,Oligo Barcode - Lower Strand,False,,,,ImagingLevel3Channels -Antibody Role,Antibody Role,AntibodyRole,"""Is this antibody acting as a primary or secondary antibody""",True,,"['Secondary', 'Neither-Dye/Stain', 'Primary']",,ImagingLevel3Channels -Excitation Wavelength,Excitation Wavelength,ExcitationWavelength,Center/peak of the excitation spectrum (nm),False,,,,ImagingLevel3Channels -Cycle Number,Cycle Number,CycleNumber,The cycle # in which the co-listed reagent(s) was(were) used. Integer >= 1 (up to number of cycles),False,,,,ImagingLevel3Channels -Emission Bandwidth,Emission Bandwidth,EmissionBandwidth,Nominal width of emission spectrum (nm),False,,,,ImagingLevel3Channels Excitation Bandwidth,Excitation Bandwidth,ExcitationBandwidth,Nominal width of excitation spectrum (nm),False,,,,ImagingLevel3Channels -Metal Isotope Element,Metal Isotope Element,MetalIsotopeElement,Element abbreviation. eg “La” or “Nd”,False,,"['Ni', 'Ba', 'Po', 'Pd', 'Zr', 'Os', 'Sg', 'Yb', 'Si', 'Zn', 'In', 'Fm', 'Fr', 'Tl', 'U', 'Tc', 'Ce', 'At', 'Rg', 'Br', 'Md', 'Dy', 'Y', 'Nb', 'Ag', 'Hg', 'Rb', 'Pa', 'Rh', 'Ca', 'Hs', 'Xe', 'Nd', 'Np', 'Tm', 'V', 'Ds', 'I', 'Cn', 'Co', 'Lv', 'Au', 'Bk', 'Ga', 'Er', 'Mc', 'Cd', 'Mo', 'Es', 'Mt', 'Al', 'Th', 'Ne', 'Na', 'Ru', 'Tb', 'He', 'Be', 'Kr', 'Ac', 'As', 'Se', 'Sn', 'Li', 'Ar', 'Pr', 'Te', 'Db', 'N', 'Bi', 'Lr', 'W', 'Re', 'Ti', 'Ir', 'Pb', 'Ra', 'no', 'Rn', 'Lu', 'Sc', 'La', 'Gd', 'Cl', 'Fl', 'H', 'Sb', 'Pt', 'S', 'F', 'Eu', 'Bh', 'Fe', 'Pu', 'Ge', 'Cs', 'Nh', 'Mg', 'Rf', 'Sr', 'Sm', 'Og', 'Am', 'Cu', 'Ho', 'O', 'C', 'Mn', 'Cf', 'Ts', 'Hf', 'K', 'Pm', 'Ta', 'Cr', 'P', 'B', '']",,ImagingLevel3Channels +Excitation Wavelength,Excitation Wavelength,ExcitationWavelength,Center/peak of the excitation spectrum (nm),False,,,,ImagingLevel3Channels +Channel Passed QC,Channel Passed QC,ChannelPassedQC,Identify stains that did not pass QC but are included in the dataset.,True,,"['No - Channel Failed QC', 'yes']",,ImagingLevel3Channels +Lot,Lot,Lot,Lot number from vendor,False,,,,ImagingLevel3Channels +Channel Name,Channel Name,ChannelName,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Blue' or 'CD45' or 'E-cadherin'),True,,,,ImagingLevel3Channels +Antibody Role,Antibody Role,AntibodyRole,"""Is this antibody acting as a primary or secondary antibody""",True,,"['Neither-Dye/Stain', 'Secondary', 'Primary']",,ImagingLevel3Channels +Vendor,Vendor,Vendor,Vendor,False,,,,ImagingLevel3Channels +Metal Isotope Element,Metal Isotope Element,MetalIsotopeElement,Element abbreviation. eg “La” or “Nd”,False,,"['Hf', 'At', 'Si', 'Co', 'Rb', 'Er', 'Mg', 'Ru', 'Ar', 'Kr', 'Yb', 'V', 'Cl', 'Sg', 'Ac', 'Pr', 'Cu', 'He', 'Og', 'Mt', 'Rh', 'Xe', 'Mn', 'Y', 'Ne', 'Ni', 'N', 'Sn', 'Po', 'B', 'Tc', 'W', 'Tm', 'Nd', 'Lv', 'Na', 'Gd', 'Pd', 'Ge', 'Sb', 'Ba', 'Hg', 'Rf', 'Fm', 'H', 'Li', 'Cr', 'Eu', 'F', 'Ts', 'Ag', 'Sc', 'Zr', 'Ca', 'Am', 'Es', 'Tl', 'Pu', 'Fl', 'Pt', 'Ta', 'K', 'Cd', 'Dy', 'Sm', 'Lr', 'S', 'Be', 'Pb', 'Ds', 'P', 'Sr', 'Ti', 'Hs', 'Rn', 'Zn', 'Tb', 'I', 'Cf', 'U', 'Mc', 'Cs', 'Ir', 'Te', 'Np', 'Th', 'Fr', 'no', 'Bh', 'Cn', 'Ho', 'Db', 'Br', 'Fe', 'Rg', 'Bi', 'C', 'Md', 'As', 'Ga', 'Al', 'La', 'O', 'Ra', 'Pa', 'Nh', 'Os', 'Bk', 'Pm', 'Ce', 'Re', 'Se', 'Lu', 'Nb', 'In', 'Mo', 'Au', '']",,ImagingLevel3Channels +Oligo Barcode Lower Strand,Oligo Barcode Lower Strand,OligoBarcodeLowerStrand,Oligo Barcode - Lower Strand,False,,,,ImagingLevel3Channels +Fluorophore,Fluorophore,Fluorophore,Fluorescent dye label (eg Alexa Fluor 488),False,,,,ImagingLevel3Channels +Dilution,Dilution,Dilution,Dilution (eg 1:1000),False,,,,ImagingLevel3Channels Catalog Number,Catalog Number,CatalogNumber,Catalog Number,False,,,,ImagingLevel3Channels +Channel ID,Channel ID,ChannelID,This must match the corresponding field in the OME-XML / TIFF header. (eg 'Channel:0:1'),True,,,,ImagingLevel3Channels RRID identifier,RRID identifier,RRIDidentifier,Research Resource Identifier (eg “RRID: AB_394606”),True,,,,ImagingLevel3Channels -Channel QC Failure Type,Channel QC Failure Type,ChannelQCFailureType,Reason the channel failed QC,False,True,"['Other/multiple channel QC faliure types', 'Staining artefacet', 'Auto-fluoresence', 'Imaging artefact', 'Off-target staining', '']","['Channel Passed QC is ""No - Channel Failed QC""']",ImagingLevel3Channels +Clone,Clone,Clone,Clone,False,,,,ImagingLevel3Channels +Channel QC Failure Type,Channel QC Failure Type,ChannelQCFailureType,Reason the channel failed QC,False,True,"['Auto-fluoresence', 'Other/multiple channel QC faliure types', 'Imaging artefact', 'Off-target staining', 'Staining artefacet', '']","['Channel Passed QC is ""No - Channel Failed QC""']",ImagingLevel3Channels Channel QC Failure Comment,Channel QC Failure Comment,ChannelQCFailureComment,Custom comment on channel QC faliure,False,True,,"['Channel is ""Other/multiple channel QC faliure types""']",ImagingLevel3Channels -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ImagingLevel4 -HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,HTAN ID for a level 3 channels table.,True,,,,ImagingLevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel4 -Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,ImagingLevel4 -Number of Objects,Number of Objects,NumberofObjects,The number of objects (eg cells) described,True,,,,ImagingLevel4 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ImagingLevel4 -Imaging Summary Statistic,Imaging Summary Statistic,ImagingSummaryStatistic,Function used to summarize object/feature intensity,False,,"['Mean', 'Not Specified', 'Median', '']",,ImagingLevel4 -Number of Features,Number of Features,NumberofFeatures,The number of features (eg channels) described,True,,,,ImagingLevel4 Filename,Filename,Filename,Name of a file,True,,,,ImagingLevel4 +Imaging Summary Statistic,Imaging Summary Statistic,ImagingSummaryStatistic,Function used to summarize object/feature intensity,False,,"['Mean', 'Not Specified', 'Median', '']",,ImagingLevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ImagingLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ImagingLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ImagingLevel4 Parameter file,Parameter file,Parameterfile,Path in Syanpse to a text file listing algorithm version numbers and relevant parameters needed to reproduce the analysis,False,,,,ImagingLevel4 +Number of Objects,Number of Objects,NumberofObjects,The number of objects (eg cells) described,True,,,,ImagingLevel4 +Number of Features,Number of Features,NumberofFeatures,The number of features (eg channels) described,True,,,,ImagingLevel4 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ImagingLevel4 +Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,ImagingLevel4 +HTAN Parent Channel Metadata ID,HTAN Parent Channel Metadata ID,HTANParentChannelMetadataID,HTAN ID for a level 3 channels table.,True,,,,ImagingLevel4 Commit SHA,Commit SHA,CommitSHA,"Short SHA for software version [8 hexadecimal characters (for github), comma separated if multiple]",False,,,,ImagingLevel4 Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,,"['Imaging Object Class is ""Imaging Object Class Other""']",ImagingLevel4 -Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Random', 'Oligo-dT', 'Feature barcoding', 'Poly-dT']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['Other', 'I1', 'R1&R2', 'R1', 'R2']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Spatial Library Construction Method,Spatial Library Construction Method,SpatialLibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['inDropsV3', 'Smart-seq2', 'inDropsV2', 'Nextera XT', '10xV3', '10xV1.1', 'Drop-seq', '10xV2', '10xV3.1', 'Smart-SeqV4', 'TruDrop', '10xV1.0']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,,"['cDNA', 'Spatial Barcode and UMI']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Slide Version,Slide Version,SlideVersion,Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.,False,,"['V4', 'V3', 'V2', 'V1', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,,"['cDNA', 'Spatial Barcode and UMI']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer IIx', 'Illumina HiSeq 2500', 'GridION', '454 GS FLX Titanium', 'Illumina NovaSeq 6000', 'NovaSeqS4', 'Illumina HiSeq X Five', 'Illumina MiSeq', 'Ion Torrent Proton', 'Other', 'PromethION', 'Illumina NextSeq', 'Revio', 'AB SOLiD 4', 'NovaSeq 6000', 'unknown', 'Ultima Genomics UG100', 'Ion Torrent PGM', 'Illumina HiSeq X Ten', 'Oxford Nanopore minION', 'Illumina NextSeq 1000', 'Illumina Next Seq 2500', 'PacBio RS', 'Illumina NextSeq 2000', 'Illumina Next Seq 500', 'AB SOLiD 2', 'Ion Torrent S5', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Complete Genomics', 'Illumina HiSeq 2000', 'AB SOLiD 3', 'Not Reported', 'Illumina Genome Analyzer II', 'Illumina HiSeq 4000']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['D', 'D1', 'A', 'C1', 'C', 'B', 'A1', 'B1', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Permeabilization Time,Permeabilization Time,PermeabilizationTime,Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Spatial Read1,Spatial Read1,SpatialRead1,Read 1 content description,True,,"['Spatial Barcode and UMI', 'cDNA']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Library Preparation Days from Index,Library Preparation Days from Index,LibraryPreparationDaysfromIndex,Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable',False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Permeabilization Time,Permeabilization Time,PermeabilizationTime,Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['C', 'D1', 'C1', 'B', 'A1', 'B1', 'A', 'D', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 Sequencing Library Construction Days from Index,Sequencing Library Construction Days from Index,SequencingLibraryConstructionDaysfromIndex,Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable',True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 RIN,RIN,RIN,A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +End Bias,End Bias,EndBias,"The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript",True,,"['Full Length Transcript', '5 Prime', '3 Prime']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Spatial Library Construction Method,Spatial Library Construction Method,SpatialLibraryConstructionMethod,Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711],True,,"['10xV3.1', 'inDropsV3', 'Nextera XT', 'Smart-SeqV4', '10xV3', '10xV2', '10xV1.1', 'Smart-seq2', 'inDropsV2', '10xV1.0', 'TruDrop', 'Drop-seq']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Read Indicator,Read Indicator,ReadIndicator,"Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other",True,,"['I1', 'R2', 'R1', 'Other', 'R1&R2']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Spatial Read2,Spatial Read2,SpatialRead2,Read 2 content description,True,,"['Spatial Barcode and UMI', 'cDNA']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +DV200,DV200,DV200,Represents the percentage of RNA fragments that are >200 nucleotides in size. Number,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 Image Re-orientation,Image Re-orientation,ImageRe-orientation,"To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.",False,,"['TRUE', 'FALSE', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Reverse Transcription Primer,Reverse Transcription Primer,ReverseTranscriptionPrimer,"An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA",True,,"['Feature barcoding', 'Poly-dT', 'Random', 'Oligo-dT']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Slide Version,Slide Version,SlideVersion,Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.,False,,"['V3', 'V4', 'V2', 'V1', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 Spatial Barcode and UMI,Spatial Barcode and UMI,SpatialBarcodeandUMI,Spot and transcript identifiers,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 Spatial Barcode Offset,Spatial Barcode Offset,SpatialBarcodeOffset,Offset in sequence for spot barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +UMI Barcode Length,UMI Barcode Length,UMIBarcodeLength,Length of UMI barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +UMI Barcode Offset,UMI Barcode Offset,UMIBarcodeOffset,"Start position of UMI barcode in the sequence. Values: number, 0 for start of read",False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 Spatial Barcode Length,Spatial Barcode Length,SpatialBarcodeLength,Length of spot barcode read (in bp): number,False,True,,"['Spatial Read2 is ""Spatial Barcode and UMI""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 -Spatial Barcode Tag,Spatial Barcode Tag,SpatialBarcodeTag,SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +cDNA Length,cDNA Length,CDNALength,Length of cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +cDNA Offset,cDNA Offset,CDNAOffset,Offset in sequence for cDNA read (in bp): number,False,True,,"['Spatial Read2 is ""cDNA""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Feature Reference Id,Feature Reference Id,FeatureReferenceId,"Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]",False,True,,"['Reverse Transcription Primer is ""Feature barcoding""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel1 +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Spatial Barcode Tag,Spatial Barcode Tag,SpatialBarcodeTag,SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['D', 'D1', 'A', 'C1', 'C', 'B', 'A1', 'B1', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 Whitelist Spatial Barcode File Link,Whitelist Spatial Barcode File Link,WhitelistSpatialBarcodeFileLink,Link to file listing all possible spatial barcodes. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Genome Annotation URL,Genome Annotation URL,GenomeAnnotationURL,Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['Yes - Applied Hard Trimming', 'no']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['C', 'D1', 'C1', 'B', 'A1', 'B1', 'A', 'D', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +Checksum,Checksum,Checksum,MD5 checksum of the BAM file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 Genomic Reference URL,Genomic Reference URL,GenomicReferenceURL,Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Applied Hard Trimming,Applied Hard Trimming,AppliedHardTrimming,Was Hard Trimming applied,True,,"['no', 'Yes - Applied Hard Trimming']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 +UMI Tag,UMI Tag,UMITag,"SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel2 Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,False,True,,"['Applied Hard Trimming is ""Yes - Applied Hard Trimming""']",10xVisiumSpatialTranscriptomics-RNA-seqLevel2 -Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,,"['unfiltered mex', 'filtered mex', 'detected jpg', 'fiducial image jpg', 'reference jpg', 'json scale factors', 'reference png', 'fiducial image png', 'probe dataset csv', 'tissue_positions', 'features', 'detected image png', 'barcodes', 'high res image', 'low res image', 'qc result html']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['D', 'D1', 'A', 'C1', 'C', 'B', 'A1', 'B1', '']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles -Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,,"['unfiltered mex', 'fiducial image jpg', 'probe dataset csv', 'filtered mex', 'high res image', 'qc result html', 'detected image png', 'json scale factors', 'detected jpg', 'reference png', 'tissue_positions', 'features', 'low res image', 'barcodes', 'reference jpg', 'fiducial image png']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['C', 'D1', 'C1', 'B', 'A1', 'B1', 'A', 'D', '']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,10xVisiumSpatialTranscriptomics-AuxiliaryFiles +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Mean Reads per Spatial Spot,Mean Reads per Spatial Spot,MeanReadsperSpatialSpot,"The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,,"['unfiltered mex', 'filtered mex', 'detected jpg', 'fiducial image jpg', 'reference jpg', 'json scale factors', 'reference png', 'fiducial image png', 'probe dataset csv', 'tissue_positions', 'features', 'detected image png', 'barcodes', 'high res image', 'low res image', 'qc result html']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Sequencing Saturation,Sequencing Saturation,SequencingSaturation,"The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['D', 'D1', 'A', 'C1', 'C', 'B', 'A1', 'B1', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Visium File Type,Visium File Type,VisiumFileType,The file type generated for the visium experiment.,True,,"['unfiltered mex', 'fiducial image jpg', 'probe dataset csv', 'filtered mex', 'high res image', 'qc result html', 'detected image png', 'json scale factors', 'detected jpg', 'reference png', 'tissue_positions', 'features', 'low res image', 'barcodes', 'reference jpg', 'fiducial image png']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Proportion Reads Mapped to Transcriptome,Proportion Reads Mapped to Transcriptome,ProportionReadsMappedtoTranscriptome,Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Median Number Genes per Spatial Spot,Median Number Genes per Spatial Spot,MedianNumberGenesperSpatialSpot,The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 -Median UMI Counts per Spot,Median UMI Counts per Spot,MedianUMICountsperSpot,The median number of UMI counts per tissue covered spot.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 Spots under tissue,Spots under tissue,Spotsundertissue,The number of barcodes associated with a spot under tissue.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Capture Area,Capture Area,CaptureArea,"Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.",False,,"['C', 'D1', 'C1', 'B', 'A1', 'B1', 'A', 'D', '']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 Proportion Reads Mapped,Proportion Reads Mapped,ProportionReadsMapped,Proportion of mapped reads collected from samtools. Number,False,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Mean Reads per Spatial Spot,Mean Reads per Spatial Spot,MeanReadsperSpatialSpot,"The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Proportion Reads Mapped to Transcriptome,Proportion Reads Mapped to Transcriptome,ProportionReadsMappedtoTranscriptome,Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Median UMI Counts per Spot,Median UMI Counts per Spot,MedianUMICountsperSpot,The median number of UMI counts per tissue covered spot.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Sequencing Saturation,Sequencing Saturation,SequencingSaturation,"The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel3 +Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 Workflow Version,Workflow Version,WorkflowVersion,Major version of the workflow (e.g. Cell Ranger v3.1),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 Workflow Link,Workflow Link,WorkflowLink,Link to workflow or command. DockStore.org recommended. URL,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Run ID,Run ID,RunID,A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 Visium Workflow Type,Visium Workflow Type,VisiumWorkflowType,Generic name for the workflow used to analyze the visium data set.,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 Visium Workflow Parameters Description,Visium Workflow Parameters Description,VisiumWorkflowParametersDescription,Parameters used to run the workflow..,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 -Filename,Filename,Filename,Name of a file,True,,,,10xVisiumSpatialTranscriptomics-RNA-seqLevel4 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -GeoMx DSP NGS Sequencing Platform,GeoMx DSP NGS Sequencing Platform,GeoMxDSPNGSSequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -GeoMx DSP NGS Library Preparation Kit Name,GeoMx DSP NGS Library Preparation Kit Name,GeoMxDSPNGSLibraryPreparationKitName,Name of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +Synapse ID of GeoMx DSP PKC File,Synapse ID of GeoMx DSP PKC File,SynapseIDofGeoMxDSPPKCFile,The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +GeoMx DSP Library Preparation Kit Version,GeoMx DSP Library Preparation Kit Version,GeoMxDSPLibraryPreparationKitVersion,Version of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +Synapse ID of GeoMx Lab Worksheet File,Synapse ID of GeoMx Lab Worksheet File,SynapseIDofGeoMxLabWorksheetFile,Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -GeoMx DSP Library Preparation Kit Vendor,GeoMx DSP Library Preparation Kit Vendor,GeoMxDSPLibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 Filename,Filename,Filename,Name of a file,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 GeoMx DSP NGS Library Selection Method,GeoMx DSP NGS Library Selection Method,GeoMxDSPNGSLibrarySelectionMethod,How RNA molecules are isolated.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -GeoMx DSP Library Preparation Kit Version,GeoMx DSP Library Preparation Kit Version,GeoMxDSPLibraryPreparationKitVersion,Version of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +GeoMx DSP Library Preparation Kit Vendor,GeoMx DSP Library Preparation Kit Vendor,GeoMxDSPLibraryPreparationKitVendor,Vendor of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -Synapse ID of GeoMx DSP PKC File,Synapse ID of GeoMx DSP PKC File,SynapseIDofGeoMxDSPPKCFile,The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -Synapse ID of GeoMx Lab Worksheet File,Synapse ID of GeoMx Lab Worksheet File,SynapseIDofGeoMxLabWorksheetFile,Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 -Segment name,Segment name,Segmentname,Name given to segment at time of generation,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +GeoMx DSP NGS Library Preparation Kit Name,GeoMx DSP NGS Library Preparation Kit Name,GeoMxDSPNGSLibraryPreparationKitName,Name of Library Preparation Kit. String,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 +GeoMx DSP NGS Sequencing Platform,GeoMx DSP NGS Sequencing Platform,GeoMxDSPNGSSequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel1 ROI Y Coordinate,ROI Y Coordinate,ROIYCoordinate,Y location within the image,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Nuclei count,Nuclei count,Nucleicount,Number of nuclei detected in the segment (if applicable),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata ROI X Coordinate,ROI X Coordinate,ROIXCoordinate,X location within the image,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Scan name,Scan name,Scanname,GeoMx Scan name (as appears in Segment Summary),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Scan Width,Scan Width,ScanWidth,Width of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Deduplicated reads,Deduplicated reads,Deduplicatedreads,Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Nuclei count,Nuclei count,Nucleicount,Number of nuclei detected in the segment (if applicable),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Scan Offset X,Scan Offset X,ScanOffsetX,Offset X of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Scan name,Scan name,Scanname,GeoMx Scan name (as appears in Segment Summary),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Raw reads,Raw reads,Rawreads,Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata Tags,Tags,Tags,Unique descriptor of a variable group (ie. MAPK+),True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Scan Offset X,Scan Offset X,ScanOffsetX,Offset X of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Stitched reads,Stitched reads,Stitchedreads,"Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads",False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Scan Width,Scan Width,ScanWidth,Width of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Scan Offset Y,Scan Offset Y,ScanOffsetY,Offset Y of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Segment name,Segment name,Segmentname,Name given to segment at time of generation,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata Slide name,Slide name,Slidename,"Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).",False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Scan Height,Scan Height,ScanHeight,Height of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata Aligned reads,Aligned reads,Alignedreads,Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Raw reads,Raw reads,Rawreads,Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Sequencing Saturation,Sequencing Saturation,SequencingSaturation,"The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).",True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Deduplicated reads,Deduplicated reads,Deduplicatedreads,Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata Biological probe median,Biological probe median,Biologicalprobemedian,Is the median count from all probes except the negative control probes. A measure of signal to background for each segment,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Scan Offset Y,Scan Offset Y,ScanOffsetY,Offset Y of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Scan Height,Scan Height,ScanHeight,Height of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +MapQ30,MapQ30,MapQ30,Number of reads with Quality >= 30.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +Stitched reads,Stitched reads,Stitchedreads,"Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads",False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata In Situ Negative median,In Situ Negative median,InSituNegativemedian,Is the median of all negative control probes for a given segment. A measure of signal to background for each segment.,False,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata -Tissue Stain,Tissue Stain,TissueStain,e.g. CD45 or PanCK (if masking was performed),False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Segment name,Segment name,Segmentname,Name given to segment at time of generation,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -ROI Y Coordinate,ROI Y Coordinate,ROIYCoordinate,Y location within the image,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Scan Height,Scan Height,ScanHeight,Height of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Sequencing Saturation,Sequencing Saturation,SequencingSaturation,"The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).",True,,,,NanoStringGeoMxDSPROIDCCSegmentAnnotationMetadata +QC status,QC status,QCstatus,ROI quality control flag as reported by the application,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Scan Offset X,Scan Offset X,ScanOffsetX,Offset X of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +ROI Y Coordinate,ROI Y Coordinate,ROIYCoordinate,Y location within the image,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata Binding Density,Binding Density,BindingDensity,The binding density as reported by the application,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -QC status,QC status,QCstatus,ROI quality control flag as reported by the application,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Nuclei count,Nuclei count,Nucleicount,Number of nuclei detected in the segment (if applicable),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata ROI X Coordinate,ROI X Coordinate,ROIXCoordinate,X location within the image,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Scan Height,Scan Height,ScanHeight,Height of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Positive norm factor,Positive norm factor,Positivenormfactor,The Positive Control Normalization factor calculated using pos-hyb controls,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata Scan name,Scan name,Scanname,GeoMx Scan name (as appears in Segment Summary),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Scan Width,Scan Width,ScanWidth,Width of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Tissue Stain,Tissue Stain,TissueStain,e.g. CD45 or PanCK (if masking was performed),False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata Tags,Tags,Tags,Unique descriptor of a variable group (ie. MAPK+),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -Positive norm factor,Positive norm factor,Positivenormfactor,The Positive Control Normalization factor calculated using pos-hyb controls,False,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Scan Width,Scan Width,ScanWidth,Width of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata Scan Offset Y,Scan Offset Y,ScanOffsetY,Offset Y of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata -GeoMx DSP Assay Type,GeoMx DSP Assay Type,GeoMxDSPAssayType,The assay type which was used for the GeoMx DSP pipeline.,True,,"['Protein nCounter', 'RNA nCounter', 'RNA NGS', 'Protein NGS']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +Nuclei count,Nuclei count,Nucleicount,Number of nuclei detected in the segment (if applicable),True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Segment name,Segment name,Segmentname,Name given to segment at time of generation,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata +Scan Offset X,Scan Offset X,ScanOffsetX,Offset X of the scan for GeoMx Analysis,True,,,,NanoStringGeoMxDSPROIRCCSegmentAnnotationMetadata HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -GeoMx DSP Genomic Reference,GeoMx DSP Genomic Reference,GeoMxDSPGenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Raw Counts', 'Scaled Counts', 'Normalized Counts', 'Batch Corrected Counts']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +GeoMx DSP Assay Type,GeoMx DSP Assay Type,GeoMxDSPAssayType,The assay type which was used for the GeoMx DSP pipeline.,True,,"['Protein NGS', 'RNA NGS', 'RNA nCounter', 'Protein nCounter']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -GeoMx DSP Unique Probe Count,GeoMx DSP Unique Probe Count,GeoMxDSPUniqueProbeCount,Total number of unique probes reported.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -GeoMx DSP Unique Target Count,GeoMx DSP Unique Target Count,GeoMxDSPUniqueTargetCount,Total number of unique genes reported.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -GeoMx DSP Workflow Link,GeoMx DSP Workflow Link,GeoMxDSPWorkflowLink,Link to workflow or command. DockStore.org recommended. URL,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 Filename,Filename,Filename,Name of a file,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -GeoMx DSP Workflow Parameter Description,GeoMx DSP Workflow Parameter Description,GeoMxDSPWorkflowParameterDescription,Parameters used to run the GeoMx DSP workflow.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -Matrix Type,Matrix Type,MatrixType,Type of data stored in matrix.,True,,"['Batch Corrected Counts', 'Raw Counts', 'Normalized Counts', 'Scaled Counts']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 GeoMx DSP Workflow Type,GeoMx DSP Workflow Type,GeoMxDSPWorkflowType,Generic name for the workflow used to analyze the GeoMx DSP data set.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +GeoMx DSP Workflow Link,GeoMx DSP Workflow Link,GeoMxDSPWorkflowLink,Link to workflow or command. DockStore.org recommended. URL,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +GeoMx DSP Workflow Parameter Description,GeoMx DSP Workflow Parameter Description,GeoMxDSPWorkflowParameterDescription,Parameters used to run the GeoMx DSP workflow.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +GeoMx DSP Genomic Reference,GeoMx DSP Genomic Reference,GeoMxDSPGenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 Synapse ID of GeoMx DSP ROI Segment Annotation File,Synapse ID of GeoMx DSP ROI Segment Annotation File,SynapseIDofGeoMxDSPROISegmentAnnotationFile,Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.,True,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 -Biotin Enrichment,Biotin Enrichment,BiotinEnrichment,Whether biotin is used for enriching ligation product,True,,"['no', 'yes']",,HI-C-seqLevel1 +GeoMx DSP Unique Probe Count,GeoMx DSP Unique Probe Count,GeoMxDSPUniqueProbeCount,Total number of unique probes reported.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +GeoMx DSP Unique Target Count,GeoMx DSP Unique Target Count,GeoMxDSPUniqueTargetCount,Total number of unique genes reported.,False,,,,NanoStringGeoMxDSPSpatialTranscriptomicsLevel3 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,HI-C-seqLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,HI-C-seqLevel1 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,HI-C-seqLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,HI-C-seqLevel1 -Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Single Nucleus', 'Micro-region', 'Bulk Nuclei', 'Single Cell']",,HI-C-seqLevel1 Crosslinking Condtion,Crosslinking Condtion,CrosslinkingCondtion,Detailed condition for DNA crosslinking,True,,,,HI-C-seqLevel1 -DNA Digestion Condition,DNA Digestion Condition,DNADigestionCondition,Enzymes and treatment length/temperature for genome digestion,True,,,,HI-C-seqLevel1 -Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,HI-C-seqLevel1 Nuclei Permeabilization Method,Nuclei Permeabilization Method,NucleiPermeabilizationMethod,Detergent and treatment condition for nuclei permeabilization and crosslinking softening,True,,,,HI-C-seqLevel1 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,HI-C-seqLevel1 -DNA Input Amount,DNA Input Amount,DNAInputAmount,"Amount of DNA for library construction, in nanograms.",True,,,,HI-C-seqLevel1 -Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['EZ-Tn5', 'Diagenode-unloaded Apex-Bio', 'Tn5', 'Tn5-059', 'In-House', 'Nextera Tn5', 'Diagenode-loaded Apex-Bio']",,HI-C-seqLevel1 Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,HI-C-seqLevel1 -Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Genome Analyzer IIx', 'Illumina HiSeq 2500', 'GridION', '454 GS FLX Titanium', 'Illumina NovaSeq 6000', 'NovaSeqS4', 'Illumina HiSeq X Five', 'Illumina MiSeq', 'Ion Torrent Proton', 'Other', 'PromethION', 'Illumina NextSeq', 'Revio', 'AB SOLiD 4', 'NovaSeq 6000', 'unknown', 'Ultima Genomics UG100', 'Ion Torrent PGM', 'Illumina HiSeq X Ten', 'Oxford Nanopore minION', 'Illumina NextSeq 1000', 'Illumina Next Seq 2500', 'PacBio RS', 'Illumina NextSeq 2000', 'Illumina Next Seq 500', 'AB SOLiD 2', 'Ion Torrent S5', 'PacBio Sequel2', 'Illumina Next Seq 550', 'Complete Genomics', 'Illumina HiSeq 2000', 'AB SOLiD 3', 'Not Reported', 'Illumina Genome Analyzer II', 'Illumina HiSeq 4000']",,HI-C-seqLevel1 +Sequencing Platform,Sequencing Platform,SequencingPlatform,A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.,True,,"['Illumina Next Seq 500', 'Ultima Genomics UG100', 'Illumina Genome Analyzer II', 'Illumina HiSeq 2000', 'Illumina NextSeq', 'Illumina NovaSeq 6000', 'Ion Torrent Proton', '454 GS FLX Titanium', 'AB SOLiD 4', 'Illumina NextSeq 2000', 'Oxford Nanopore minION', 'Illumina Next Seq 550', 'PacBio RS', 'Illumina HiSeq 2500', 'Ion Torrent S5', 'Other', 'Illumina MiSeq', 'PacBio Sequel2', 'Ion Torrent PGM', 'AB SOLiD 2', 'Illumina HiSeq X Five', 'Illumina Genome Analyzer IIx', 'unknown', 'Illumina HiSeq X Ten', 'Illumina NextSeq 1000', 'Not Reported', 'GridION', 'NovaSeqS4', 'Illumina HiSeq 4000', 'AB SOLiD 3', 'Illumina Next Seq 2500', 'NovaSeq 6000', 'Complete Genomics', 'Revio', 'PromethION']",,HI-C-seqLevel1 +Transposition Reaction,Transposition Reaction,TranspositionReaction,"Name of the transposase, transposon sequences",True,,"['Tn5', 'Diagenode-loaded Apex-Bio', 'Diagenode-unloaded Apex-Bio', 'Tn5-059', 'EZ-Tn5', 'In-House', 'Nextera Tn5']",,HI-C-seqLevel1 +DNA Digestion Condition,DNA Digestion Condition,DNADigestionCondition,Enzymes and treatment length/temperature for genome digestion,True,,,,HI-C-seqLevel1 +Nucleic Acid Source,Nucleic Acid Source,NucleicAcidSource,The source of the input nucleic molecule,True,,"['Bulk Whole Cell', 'Bulk Nuclei', 'Single Cell', 'Micro-region', 'Single Nucleus']",,HI-C-seqLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel1 Ligation Condition,Ligation Condition,LigationCondition,Name of ligase and condition for proximity ligation,True,,,,HI-C-seqLevel1 Technical Replicate Group,Technical Replicate Group,TechnicalReplicateGroup,A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch),False,,,,HI-C-seqLevel1 +Biotin Enrichment,Biotin Enrichment,BiotinEnrichment,Whether biotin is used for enriching ligation product,True,,"['yes', 'no']",,HI-C-seqLevel1 +Total Reads,Total Reads,TotalReads,Total number of reads per sample. Integer,False,,,,HI-C-seqLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,HI-C-seqLevel1 +DNA Input Amount,DNA Input Amount,DNAInputAmount,"Amount of DNA for library construction, in nanograms.",True,,,,HI-C-seqLevel1 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,HI-C-seqLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,HI-C-seqLevel2 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,HI-C-seqLevel2 +Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel2 Aligned Read Length,Aligned Read Length,AlignedReadLength,Read length used for alignment if hard trimming was applied,True,,,,HI-C-seqLevel2 +Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,HI-C-seqLevel2 HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,HI-C-seqLevel2 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,HI-C-seqLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,HI-C-seqLevel2 Resolution,Resolution,Resolution,"Binning size used for generating contact matrix, in basepair.",True,,,,HI-C-seqLevel2 -Tool,Tool,Tool,Were any software or computational tools generated for this content,True,,"['no', 'yes']",,HI-C-seqLevel2 -Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,HI-C-seqLevel2 -Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel2 +Tool,Tool,Tool,Were any software or computational tools generated for this content,True,,"['yes', 'no']",,HI-C-seqLevel2 +Loop Calling,Loop Calling,LoopCalling,Tool used for identifying loop interactions,True,,"['Cooltools', 'Other', 'HiCCUPS']",,HI-C-seqLevel3 Genomic Reference,Genomic Reference,GenomicReference,Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39),True,,,,HI-C-seqLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,HI-C-seqLevel3 -Loop Calling,Loop Calling,LoopCalling,Tool used for identifying loop interactions,True,,"['Other', 'HiCCUPS', 'Cooltools']",,HI-C-seqLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,HI-C-seqLevel3 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,HI-C-seqLevel3 -Stripe Window,Stripe Window,StripeWindow,Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.,True,,,,HI-C-seqLevel3 -Stripe Calling,Stripe Calling,StripeCalling,"Tool used for identifying architectural stripe-forming, interaction hotspots.",True,,,,HI-C-seqLevel3 Filename,Filename,Filename,Name of a file,True,,,,HI-C-seqLevel3 +Stripe Window,Stripe Window,StripeWindow,Binning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.,True,,,,HI-C-seqLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,HI-C-seqLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,HI-C-seqLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,HI-C-seqLevel3 Loop Window,Loop Window,LoopWindow,Binning size used for calling significant dot interactions (loops),True,,,,HI-C-seqLevel3 -SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 -Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['mIHC', 'IMC', 'IHC', 'Not Applicable', 'CyCIF', 'ExSeq', 't-CyCIF', 'H&E', 'GeoMX-DSP', 'CODEX', 'MERFISH', 'MxIF', 'RareCyte Orion', 'MIBI', 'SABER']",,SRRSImagingLevel2 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,SRRSImagingLevel2 -Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,SRRSImagingLevel2 -PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['double', 'int16', 'int32', 'uint8', 'bit', 'int8', 'uint16', 'float', 'uint32']",,SRRSImagingLevel2 -PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2 +Stripe Calling,Stripe Calling,StripeCalling,"Tool used for identifying architectural stripe-forming, interaction hotspots.",True,,"['Other', 'MACS2']",,HI-C-seqLevel3 +Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['yes', 'no']",,SRRSImagingLevel2 SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,SRRSImagingLevel2 -Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,SRRSImagingLevel2 +Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['false', 'true']",,SRRSImagingLevel2 +SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,SRRSImagingLevel2 +Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,SRRSImagingLevel2 +SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 +NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,SRRSImagingLevel2 +PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,SRRSImagingLevel2 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,SRRSImagingLevel2 +Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['yes', 'no']",,SRRSImagingLevel2 +Imaging Assay Type,Imaging Assay Type,ImagingAssayType,Type of imaging assay,True,,"['MxIF', 'mIHC', 'CODEX', 'SABER', 'IHC', 'H&E', 'MIBI', 'RareCyte Orion', 'IMC', 'GeoMX-DSP', 't-CyCIF', 'Not Applicable', 'ExSeq', 'CyCIF', 'MERFISH']",,SRRSImagingLevel2 Objective,Objective,Objective,Objective,False,,,,SRRSImagingLevel2 -Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,SRRSImagingLevel2 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSImagingLevel2 +DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['XYTZC', 'XYZTC', 'ZYX', 'XYCTZ', 'XYCZT', 'XYZCT']",,SRRSImagingLevel2 +SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 +Filename,Filename,Filename,Name of a file,True,,,,SRRSImagingLevel2 +SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 +PixelType,PixelType,PixelType,"Data type for each pixel value. E.g. ""uint16""",True,,"['bit', 'double', 'uint8', 'float', 'int8', 'uint32', 'uint16', 'int32', 'int16']",,SRRSImagingLevel2 Microscope,Microscope,Microscope,"Microscope type (manufacturer, model, etc) used for this experiment",True,,,,SRRSImagingLevel2 -PlaneCount,PlaneCount,PlaneCount,"Number of Z-planes (not to be confused with downsampled ""pyramid""). Integer >=1",True,,,,SRRSImagingLevel2 +Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['yes', 'no']",,SRRSImagingLevel2 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,SRRSImagingLevel2 -PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,SRRSImagingLevel2 -PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSImagingLevel2 -SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 -DimensionOrder,DimensionOrder,DimensionOrder,The order in which the individual planes of data are interleaved.,True,,"['ZYX', 'XYTZC', 'XYCTZ', 'XYCZT', 'XYZTC', 'XYZCT']",,SRRSImagingLevel2 -Filename,Filename,Filename,Name of a file,True,,,,SRRSImagingLevel2 -SizeT,SizeT,SizeT,Number of time points. Integer >= 1,True,,,,SRRSImagingLevel2 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,SRRSImagingLevel2 -Pixels BigEndian,Pixels BigEndian,PixelsBigEndian,Boolean (True/False),True,,"['true', 'false']",,SRRSImagingLevel2 -NominalMagnification,NominalMagnification,NominalMagnification,The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. floating point value > 1(no units),True,,,,SRRSImagingLevel2 -Image ID,Image ID,ImageID,"Unique internal image identifier. eg ""Image:0"". (To be extracted from OME-XML)",True,,,,SRRSImagingLevel2 -Tseries,Tseries,Tseries,Does data file contain a time-series of images,True,,"['no', 'yes']",,SRRSImagingLevel2 +PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2 +PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),True,,"['mm', 'Å', 'nm', 'cm', 'µm']",,SRRSImagingLevel2 +Channel Metadata Filename,Channel Metadata Filename,ChannelMetadataFilename,Full path within Synapse project of uploaded companion CSV file containing channel-level metadata details,True,,,,SRRSImagingLevel2 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,SRRSImagingLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,SRRSImagingLevel2 -SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,SRRSImagingLevel2 -Zstack,Zstack,Zstack,Does data file contain a Z-stack of images,True,,"['no', 'yes']",,SRRSImagingLevel2 +Frame Averaging,Frame Averaging,FrameAveraging,"Number of frames averaged together (if no averaging, set to 1). Integer >= 1",False,,,,SRRSImagingLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,SRRSImagingLevel2 -PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,SRRSImagingLevel2 -Pyramid,Pyramid,Pyramid,Does data file contain pyramid of images,True,,"['no', 'yes']",,SRRSImagingLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,SRRSImagingLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,SRRSImagingLevel2 +Passed QC,Passed QC,PassedQC,Did all channels pass QC (if not add free text Comment),True,,"['No - Channels QC', 'yes']",,SRRSImagingLevel2 +PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,SRRSImagingLevel2 +PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,SRRSImagingLevel2 Comment,Comment,Comment,Free text field (generally for QC comment),False,True,,"['Passed QC is ""No - Channels QC""']",SRRSImagingLevel2 -Experiment IF Channels,Experiment IF Channels,ExperimentIFChannels,"A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)",True,,,,10XGenomicsXeniumISSExperiment -Transcripts per Cell,Transcripts per Cell,TranscriptsperCell,Mean or Median transcript count per cell analyzed on the flow cell or slide,True,,,,10XGenomicsXeniumISSExperiment -Decoded Transcripts,Decoded Transcripts,DecodedTranscripts,"In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).",True,,,,10XGenomicsXeniumISSExperiment -Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,10XGenomicsXeniumISSExperiment Total Number of Cells,Total Number of Cells,TotalNumberofCells,The total number of cells analyzed on the flow cell,True,,,,10XGenomicsXeniumISSExperiment -Percent of Transcripts within Cells,Percent of Transcripts within Cells,PercentofTranscriptswithinCells,The percentage of transcripts assigned to assayed cells,True,,,,10XGenomicsXeniumISSExperiment -Xenium Bundle Contents,Xenium Bundle Contents,XeniumBundleContents,A comma separated list of filenames within the Xenium bundle zip file,True,,,,10XGenomicsXeniumISSExperiment -Xenium HE image HTAN File ID,Xenium HE image HTAN File ID,XeniumHEimageHTANFileID,The HTAN Data File ID of a Imaging Level 2 file,False,,,,10XGenomicsXeniumISSExperiment -ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,10XGenomicsXeniumISSExperiment -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,10XGenomicsXeniumISSExperiment -Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,10XGenomicsXeniumISSExperiment -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10XGenomicsXeniumISSExperiment -Filename,Filename,Filename,Name of a file,True,,,,10XGenomicsXeniumISSExperiment -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,10XGenomicsXeniumISSExperiment Xenium IF image HTAN File ID,Xenium IF image HTAN File ID,XeniumIFimageHTANFileID,The HTAN Data File ID of a Imaging Level 2 file,False,,,,10XGenomicsXeniumISSExperiment +Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,10XGenomicsXeniumISSExperiment +Panel Name,Panel Name,PanelName,"The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))",True,,,,10XGenomicsXeniumISSExperiment Total Number of Targets,Total Number of Targets,TotalNumberofTargets,Refers to the target of an assay. Can be genes/transcripts or probes,True,,,,10XGenomicsXeniumISSExperiment +Experiment IF Channels,Experiment IF Channels,ExperimentIFChannels,"A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)",True,,,,10XGenomicsXeniumISSExperiment +ROI name,ROI name,ROIname,ROI name (application generated). For Xenium this is referred to as the “region name”,True,,,,10XGenomicsXeniumISSExperiment +Xenium HE image HTAN File ID,Xenium HE image HTAN File ID,XeniumHEimageHTANFileID,The HTAN Data File ID of a Imaging Level 2 file,False,,,,10XGenomicsXeniumISSExperiment +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,10XGenomicsXeniumISSExperiment +Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,10XGenomicsXeniumISSExperiment +Filename,Filename,Filename,Name of a file,True,,,,10XGenomicsXeniumISSExperiment +Decoded Transcripts,Decoded Transcripts,DecodedTranscripts,"In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).",True,,,,10XGenomicsXeniumISSExperiment +Transcripts per Cell,Transcripts per Cell,TranscriptsperCell,Mean or Median transcript count per cell analyzed on the flow cell or slide,True,,,,10XGenomicsXeniumISSExperiment +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,10XGenomicsXeniumISSExperiment HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,10XGenomicsXeniumISSExperiment -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,10XGenomicsXeniumISSExperiment Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,10XGenomicsXeniumISSExperiment -Panel Name,Panel Name,PanelName,"The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))",True,,,,10XGenomicsXeniumISSExperiment +Xenium Bundle Contents,Xenium Bundle Contents,XeniumBundleContents,A comma separated list of filenames within the Xenium bundle zip file,True,,,,10XGenomicsXeniumISSExperiment +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,10XGenomicsXeniumISSExperiment +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,10XGenomicsXeniumISSExperiment +Percent of Transcripts within Cells,Percent of Transcripts within Cells,PercentofTranscriptswithinCells,The percentage of transcripts assigned to assayed cells,True,,,,10XGenomicsXeniumISSExperiment HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,RPPALevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,RPPALevel3 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,RPPALevel3 -Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel3 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel3 -Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,RPPALevel3 Filename,Filename,Filename,Name of a file,True,,,,RPPALevel3 +Normalization Method,Normalization Method,NormalizationMethod,Description of Normalization Process,False,,,,RPPALevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,RPPALevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,RPPALevel3 +Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel3 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel3 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,RPPALevel3 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,RPPALevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,RPPALevel4 -HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,RPPALevel4 -Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel4 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,RPPALevel4 -Batch Correction Method,Batch Correction Method,BatchCorrectionMethod,Method that was used to batch correct Level 3 data,False,,,,RPPALevel4 Filename,Filename,Filename,Name of a file,True,,,,RPPALevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,RPPALevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,RPPALevel4 +Batch Correction Method,Batch Correction Method,BatchCorrectionMethod,Method that was used to batch correct Level 3 data,False,,,,RPPALevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,RPPALevel4 +Assay Type,Assay Type,AssayType,"The type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)",True,,,,RPPALevel4 +HTAN Participant ID,HTAN Participant ID,HTANParticipantID,HTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy ),True,,,,RPPALevel4 +Total Number of Cells,Total Number of Cells,TotalNumberofCells,The total number of cells analyzed on the flow cell,True,,,,NanostringCosMxSMIExperiment +Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,NanostringCosMxSMIExperiment Number of FOVs,Number of FOVs,NumberofFOVs,The total number of FOVs recorded for the sample on a single flow cell,True,,,,NanostringCosMxSMIExperiment +Panel Name,Panel Name,PanelName,"The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))",True,,,,NanostringCosMxSMIExperiment +Total Number of Targets,Total Number of Targets,TotalNumberofTargets,Refers to the target of an assay. Can be genes/transcripts or probes,True,,,,NanostringCosMxSMIExperiment Experiment IF Channels,Experiment IF Channels,ExperimentIFChannels,"A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)",True,,,,NanostringCosMxSMIExperiment -Transcripts per Cell,Transcripts per Cell,TranscriptsperCell,Mean or Median transcript count per cell analyzed on the flow cell or slide,True,,,,NanostringCosMxSMIExperiment Unique Genes,Unique Genes,UniqueGenes,The total unique genes detected above background,False,,,,NanostringCosMxSMIExperiment +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,NanostringCosMxSMIExperiment Surface area,Surface area,Surfacearea,"Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area",True,,,,NanostringCosMxSMIExperiment -Total Number of Cells,Total Number of Cells,TotalNumberofCells,The total number of cells analyzed on the flow cell,True,,,,NanostringCosMxSMIExperiment -Percent of Transcripts within Cells,Percent of Transcripts within Cells,PercentofTranscriptswithinCells,The percentage of transcripts assigned to assayed cells,True,,,,NanostringCosMxSMIExperiment -CosMx Assay Type,CosMx Assay Type,CosMxAssayType,The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay,True,,"['protein', 'RNA']",,NanostringCosMxSMIExperiment -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,NanostringCosMxSMIExperiment -Slide ID,Slide ID,SlideID,"For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.",False,,,,NanostringCosMxSMIExperiment -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanostringCosMxSMIExperiment -Mean Total Transcripts per Area,Mean Total Transcripts per Area,MeanTotalTranscriptsperArea,The mean total transcripts per um3,True,,,,NanostringCosMxSMIExperiment CosMx Bundle Contents,CosMx Bundle Contents,CosMxBundleContents,A comma separated list of filenames within the CosMx bundle zip file,True,,,,NanostringCosMxSMIExperiment +CosMx Assay Type,CosMx Assay Type,CosMxAssayType,The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay,True,,"['RNA', 'protein']",,NanostringCosMxSMIExperiment Filename,Filename,Filename,Name of a file,True,,,,NanostringCosMxSMIExperiment -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,NanostringCosMxSMIExperiment +Transcripts per Cell,Transcripts per Cell,TranscriptsperCell,Mean or Median transcript count per cell analyzed on the flow cell or slide,True,,,,NanostringCosMxSMIExperiment Total Negative Probe Counts,Total Negative Probe Counts,TotalNegativeProbeCounts,Mean Total Negative probe counts/cell,True,,,,NanostringCosMxSMIExperiment -Total Number of Targets,Total Number of Targets,TotalNumberofTargets,Refers to the target of an assay. Can be genes/transcripts or probes,True,,,,NanostringCosMxSMIExperiment +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,NanostringCosMxSMIExperiment HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,NanostringCosMxSMIExperiment -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,NanostringCosMxSMIExperiment Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,NanostringCosMxSMIExperiment -Panel Name,Panel Name,PanelName,"The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))",True,,,,NanostringCosMxSMIExperiment +Mean Total Transcripts per Area,Mean Total Transcripts per Area,MeanTotalTranscriptsperArea,The mean total transcripts per um3,True,,,,NanostringCosMxSMIExperiment +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,NanostringCosMxSMIExperiment +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,NanostringCosMxSMIExperiment +Percent of Transcripts within Cells,Percent of Transcripts within Cells,PercentofTranscriptswithinCells,The percentage of transcripts assigned to assayed cells,True,,,,NanostringCosMxSMIExperiment +LC Flow Rate,LC Flow Rate,LCFlowRate,LC flow rate in nL/min.,True,,,,MassSpectrometryLevel1 +MS-based Targeted,MS-based Targeted,MS-basedTargeted,Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.,True,,"['Targeted', 'Untargeted']",,MassSpectrometryLevel1 +LC Column Vendor and Model,LC Column Vendor and Model,LCColumnVendorandModel,"The manufacturer of the LC Column unless self-packed, pulled tip capilary is used and the model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter 'Pulled tip capilary'",True,,,,MassSpectrometryLevel1 LC Length Value,LC Length Value,LCLengthValue,LC column length in cm.,True,,,,MassSpectrometryLevel1 -MS Source,MS Source,MSSource,"The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)",True,,"['Other', 'MALDI-2', 'DESI', 'nESI', 'MALDI', 'SIMS']",,MassSpectrometryLevel1 -MS Batch ID,MS Batch ID,MSBatchID,Batch ID indicating a set of samples that were run together.,True,,,,MassSpectrometryLevel1 +Mass Range Low Value,Mass Range Low Value,MassRangeLowValue,The low value of the scanned mass range for MS1 in m/z.,True,,,,MassSpectrometryLevel1 +Mass Range High Value,Mass Range High Value,MassRangeHighValue,The high value of the scanned mass range for MS1 in m/z.,True,,,,MassSpectrometryLevel1 +MS Scan Mode,MS Scan Mode,MSScanMode,"Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)",True,,"['Other', 'MS', 'MS3', 'MS/MS']",,MassSpectrometryLevel1 MS Instrument Metadata File,MS Instrument Metadata File,MSInstrumentMetadataFile,Additional file containing instrument metadata details. Use either synapse_path or entity_Id,False,,,,MassSpectrometryLevel1 -Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,True,,"['RNA Analyte', 'protein', 'cfDNA Analyte', 'DNA Analyte', 'PBMCs', 'metabolite', 'Total RNA Analyte', 'Serum Analyte', 'lipid', 'Tissue Block Analyte', 'PBMCs or Plasma or Serum Analyte', 'cDNA Libraries Analyte', 'Tissue Section Analyte', 'Plasma']",,MassSpectrometryLevel1 -LC Gradient,LC Gradient,LCGradient,The program dictates the mobile phase solvent composition over the course of the chromatographic run.,True,,,,MassSpectrometryLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,MassSpectrometryLevel1 +MS Batch ID,MS Batch ID,MSBatchID,Batch ID indicating a set of samples that were run together.,True,,,,MassSpectrometryLevel1 +MS-based Assay Type,MS-based Assay Type,MS-basedAssayType,Analytes are the target molecules being measured with the assay.,True,,"['TMT', 'LC-MS/MS', 'MS', 'LC-MS']",,MassSpectrometryLevel1 +Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel1 +Data Collection Mode,Data Collection Mode,DataCollectionMode,Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.,True,,"['Other', 'DIA', 'DDA']",,MassSpectrometryLevel1 +Polarity,Polarity,Polarity,The polarity of the mass analysis (positive or negative ion modes),True,,"['negative', 'positive']",,MassSpectrometryLevel1 LC ID Value,LC ID Value,LCIDValue,LC column inner diameter in microns.,True,,,,MassSpectrometryLevel1 -LC Flow Rate,LC Flow Rate,LCFlowRate,LC flow rate in nL/min.,True,,,,MassSpectrometryLevel1 +Analyte Type,Analyte Type,AnalyteType,The kind of molecular specimen analyte: a molecular derivative (I.e. RNA / DNA / Protein Lysate) obtained from a specimen,True,,"['lipid', 'Tissue Section Analyte', 'PBMCs or Plasma or Serum Analyte', 'metabolite', 'RNA Analyte', 'cfDNA Analyte', 'Total RNA Analyte', 'Tissue Block Analyte', 'DNA Analyte', 'cDNA Libraries Analyte', 'PBMCs', 'protein', 'Plasma', 'Serum Analyte']",,MassSpectrometryLevel1 +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel1 LC Temp Value,LC Temp Value,LCTempValue,LC temperature in C.,True,,,,MassSpectrometryLevel1 MS Instrument Vendor and Model,MS Instrument Vendor and Model,MSInstrumentVendorandModel,An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.,True,,,,MassSpectrometryLevel1 -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel1 -Data Collection Mode,Data Collection Mode,DataCollectionMode,Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition) or DIA (Data-indemendent acquisition.,True,,"['Other', 'DDA', 'DIA']",,MassSpectrometryLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel1 +LC Gradient,LC Gradient,LCGradient,The program dictates the mobile phase solvent composition over the course of the chromatographic run.,True,,,,MassSpectrometryLevel1 +HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel1 +LC Resin,LC Resin,LCResin,"Details of the resin used for lc, including vendor, particle size, pore size",True,,,,MassSpectrometryLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel1 MS Labeling,MS Labeling,MSLabeling,"Indicates whether samples were labeled prior to MS analysis (e.g., TMT)",True,,,,MassSpectrometryLevel1 -Polarity,Polarity,Polarity,The polarity of the mass analysis (positive or negative ion modes),True,,"['negative', 'positive']",,MassSpectrometryLevel1 -LC Instrument Vendor and Model,LC Instrument Vendor and Model,LCInstrumentVendorandModel,The manufacturer of the instrument used for LC.,True,,,,MassSpectrometryLevel1 -Mass Range High Value,Mass Range High Value,MassRangeHighValue,The high value of the scanned mass range for MS1 in m/z.,True,,,,MassSpectrometryLevel1 -Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel1 +MS Source,MS Source,MSSource,"The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)",True,,"['nESI', 'MALDI', 'MALDI-2', 'SIMS', 'DESI', 'Other']",,MassSpectrometryLevel1 LC Mobile Phase B,LC Mobile Phase B,LCMobilePhaseB,Composition of mobile phase B,True,,,,MassSpectrometryLevel1 -MS Scan Mode,MS Scan Mode,MSScanMode,"Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)",True,,"['Other', 'MS3', 'MS/MS', 'MS']",,MassSpectrometryLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,MassSpectrometryLevel1 -Mass Range Low Value,Mass Range Low Value,MassRangeLowValue,The low value of the scanned mass range for MS1 in m/z.,True,,,,MassSpectrometryLevel1 -MS-based Assay Type,MS-based Assay Type,MS-basedAssayType,Analytes are the target molecules being measured with the assay.,True,,"['LC-MS/MS', 'LC-MS', 'MS', 'TMT']",,MassSpectrometryLevel1 -HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel1 -MS-based Targeted,MS-based Targeted,MS-basedTargeted,Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. Example: The MALDI Imaging analyte is lipids.,True,,"['Untargeted', 'Targeted']",,MassSpectrometryLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,MassSpectrometryLevel1 -LC Column Vendor and Model,LC Column Vendor and Model,LCColumnVendorandModel,"The manufacturer of the LC Column unless self-packed, pulled tip capilary is used and the model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter 'Pulled tip capilary'",True,,,,MassSpectrometryLevel1 +LC Instrument Vendor and Model,LC Instrument Vendor and Model,LCInstrumentVendorandModel,The manufacturer of the instrument used for LC.,True,,,,MassSpectrometryLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,MassSpectrometryLevel1 LC Mobile Phase A,LC Mobile Phase A,LCMobilePhaseA,Composition of mobile phase A,True,,,,MassSpectrometryLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel1 -LC Resin,LC Resin,LCResin,"Details of the resin used for lc, including vendor, particle size, pore size",True,,,,MassSpectrometryLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,MassSpectrometryLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MassSpectrometryLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel2 +Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel2 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MassSpectrometryLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel2 +MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel2 Mass Spectrometry Auxiliary File,Mass Spectrometry Auxiliary File,MassSpectrometryAuxiliaryFile,"Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).",False,,,,MassSpectrometryLevel2 -Filename,Filename,Filename,Name of a file,False,,,,MassSpectrometryLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf', '']",,MassSpectrometryLevel2 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel2 -MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel2 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel3 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,MassSpectrometryLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MassSpectrometryLevel3 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel3 +Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MassSpectrometryLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel3 +MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel3 Mass Spectrometry Auxiliary File,Mass Spectrometry Auxiliary File,MassSpectrometryAuxiliaryFile,"Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).",False,,,,MassSpectrometryLevel3 -Filename,Filename,Filename,Name of a file,False,,,,MassSpectrometryLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf', '']",,MassSpectrometryLevel3 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel3 -MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel3 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,MassSpectrometryLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,MassSpectrometryLevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MassSpectrometryLevel4 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,MassSpectrometryLevel4 +Filename,Filename,Filename,Name of a file,True,,,,MassSpectrometryLevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,MassSpectrometryLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,MassSpectrometryLevel4 +MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel4 Mass Spectrometry Auxiliary File,Mass Spectrometry Auxiliary File,MassSpectrometryAuxiliaryFile,"Auxiliary software parameter file used in mass spectrometry data processing, recorded as synapse ID (syn12345).",False,,,,MassSpectrometryLevel4 -Filename,Filename,Filename,Name of a file,False,,,,MassSpectrometryLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",False,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf', '']",,MassSpectrometryLevel4 Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,MassSpectrometryLevel4 -MS Assay Category,MS Assay Category,MSAssayCategory,Type of Mass Spectrometry performed.,True,,,,MassSpectrometryLevel4 -EM instrument,EM instrument,EMinstrument,Make and model of the EM instrument used,True,,,,ElectronMicroscopyLevel1 -SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ElectronMicroscopyLevel1 -PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1 -PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1 -SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,ElectronMicroscopyLevel1 -EM dwell or exposure time,EM dwell or exposure time,EMdwellorexposuretime,Duration in microseconds (µs) of electron beam data collection per pixel or frame,False,,,,ElectronMicroscopyLevel1 -EM signal or contrast mech,EM signal or contrast mech,EMsignalorcontrastmech,How the electron microscopy signal is generated from the sample,True,,"['BSE', 'SE', 'phase', 'dark-field', 'bright-field']",,ElectronMicroscopyLevel1 -Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ElectronMicroscopyLevel1 PhysicalSizeY,PhysicalSizeY,PhysicalSizeY,Physical size (Y-dimension) of a pixel. Units are set by PhysicalSizeYUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel1 +EM signal or contrast mech,EM signal or contrast mech,EMsignalorcontrastmech,How the electron microscopy signal is generated from the sample,True,,"['SE', 'phase', 'BSE', 'bright-field', 'dark-field']",,ElectronMicroscopyLevel1 +EM contrast type,EM contrast type,EMcontrasttype,Does the image use standard SEM contrast or TEM contrast,False,,"['SEM', 'TEM', '']",,ElectronMicroscopyLevel1 +SizeC,SizeC,SizeC,Number of channels. Integer >= 1,True,,,,ElectronMicroscopyLevel1 SizeZ,SizeZ,SizeZ,Size of image: Z dimension (in pixels). Integer >= 1,True,,,,ElectronMicroscopyLevel1 +EM method,EM method,EMmethod,Electron microscopy method used,True,,"['cryo ET', 'ssTEM', 'ET', 'TEM', 'SBF-SEM', 'SEM', 'FIB-SEM', 'AT']",,ElectronMicroscopyLevel1 +EM stage tilt,EM stage tilt,EMstagetilt,Physical stage tilt in degrees with respect to the electron beam,False,,,,ElectronMicroscopyLevel1 +Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ElectronMicroscopyLevel1 EM spot size,EM spot size,EMspotsize,Beam spot size in micrometers (µm),False,,,,ElectronMicroscopyLevel1 Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel1 -Protocol Link,Protocol Link,ProtocolLink,"Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated.",True,,,,ElectronMicroscopyLevel1 -EM stage tilt,EM stage tilt,EMstagetilt,Physical stage tilt in degrees with respect to the electron beam,False,,,,ElectronMicroscopyLevel1 -EM method,EM method,EMmethod,Electron microscopy method used,True,,"['SBF-SEM', 'TEM', 'cryo ET', 'AT', 'ssTEM', 'FIB-SEM', 'SEM', 'ET']",,ElectronMicroscopyLevel1 +SizeX,SizeX,SizeX,Size of image: X dimension (in pixels). Integer >= 1,True,,,,ElectronMicroscopyLevel1 +EM instrument,EM instrument,EMinstrument,Make and model of the EM instrument used,True,,,,ElectronMicroscopyLevel1 +Software and Version,Software and Version,SoftwareandVersion,Name of software used to generate expression values. String,True,,,,ElectronMicroscopyLevel1 +PhysicalSizeX,PhysicalSizeX,PhysicalSizeX,Physical size (X-dimension) of a pixel. Units are set by PhysicalSizeXUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1 HTAN Parent Biospecimen ID,HTAN Parent Biospecimen ID,HTANParentBiospecimenID,HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated,True,,,,ElectronMicroscopyLevel1 +Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel1 +PhysicalSizeZ,PhysicalSizeZ,PhysicalSizeZ,Physical size (Z-dimension) of a pixel. Units are set by PhysicalSizeZUnit. Floating point value > 0.,True,,,,ElectronMicroscopyLevel1 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel1 +EM signal processing,EM signal processing,EMsignalprocessing,SNR improvement strategies used,False,,"['frame averaging', 'line integration', 'frame integration', 'None', '']",,ElectronMicroscopyLevel1 +EM dwell or exposure time,EM dwell or exposure time,EMdwellorexposuretime,Duration in microseconds (µs) of electron beam data collection per pixel or frame,False,,,,ElectronMicroscopyLevel1 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ElectronMicroscopyLevel1 EM voltage,EM voltage,EMvoltage,Accelerating voltage in kiloelectronvolts (keV),False,,,,ElectronMicroscopyLevel1 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ElectronMicroscopyLevel1 -EM contrast type,EM contrast type,EMcontrasttype,Does the image use standard SEM contrast or TEM contrast,False,,"['SEM', 'TEM', '']",,ElectronMicroscopyLevel1 SizeY,SizeY,SizeY,Size of image: Y dimension (in pixels). Integer >= 1,True,,,,ElectronMicroscopyLevel1 EM beam current,EM beam current,EMbeamcurrent,Beam current in nanoamps (nA),False,,,,ElectronMicroscopyLevel1 -Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel1 -EM signal processing,EM signal processing,EMsignalprocessing,SNR improvement strategies used,False,,"['frame averaging', 'None', 'frame integration', 'line integration', '']",,ElectronMicroscopyLevel1 -PhysicalSizeZUnit,PhysicalSizeZUnit,PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,ElectronMicroscopyLevel1 -PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,ElectronMicroscopyLevel1 -PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['nm', 'mm', 'µm', 'cm', 'Å', '']",,ElectronMicroscopyLevel1 +PhysicalSizeYUnit,PhysicalSizeYUnit,PhysicalSizeYUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ElectronMicroscopyLevel1 +PhysicalSizeXUnit,PhysicalSizeXUnit,PhysicalSizeXUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ElectronMicroscopyLevel1 +PhysicalSizeZUnit,PhysicalSizeZUnit,PhysicalSizeZUnit,The units of the physical size of a pixel. See OME enumeration of allowed values for the UnitsLength attribute -- default: microns (um),False,,"['mm', 'Å', 'nm', 'cm', 'µm', '']",,ElectronMicroscopyLevel1 Tile overlap Y,Tile overlap Y,TileoverlapY,Percentage of image overlap to allow tile stitching in x direction,True,,,,ElectronMicroscopyLevel2 -EM contrast type,EM contrast type,EMcontrasttype,Does the image use standard SEM contrast or TEM contrast,False,,"['SEM', 'TEM', '']",,ElectronMicroscopyLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel2 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ElectronMicroscopyLevel2 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel2 -Tile overlap X,Tile overlap X,TileoverlapX,Percentage of image overlap to allow tile stitching in x direction,True,,,,ElectronMicroscopyLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel2 +Tile overlap X,Tile overlap X,TileoverlapX,Percentage of image overlap to allow tile stitching in x direction,True,,,,ElectronMicroscopyLevel2 Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel2 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel3 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ElectronMicroscopyLevel3 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel3 -Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,ElectronMicroscopyLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel2 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel2 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ElectronMicroscopyLevel2 +EM contrast type,EM contrast type,EMcontrasttype,Does the image use standard SEM contrast or TEM contrast,False,,"['SEM', 'TEM', '']",,ElectronMicroscopyLevel2 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel3 Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel3 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel3 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel3 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ElectronMicroscopyLevel3 +Imaging Object Class,Imaging Object Class,ImagingObjectClass,Defines the structure that the mask delineates,True,,,,ElectronMicroscopyLevel3 Imaging Object Class Description,Imaging Object Class Description,ImagingObjectClassDescription,Free text description of object class [string],False,True,,"['Imaging Object Class is ""Imaging Object Class Other""']",ElectronMicroscopyLevel3 -Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ElectronMicroscopyLevel4 -HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel4 -File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['gct', 'xml', 'bpm', 'sqlite', 'tiff', 'OME-TIFF', 'mpg', 'pkc', 'Md', 'hic', 'tsv', 'sav', 'sam', 'doc', 'mzML', 'sif', 'mov', 'pdf', 'jpg', 'sdf', 'rcc', 'fasta', 'recal', 'png', 'bcf', 'gzip', 'raw', 'chp', 'tagAlign', 'svs', 'seg', 'flagstat', 'bed narrowPeak', '7z', 'plink', 'msf', 'excel', 'txt', 'bed broadPeak', 'Sentrix descriptor file', 'svg', 'csv', 'hdf5', 'html', 'bam', 'dat', 'bai', 'mtx', 'bedgraph', 'powerpoint', 'locs', 'bed gappedPeak', 'cel', 'sf', 'idat', 'avi', 'tif', 'R script', 'Python script', 'cloupe', 'wiggle', 'pzfx', 'dcc', 'hyperlink', 'gff3', 'bedpe', 'mex', 'zip', 'fig', 'gtf', 'Am', 'tar', 'dup', 'sra', 'cell am', 'abf', 'bed', 'M', 'idx', 'rmd', 'maf', 'ab1', 'json', 'scn', 'bigwig', 'bgzip', 'DICOM', 'tranches', 'fastq', 'RData', 'czi', 'vcf']",,ElectronMicroscopyLevel4 -HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel4 Component,Component,Component,"Category of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.",True,,,,ElectronMicroscopyLevel4 Filename,Filename,Filename,Name of a file,True,,,,ElectronMicroscopyLevel4 +Comment,Comment,Comment,Free text field (generally for QC comment),False,,,,ElectronMicroscopyLevel4 +HTAN Parent Data File ID,HTAN Parent Data File ID,HTANParentDataFileID,HTAN Data File Identifier indicating the file(s) from which these files were derived,True,,,,ElectronMicroscopyLevel4 +HTAN Data File ID,HTAN Data File ID,HTANDataFileID,Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz),True,,,,ElectronMicroscopyLevel4 +File Format,File Format,FileFormat,"Format of a file (e.g. txt, csv, fastq, bam, etc.)",True,,"['7z', 'gff3', 'scn', 'raw', 'excel', 'bed broadPeak', 'seg', 'fasta', 'chp', 'gzip', 'gtf', 'cloupe', 'recal', 'hdf5', 'gct', 'bigwig', 'fig', 'bed', 'sdf', 'avi', 'sif', 'zip', 'hic', 'json', 'RData', 'svg', 'mpg', 'plink', 'tiff', 'pzfx', 'cell am', 'rcc', 'R script', 'sra', 'bai', 'mex', 'html', 'Sentrix descriptor file', 'Am', 'svs', 'csv', 'txt', 'sav', 'flagstat', 'bgzip', 'mov', 'DICOM', 'idx', 'bpm', 'cel', 'idat', 'sf', 'mtx', 'sam', 'rmd', 'pkc', 'bcf', 'wiggle', 'dup', 'Python script', 'tar', 'dat', 'mzML', 'hyperlink', 'sqlite', 'powerpoint', 'tranches', 'tsv', 'msf', 'OME-TIFF', 'png', 'maf', 'xml', 'bedpe', 'M', 'doc', 'bed gappedPeak', 'czi', 'tif', 'bam', 'Md', 'jpg', 'bed narrowPeak', 'ab1', 'tagAlign', 'bedgraph', 'abf', 'fastq', 'dcc', 'pdf', 'locs', 'vcf']",,ElectronMicroscopyLevel4