diff --git a/.github/ISSUE_TEMPLATE/new_sssom_element.md b/.github/ISSUE_TEMPLATE/new_sssom_element.md index 08bc3604..79b7462e 100644 --- a/.github/ISSUE_TEMPLATE/new_sssom_element.md +++ b/.github/ISSUE_TEMPLATE/new_sssom_element.md @@ -22,4 +22,26 @@ xsd:string **Description** (Provide a human-readable description that clarifies the intended use of the metadata element.) -Example description. \ No newline at end of file +Example description. + +**Complete example to a SSSOM file with this element** +(This example can be given as a markdown table or a linked SSSOM file, feel free to edit the markdown table below) + +``` +# curie_map: +# HP: http://purl.obolibrary.org/obo/FBbt_ +# MP: http://purl.obolibrary.org/obo/UBERON_ +# owl: http://www.w3.org/2002/07/owl# +# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# +# rdfs: http://www.w3.org/2000/01/rdf-schema# +# semapv: https://w3id.org/semapv/vocab/ +# skos: http://www.w3.org/2004/02/skos/core# +# sssom: https://w3id.org/sssom/ +# license: https://w3id.org/sssom/license/unspecified +# mapping_set_id: https://w3id.org/sssom/mappings/ac9e1878-73f4-4767-8402-a6c40e1b0835 +``` + +| subject_id | predicate_id | object_id | mapping_justification | element_id_example | +| ----------- | --------------- | ----------- | ----------------------- | ------------------- | +| HP:0009124 | skos:exactMatch | MP:0000003 | semapv:LexicalMatching | YOUR EXAMPLE VALUE | +| HP:0008551 | skos:exactMatch | MP:0000018 | semapv:LexicalMatching | YOUR EXAMPLE VALUE | diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index aee19faa..305bc2e5 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -3,6 +3,13 @@ Resolves [#ISSUE, #ISSUE] - [ ] `docs/` have been added/updated if necessary - [ ] `make test` has been run locally - [ ] tests have been added/updated (if applicable) -- [ ] [CHANGELOG.md](https://github.com/mapping-commons/sssom/blob/0.9.0/CHANGELOG.md) has been updated. +- [ ] [CHANGELOG.md](https://github.com/mapping-commons/sssom/blob/master/CHANGELOG.md) has been updated. -[Description, mentioning at least relevant #ISSUE and how it was addressed. A bulleted list of all changes performed by the PR is is helpful.] \ No newline at end of file +If you are proposing a change to the SSSOM metadata model, you must + +- [ ] provide a full, working and valid example in `examples/` +- [ ] provide a link to the related GitHub issue in the `see_also` field of the linkml model +- [ ] provide a link to a valid example in the `see_also` field of the linkml model + + +[Add a description, mentioning at least relevant #ISSUE and how it was addressed. A bulleted list of all changes performed by the PR is is helpful.] diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml new file mode 100644 index 00000000..02d6ef99 --- /dev/null +++ b/.github/workflows/qc.yml @@ -0,0 +1,31 @@ +# Basic ODK workflow + +name: CI + +# Controls when the action will run. +on: + # Triggers the workflow on push or pull request events but only for the master branch + push: + branches: [ master ] + pull_request: + branches: [ master ] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + sssom_validation: + runs-on: ubuntu-latest + container: obolibrary/odkfull:v1.4 + steps: + - name: Install latest SSSOM + env: + DEFAULT_BRANCH: master + run: pip install --upgrade pip && pip install -U sssom sssom-schema + - uses: actions/checkout@v2 + - name: Run Mapping QC checks + env: + DEFAULT_BRANCH: master + run: make validate_mappings + diff --git a/CHANGELOG.md b/CHANGELOG.md index 6ab25bce..bfe21183 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,37 @@ # Changelog for SSSOM -## SSSOM version 1.0 +## SSSOM version 0.13.0 -- TBD +- The necessity of the "canonical column ordering" was downgraded from MUST to SHOULD (https://github.com/mapping-commons/sssom/pull/285) +- Documents clearly that built-in prefixes MUST NOT be redefined (https://github.com/mapping-commons/sssom/pull/285) + +## SSSOM version 0.11.0 + +- see https://github.com/mapping-commons/sssom/releases/tag/0.11.0 + +### Summary + +#### New elements: +- `mapping_set_title` to capture a human readable title for a mapping set +- `registry_title` and `registry_description` to capture the human readable title and description of an SSSOM mapping set registry +- `curation_rule` to capture a (potentially) complex (set of) condition(s) executed by an agent (usually human) that led to the establishment of a mapping. + +#### Updated elements: +- Adding mapping_source slot to Mapping by @matentzn in #230 +- Improve documentation for `subject_category` and `object_category` elements + +#### Documentation +- Compiled a list of all SSSOM talks: https://mapping-commons.github.io/sssom/presentations/ +- Document chaining rules: https://mapping-commons.github.io/sssom/chaining_rules/ + +#### Quality control and Technical infrastructure + +- Make adding a concrete SSSOM example part of the new element request +- Adding QC checks for example SSSOM files hosted in the repo + +## SSSOM version 0.10.1 + +- see https://github.com/mapping-commons/sssom/releases/tag/0.10.1 ## SSSOM version 0.9.4 diff --git a/Makefile b/Makefile index b017f82e..23f0d235 100644 --- a/Makefile +++ b/Makefile @@ -40,7 +40,7 @@ install: poetry install .PHONY: install -all: gen-project gendoc gen-excel +all: gen-project gendoc gen-excel get-context %.yaml: gen-project deploy: all mkd-gh-deploy @@ -57,6 +57,10 @@ check-config: convert-examples-to-%: $(patsubst %, $(RUN) linkml-convert % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell find src/data/examples -name "*.yaml")) +get-context: + mkdir -p $(SRC)/$(SCHEMA_NAME)/context + cp $(DEST)/jsonld/* $(SRC)/$(SCHEMA_NAME)/context + examples/%.yaml: src/data/examples/%.yaml $(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@ examples/%.json: src/data/examples/%.yaml diff --git a/README.md b/README.md index 09218b77..2442add9 100644 --- a/README.md +++ b/README.md @@ -58,3 +58,5 @@ Nicolas Matentzoglu, James P Balhoff, Susan M Bello, Chris Bizon, Matthew Brush, eprint = {https://academic.oup.com/database/article-pdf/doi/10.1093/database/baac035/43832024/baac035.pdf}, } ``` + +A [second report with updates since the primary SSSOM publication](https://ceur-ws.org/Vol-3324/om2022_LTpaper6.pdf) above was published as part of the proceedings of the Ontology Matching Workshop 2022. diff --git a/examples/embedded/foodie-inc-2022-05-01.sssom.tsv b/examples/embedded/foodie-inc-2022-05-01.sssom.tsv index 16f19b50..4643f907 100644 --- a/examples/embedded/foodie-inc-2022-05-01.sssom.tsv +++ b/examples/embedded/foodie-inc-2022-05-01.sssom.tsv @@ -1,20 +1,26 @@ -# mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv +# comment: We could map to FOODON:00004187 instead which more specifically refers to +# 'raw' Pink apples. Decided against to be consistent with other mapping choices. +# curie_map: +# FOODON: http://purl.obolibrary.org/obo/FOODON_ +# KF_FOOD: https://kewl-foodie.inc/food/ +# orcid: https://orcid.org/ +# owl: http://www.w3.org/2002/07/owl# +# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# +# rdfs: http://www.w3.org/2000/01/rdf-schema# +# semapv: https://w3id.org/semapv/vocab/ +# skos: http://www.w3.org/2004/02/skos/core# +# sssom: https://w3id.org/sssom/ +# wikidata: https://www.wikidata.org/wiki/ # license: https://creativecommons.org/licenses/by/4.0/ # mapping_date: '2022-05-02' # mapping_set_description: Manually curated alignment of KEWL FOODIE INC internal food # and nutrition database with Food Ontology (FOODON). Intended to be used for ontological # analysis and grouping of KEWL FOODIE INC related data. +# mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv # mapping_set_version: '2022-05-01' # object_source: wikidata:Q55118395 # object_source_version: http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl # subject_source: KF_FOOD:DB -# comment: We could map to FOODON:00004187 instead which more specifically refers to -# 'raw' Pink apples. Decided against to be consistent with other mapping choices. -# curie_map: -# FOODON: http://purl.obolibrary.org/obo/FOODON_ -# KF_FOOD: https://kewl-foodie.inc/food/ -# skos: http://www.w3.org/2004/02/skos/core# -# sssom: https://w3id.org/sssom/ subject_id subject_label predicate_id object_id object_label mapping_justification author_id object_source_version mapping_date confidence comment KF_FOOD:F001 apple skos:exactMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.95 "We could map to FOODON:03310788 instead to cover sliced apples, but only ""whole"" apple types exist." KF_FOOD:F002 gala skos:exactMatch FOODON:00003348 Gala apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0 diff --git a/examples/embedded/mp-hp-exact-0.0.1.sssom.tsv b/examples/embedded/mp-hp-exact-0.0.1.sssom.tsv index d7fda6aa..6e45d4dd 100644 --- a/examples/embedded/mp-hp-exact-0.0.1.sssom.tsv +++ b/examples/embedded/mp-hp-exact-0.0.1.sssom.tsv @@ -1,1492 +1,56 @@ -#creator_id: "https://orcid.org/0000-0002-7356-1779" -#curie_map: -# HP: "http://purl.obolibrary.org/obo/HP_" -# MP: "http://purl.obolibrary.org/obo/MP_" -# skos: "http://www.w3.org/2004/02/skos/core" -#license: "https://creativecommons.org/publicdomain/zero/1.0/" -#mapping_provider: "http://purl.obolibrary.org/obo/upheno.owl" -subject_id predicate_id object_id mapping_justification subject_label object_label -HP:0009124 skos:exactMatch MP:0000003 semapv:LexicalMatching Abnormal adipose tissue morphology abnormal adipose tissue morphology -HP:0008551 skos:exactMatch MP:0000018 semapv:LexicalMatching Microtia small ears -HP:0000411 skos:exactMatch MP:0000021 semapv:LexicalMatching Protruding ear prominent ears -HP:0000375 skos:exactMatch MP:0000031 semapv:LexicalMatching Abnormal cochlea morphology abnormal cochlea morphology -HP:0009910 skos:exactMatch MP:0000040 semapv:LexicalMatching Aplasia of the middle ear ossicles absent middle ear ossicles -HP:0002659 skos:exactMatch MP:0000061 semapv:LexicalMatching Increased susceptibility to fractures fragile skeleton -HP:0004349 skos:exactMatch MP:0000063 semapv:LexicalMatching Reduced bone mineral density decreased bone mineral density -HP:0011002 skos:exactMatch MP:0000067 semapv:LexicalMatching Osteopetrosis osteopetrosis -HP:0001363 skos:exactMatch MP:0000081 semapv:LexicalMatching Craniosynostosis premature cranial suture closure -HP:0000260 skos:exactMatch MP:0000085 semapv:LexicalMatching Wide anterior fontanel large anterior fontanelle -HP:0009939 skos:exactMatch MP:0000087 semapv:LexicalMatching Mandibular aplasia absent mandible -HP:0100629 skos:exactMatch MP:0000108 semapv:LexicalMatching Midline facial cleft midline facial cleft -HP:0000175 skos:exactMatch MP:0000111 semapv:LexicalMatching Cleft palate cleft palate -HP:0400001 skos:exactMatch MP:0000114 semapv:LexicalMatching Chin with vertical crease cleft chin -HP:0006288 skos:exactMatch MP:0000122 semapv:LexicalMatching Advanced eruption of teeth premature tooth eruption -HP:0100671 skos:exactMatch MP:0000130 semapv:LexicalMatching Abnormal trabecular bone morphology abnormal trabecular bone morphology -HP:0003307 skos:exactMatch MP:0000162 semapv:LexicalMatching Hyperlordosis lordosis -HP:0002763 skos:exactMatch MP:0000163 semapv:LexicalMatching Abnormal cartilage morphology abnormal cartilage morphology -HP:0031851 skos:exactMatch MP:0000208 semapv:LexicalMatching Reduced hematocrit decreased hematocrit -HP:0001974 skos:exactMatch MP:0000218 semapv:LexicalMatching Leukocytosis increased leukocyte cell number -HP:0011897 skos:exactMatch MP:0000219 semapv:LexicalMatching Neutrophilia increased neutrophil cell number -HP:0001882 skos:exactMatch MP:0000221 semapv:LexicalMatching Leukopenia decreased leukocyte cell number -HP:0025065 skos:exactMatch MP:0000226 semapv:LexicalMatching Abnormal mean corpuscular volume abnormal mean corpuscular volume -HP:0000822 skos:exactMatch MP:0000231 semapv:LexicalMatching Hypertension hypertension -HP:0001978 skos:exactMatch MP:0000240 semapv:LexicalMatching Extramedullary hematopoiesis extramedullary hematopoiesis -HP:0001336 skos:exactMatch MP:0000243 semapv:LexicalMatching Myoclonus myoclonus -HP:0001627 skos:exactMatch MP:0000266 semapv:LexicalMatching Abnormal heart morphology abnormal heart morphology -HP:0001679 skos:exactMatch MP:0000272 semapv:LexicalMatching Abnormal aortic morphology abnormal aorta morphology -HP:0001667 skos:exactMatch MP:0000276 semapv:LexicalMatching Right ventricular hypertrophy heart right ventricle hypertrophy -HP:0001719 skos:exactMatch MP:0000284 semapv:LexicalMatching Double outlet right ventricle double outlet right ventricle -HP:0001633 skos:exactMatch MP:0000286 semapv:LexicalMatching Abnormal mitral valve morphology abnormal mitral valve morphology -HP:0001981 skos:exactMatch MP:0000314 semapv:LexicalMatching Schistocytosis schistocytosis -HP:0032310 skos:exactMatch MP:0000322 semapv:LexicalMatching Granulocytosis increased granulocyte number -HP:0012543 skos:exactMatch MP:0000327 semapv:LexicalMatching Hemosiderinuria hemosiderinuria -HP:0001913 skos:exactMatch MP:0000334 semapv:LexicalMatching Granulocytopenia decreased granulocyte number -HP:0012234 skos:exactMatch MP:0000334 semapv:LexicalMatching Agranulocytosis decreased granulocyte number -HP:0031377 skos:exactMatch MP:0000350 semapv:LexicalMatching Abnormal cell proliferation abnormal cell proliferation -HP:0025084 skos:exactMatch MP:0000376 semapv:LexicalMatching Folliculitis folliculitis -HP:0002212 skos:exactMatch MP:0000410 semapv:LexicalMatching Curly hair waved hair -HP:0001596 skos:exactMatch MP:0000414 semapv:LexicalMatching Alopecia alopecia -HP:0011457 skos:exactMatch MP:0000425 semapv:LexicalMatching Loss of eyelashes loss of eyelid cilia -HP:0000252 skos:exactMatch MP:0000433 semapv:LexicalMatching Microcephaly microcephaly -HP:0000256 skos:exactMatch MP:0000434 semapv:LexicalMatching Macrocephaly megacephaly -HP:0002457 skos:exactMatch MP:0000436 semapv:LexicalMatching Abnormal head movements abnormal head movements -HP:0030791 skos:exactMatch MP:0000454 semapv:LexicalMatching Abnormal jaw morphology abnormal jaw morphology -HP:0000347 skos:exactMatch MP:0000460 semapv:LexicalMatching Micrognathia mandible hypoplasia -HP:0002031 skos:exactMatch MP:0000467 semapv:LexicalMatching Abnormal esophagus morphology abnormal esophagus morphology -HP:0002242 skos:exactMatch MP:0000477 semapv:LexicalMatching Abnormal intestine morphology abnormal intestine morphology -HP:0031855 skos:exactMatch MP:0000508 semapv:LexicalMatching Right isomerism right-sided isomerism -HP:0000126 skos:exactMatch MP:0000519 semapv:LexicalMatching Hydronephrosis hydronephrosis -HP:0010958 skos:exactMatch MP:0000520 semapv:LexicalMatching Bilateral renal agenesis absent kidney -HP:0000803 skos:exactMatch MP:0000522 semapv:LexicalMatching Renal cortical cysts kidney cortex cysts -HP:0001947 skos:exactMatch MP:0000525 semapv:LexicalMatching Renal tubular acidosis renal tubular acidosis -HP:0000072 skos:exactMatch MP:0000536 semapv:LexicalMatching Hydroureter hydroureter -HP:0000021 skos:exactMatch MP:0000539 semapv:LexicalMatching Megacystis distended urinary bladder -HP:0031854 skos:exactMatch MP:0000542 semapv:LexicalMatching Left Isomerism left-sided isomerism -HP:0009826 skos:exactMatch MP:0000547 semapv:LexicalMatching Limb undergrowth short limbs -HP:0004231 skos:exactMatch MP:0000555 semapv:LexicalMatching Carpal bone aplasia absent carpal bone -HP:0009776 skos:exactMatch MP:0000561 semapv:LexicalMatching Adactyly adactyly -HP:0001159 skos:exactMatch MP:0000564 semapv:LexicalMatching Syndactyly syndactyly -HP:0001762 skos:exactMatch MP:0000576 semapv:LexicalMatching Talipes equinovarus clubfoot -HP:0002164 skos:exactMatch MP:0000579 semapv:LexicalMatching Nail dysplasia abnormal nail morphology -HP:0008404 skos:exactMatch MP:0000579 semapv:LexicalMatching Nail dystrophy abnormal nail morphology -HP:0002910 skos:exactMatch MP:0000609 semapv:LexicalMatching Elevated hepatic transaminase abnormal liver physiology -HP:0031865 skos:exactMatch MP:0000609 semapv:LexicalMatching Abnormal liver physiology abnormal liver physiology -HP:0001396 skos:exactMatch MP:0000610 semapv:LexicalMatching Cholestasis cholestasis -HP:0000952 skos:exactMatch MP:0000611 semapv:LexicalMatching Jaundice jaundice -HP:0010286 skos:exactMatch MP:0000613 semapv:LexicalMatching Abnormal salivary gland morphology abnormal salivary gland morphology -HP:0002307 skos:exactMatch MP:0000622 semapv:LexicalMatching Drooling increased salivation -HP:0003781 skos:exactMatch MP:0000622 semapv:LexicalMatching Excessive salivation increased salivation -HP:0000217 skos:exactMatch MP:0000623 semapv:LexicalMatching Xerostomia decreased salivation -HP:0100783 skos:exactMatch MP:0000629 semapv:LexicalMatching Breast aplasia absent mammary gland -HP:0008216 skos:exactMatch MP:0000639 semapv:LexicalMatching Adrenal gland dysgenesis abnormal adrenal gland morphology -HP:0001651 skos:exactMatch MP:0000644 semapv:LexicalMatching Dextrocardia dextrocardia -HP:0032226 skos:exactMatch MP:0000647 semapv:LexicalMatching Abnormal sebaceous gland morphology abnormal sebaceous gland morphology -HP:0410400 skos:exactMatch MP:0000648 semapv:LexicalMatching Absent sebaceous glands absent sebaceous gland -HP:0011599 skos:exactMatch MP:0000650 semapv:LexicalMatching Mesocardia mesocardia -HP:0000971 skos:exactMatch MP:0000674 semapv:LexicalMatching Abnormal sweat gland morphology abnormal sweat gland morphology -HP:0008188 skos:exactMatch MP:0000681 semapv:LexicalMatching Thyroid dysgenesis abnormal thyroid gland morphology -HP:0025408 skos:exactMatch MP:0000689 semapv:LexicalMatching Abnormal spleen morphology abnormal spleen morphology -HP:0002716 skos:exactMatch MP:0000702 semapv:LexicalMatching Lymphadenopathy enlarged lymph nodes -HP:0000778 skos:exactMatch MP:0000706 semapv:LexicalMatching Hypoplasia of the thymus small thymus -HP:0002487 skos:exactMatch MP:0000743 semapv:LexicalMatching Hyperkinetic movements muscle spasm -HP:0003394 skos:exactMatch MP:0000743 semapv:LexicalMatching Muscle spasm muscle spasm -HP:0001337 skos:exactMatch MP:0000745 semapv:LexicalMatching Tremor tremors -HP:0003202 skos:exactMatch MP:0000749 semapv:LexicalMatching Skeletal muscle atrophy muscle degeneration -HP:0003470 skos:exactMatch MP:0000753 semapv:LexicalMatching Paralysis paralysis -HP:0001543 skos:exactMatch MP:0000757 semapv:LexicalMatching Gastroschisis herniated abdominal wall -HP:0011805 skos:exactMatch MP:0000759 semapv:LexicalMatching Abnormal skeletal muscle morphology abnormal skeletal muscle morphology -HP:0030809 skos:exactMatch MP:0000762 semapv:LexicalMatching Abnormal tongue morphology abnormal tongue morphology -HP:0001273 skos:exactMatch MP:0000780 semapv:LexicalMatching Abnormal corpus callosum morphology abnormal corpus callosum morphology -HP:0025101 skos:exactMatch MP:0000808 semapv:LexicalMatching Dysgenesis of the hippocampus abnormal hippocampus development -HP:0001317 skos:exactMatch MP:0000849 semapv:LexicalMatching Abnormal cerebellum morphology abnormal cerebellum morphology -HP:0007033 skos:exactMatch MP:0000849 semapv:LexicalMatching Cerebellar dysplasia abnormal cerebellum morphology -HP:0001321 skos:exactMatch MP:0000852 semapv:LexicalMatching Cerebellar hypoplasia small cerebellum -HP:0030769 skos:exactMatch MP:0000914 semapv:LexicalMatching Exencephaly exencephaly -HP:0012447 skos:exactMatch MP:0000920 semapv:LexicalMatching Abnormal myelination abnormal myelination -HP:0011096 skos:exactMatch MP:0000921 semapv:LexicalMatching Peripheral demyelination demyelination -HP:0007373 skos:exactMatch MP:0000938 semapv:LexicalMatching Motor neuron atrophy motor neuron degeneration -HP:0001291 skos:exactMatch MP:0001056 semapv:LexicalMatching Abnormal cranial nerve morphology abnormal cranial nerve morphology -HP:0000135 skos:exactMatch MP:0001116 semapv:LexicalMatching Hypogonadism small gonad -HP:0031105 skos:exactMatch MP:0001120 semapv:LexicalMatching Abnormal uterus morphology abnormal uterus morphology -HP:0000142 skos:exactMatch MP:0001139 semapv:LexicalMatching Abnormal vagina morphology abnormal vagina morphology -HP:0000035 skos:exactMatch MP:0001146 semapv:LexicalMatching Abnormal testis morphology abnormal testis morphology -HP:0000053 skos:exactMatch MP:0001148 semapv:LexicalMatching Macroorchidism enlarged testis -HP:0008669 skos:exactMatch MP:0001156 semapv:LexicalMatching Abnormal spermatogenesis abnormal spermatogenesis -HP:0008775 skos:exactMatch MP:0001158 semapv:LexicalMatching Abnormal prostate morphology abnormal prostate gland morphology -HP:0002088 skos:exactMatch MP:0001175 semapv:LexicalMatching Abnormal lung morphology abnormal lung morphology -HP:0100750 skos:exactMatch MP:0001177 semapv:LexicalMatching Atelectasis atelectasis -HP:0005944 skos:exactMatch MP:0001181 semapv:LexicalMatching Bilateral lung agenesis absent lungs -HP:0040223 skos:exactMatch MP:0001182 semapv:LexicalMatching Pulmonary hemorrhage lung hemorrhage -HP:0010783 skos:exactMatch MP:0001190 semapv:LexicalMatching Erythema reddish skin -HP:0040189 skos:exactMatch MP:0001192 semapv:LexicalMatching Scaling skin scaly skin -HP:0000963 skos:exactMatch MP:0001199 semapv:LexicalMatching Thin skin thin skin -HP:0001072 skos:exactMatch MP:0001200 semapv:LexicalMatching Thickened skin thick skin -HP:0010648 skos:exactMatch MP:0001201 semapv:LexicalMatching Dermal translucency translucent skin -HP:0000992 skos:exactMatch MP:0001202 semapv:LexicalMatching Cutaneous photosensitivity skin photosensitivity -HP:0200037 skos:exactMatch MP:0001208 semapv:LexicalMatching Skin vesicle blistering -HP:0000962 skos:exactMatch MP:0001242 semapv:LexicalMatching Hyperkeratosis hyperkeratosis -HP:0001552 skos:exactMatch MP:0001268 semapv:LexicalMatching Barrel-shaped chest barrel chest -HP:0000528 skos:exactMatch MP:0001293 semapv:LexicalMatching Anophthalmia anophthalmia -HP:0000568 skos:exactMatch MP:0001297 semapv:LexicalMatching Microphthalmia microphthalmia -HP:0012376 skos:exactMatch MP:0001306 semapv:LexicalMatching Microphakia small lens -HP:0007957 skos:exactMatch MP:0001314 semapv:LexicalMatching Corneal opacity corneal opacity -HP:0007973 skos:exactMatch MP:0001325 semapv:LexicalMatching Retinal dysplasia abnormal retina morphology -HP:0000546 skos:exactMatch MP:0001326 semapv:LexicalMatching Retinal degeneration retinal degeneration -HP:0001093 skos:exactMatch MP:0001330 semapv:LexicalMatching Optic nerve dysplasia abnormal optic nerve morphology -HP:0001097 skos:exactMatch MP:0001337 semapv:LexicalMatching Keratoconjunctivitis sicca dry eyes -HP:0000492 skos:exactMatch MP:0001340 semapv:LexicalMatching Abnormal eyelid morphology abnormal eyelid morphology -HP:0011224 skos:exactMatch MP:0001341 semapv:LexicalMatching Ablepharon absent eyelids -HP:0000508 skos:exactMatch MP:0001344 semapv:LexicalMatching Ptosis blepharoptosis -HP:0007656 skos:exactMatch MP:0001347 semapv:LexicalMatching Lacrimal gland aplasia absent lacrimal glands -HP:0009926 skos:exactMatch MP:0001349 semapv:LexicalMatching Epiphora excessive tearing -HP:0012875 skos:exactMatch MP:0001378 semapv:LexicalMatching Abnormal ejaculation abnormal ejaculation -HP:0000496 skos:exactMatch MP:0001389 semapv:LexicalMatching Abnormality of eye movement abnormal eye movement -HP:0001251 skos:exactMatch MP:0001393 semapv:LexicalMatching Ataxia ataxia -HP:0000752 skos:exactMatch MP:0001399 semapv:LexicalMatching Hyperactivity hyperactivity -HP:0001288 skos:exactMatch MP:0001406 semapv:LexicalMatching Gait disturbance abnormal gait -HP:0000733 skos:exactMatch MP:0001408 semapv:LexicalMatching Stereotypy stereotypic behavior -HP:0030082 skos:exactMatch MP:0001422 semapv:LexicalMatching Abnormal drinking behavior abnormal drinking behavior -HP:0001959 skos:exactMatch MP:0001426 semapv:LexicalMatching Polydipsia polydipsia -HP:0001944 skos:exactMatch MP:0001429 semapv:LexicalMatching Dehydration dehydration -HP:0100738 skos:exactMatch MP:0001431 semapv:LexicalMatching Abnormal eating behavior abnormal eating behavior -HP:0010831 skos:exactMatch MP:0001516 semapv:LexicalMatching Impaired proprioception abnormal motor coordination/balance -HP:0002305 skos:exactMatch MP:0001527 semapv:LexicalMatching Athetosis athetotic walking movements -HP:0030781 skos:exactMatch MP:0001554 semapv:LexicalMatching Increased circulating free fatty acid level increased circulating free fatty acid level -HP:0040214 skos:exactMatch MP:0001560 semapv:LexicalMatching Abnormal insulin level abnormal circulating insulin level -HP:0040215 skos:exactMatch MP:0001560 semapv:LexicalMatching Abnormal circulating insulin level abnormal circulating insulin level -HP:0000961 skos:exactMatch MP:0001575 semapv:LexicalMatching Cyanosis cyanosis -HP:0001903 skos:exactMatch MP:0001577 semapv:LexicalMatching Anemia anemia -HP:0001878 skos:exactMatch MP:0001585 semapv:LexicalMatching Hemolytic anemia hemolytic anemia -HP:0020058 skos:exactMatch MP:0001586 semapv:LexicalMatching Abnormal red blood cell count abnormal erythrocyte cell number -HP:0011902 skos:exactMatch MP:0001588 semapv:LexicalMatching Abnormal hemoglobin abnormal hemoglobin -HP:0025546 skos:exactMatch MP:0001589 semapv:LexicalMatching Abnormal mean corpuscular hemoglobin concentration abnormal mean corpuscular hemoglobin -HP:0002615 skos:exactMatch MP:0001596 semapv:LexicalMatching Hypotension hypotension -HP:0011675 skos:exactMatch MP:0001629 semapv:LexicalMatching Arrhythmia abnormal heart rate -HP:0011675 skos:exactMatch MP:0001636 semapv:LexicalMatching Arrhythmia irregular heartbeat -HP:0002605 skos:exactMatch MP:0001654 semapv:LexicalMatching Hepatic necrosis hepatic necrosis -HP:0002028 skos:exactMatch MP:0001665 semapv:LexicalMatching Chronic diarrhea chronic diarrhea -HP:0008897 skos:exactMatch MP:0001732 semapv:LexicalMatching Postnatal growth retardation postnatal growth retardation -HP:0008232 skos:exactMatch MP:0001750 semapv:LexicalMatching Elevated circulating follicle stimulating hormone level increased circulating follicle stimulating hormone level -HP:0012337 skos:exactMatch MP:0001764 semapv:LexicalMatching Abnormal homeostasis abnormal homeostasis -HP:0000777 skos:exactMatch MP:0001823 semapv:LexicalMatching Abnormality of the thymus thymus hypoplasia -HP:0410035 skos:exactMatch MP:0001828 semapv:LexicalMatching Abnormal T cell activation abnormal T cell activation -HP:0012647 skos:exactMatch MP:0001845 semapv:LexicalMatching Abnormal inflammatory response abnormal inflammatory response -HP:0002383 skos:exactMatch MP:0001847 semapv:LexicalMatching Encephalitis brain inflammation -HP:0012123 skos:exactMatch MP:0001848 semapv:LexicalMatching Posterior uveitis choroid inflammation -HP:0000509 skos:exactMatch MP:0001852 semapv:LexicalMatching Conjunctivitis conjunctivitis -HP:0012819 skos:exactMatch MP:0001856 semapv:LexicalMatching Myocarditis myocarditis -HP:0001701 skos:exactMatch MP:0001857 semapv:LexicalMatching Pericarditis pericarditis -HP:0000123 skos:exactMatch MP:0001859 semapv:LexicalMatching Nephritis kidney inflammation -HP:0012115 skos:exactMatch MP:0001860 semapv:LexicalMatching Hepatitis liver inflammation -HP:0002090 skos:exactMatch MP:0001861 semapv:LexicalMatching Pneumonia lung inflammation -HP:0006515 skos:exactMatch MP:0001862 semapv:LexicalMatching Interstitial pneumonitis interstitial pneumonia -HP:0012384 skos:exactMatch MP:0001866 semapv:LexicalMatching Rhinitis nasal inflammation -HP:0012384 skos:exactMatch MP:0001867 semapv:LexicalMatching Rhinitis rhinitis -HP:0031259 skos:exactMatch MP:0001868 semapv:LexicalMatching Oophoritis ovary inflammation -HP:0001733 skos:exactMatch MP:0001869 semapv:LexicalMatching Pancreatitis pancreas inflammation -HP:0031281 skos:exactMatch MP:0001870 semapv:LexicalMatching Sialadenitis salivary gland inflammation -HP:0000246 skos:exactMatch MP:0001872 semapv:LexicalMatching Sinusitis sinus inflammation -HP:0005263 skos:exactMatch MP:0001873 semapv:LexicalMatching Gastritis stomach inflammation -HP:0025092 skos:exactMatch MP:0001874 semapv:LexicalMatching Epidermal acanthosis acanthosis -HP:0100796 skos:exactMatch MP:0001875 semapv:LexicalMatching Orchitis testis inflammation -HP:0031094 skos:exactMatch MP:0001881 semapv:LexicalMatching Abnormal breast physiology abnormal mammary gland physiology -HP:0002323 skos:exactMatch MP:0001890 semapv:LexicalMatching Anencephaly anencephaly -HP:0000238 skos:exactMatch MP:0001891 semapv:LexicalMatching Hydrocephalus hydrocephaly -HP:0001334 skos:exactMatch MP:0001893 semapv:LexicalMatching Communicating hydrocephalus non-obstructive hydrocephaly -HP:0001342 skos:exactMatch MP:0001916 semapv:LexicalMatching Cerebral hemorrhage intracerebral hemorrhage -HP:0030746 skos:exactMatch MP:0001917 semapv:LexicalMatching Intraventricular hemorrhage intraventricular hemorrhage -HP:0008734 skos:exactMatch MP:0001940 semapv:LexicalMatching Decreased testicular size testis hypoplasia -HP:0002795 skos:exactMatch MP:0001943 semapv:LexicalMatching Functional respiratory abnormality abnormal respiration -HP:0005232 skos:exactMatch MP:0001944 semapv:LexicalMatching Pancreatic dysplasia abnormal pancreas morphology -HP:0031602 skos:exactMatch MP:0001947 semapv:LexicalMatching Abnormal mucociliary clearance abnormal mucociliary clearance -HP:0000076 skos:exactMatch MP:0001948 semapv:LexicalMatching Vesicoureteral reflux vesicoureteral reflux -HP:0002878 skos:exactMatch MP:0001953 semapv:LexicalMatching Respiratory failure respiratory failure -HP:0002094 skos:exactMatch MP:0001954 semapv:LexicalMatching Dyspnea respiratory distress -HP:0002098 skos:exactMatch MP:0001954 semapv:LexicalMatching Respiratory distress respiratory distress -HP:0040213 skos:exactMatch MP:0001956 semapv:LexicalMatching Hypopnea hypopnea -HP:0031826 skos:exactMatch MP:0001961 semapv:LexicalMatching Abnormal reflex abnormal reflex -HP:0000992 skos:exactMatch MP:0001999 semapv:LexicalMatching Cutaneous photosensitivity photosensitivity -HP:0002664 skos:exactMatch MP:0002006 semapv:LexicalMatching Neoplasm neoplasm -HP:0030434 skos:exactMatch MP:0002013 semapv:LexicalMatching Pilomatrixoma increased pilomatricoma incidence -HP:0100243 skos:exactMatch MP:0002035 semapv:LexicalMatching Leiomyosarcoma increased leiomyosarcoma incidence -HP:0002859 skos:exactMatch MP:0002036 semapv:LexicalMatching Rhabdomyosarcoma increased rhabdomyosarcoma incidence -HP:0001250 skos:exactMatch MP:0002064 semapv:LexicalMatching Seizures seizures -HP:0100852 skos:exactMatch MP:0002065 semapv:LexicalMatching Abnormal fear/anxiety-related behavior abnormal fear/anxiety-related behavior -HP:0040202 skos:exactMatch MP:0002069 semapv:LexicalMatching Abnormal consumption behavior abnormal consumption behavior -HP:0011014 skos:exactMatch MP:0002078 semapv:LexicalMatching Abnormal glucose homeostasis abnormal glucose homeostasis -HP:0001000 skos:exactMatch MP:0002095 semapv:LexicalMatching Abnormality of skin pigmentation abnormal skin pigmentation -HP:0031703 skos:exactMatch MP:0002102 semapv:LexicalMatching Abnormal ear morphology abnormal ear morphology -HP:0011805 skos:exactMatch MP:0002108 semapv:LexicalMatching Abnormal skeletal muscle morphology abnormal muscle morphology -HP:0011297 skos:exactMatch MP:0002110 semapv:LexicalMatching Abnormal digit morphology abnormal digit morphology -HP:0000110 skos:exactMatch MP:0002135 semapv:LexicalMatching Renal dysplasia abnormal kidney morphology -HP:0012210 skos:exactMatch MP:0002135 semapv:LexicalMatching Abnormal renal morphology abnormal kidney morphology -HP:0002171 skos:exactMatch MP:0002183 semapv:LexicalMatching Gliosis gliosis -HP:0001961 skos:exactMatch MP:0002188 semapv:LexicalMatching Hypoplastic heart small heart -HP:0012244 skos:exactMatch MP:0002210 semapv:LexicalMatching Abnormal sex determination abnormal sex determination -HP:0010459 skos:exactMatch MP:0002213 semapv:LexicalMatching True hermaphroditism true hermaphroditism -HP:0002180 skos:exactMatch MP:0002229 semapv:LexicalMatching Neurodegeneration neurodegeneration -HP:0025423 skos:exactMatch MP:0002249 semapv:LexicalMatching Abnormal larynx morphology abnormal larynx morphology -HP:0025426 skos:exactMatch MP:0002264 semapv:LexicalMatching Abnormal bronchus morphology abnormal bronchus morphology -HP:0003202 skos:exactMatch MP:0002269 semapv:LexicalMatching Skeletal muscle atrophy muscular atrophy -HP:0001311 skos:exactMatch MP:0002272 semapv:LexicalMatching Abnormal nervous system electrophysiology abnormal nervous system electrophysiology -HP:0002778 skos:exactMatch MP:0002282 semapv:LexicalMatching Abnormal trachea morphology abnormal trachea morphology -HP:0000028 skos:exactMatch MP:0002286 semapv:LexicalMatching Cryptorchidism cryptorchism -HP:0030875 skos:exactMatch MP:0002295 semapv:LexicalMatching Abnormality of pulmonary circulation abnormal pulmonary circulation -HP:0002835 skos:exactMatch MP:0002296 semapv:LexicalMatching Aspiration aspiration -HP:0012416 skos:exactMatch MP:0002318 semapv:LexicalMatching Hypercapnia hypercapnia -HP:0012415 skos:exactMatch MP:0002329 semapv:LexicalMatching Abnormal blood gas level abnormal blood gas level -HP:0025035 skos:exactMatch MP:0002416 semapv:LexicalMatching Abnormal proerythroblast morphology abnormal proerythroblast morphology -HP:0012143 skos:exactMatch MP:0002417 semapv:LexicalMatching Abnormal megakaryocyte morphology abnormal megakaryocyte morphology -HP:0001912 skos:exactMatch MP:0002422 semapv:LexicalMatching Abnormal basophil morphology abnormal basophil morphology -HP:0004312 skos:exactMatch MP:0002424 semapv:LexicalMatching Abnormal reticulocyte morphology abnormal reticulocyte morphology -HP:0001911 skos:exactMatch MP:0002441 semapv:LexicalMatching Abnormal granulocyte morphology abnormal granulocyte morphology -HP:0001877 skos:exactMatch MP:0002447 semapv:LexicalMatching Abnormal erythrocyte morphology abnormal erythrocyte morphology -HP:0100845 skos:exactMatch MP:0002531 semapv:LexicalMatching Anaphylactic shock abnormal type I hypersensitivity reaction -HP:0009803 skos:exactMatch MP:0002543 semapv:LexicalMatching Short phalanx of finger brachyphalangia -HP:0001156 skos:exactMatch MP:0002544 semapv:LexicalMatching Brachydactyly brachydactyly -HP:0011499 skos:exactMatch MP:0002546 semapv:LexicalMatching Mydriasis mydriasis -HP:0012433 skos:exactMatch MP:0002557 semapv:LexicalMatching Abnormal social behavior abnormal social/conspecific interaction -HP:0100851 skos:exactMatch MP:0002572 semapv:LexicalMatching Abnormal emotion/affect behavior abnormal emotion/affect behavior -HP:0410175 skos:exactMatch MP:0002575 semapv:LexicalMatching Hyperketonemia increased circulating ketone body level -HP:0005518 skos:exactMatch MP:0002590 semapv:LexicalMatching Increased mean corpuscular volume increased mean corpuscular volume -HP:0025066 skos:exactMatch MP:0002591 semapv:LexicalMatching Decreased mean corpuscular volume decreased mean corpuscular volume -HP:0031850 skos:exactMatch MP:0002596 semapv:LexicalMatching Abnormal hematocrit abnormal hematocrit -HP:0020064 skos:exactMatch MP:0002602 semapv:LexicalMatching Abnormal eosinophil count abnormal eosinophil cell number -HP:0001899 skos:exactMatch MP:0002608 semapv:LexicalMatching Increased hematocrit increased hematocrit -HP:0004332 skos:exactMatch MP:0002619 semapv:LexicalMatching Abnormal lymphocyte morphology abnormal lymphocyte morphology -HP:0001702 skos:exactMatch MP:0002624 semapv:LexicalMatching Abnormal tricuspid valve morphology abnormal tricuspid valve morphology -HP:0030732 skos:exactMatch MP:0002624 semapv:LexicalMatching Dysplastic tricuspid valve abnormal tricuspid valve morphology -HP:0001712 skos:exactMatch MP:0002625 semapv:LexicalMatching Left ventricular hypertrophy heart left ventricle hypertrophy -HP:0001649 skos:exactMatch MP:0002626 semapv:LexicalMatching Tachycardia increased heart rate -HP:0001397 skos:exactMatch MP:0002628 semapv:LexicalMatching Hepatic steatosis hepatic steatosis -HP:0001660 skos:exactMatch MP:0002633 semapv:LexicalMatching Truncus arteriosus persistent truncus arteriosis -HP:0000013 skos:exactMatch MP:0002637 semapv:LexicalMatching Hypoplasia of the uterus small uterus -HP:0000347 skos:exactMatch MP:0002639 semapv:LexicalMatching Micrognathia micrognathia -HP:0011273 skos:exactMatch MP:0002642 semapv:LexicalMatching Anisocytosis anisocytosis -HP:0008707 skos:exactMatch MP:0002670 semapv:LexicalMatching Absent scrotum absent scrotum -HP:0012206 skos:exactMatch MP:0002674 semapv:LexicalMatching Abnormal sperm motility abnormal sperm motility -HP:0012207 skos:exactMatch MP:0002675 semapv:LexicalMatching Reduced sperm motility asthenozoospermia -HP:0012205 skos:exactMatch MP:0002686 semapv:LexicalMatching Globozoospermia globozoospermia -HP:0000798 skos:exactMatch MP:0002687 semapv:LexicalMatching Oligospermia oligozoospermia -HP:0002304 skos:exactMatch MP:0002690 semapv:LexicalMatching Akinesia akinesia -HP:0030687 skos:exactMatch MP:0002695 semapv:LexicalMatching Abnormal glucagon level abnormal circulating glucagon level -HP:0040299 skos:exactMatch MP:0002702 semapv:LexicalMatching Decreased circulating free fatty acid level decreased circulating free fatty acid level -HP:0000787 skos:exactMatch MP:0002708 semapv:LexicalMatching Nephrolithiasis nephrolithiasis -HP:0009556 skos:exactMatch MP:0002728 semapv:LexicalMatching Absent tibia absent tibia -HP:0002251 skos:exactMatch MP:0002731 semapv:LexicalMatching Aganglionic megacolon megacolon -HP:0025367 skos:exactMatch MP:0002732 semapv:LexicalMatching Trichoepithelioma increased trichoepithelioma incidence -HP:0000099 skos:exactMatch MP:0002743 semapv:LexicalMatching Glomerulonephritis glomerulonephritis -HP:0001646 skos:exactMatch MP:0002747 semapv:LexicalMatching Abnormal aortic valve morphology abnormal aortic valve morphology -HP:0001641 skos:exactMatch MP:0002748 semapv:LexicalMatching Abnormal pulmonary valve morphology abnormal pulmonary valve morphology -HP:0005164 skos:exactMatch MP:0002748 semapv:LexicalMatching Dysplastic pulmonary valve abnormal pulmonary valve morphology -HP:0000520 skos:exactMatch MP:0002750 semapv:LexicalMatching Proptosis exophthalmos -HP:0005133 skos:exactMatch MP:0002754 semapv:LexicalMatching Right ventricular dilatation dilated heart right ventricle -HP:0005736 skos:exactMatch MP:0002764 semapv:LexicalMatching Short tibia short tibia -HP:0003038 skos:exactMatch MP:0002765 semapv:LexicalMatching Fibular hypoplasia short fibula -HP:0003363 skos:exactMatch MP:0002766 semapv:LexicalMatching Abdominal situs inversus situs inversus -HP:0000835 skos:exactMatch MP:0002768 semapv:LexicalMatching Adrenal hypoplasia small adrenal glands -HP:0012872 skos:exactMatch MP:0002769 semapv:LexicalMatching Abnormal vas deferens morphology abnormal vas deferens morphology -HP:0030341 skos:exactMatch MP:0002790 semapv:LexicalMatching Decreased circulating follicle stimulating hormone level decreased circulating follicle stimulating hormone level -HP:0002570 skos:exactMatch MP:0002791 semapv:LexicalMatching Steatorrhea steatorrhea -HP:0001142 skos:exactMatch MP:0002794 semapv:LexicalMatching Lenticonus lenticonus -HP:0001644 skos:exactMatch MP:0002795 semapv:LexicalMatching Dilated cardiomyopathy dilated cardiomyopathy -HP:0001935 skos:exactMatch MP:0002810 semapv:LexicalMatching Microcytic anemia microcytic anemia -HP:0001972 skos:exactMatch MP:0002811 semapv:LexicalMatching Macrocytic anemia macrocytic anemia -HP:0025066 skos:exactMatch MP:0002813 semapv:LexicalMatching Decreased mean corpuscular volume microcytosis -HP:0002583 skos:exactMatch MP:0002816 semapv:LexicalMatching Colitis colitis -HP:0031263 skos:exactMatch MP:0002827 semapv:LexicalMatching Abnormal renal corpuscle morphology abnormal renal corpuscle morphology -HP:0031264 skos:exactMatch MP:0002828 semapv:LexicalMatching Abnormal morphology of Bowman capsule abnormal renal glomerular capsule morphology -HP:0001081 skos:exactMatch MP:0002830 semapv:LexicalMatching Cholelithiasis gallstones -HP:0002615 skos:exactMatch MP:0002843 semapv:LexicalMatching Hypotension decreased systemic arterial blood pressure -HP:0012212 skos:exactMatch MP:0002847 semapv:LexicalMatching Abnormal glomerular filtration rate abnormal renal glomerular filtration rate -HP:0012592 skos:exactMatch MP:0002871 semapv:LexicalMatching Albuminuria albuminuria -HP:0020060 skos:exactMatch MP:0002875 semapv:LexicalMatching Decreased red blood cell count decreased erythrocyte cell number -HP:0002179 skos:exactMatch MP:0002880 semapv:LexicalMatching Opisthotonus opisthotonus -HP:0002919 skos:exactMatch MP:0002893 semapv:LexicalMatching Ketonuria ketoaciduria -HP:0012378 skos:exactMatch MP:0002899 semapv:LexicalMatching Fatigue fatigue -HP:0003109 skos:exactMatch MP:0002901 semapv:LexicalMatching Hyperphosphaturia increased urine phosphate level -HP:0012365 skos:exactMatch MP:0002902 semapv:LexicalMatching Hypophosphaturia decreased urine phosphate level -HP:0031817 skos:exactMatch MP:0002905 semapv:LexicalMatching Decreased circulating parathyroid hormone level decreased circulating parathyroid hormone level -HP:0030191 skos:exactMatch MP:0002913 semapv:LexicalMatching Abnormal peripheral nervous system synaptic transmission abnormal PNS synaptic transmission -HP:0002251 skos:exactMatch MP:0002926 semapv:LexicalMatching Aganglionic megacolon aganglionic megacolon -HP:0001367 skos:exactMatch MP:0002932 semapv:LexicalMatching Abnormal joint morphology abnormal joint morphology -HP:0100769 skos:exactMatch MP:0002933 semapv:LexicalMatching Synovitis joint inflammation -HP:0012594 skos:exactMatch MP:0002959 semapv:LexicalMatching Microalbuminuria increased urine microalbumin level -HP:0012117 skos:exactMatch MP:0002965 semapv:LexicalMatching Hyperalbuminemia increased circulating serum albumin level -HP:0012861 skos:exactMatch MP:0002996 semapv:LexicalMatching Ovotestis ovotestis -HP:0001948 skos:exactMatch MP:0003028 semapv:LexicalMatching Alkalosis alkalosis -HP:0032369 skos:exactMatch MP:0003029 semapv:LexicalMatching Alkalemia alkalemia -HP:0032368 skos:exactMatch MP:0003030 semapv:LexicalMatching Acidemia acidemia -HP:0012417 skos:exactMatch MP:0003032 semapv:LexicalMatching Hypocapnia hypocapnia -HP:0005317 skos:exactMatch MP:0003034 semapv:LexicalMatching Increased pulmonary vascular resistance increased pulmonary vascular resistance -HP:0001394 skos:exactMatch MP:0003046 semapv:LexicalMatching Cirrhosis liver cirrhosis -HP:0001539 skos:exactMatch MP:0003052 semapv:LexicalMatching Omphalocele omphalocele -HP:0000684 skos:exactMatch MP:0003053 semapv:LexicalMatching Delayed eruption of teeth delayed tooth eruption -HP:0002414 skos:exactMatch MP:0003054 semapv:LexicalMatching Spina bifida spina bifida -HP:0010301 skos:exactMatch MP:0003054 semapv:LexicalMatching Spinal dysraphism spina bifida -HP:0004303 skos:exactMatch MP:0003084 semapv:LexicalMatching Abnormal muscle fiber morphology abnormal skeletal muscle fiber morphology -HP:0100565 skos:exactMatch MP:0003086 semapv:LexicalMatching Hydromyelia hydromyelia -HP:0000541 skos:exactMatch MP:0003099 semapv:LexicalMatching Retinal detachment retinal detachment -HP:0000545 skos:exactMatch MP:0003100 semapv:LexicalMatching Myopia myopia -HP:0011003 skos:exactMatch MP:0003101 semapv:LexicalMatching High myopia high myopia -HP:0030716 skos:exactMatch MP:0003104 semapv:LexicalMatching Acrania acrania -HP:0002748 skos:exactMatch MP:0003116 semapv:LexicalMatching Rickets rickets -HP:0000047 skos:exactMatch MP:0003124 semapv:LexicalMatching Hypospadias hypospadia -HP:0012621 skos:exactMatch MP:0003129 semapv:LexicalMatching Persistent cloaca persistent cloaca -HP:0009892 skos:exactMatch MP:0003142 semapv:LexicalMatching Anotia anotia -HP:0100736 skos:exactMatch MP:0003154 semapv:LexicalMatching Abnormal soft palate morphology abnormal soft palate morphology -HP:0002015 skos:exactMatch MP:0003158 semapv:LexicalMatching Dysphagia dysphagia -HP:0012533 skos:exactMatch MP:0003177 semapv:LexicalMatching Allodynia allodynia -HP:0003761 skos:exactMatch MP:0003195 semapv:LexicalMatching Calcinosis calcinosis -HP:0000121 skos:exactMatch MP:0003197 semapv:LexicalMatching Nephrocalcinosis nephrocalcinosis -HP:0002185 skos:exactMatch MP:0003214 semapv:LexicalMatching Neurofibrillary tangles neurofibrillary tangles -HP:0005576 skos:exactMatch MP:0003215 semapv:LexicalMatching Tubulointerstitial fibrosis renal interstitial fibrosis -HP:0002121 skos:exactMatch MP:0003216 semapv:LexicalMatching Absence seizure absence seizures -HP:0001657 skos:exactMatch MP:0003233 semapv:LexicalMatching Prolonged QT interval prolonged QT interval -HP:0011467 skos:exactMatch MP:0003250 semapv:LexicalMatching Absent gallbladder absent gallbladder -HP:0001082 skos:exactMatch MP:0003251 semapv:LexicalMatching Cholecystitis gallbladder inflammation -HP:0030151 skos:exactMatch MP:0003254 semapv:LexicalMatching Cholangitis bile duct inflammation -HP:0001408 skos:exactMatch MP:0003255 semapv:LexicalMatching Bile duct proliferation bile duct proliferation -HP:0002613 skos:exactMatch MP:0003256 semapv:LexicalMatching Biliary cirrhosis biliary cirrhosis -HP:0002036 skos:exactMatch MP:0003258 semapv:LexicalMatching Hiatus hernia hiatal hernia -HP:0002018 skos:exactMatch MP:0003259 semapv:LexicalMatching Nausea nausea -HP:0002013 skos:exactMatch MP:0003260 semapv:LexicalMatching Vomiting vomiting -HP:0002248 skos:exactMatch MP:0003261 semapv:LexicalMatching Hematemesis hematemesis -HP:0100890 skos:exactMatch MP:0003266 semapv:LexicalMatching Cyst of the ductus choledochus biliary cyst -HP:0012450 skos:exactMatch MP:0003268 semapv:LexicalMatching Chronic constipation chronic constipation -HP:0100633 skos:exactMatch MP:0003278 semapv:LexicalMatching Esophagitis esophageal inflammation -HP:0000020 skos:exactMatch MP:0003280 semapv:LexicalMatching Urinary incontinence urinary incontinence -HP:0002607 skos:exactMatch MP:0003281 semapv:LexicalMatching Bowel incontinence fecal incontinence -HP:0002020 skos:exactMatch MP:0003286 semapv:LexicalMatching Gastroesophageal reflux gastroesophageal reflux -HP:0002573 skos:exactMatch MP:0003293 semapv:LexicalMatching Hematochezia rectal hemorrhage -HP:0002576 skos:exactMatch MP:0003294 semapv:LexicalMatching Intussusception intussusception -HP:0004398 skos:exactMatch MP:0003301 semapv:LexicalMatching Peptic ulcer peptic ulcer -HP:0002021 skos:exactMatch MP:0003307 semapv:LexicalMatching Pyloric stenosis pyloric stenosis -HP:0001310 skos:exactMatch MP:0003314 semapv:LexicalMatching Dysmetria dysmetria -HP:0005218 skos:exactMatch MP:0003317 semapv:LexicalMatching Anoperineal fistula anoperineal fistula -HP:0004792 skos:exactMatch MP:0003318 semapv:LexicalMatching Rectoperineal fistula rectoperineal fistula -HP:0000143 skos:exactMatch MP:0003320 semapv:LexicalMatching Rectovaginal fistula rectovaginal fistula -HP:0001395 skos:exactMatch MP:0003333 semapv:LexicalMatching Hepatic fibrosis liver fibrosis -HP:0100732 skos:exactMatch MP:0003334 semapv:LexicalMatching Pancreatic fibrosis pancreas fibrosis -HP:0006280 skos:exactMatch MP:0003341 semapv:LexicalMatching Chronic pancreatitis chronic pancreas inflammation -HP:0001747 skos:exactMatch MP:0003342 semapv:LexicalMatching Accessory spleen accessory spleen -HP:0001748 skos:exactMatch MP:0003342 semapv:LexicalMatching Polysplenia accessory spleen -HP:0003187 skos:exactMatch MP:0003344 semapv:LexicalMatching Breast hypoplasia mammary gland hypoplasia -HP:0011957 skos:exactMatch MP:0003346 semapv:LexicalMatching Abnormal pectoral muscle morphology abnormal pectoral muscle morphology -HP:0002446 skos:exactMatch MP:0003354 semapv:LexicalMatching Astrocytosis astrocytosis -HP:0030338 skos:exactMatch MP:0003361 semapv:LexicalMatching Abnormal circulating gonadotropin level abnormal circulating gonadotropin level -HP:0000837 skos:exactMatch MP:0003362 semapv:LexicalMatching Increased circulating gonadotropin level increased circulating gonadotropin level -HP:0030339 skos:exactMatch MP:0003363 semapv:LexicalMatching Decreased circulating gonadotropin level decreased circulating gonadotropin level -HP:0025132 skos:exactMatch MP:0003369 semapv:LexicalMatching Abnormal circulating estrogen level abnormal circulating estrogen level -HP:0000826 skos:exactMatch MP:0003378 semapv:LexicalMatching Precocious puberty early sexual maturation -HP:0001680 skos:exactMatch MP:0003387 semapv:LexicalMatching Coarctation of aorta aorta coarctation -HP:0001004 skos:exactMatch MP:0003390 semapv:LexicalMatching Lymphedema lymphedema -HP:0031251 skos:exactMatch MP:0003395 semapv:LexicalMatching Abnormal subclavian artery morphology abnormal subclavian artery morphology -HP:0200040 skos:exactMatch MP:0003414 semapv:LexicalMatching Epidermoid cyst epidermal cyst -HP:0001036 skos:exactMatch MP:0003427 semapv:LexicalMatching Parakeratosis parakeratosis -HP:0000843 skos:exactMatch MP:0003432 semapv:LexicalMatching Hyperparathyroidism increased activity of parathyroid -HP:0000829 skos:exactMatch MP:0003433 semapv:LexicalMatching Hypoparathyroidism decreased activity of parathyroid -HP:0031794 skos:exactMatch MP:0003442 semapv:LexicalMatching Decreased circulating glycerol level decreased circulating glycerol level -HP:0010497 skos:exactMatch MP:0003445 semapv:LexicalMatching Sirenomelia sirenomelia -HP:0000197 skos:exactMatch MP:0003452 semapv:LexicalMatching Abnormal parotid gland morphology abnormal parotid gland morphology -HP:0001019 skos:exactMatch MP:0003454 semapv:LexicalMatching Erythroderma erythroderma -HP:0100646 skos:exactMatch MP:0003504 semapv:LexicalMatching Thyroiditis thyroid gland inflammation -HP:0012882 skos:exactMatch MP:0003517 semapv:LexicalMatching Hyperplastic labia majora enlarged labia majora -HP:0000059 skos:exactMatch MP:0003518 semapv:LexicalMatching Hypoplastic labia majora small labia majora -HP:0008665 skos:exactMatch MP:0003529 semapv:LexicalMatching Clitoral hypertrophy enlarged clitoris -HP:0000060 skos:exactMatch MP:0003530 semapv:LexicalMatching Clitoral hypoplasia small clitoris -HP:0001153 skos:exactMatch MP:0003533 semapv:LexicalMatching Septate vagina bifid vagina -HP:0040314 skos:exactMatch MP:0003534 semapv:LexicalMatching Blind vagina blind vagina -HP:0031088 skos:exactMatch MP:0003536 semapv:LexicalMatching Vaginal dryness vagina dryness -HP:0030010 skos:exactMatch MP:0003537 semapv:LexicalMatching Hydrometrocolpos hydrometrocolpos -HP:0030011 skos:exactMatch MP:0003540 semapv:LexicalMatching Imperforate hymen imperforate hymen -HP:0030683 skos:exactMatch MP:0003541 semapv:LexicalMatching Vaginitis vaginal inflammation -HP:0001741 skos:exactMatch MP:0003554 semapv:LexicalMatching Phimosis phimosis -HP:0000041 skos:exactMatch MP:0003555 semapv:LexicalMatching Chordee chordee -HP:0012873 skos:exactMatch MP:0003557 semapv:LexicalMatching Absent vas deferens absent vas deferens -HP:0002758 skos:exactMatch MP:0003560 semapv:LexicalMatching Osteoarthritis osteoarthritis -HP:0001370 skos:exactMatch MP:0003561 semapv:LexicalMatching Rheumatoid arthritis rheumatoid arthritis -HP:0010463 skos:exactMatch MP:0003578 semapv:LexicalMatching Aplasia of the ovary absent ovary -HP:0025318 skos:exactMatch MP:0003579 semapv:LexicalMatching Ovarian carcinoma increased ovarian carcinoma incidence -HP:0000072 skos:exactMatch MP:0003585 semapv:LexicalMatching Hydroureter large ureter -HP:0025634 skos:exactMatch MP:0003589 semapv:LexicalMatching Abnormal ureter physiology abnormal ureter physiology -HP:0000076 skos:exactMatch MP:0003590 semapv:LexicalMatching Vesicoureteral reflux ureteral reflux -HP:0008716 skos:exactMatch MP:0003593 semapv:LexicalMatching Urethrovaginal fistula urethrovaginal fistula -HP:0030424 skos:exactMatch MP:0003595 semapv:LexicalMatching Epididymal cyst epididymal cyst -HP:0000039 skos:exactMatch MP:0003598 semapv:LexicalMatching Epispadias epispadia -HP:0008696 skos:exactMatch MP:0003602 semapv:LexicalMatching Renal hamartoma increased renal hamartoma incidence -HP:0000122 skos:exactMatch MP:0003604 semapv:LexicalMatching Unilateral renal agenesis single kidney -HP:0000024 skos:exactMatch MP:0003608 semapv:LexicalMatching Prostatitis prostate gland inflammation -HP:0030276 skos:exactMatch MP:0003609 semapv:LexicalMatching Small scrotum small scrotum -HP:0100645 skos:exactMatch MP:0003614 semapv:LexicalMatching Cystocele urinary bladder prolapse -HP:0000015 skos:exactMatch MP:0003615 semapv:LexicalMatching Bladder diverticulum urinary bladder diverticulum -HP:0100520 skos:exactMatch MP:0003620 semapv:LexicalMatching Oliguria oliguria -HP:0100518 skos:exactMatch MP:0003621 semapv:LexicalMatching Dysuria dysuria -HP:0000016 skos:exactMatch MP:0003622 semapv:LexicalMatching Urinary retention ischuria -HP:0012535 skos:exactMatch MP:0003635 semapv:LexicalMatching Abnormal synaptic transmission abnormal synaptic transmission -HP:0002089 skos:exactMatch MP:0003641 semapv:LexicalMatching Pulmonary hypoplasia small lung -HP:0010310 skos:exactMatch MP:0003660 semapv:LexicalMatching Chylothorax chylothorax -HP:0200058 skos:exactMatch MP:0003667 semapv:LexicalMatching Angiosarcoma increased hemangiosarcoma incidence -HP:0000387 skos:exactMatch MP:0003678 semapv:LexicalMatching Absent earlobe absent ear lobes -HP:0009748 skos:exactMatch MP:0003680 semapv:LexicalMatching Large earlobe thick ear lobes -HP:0009748 skos:exactMatch MP:0003683 semapv:LexicalMatching Large earlobe prominent ear lobes -HP:0000597 skos:exactMatch MP:0003688 semapv:LexicalMatching Ophthalmoparesis ophthalmoparesis -HP:0001114 skos:exactMatch MP:0003692 semapv:LexicalMatching Xanthelasma xanthoma -HP:0020156 skos:exactMatch MP:0003696 semapv:LexicalMatching Abnormal zona pellucida morphology abnormal zona pellucida morphology -HP:0000980 skos:exactMatch MP:0003717 semapv:LexicalMatching Pallor pallor -HP:0000378 skos:exactMatch MP:0003735 semapv:LexicalMatching Cupped ear cup-shaped ears -HP:0005103 skos:exactMatch MP:0003737 semapv:LexicalMatching Calcification of the auricular cartilage ossification of pinnae -HP:0005473 skos:exactMatch MP:0003740 semapv:LexicalMatching Fusion of middle ear ossicles fusion of middle ear ossicles -HP:0000360 skos:exactMatch MP:0003741 semapv:LexicalMatching Tinnitus tinnitus -HP:0000268 skos:exactMatch MP:0003742 semapv:LexicalMatching Dolichocephaly narrow head -HP:0010280 skos:exactMatch MP:0003746 semapv:LexicalMatching Stomatitis stomatitis -HP:0002714 skos:exactMatch MP:0003749 semapv:LexicalMatching Downturned corners of mouth down-turned corners of mouth -HP:0002745 skos:exactMatch MP:0003751 semapv:LexicalMatching Oral leukoplakia oral leukoplakia -HP:0000174 skos:exactMatch MP:0003755 semapv:LexicalMatching Abnormal palate morphology abnormal palate morphology -HP:0012472 skos:exactMatch MP:0003773 semapv:LexicalMatching Eclabion eclabion -HP:0012471 skos:exactMatch MP:0003774 semapv:LexicalMatching Thick vermilion border thick lip -HP:0100825 skos:exactMatch MP:0003777 semapv:LexicalMatching Cheilitis lip inflammation -HP:0003103 skos:exactMatch MP:0003797 semapv:LexicalMatching Abnormal cortical bone morphology abnormal compact bone morphology -HP:0012385 skos:exactMatch MP:0003807 semapv:LexicalMatching Camptodactyly camptodactyly -HP:0002299 skos:exactMatch MP:0003848 semapv:LexicalMatching Brittle hair brittle hair -HP:0000958 skos:exactMatch MP:0003853 semapv:LexicalMatching Dry skin dry skin -HP:0002840 skos:exactMatch MP:0003865 semapv:LexicalMatching Lymphadenitis lymph node inflammation -HP:0031685 skos:exactMatch MP:0003868 semapv:LexicalMatching Abnormal stool composition abnormal feces composition -HP:0012575 skos:exactMatch MP:0003881 semapv:LexicalMatching Abnormal nephron morphology abnormal nephron morphology -HP:0030850 skos:exactMatch MP:0003882 semapv:LexicalMatching Abnormal pulse pressure abnormal pulse pressure -HP:0012248 skos:exactMatch MP:0003896 semapv:LexicalMatching Prolonged PR interval prolonged PR interval -HP:0012249 skos:exactMatch MP:0003897 semapv:LexicalMatching Abnormal ST segment abnormal ST segment -HP:0025074 skos:exactMatch MP:0003898 semapv:LexicalMatching Abnormal QRS complex abnormal QRS complex -HP:0031547 skos:exactMatch MP:0003899 semapv:LexicalMatching Abnormal QT interval abnormal QT interval -HP:0012232 skos:exactMatch MP:0003900 semapv:LexicalMatching Shortened QT interval shortened QT interval -HP:0031593 skos:exactMatch MP:0003901 semapv:LexicalMatching Abnormal PR interval abnormal PR interval -HP:0000776 skos:exactMatch MP:0003924 semapv:LexicalMatching Congenital diaphragmatic hernia diaphragmatic hernia -HP:0031862 skos:exactMatch MP:0003928 semapv:LexicalMatching Increased heart rate variability increased heart rate variability -HP:0031861 skos:exactMatch MP:0003929 semapv:LexicalMatching Decreased heart rate variability decreased heart rate variability -HP:0011054 skos:exactMatch MP:0003931 semapv:LexicalMatching Agenesis of molar absent molars -HP:0031409 skos:exactMatch MP:0003945 semapv:LexicalMatching Abnormal lymphocyte physiology abnormal lymphocyte physiology -HP:0032367 skos:exactMatch MP:0003968 semapv:LexicalMatching Abnormal growth hormone level abnormal growth hormone level -HP:0030345 skos:exactMatch MP:0003969 semapv:LexicalMatching Abnormal circulating luteinizing hormone level abnormal luteinizing hormone level -HP:0040086 skos:exactMatch MP:0003970 semapv:LexicalMatching Abnormal prolactin level abnormal prolactin level -HP:0031097 skos:exactMatch MP:0003971 semapv:LexicalMatching Abnormal thyroid-stimulating hormone level abnormal thyroid-stimulating hormone level -HP:0030760 skos:exactMatch MP:0003985 semapv:LexicalMatching Renal fibrosis renal fibrosis -HP:0002634 skos:exactMatch MP:0003991 semapv:LexicalMatching Arteriosclerosis arteriosclerosis -HP:0002069 skos:exactMatch MP:0003997 semapv:LexicalMatching Generalized tonic-clonic seizures tonic-clonic seizures -HP:0004890 skos:exactMatch MP:0004012 semapv:LexicalMatching Elevated pulmonary artery pressure increased pulmonary artery pressure -HP:0001561 skos:exactMatch MP:0004020 semapv:LexicalMatching Polyhydramnios polyhydramnios -HP:0040012 skos:exactMatch MP:0004028 semapv:LexicalMatching Chromosome breakage chromosome breakage -HP:0002647 skos:exactMatch MP:0004044 semapv:LexicalMatching Aortic dissection aortic dissection -HP:0031196 skos:exactMatch MP:0004057 semapv:LexicalMatching Thin myocardium compact layer thin myocardium compact layer -HP:0030718 skos:exactMatch MP:0004062 semapv:LexicalMatching Right atrial enlargement dilated heart right atrium -HP:0031595 skos:exactMatch MP:0004070 semapv:LexicalMatching Abnormal P wave abnormal P wave -HP:0002339 skos:exactMatch MP:0004078 semapv:LexicalMatching Abnormal caudate nucleus morphology abnormal caudate nucleus morphology -HP:0031982 skos:exactMatch MP:0004079 semapv:LexicalMatching Abnormal putamen morphology abnormal putamen morphology -HP:0002453 skos:exactMatch MP:0004081 semapv:LexicalMatching Abnormal globus pallidus morphology abnormal globus pallidus morphology -HP:0004303 skos:exactMatch MP:0004087 semapv:LexicalMatching Abnormal muscle fiber morphology abnormal muscle fiber morphology -HP:0006704 skos:exactMatch MP:0004111 semapv:LexicalMatching Abnormal coronary artery morphology abnormal coronary artery morphology -HP:0002900 skos:exactMatch MP:0004119 semapv:LexicalMatching Hypokalemia hypokalemia -HP:0030853 skos:exactMatch MP:0004133 semapv:LexicalMatching Heterotaxy heterotaxia -HP:0001257 skos:exactMatch MP:0004143 semapv:LexicalMatching Spasticity muscle hypertonia -HP:0008682 skos:exactMatch MP:0004154 semapv:LexicalMatching Acute tubular necrosis renal tubular necrosis -HP:0011611 skos:exactMatch MP:0004157 semapv:LexicalMatching Interrupted aortic arch interrupted aortic arch -HP:0012020 skos:exactMatch MP:0004158 semapv:LexicalMatching Right aortic arch right aortic arch -HP:0011590 skos:exactMatch MP:0004159 semapv:LexicalMatching Double aortic arch double aortic arch -HP:0011588 skos:exactMatch MP:0004161 semapv:LexicalMatching Cervical aortic arch cervical aortic arch -HP:0005344 skos:exactMatch MP:0004181 semapv:LexicalMatching Abnormal carotid artery morphology abnormal carotid artery morphology -HP:0010944 skos:exactMatch MP:0004194 semapv:LexicalMatching Abnormal renal pelvis morphology abnormal kidney pelvis morphology -HP:0100792 skos:exactMatch MP:0004241 semapv:LexicalMatching Acantholysis acantholysis -HP:0011970 skos:exactMatch MP:0004254 semapv:LexicalMatching Cerebral amyloid angiopathy cerebral amyloid angiopathy -HP:0000278 skos:exactMatch MP:0004282 semapv:LexicalMatching Retrognathia retrognathia -HP:0031000 skos:exactMatch MP:0004329 semapv:LexicalMatching Vestibular saccular degeneration vestibular saccular degeneration -HP:0000894 skos:exactMatch MP:0004337 semapv:LexicalMatching Short clavicles clavicle hypoplasia -HP:0010317 skos:exactMatch MP:0004341 semapv:LexicalMatching Scapular aplasia absent scapula -HP:0000882 skos:exactMatch MP:0004343 semapv:LexicalMatching Hypoplastic scapulae small scapula -HP:0002984 skos:exactMatch MP:0004355 semapv:LexicalMatching Hypoplasia of the radius short radius -HP:0003022 skos:exactMatch MP:0004359 semapv:LexicalMatching Hypoplasia of the ulna short ulna -HP:0100616 skos:exactMatch MP:0004478 semapv:LexicalMatching Testicular teratoma increased testicular teratoma incidence -HP:0100614 skos:exactMatch MP:0004510 semapv:LexicalMatching Myositis myositis -HP:0000458 skos:exactMatch MP:0004512 semapv:LexicalMatching Anosmia anosmia -HP:0010667 skos:exactMatch MP:0004539 semapv:LexicalMatching Aplasia of the maxilla absent maxilla -HP:0000327 skos:exactMatch MP:0004540 semapv:LexicalMatching Hypoplasia of the maxilla small maxilla -HP:0040116 skos:exactMatch MP:0004541 semapv:LexicalMatching Aplasia of the Eustachian tube absent auditory tube -HP:0000347 skos:exactMatch MP:0004592 semapv:LexicalMatching Micrognathia small mandible -HP:0002948 skos:exactMatch MP:0004609 semapv:LexicalMatching Vertebral fusion vertebral fusion -HP:0008479 skos:exactMatch MP:0004610 semapv:LexicalMatching Hypoplastic vertebral bodies small vertebrae -HP:0002948 skos:exactMatch MP:0004612 semapv:LexicalMatching Vertebral fusion fusion of vertebral bodies -HP:0002953 skos:exactMatch MP:0004626 semapv:LexicalMatching Vertebral compression fractures vertebral compression -HP:0030304 skos:exactMatch MP:0004643 semapv:LexicalMatching Abnormal number of vertebrae abnormal vertebrae number -HP:0100891 skos:exactMatch MP:0004678 semapv:LexicalMatching Bifid xiphoid process split xiphoid process -HP:0009900 skos:exactMatch MP:0004699 semapv:LexicalMatching Unilateral deafness unilateral deafness -HP:0500166 skos:exactMatch MP:0004730 semapv:LexicalMatching Abnormal circulating gastrin level abnormal circulating gastrin level -HP:0000405 skos:exactMatch MP:0004739 semapv:LexicalMatching Conductive hearing impairment conductive hearing loss -HP:0000407 skos:exactMatch MP:0004740 semapv:LexicalMatching Sensorineural hearing impairment sensorineural hearing loss -HP:0000410 skos:exactMatch MP:0004741 semapv:LexicalMatching Mixed hearing impairment mixed hearing loss -HP:0006560 skos:exactMatch MP:0004839 semapv:LexicalMatching Biliary hyperplasia bile duct hyperplasia -HP:0007670 skos:exactMatch MP:0004844 semapv:LexicalMatching Abnormal vestibulo-ocular reflex abnormal vestibuloocular reflex -HP:0012114 skos:exactMatch MP:0004868 semapv:LexicalMatching Endometrial carcinoma increased endometrial carcinoma incidence -HP:0010650 skos:exactMatch MP:0004870 semapv:LexicalMatching Hypoplasia of the premaxilla small premaxilla -HP:0005273 skos:exactMatch MP:0004872 semapv:LexicalMatching Absent nasal septal cartilage absent nasal septum -HP:0030684 skos:exactMatch MP:0004891 semapv:LexicalMatching Abnormal adiponectin level abnormal adiponectin level -HP:0030686 skos:exactMatch MP:0004892 semapv:LexicalMatching Increased adiponectin level increased adiponectin level -HP:0030685 skos:exactMatch MP:0004893 semapv:LexicalMatching Decreased adiponectin level decreased adiponectin level -HP:0000362 skos:exactMatch MP:0004897 semapv:LexicalMatching Otosclerosis otosclerosis -HP:0011123 skos:exactMatch MP:0004947 semapv:LexicalMatching Inflammatory abnormality of the skin skin inflammation -HP:0002797 skos:exactMatch MP:0004992 semapv:LexicalMatching Osteolysis increased bone resorption -HP:0001880 skos:exactMatch MP:0005011 semapv:LexicalMatching Eosinophilia increased eosinophil cell number -HP:0031891 skos:exactMatch MP:0005012 semapv:LexicalMatching Decreased eosinophil count decreased eosinophil cell number -HP:0100827 skos:exactMatch MP:0005013 semapv:LexicalMatching Lymphocytosis increased lymphocyte cell number -HP:0001888 skos:exactMatch MP:0005016 semapv:LexicalMatching Lymphopenia decreased lymphocyte cell number -HP:0100806 skos:exactMatch MP:0005044 semapv:LexicalMatching Sepsis sepsis -HP:0001977 skos:exactMatch MP:0005048 semapv:LexicalMatching Abnormal thrombosis abnormal thrombosis -HP:0001879 skos:exactMatch MP:0005061 semapv:LexicalMatching Abnormal eosinophil morphology abnormal eosinophil morphology -HP:0012437 skos:exactMatch MP:0005084 semapv:LexicalMatching Abnormal gallbladder morphology abnormal gallbladder morphology -HP:0031379 skos:exactMatch MP:0005094 semapv:LexicalMatching Abnormal T cell proliferation abnormal T cell proliferation -HP:0000610 skos:exactMatch MP:0005098 semapv:LexicalMatching Abnormal choroid morphology abnormal optic choroid morphology -HP:0008034 skos:exactMatch MP:0005102 semapv:LexicalMatching Abnormal iris pigmentation abnormal iris pigmentation -HP:0000870 skos:exactMatch MP:0005124 semapv:LexicalMatching Increased circulating prolactin concentration increased circulating prolactin level -HP:0031098 skos:exactMatch MP:0005134 semapv:LexicalMatching Decreased thyroid-stimulating hormone level decreased thyroid-stimulating hormone level -HP:0002925 skos:exactMatch MP:0005135 semapv:LexicalMatching Increased thyroid-stimulating hormone level increased thyroid-stimulating hormone level -HP:0031380 skos:exactMatch MP:0005153 semapv:LexicalMatching Abnormal B cell proliferation abnormal B cell proliferation -HP:0002067 skos:exactMatch MP:0005156 semapv:LexicalMatching Bradykinesia bradykinesia -HP:0001360 skos:exactMatch MP:0005157 semapv:LexicalMatching Holoprosencephaly holoprosencephaly -HP:0000027 skos:exactMatch MP:0005159 semapv:LexicalMatching Azoospermia azoospermia -HP:0000790 skos:exactMatch MP:0005161 semapv:LexicalMatching Hematuria hematuria -HP:0031189 skos:exactMatch MP:0005162 semapv:LexicalMatching Wrist drop carpoptosis -HP:0009914 skos:exactMatch MP:0005163 semapv:LexicalMatching Cyclopia cyclopia -HP:0000204 skos:exactMatch MP:0005170 semapv:LexicalMatching Cleft upper lip cleft upper lip -HP:0031212 skos:exactMatch MP:0005184 semapv:LexicalMatching Abnormal circulating progesterone level abnormal circulating progesterone level -HP:0000054 skos:exactMatch MP:0005188 semapv:LexicalMatching Micropenis small penis -HP:0030260 skos:exactMatch MP:0005188 semapv:LexicalMatching Microphallus small penis -HP:0002754 skos:exactMatch MP:0005190 semapv:LexicalMatching Osteomyelitis osteomyelitis -HP:0000553 skos:exactMatch MP:0005197 semapv:LexicalMatching Abnormal uvea morphology abnormal uvea morphology -HP:0001254 skos:exactMatch MP:0005202 semapv:LexicalMatching Lethargy lethargy -HP:0012630 skos:exactMatch MP:0005203 semapv:LexicalMatching Abnormal trabecular meshwork morphology abnormal trabecular meshwork morphology -HP:0100257 skos:exactMatch MP:0005230 semapv:LexicalMatching Ectrodactyly ectrodactyly -HP:0001126 skos:exactMatch MP:0005242 semapv:LexicalMatching Cryptophthalmos cryptophthalmos -HP:0012151 skos:exactMatch MP:0005243 semapv:LexicalMatching Hemothorax hemothorax -HP:0011851 skos:exactMatch MP:0005244 semapv:LexicalMatching Hemopericardium hemopericardium -HP:0000498 skos:exactMatch MP:0005251 semapv:LexicalMatching Blepharitis blepharitis -HP:0000486 skos:exactMatch MP:0005254 semapv:LexicalMatching Strabismus strabismus -HP:0000577 skos:exactMatch MP:0005255 semapv:LexicalMatching Exotropia exotropia -HP:0000565 skos:exactMatch MP:0005256 semapv:LexicalMatching Esotropia esotropia -HP:0012632 skos:exactMatch MP:0005257 semapv:LexicalMatching Abnormal intraocular pressure abnormal intraocular pressure -HP:0007906 skos:exactMatch MP:0005258 semapv:LexicalMatching Ocular hypertension ocular hypertension -HP:0000589 skos:exactMatch MP:0005262 semapv:LexicalMatching Coloboma coloboma -HP:0000096 skos:exactMatch MP:0005264 semapv:LexicalMatching Glomerulosclerosis glomerulosclerosis -HP:0009911 skos:exactMatch MP:0005272 semapv:LexicalMatching Abnormal temporal bone morphology abnormal temporal bone morphology -HP:0002508 skos:exactMatch MP:0005277 semapv:LexicalMatching Brainstem dysplasia abnormal brainstem morphology -HP:0003107 skos:exactMatch MP:0005278 semapv:LexicalMatching Abnormal circulating cholesterol concentration abnormal cholesterol homeostasis -HP:0030050 skos:exactMatch MP:0005279 semapv:LexicalMatching Narcolepsy narcolepsy -HP:0000581 skos:exactMatch MP:0005287 semapv:LexicalMatching Blepharophimosis narrow eye opening -HP:0001952 skos:exactMatch MP:0005293 semapv:LexicalMatching Glucose intolerance impaired glucose tolerance -HP:0040270 skos:exactMatch MP:0005293 semapv:LexicalMatching Impaired glucose tolerance impaired glucose tolerance -HP:0031095 skos:exactMatch MP:0005296 semapv:LexicalMatching Abnormal humerus morphology abnormal humerus morphology -HP:0003298 skos:exactMatch MP:0005297 semapv:LexicalMatching Spina bifida occulta spina bifida occulta -HP:0000011 skos:exactMatch MP:0005302 semapv:LexicalMatching Neurogenic bladder neurogenic bladder -HP:0001698 skos:exactMatch MP:0005312 semapv:LexicalMatching Pericardial effusion pericardial effusion -HP:0010626 skos:exactMatch MP:0005315 semapv:LexicalMatching Anterior pituitary agenesis absent pituitary gland -HP:0001332 skos:exactMatch MP:0005323 semapv:LexicalMatching Dystonia dystonia -HP:0001541 skos:exactMatch MP:0005324 semapv:LexicalMatching Ascites ascites -HP:0012100 skos:exactMatch MP:0005328 semapv:LexicalMatching Abnormal circulating creatinine level abnormal circulating creatinine level -HP:0001662 skos:exactMatch MP:0005333 semapv:LexicalMatching Bradycardia decreased heart rate -HP:0012112 skos:exactMatch MP:0005345 semapv:LexicalMatching Abnormal circulating corticosterone level abnormal circulating corticosterone level -HP:0000252 skos:exactMatch MP:0005352 semapv:LexicalMatching Microcephaly small cranium -HP:0003045 skos:exactMatch MP:0005353 semapv:LexicalMatching Abnormal patella morphology abnormal patella morphology -HP:0040129 skos:exactMatch MP:0005403 semapv:LexicalMatching Abnormal nerve conduction velocity abnormal nerve conduction -HP:0040078 skos:exactMatch MP:0005405 semapv:LexicalMatching Axonal degeneration axon degeneration -HP:0031005 skos:exactMatch MP:0005407 semapv:LexicalMatching Hyperalgesia hyperalgesia -HP:0001010 skos:exactMatch MP:0005408 semapv:LexicalMatching Hypopigmentation of the skin hypopigmentation -HP:0012334 skos:exactMatch MP:0005414 semapv:LexicalMatching Extrahepatic cholestasis extrahepatic cholestasis -HP:0001406 skos:exactMatch MP:0005415 semapv:LexicalMatching Intrahepatic cholestasis intrahepatic cholestasis -HP:0010876 skos:exactMatch MP:0005416 semapv:LexicalMatching Abnormal circulating protein level abnormal circulating protein level -HP:0000973 skos:exactMatch MP:0005421 semapv:LexicalMatching Cutis laxa loose skin -HP:0011001 skos:exactMatch MP:0005422 semapv:LexicalMatching Increased bone mineral density osteosclerosis -HP:0002789 skos:exactMatch MP:0005426 semapv:LexicalMatching Tachypnea tachypnea -HP:0011854 skos:exactMatch MP:0005435 semapv:LexicalMatching Hemoperitoneum hemoperitoneum -HP:0031508 skos:exactMatch MP:0005468 semapv:LexicalMatching Abnormal thyroid hormone level abnormal thyroid hormone level -HP:0031505 skos:exactMatch MP:0005475 semapv:LexicalMatching Abnormal circulating thyroxine level abnormal circulating thyroxine level -HP:0031506 skos:exactMatch MP:0005477 semapv:LexicalMatching Increased circulating thyroxine level increased circulating thyroxine level -HP:0031507 skos:exactMatch MP:0005478 semapv:LexicalMatching Decreased circulating thyroxine level decreased circulating thyroxine level -HP:0005506 skos:exactMatch MP:0005481 semapv:LexicalMatching Chronic myelogenous leukemia increased chronic myelocytic leukemia incidence -HP:0001894 skos:exactMatch MP:0005505 semapv:LexicalMatching Thrombocytosis thrombocytosis -HP:0000554 skos:exactMatch MP:0005515 semapv:LexicalMatching Uveitis uveitis -HP:0012214 skos:exactMatch MP:0005527 semapv:LexicalMatching Increased glomerular filtration rate increased renal glomerular filtration rate -HP:0012213 skos:exactMatch MP:0005528 semapv:LexicalMatching Decreased glomerular filtration rate decreased renal glomerular filtration rate -HP:0002045 skos:exactMatch MP:0005534 semapv:LexicalMatching Hypothermia decreased body temperature -HP:0011496 skos:exactMatch MP:0005542 semapv:LexicalMatching Corneal neovascularization corneal vascularization -HP:0000531 skos:exactMatch MP:0005544 semapv:LexicalMatching Corneal crystals corneal deposits -HP:0011506 skos:exactMatch MP:0005546 semapv:LexicalMatching Choroidal neovascularization choroidal neovascularization -HP:0012213 skos:exactMatch MP:0005558 semapv:LexicalMatching Decreased glomerular filtration rate decreased creatinine clearance -HP:0025548 skos:exactMatch MP:0005561 semapv:LexicalMatching Increased mean corpuscular hemoglobin concentration increased mean corpuscular hemoglobin -HP:0032231 skos:exactMatch MP:0005562 semapv:LexicalMatching Hypochromia decreased mean corpuscular hemoglobin -HP:0031969 skos:exactMatch MP:0005566 semapv:LexicalMatching Reduced blood urea nitrogen decreased blood urea nitrogen level -HP:0002152 skos:exactMatch MP:0005568 semapv:LexicalMatching Hyperproteinemia increased circulating total protein level -HP:0012864 skos:exactMatch MP:0005578 semapv:LexicalMatching Abnormal sperm morphology teratozoospermia -HP:0012379 skos:exactMatch MP:0005584 semapv:LexicalMatching Abnormal enzyme/coenzyme activity abnormal enzyme/coenzyme activity -HP:0003010 skos:exactMatch MP:0005606 semapv:LexicalMatching Prolonged bleeding time increased bleeding time -HP:0025546 skos:exactMatch MP:0005640 semapv:LexicalMatching Abnormal mean corpuscular hemoglobin concentration abnormal mean corpuscular hemoglobin concentration -HP:0025548 skos:exactMatch MP:0005641 semapv:LexicalMatching Increased mean corpuscular hemoglobin concentration increased mean corpuscular hemoglobin concentration -HP:0025547 skos:exactMatch MP:0005642 semapv:LexicalMatching Decreased mean corpuscular hemoglobin concentration decreased mean corpuscular hemoglobin concentration -HP:0012245 skos:exactMatch MP:0005652 semapv:LexicalMatching Sex reversal sex reversal -HP:0002269 skos:exactMatch MP:0006009 semapv:LexicalMatching Abnormality of neuronal migration abnormal neuronal migration -HP:0002206 skos:exactMatch MP:0006050 semapv:LexicalMatching Pulmonary fibrosis pulmonary fibrosis -HP:0011536 skos:exactMatch MP:0006061 semapv:LexicalMatching Right atrial isomerism right atrial isomerism -HP:0000023 skos:exactMatch MP:0006077 semapv:LexicalMatching Inguinal hernia inguinal hernia -HP:0004404 skos:exactMatch MP:0006078 semapv:LexicalMatching Abnormal nipple morphology abnormal nipple morphology -HP:0001700 skos:exactMatch MP:0006085 semapv:LexicalMatching Myocardial necrosis myocardium necrosis -HP:0045082 skos:exactMatch MP:0006086 semapv:LexicalMatching Decreased body mass index decreased body mass index -HP:0031418 skos:exactMatch MP:0006087 semapv:LexicalMatching Increased body mass index increased body mass index -HP:0030999 skos:exactMatch MP:0006089 semapv:LexicalMatching Abnormal vestibular saccule morphology abnormal vestibular saccule morphology -HP:0004947 skos:exactMatch MP:0006093 semapv:LexicalMatching Arteriovenous fistula arteriovenous malformation -HP:0030759 skos:exactMatch MP:0006094 semapv:LexicalMatching Adipocyte hypertrophy increased fat cell size -HP:0001663 skos:exactMatch MP:0006110 semapv:LexicalMatching Ventricular fibrillation ventricular fibrillation -HP:0001681 skos:exactMatch MP:0006112 semapv:LexicalMatching Angina pectoris angina -HP:0030148 skos:exactMatch MP:0006114 semapv:LexicalMatching Heart murmur cardiac murmur -HP:0025578 skos:exactMatch MP:0006118 semapv:LexicalMatching Aortic valve prolapse aortic valve prolapse -HP:0011560 skos:exactMatch MP:0006119 semapv:LexicalMatching Mitral atresia mitral valve atresia -HP:0011662 skos:exactMatch MP:0006123 semapv:LexicalMatching Tricuspid atresia tricuspid valve atresia -HP:0010446 skos:exactMatch MP:0006124 semapv:LexicalMatching Tricuspid stenosis tricuspid valve stenosis -HP:0025324 skos:exactMatch MP:0006134 semapv:LexicalMatching Arterial occlusion artery occlusion -HP:0002619 skos:exactMatch MP:0006136 semapv:LexicalMatching Varicose veins varicose veins -HP:0001635 skos:exactMatch MP:0006138 semapv:LexicalMatching Congestive heart failure congestive heart failure -HP:0000622 skos:exactMatch MP:0006149 semapv:LexicalMatching Blurred vision decreased visual acuity -HP:0007663 skos:exactMatch MP:0006149 semapv:LexicalMatching Reduced visual acuity decreased visual acuity -HP:0000651 skos:exactMatch MP:0006150 semapv:LexicalMatching Diplopia double vision -HP:0000540 skos:exactMatch MP:0006153 semapv:LexicalMatching Hypermetropia hypermetropia -HP:0001107 skos:exactMatch MP:0006159 semapv:LexicalMatching Ocular albinism ocular albinism -HP:0030939 skos:exactMatch MP:0006162 semapv:LexicalMatching Palpebral thickening thick eyelids -HP:0000621 skos:exactMatch MP:0006165 semapv:LexicalMatching Entropion entropion -HP:0500043 skos:exactMatch MP:0006166 semapv:LexicalMatching Eyelid retraction eyelid retraction -HP:0000537 skos:exactMatch MP:0006168 semapv:LexicalMatching Epicanthus inversus epicanthus inversus -HP:0001096 skos:exactMatch MP:0006194 semapv:LexicalMatching Keratoconjunctivitis keratoconjunctivitis -HP:0000490 skos:exactMatch MP:0006198 semapv:LexicalMatching Deeply set eye enophthalmos -HP:0025586 skos:exactMatch MP:0006199 semapv:LexicalMatching Hypertropia hypertropia -HP:0032479 skos:exactMatch MP:0006204 semapv:LexicalMatching Preimplantation lethality embryonic lethality before implantation -HP:0007807 skos:exactMatch MP:0006220 semapv:LexicalMatching Optic nerve compression optic nerve compression -HP:0000538 skos:exactMatch MP:0006223 semapv:LexicalMatching Pseudopapilledema optic nerve swelling -HP:0001085 skos:exactMatch MP:0006223 semapv:LexicalMatching Papilledema optic nerve swelling -HP:0000657 skos:exactMatch MP:0006224 semapv:LexicalMatching Oculomotor apraxia oculomotor apraxia -HP:0011500 skos:exactMatch MP:0006235 semapv:LexicalMatching Polycoria polycoria -HP:0009916 skos:exactMatch MP:0006240 semapv:LexicalMatching Anisocoria anisocoria -HP:0009918 skos:exactMatch MP:0006241 semapv:LexicalMatching Ectopia pupillae abnormal placement of pupils -HP:0000555 skos:exactMatch MP:0006242 semapv:LexicalMatching Leukocoria white pupil -HP:0000643 skos:exactMatch MP:0006244 semapv:LexicalMatching Blepharospasm eyelid muscle spasm -HP:0031786 skos:exactMatch MP:0006244 semapv:LexicalMatching Cogan lid twitch eyelid muscle spasm -HP:0012019 skos:exactMatch MP:0006245 semapv:LexicalMatching Lens luxation dislocated lens -HP:0000667 skos:exactMatch MP:0006249 semapv:LexicalMatching Phthisis bulbi phthisis bulbi -HP:0030084 skos:exactMatch MP:0006253 semapv:LexicalMatching Clinodactyly clinodactyly -HP:0001734 skos:exactMatch MP:0006261 semapv:LexicalMatching Annular pancreas annular pancreas -HP:0500104 skos:exactMatch MP:0006263 semapv:LexicalMatching Decreased diastolic blood pressure decreased systemic arterial diastolic blood pressure -HP:0500105 skos:exactMatch MP:0006264 semapv:LexicalMatching Decreased systolic blood pressure decreased systemic arterial systolic blood pressure -HP:0004942 skos:exactMatch MP:0006278 semapv:LexicalMatching Aortic aneurysm aortic aneurysm -HP:0012806 skos:exactMatch MP:0006290 semapv:LexicalMatching Proboscis proboscis -HP:0007268 skos:exactMatch MP:0006291 semapv:LexicalMatching Aprosencephaly aprosencephaly -HP:0001166 skos:exactMatch MP:0006296 semapv:LexicalMatching Arachnodactyly arachnodactyly -HP:0020119 skos:exactMatch MP:0006303 semapv:LexicalMatching Abnormal retinal nerve fiber layer morphology abnormal retinal nerve fiber layer morphology -HP:0020129 skos:exactMatch MP:0006315 semapv:LexicalMatching Abnormal urine protein level abnormal urine protein level -HP:0000405 skos:exactMatch MP:0006326 semapv:LexicalMatching Conductive hearing impairment conductive hearing impairment -HP:0000410 skos:exactMatch MP:0006327 semapv:LexicalMatching Mixed hearing impairment mixed hearing impairment -HP:0000407 skos:exactMatch MP:0006329 semapv:LexicalMatching Sensorineural hearing impairment sensorineural hearing impairment -HP:0030869 skos:exactMatch MP:0006415 semapv:LexicalMatching Anorchism absent testes -HP:0100615 skos:exactMatch MP:0008000 semapv:LexicalMatching Ovarian neoplasm increased ovary tumor incidence -HP:0032448 skos:exactMatch MP:0008003 semapv:LexicalMatching Achlorhydria achlorhydria -HP:0200008 skos:exactMatch MP:0008011 semapv:LexicalMatching Intestinal polyposis intestine polyps -HP:0004783 skos:exactMatch MP:0008012 semapv:LexicalMatching Duodenal polyposis duodenum polyps -HP:0031871 skos:exactMatch MP:0008117 semapv:LexicalMatching Abnormal Langerhans cell morphology abnormal Langerhans cell morphology -HP:0031266 skos:exactMatch MP:0008140 semapv:LexicalMatching Podocyte foot process effacement podocyte foot process effacement -HP:0000662 skos:exactMatch MP:0008144 semapv:LexicalMatching Nyctalopia nyctalopia -HP:0012047 skos:exactMatch MP:0008145 semapv:LexicalMatching Hemeralopia hemeralopia -HP:0003100 skos:exactMatch MP:0008150 semapv:LexicalMatching Slender long bone decreased diameter of long bones -HP:0031107 skos:exactMatch MP:0008153 semapv:LexicalMatching Decreased fibular diameter decreased diameter of fibula -HP:0012107 skos:exactMatch MP:0008159 semapv:LexicalMatching Increased fibular diameter increased diameter of fibula -HP:0001881 skos:exactMatch MP:0008246 semapv:LexicalMatching Abnormal leukocyte morphology abnormal leukocyte morphology -HP:0011849 skos:exactMatch MP:0008271 semapv:LexicalMatching Abnormal bone ossification abnormal bone ossification -HP:0012790 skos:exactMatch MP:0008273 semapv:LexicalMatching Abnormal intramembranous ossification abnormal intramembranous bone ossification -HP:0100961 skos:exactMatch MP:0008282 semapv:LexicalMatching Enlarged hippocampus enlarged hippocampus -HP:0025517 skos:exactMatch MP:0008283 semapv:LexicalMatching Hypoplastic hippocampus small hippocampus -HP:0001931 skos:exactMatch MP:0008387 semapv:LexicalMatching Hypochromic anemia hypochromic anemia -HP:0004840 skos:exactMatch MP:0008388 semapv:LexicalMatching Hypochromic microcytic anemia hypochromic microcytic anemia -HP:0030334 skos:exactMatch MP:0008397 semapv:LexicalMatching "Abnormal CD4-positive CD25-positive alpha-beta regulatory T cell morphology" "abnormal CD4-positive CD25-positive alpha-beta regulatory T cell morphology" -HP:0025082 skos:exactMatch MP:0008418 semapv:LexicalMatching Abnormal cutaneous elastic fiber morphology abnormal cutaneous elastic fiber morphology -HP:0031512 skos:exactMatch MP:0008438 semapv:LexicalMatching Abnormal cutaneous collagen fibril morphology abnormal cutaneous collagen fibril morphology -HP:0011537 skos:exactMatch MP:0008461 semapv:LexicalMatching Left atrial isomerism left atrial isomerism -HP:0006956 skos:exactMatch MP:0008535 semapv:LexicalMatching Dilation of lateral ventricles enlarged lateral ventricles -HP:0005110 skos:exactMatch MP:0008543 semapv:LexicalMatching Atrial fibrillation atrial fibrillation -HP:0004409 skos:exactMatch MP:0008544 semapv:LexicalMatching Hyposmia impaired olfaction -HP:0010633 skos:exactMatch MP:0008544 semapv:LexicalMatching Partial anosmia impaired olfaction -HP:0032558 skos:exactMatch MP:0008545 semapv:LexicalMatching Absent sperm flagella absent sperm flagellum -HP:0040238 skos:exactMatch MP:0008720 semapv:LexicalMatching Impaired neutrophil chemotaxis impaired neutrophil chemotaxis -HP:0002983 skos:exactMatch MP:0008736 semapv:LexicalMatching Micromelia micromelia -HP:0040134 skos:exactMatch MP:0008738 semapv:LexicalMatching Abnormal hepatic iron concentration abnormal liver iron level -HP:0030770 skos:exactMatch MP:0008784 semapv:LexicalMatching Craniorachischisis craniorachischisis -HP:0100731 skos:exactMatch MP:0008798 semapv:LexicalMatching Transverse facial cleft lateral facial cleft -HP:0410282 skos:exactMatch MP:0008804 semapv:LexicalMatching Abnormal circulating amylase level abnormal circulating amylase level -HP:0410289 skos:exactMatch MP:0008805 semapv:LexicalMatching Hypoamylasemia decreased circulating amylase level -HP:0410288 skos:exactMatch MP:0008806 semapv:LexicalMatching Hyperamylasemia increased circulating amylase level -HP:0000762 skos:exactMatch MP:0008814 semapv:LexicalMatching Decreased nerve conduction velocity decreased nerve conduction velocity -HP:0030855 skos:exactMatch MP:0008815 semapv:LexicalMatching Anterior staphyloma anterior staphyloma -HP:0000967 skos:exactMatch MP:0008816 semapv:LexicalMatching Petechiae petechiae -HP:0002937 skos:exactMatch MP:0008832 semapv:LexicalMatching Hemivertebrae hemivertebra -HP:0030666 skos:exactMatch MP:0008852 semapv:LexicalMatching Retinal neovascularization retinal neovascularization -HP:0004484 skos:exactMatch MP:0008863 semapv:LexicalMatching Craniofacial asymmetry craniofacial asymmetry -HP:0009702 skos:exactMatch MP:0008915 semapv:LexicalMatching Carpal synostosis fused carpal bones -HP:0005537 skos:exactMatch MP:0008935 semapv:LexicalMatching Decreased mean platelet volume decreased mean platelet volume -HP:0004857 skos:exactMatch MP:0008945 semapv:LexicalMatching Hyperchromic macrocytic anemia hyperchromic macrocytic anemia -HP:0004756 skos:exactMatch MP:0008950 semapv:LexicalMatching Ventricular tachycardia ventricular tachycardia -HP:0030146 skos:exactMatch MP:0008986 semapv:LexicalMatching Abnormal liver parenchyma morphology abnormal liver parenchyma morphology -HP:0002023 skos:exactMatch MP:0008999 semapv:LexicalMatching Anal atresia absent anus -HP:0012386 skos:exactMatch MP:0009001 semapv:LexicalMatching Absent hallux absent hallux -HP:0012703 skos:exactMatch MP:0009027 semapv:LexicalMatching Abnormal subarachnoid space morphology abnormal subarachnoid space morphology -HP:0025246 skos:exactMatch MP:0009042 semapv:LexicalMatching Trichilemmal cyst pilar cyst -HP:0002380 skos:exactMatch MP:0009046 semapv:LexicalMatching Fasciculations muscle twitch -HP:0012673 skos:exactMatch MP:0009072 semapv:LexicalMatching Aplasia of the upper vagina absent cranial vagina -HP:0012094 skos:exactMatch MP:0009106 semapv:LexicalMatching Abnormal pancreas size abnormal pancreas size -HP:0002894 skos:exactMatch MP:0009153 semapv:LexicalMatching Neoplasm of the pancreas increased pancreas tumor incidence -HP:0010461 skos:exactMatch MP:0009198 semapv:LexicalMatching Abnormality of the male genitalia abnormal male genitalia morphology -HP:0010784 skos:exactMatch MP:0009222 semapv:LexicalMatching Uterine neoplasm increased uterus tumor incidence -HP:0030160 skos:exactMatch MP:0009228 semapv:LexicalMatching Cervicitis uterine cervix inflammation -HP:0003270 skos:exactMatch MP:0009247 semapv:LexicalMatching Abdominal distention meteorism -HP:0000557 skos:exactMatch MP:0009274 semapv:LexicalMatching Buphthalmos buphthalmos -HP:0031364 skos:exactMatch MP:0009276 semapv:LexicalMatching Ecchymosis ecchymosis -HP:0006771 skos:exactMatch MP:0009311 semapv:LexicalMatching Duodenal adenocarcinoma increased duodenum adenocarcinoma incidence -HP:0030439 skos:exactMatch MP:0009316 semapv:LexicalMatching Anal canal adenocarcinoma increased anal adenocarcinoma incidence -HP:0002213 skos:exactMatch MP:0009351 semapv:LexicalMatching Fine hair thin hair shaft -HP:0025636 skos:exactMatch MP:0009360 semapv:LexicalMatching Endometritis endometrium inflammation -HP:0020157 skos:exactMatch MP:0009375 semapv:LexicalMatching Thin zona pellucida thin zona pellucida -HP:0003687 skos:exactMatch MP:0009404 semapv:LexicalMatching Centrally nucleated skeletal muscle fibers centrally nucleated skeletal muscle fibers -HP:0003202 skos:exactMatch MP:0009417 semapv:LexicalMatching Skeletal muscle atrophy skeletal muscle atrophy -HP:0030951 skos:exactMatch MP:0009419 semapv:LexicalMatching Skeletal muscle fibrosis skeletal muscle fibrosis -HP:0002385 skos:exactMatch MP:0009434 semapv:LexicalMatching Paraparesis paraparesis -HP:0025274 skos:exactMatch MP:0009442 semapv:LexicalMatching Ovarian dermoid cyst increased ovarian teratoma incidence -HP:0003712 skos:exactMatch MP:0009461 semapv:LexicalMatching Skeletal muscle hypertrophy skeletal muscle hypertrophy -HP:0031111 skos:exactMatch MP:0009469 semapv:LexicalMatching Cutaneous hamartoma increased skin hamartoma incidence -HP:0032564 skos:exactMatch MP:0009482 semapv:LexicalMatching Ileitis ileum inflammation -HP:0030075 skos:exactMatch MP:0009508 semapv:LexicalMatching Ductal carcinoma in situ increased mammary gland ductal carcinoma incidence -HP:0030187 skos:exactMatch MP:0009514 semapv:LexicalMatching Titubation titubation -HP:0004445 skos:exactMatch MP:0009547 semapv:LexicalMatching Elliptocytosis elliptocytosis -HP:0030402 skos:exactMatch MP:0009548 semapv:LexicalMatching Abnormal platelet aggregation abnormal platelet aggregation -HP:0003540 skos:exactMatch MP:0009549 semapv:LexicalMatching Impaired platelet aggregation decreased platelet aggregation -HP:0025114 skos:exactMatch MP:0009600 semapv:LexicalMatching Hypergranulosis hypergranulosis -HP:0012585 skos:exactMatch MP:0009641 semapv:LexicalMatching Renal atrophy kidney degeneration -HP:0002157 skos:exactMatch MP:0009644 semapv:LexicalMatching Azotemia uremia -HP:0020074 skos:exactMatch MP:0009645 semapv:LexicalMatching Crystalluria crystalluria -HP:0100577 skos:exactMatch MP:0009646 semapv:LexicalMatching Urinary bladder inflammation urinary bladder inflammation -HP:0031456 skos:exactMatch MP:0009668 semapv:LexicalMatching Ectopic pregnancy ectopic pregnancy -HP:0025080 skos:exactMatch MP:0009675 semapv:LexicalMatching Orthokeratotic hyperkeratosis orthokeratosis -HP:0040162 skos:exactMatch MP:0009675 semapv:LexicalMatching Orthokeratosis orthokeratosis -HP:0012238 skos:exactMatch MP:0009699 semapv:LexicalMatching Increased circulating chylomicron concentration hyperchylomicronemia -HP:0000413 skos:exactMatch MP:0009707 semapv:LexicalMatching Atresia of the external auditory canal absent external auditory canal -HP:0012154 skos:exactMatch MP:0009710 semapv:LexicalMatching Anhedonia anhedonia -HP:0100258 skos:exactMatch MP:0009743 semapv:LexicalMatching Preaxial polydactyly preaxial polydactyly -HP:0100259 skos:exactMatch MP:0009744 semapv:LexicalMatching Postaxial polydactyly postaxial polydactyly -HP:0001051 skos:exactMatch MP:0009792 semapv:LexicalMatching Seborrheic dermatitis seborrheic dermatitis -HP:0012804 skos:exactMatch MP:0009825 semapv:LexicalMatching Corneal ulceration cornea ulcer -HP:0032156 skos:exactMatch MP:0009827 semapv:LexicalMatching Skin detachment skin detachment -HP:0002578 skos:exactMatch MP:0009854 semapv:LexicalMatching Gastroparesis impaired gastric peristalsis -HP:0011800 skos:exactMatch MP:0009855 semapv:LexicalMatching Midface retrusion midface retrusion -HP:0009741 skos:exactMatch MP:0009860 semapv:LexicalMatching Nephrosclerosis nephrosclerosis -HP:0031784 skos:exactMatch MP:0009867 semapv:LexicalMatching Abnormal ascending aorta morphology abnormal ascending aorta morphology -HP:0031934 skos:exactMatch MP:0009869 semapv:LexicalMatching Abnormal descending aorta morphology abnormal descending aorta morphology -HP:0000160 skos:exactMatch MP:0009880 semapv:LexicalMatching Narrow mouth microstomia -HP:0000154 skos:exactMatch MP:0009881 semapv:LexicalMatching Wide mouth macrostomia -HP:0000171 skos:exactMatch MP:0009904 semapv:LexicalMatching Microglossia tongue hypoplasia -HP:0012730 skos:exactMatch MP:0009905 semapv:LexicalMatching Aglossia absent tongue -HP:0010297 skos:exactMatch MP:0009910 semapv:LexicalMatching Bifid tongue bifurcated tongue -HP:0002475 skos:exactMatch MP:0009929 semapv:LexicalMatching Myelomeningocele meningomyelocele -HP:0002213 skos:exactMatch MP:0009930 semapv:LexicalMatching Fine hair fuzzy hair -HP:0001045 skos:exactMatch MP:0010016 semapv:LexicalMatching Vitiligo variable depigmentation -HP:0012072 skos:exactMatch MP:0010028 semapv:LexicalMatching Aciduria aciduria -HP:0100588 skos:exactMatch MP:0010033 semapv:LexicalMatching Paraphimosis paraphimosis -HP:0012113 skos:exactMatch MP:0010063 semapv:LexicalMatching Abnormal circulating creatine concentration abnormal circulating creatine level -HP:0031965 skos:exactMatch MP:0010067 semapv:LexicalMatching Increased RBC distribution width increased red blood cell distribution width -HP:0004446 skos:exactMatch MP:0010074 semapv:LexicalMatching Stomatocytosis stomatocytosis -HP:0030431 skos:exactMatch MP:0010079 semapv:LexicalMatching Osteochondroma increased osteochondroma incidence -HP:0005107 skos:exactMatch MP:0010113 semapv:LexicalMatching Abnormal sacrum morphology abnormal sacrum morphology -HP:0011105 skos:exactMatch MP:0010127 semapv:LexicalMatching Hypervolemia hypervolemia -HP:0011106 skos:exactMatch MP:0010128 semapv:LexicalMatching Hypovolemia hypovolemia -HP:0012089 skos:exactMatch MP:0010138 semapv:LexicalMatching Arteritis arteritis -HP:0001537 skos:exactMatch MP:0010146 semapv:LexicalMatching Umbilical hernia umbilical hernia -HP:0001878 skos:exactMatch MP:0010163 semapv:LexicalMatching Hemolytic anemia hemolysis -HP:0032563 skos:exactMatch MP:0010176 semapv:LexicalMatching Dacryocytosis dacryocytosis -HP:0001927 skos:exactMatch MP:0010177 semapv:LexicalMatching Acanthocytosis acanthocytosis -HP:0045006 skos:exactMatch MP:0010194 semapv:LexicalMatching Aplasia of lymphatic vessels absent lymphatic vessels -HP:0031109 skos:exactMatch MP:0010249 semapv:LexicalMatching Agalactia lactation failure -HP:0000523 skos:exactMatch MP:0010251 semapv:LexicalMatching Subcapsular cataract subcapsular cataracts -HP:0025201 skos:exactMatch MP:0010331 semapv:LexicalMatching Abnormal apolipoprotein level abnormal apolipoprotein level -HP:0002202 skos:exactMatch MP:0010334 semapv:LexicalMatching Pleural effusion pleural effusion -HP:0005483 skos:exactMatch MP:0010371 semapv:LexicalMatching Abnormal epiglottis morphology abnormal epiglottis morphology -HP:0010445 skos:exactMatch MP:0010404 semapv:LexicalMatching Primum atrial septal defect ostium primum atrial septal defect -HP:0001684 skos:exactMatch MP:0010405 semapv:LexicalMatching Secundum atrial septal defect ostium secundum atrial septal defect -HP:0011565 skos:exactMatch MP:0010406 semapv:LexicalMatching Common atrium common atrium -HP:0011643 skos:exactMatch MP:0010407 semapv:LexicalMatching Coronary sinus atrial septal defect coronary sinus atrial septal defect -HP:0011567 skos:exactMatch MP:0010408 semapv:LexicalMatching Sinus venosus atrial septal defect sinus venosus atrial septal defect -HP:0010774 skos:exactMatch MP:0010409 semapv:LexicalMatching Cor triatriatum cor triatriatum -HP:0011566 skos:exactMatch MP:0010411 semapv:LexicalMatching Cor triatriatum dexter cor triatriatum dextrum -HP:0006695 skos:exactMatch MP:0010412 semapv:LexicalMatching Atrioventricular canal defect atrioventricular septal defect -HP:0001674 skos:exactMatch MP:0010413 semapv:LexicalMatching Complete atrioventricular canal defect complete atrioventricular septal defect -HP:0011577 skos:exactMatch MP:0010414 semapv:LexicalMatching Partial atrioventricular canal defect partial atrioventricular septal defect -HP:0011576 skos:exactMatch MP:0010415 semapv:LexicalMatching Intermediate atrioventricular canal defect intermediate atrioventricular septal defect -HP:0030958 skos:exactMatch MP:0010416 semapv:LexicalMatching Membranous ventricular septal aneurysm interventricular septum membranous part aneurysm -HP:0011681 skos:exactMatch MP:0010417 semapv:LexicalMatching Subarterial ventricular septal defect subarterial ventricular septal defect -HP:0011682 skos:exactMatch MP:0010418 semapv:LexicalMatching Perimembranous ventricular septal defect perimembraneous ventricular septal defect -HP:0011622 skos:exactMatch MP:0010419 semapv:LexicalMatching Inlet ventricular septal defect inlet ventricular septal defect -HP:0011623 skos:exactMatch MP:0010420 semapv:LexicalMatching Muscular ventricular septal defect muscular ventricular septal defect -HP:0011581 skos:exactMatch MP:0010427 semapv:LexicalMatching Double outlet left ventricle double outlet left ventricle -HP:0011719 skos:exactMatch MP:0010430 semapv:LexicalMatching Supracardiac total anomalous pulmonary venous connection "total anomalous pulmonary venous connection supracardiac" -HP:0011538 skos:exactMatch MP:0010431 semapv:LexicalMatching Atrial situs inversus atrial situs inversus -HP:0001750 skos:exactMatch MP:0010432 semapv:LexicalMatching Single ventricle common ventricle -HP:0011555 skos:exactMatch MP:0010433 semapv:LexicalMatching Double inlet left ventricle double inlet heart left ventricle -HP:0011556 skos:exactMatch MP:0010434 semapv:LexicalMatching Double inlet right ventricle double inlet heart right ventricle -HP:0005160 skos:exactMatch MP:0010441 semapv:LexicalMatching Total anomalous pulmonary venous return total anomalous pulmonary venous connection -HP:0010773 skos:exactMatch MP:0010442 semapv:LexicalMatching Partial anomalous pulmonary venous return partial anomalous pulmonary venous connection -HP:0011720 skos:exactMatch MP:0010443 semapv:LexicalMatching Cardiac total anomalous pulmonary venous connection "total anomalous pulmonary venous connection intracardiac" -HP:0011722 skos:exactMatch MP:0010445 semapv:LexicalMatching Mixed total anomalous pulmonary venous connection "total anomalous pulmonary venous connection mixed" -HP:0004383 skos:exactMatch MP:0010446 semapv:LexicalMatching Hypoplastic left heart heart left ventricle hypoplasia -HP:0011604 skos:exactMatch MP:0010455 semapv:LexicalMatching Aortopulmonary window aortopulmonary window -HP:0011660 skos:exactMatch MP:0010456 semapv:LexicalMatching Anomalous origin of one pulmonary artery from ascending aorta hemitruncus -HP:0004937 skos:exactMatch MP:0010462 semapv:LexicalMatching Pulmonary artery aneurysm pulmonary artery aneurysm -HP:0010775 skos:exactMatch MP:0010466 semapv:LexicalMatching Vascular ring vascular ring -HP:0004961 skos:exactMatch MP:0010467 semapv:LexicalMatching Pulmonary artery sling pulmonary artery sling -HP:0031935 skos:exactMatch MP:0010469 semapv:LexicalMatching Ascending aorta hypoplasia ascending aorta hypoplasia -HP:0004381 skos:exactMatch MP:0010471 semapv:LexicalMatching Supravalvular aortic stenosis supravalvar aortic stenosis -HP:0025495 skos:exactMatch MP:0010474 semapv:LexicalMatching Descending aorta hypoplasia descending aorta hypoplasia -HP:0011638 skos:exactMatch MP:0010475 semapv:LexicalMatching Anomalous origin of left coronary artery from the pulmonary artery anomalous pulmonary origin of left coronary artery -HP:0011641 skos:exactMatch MP:0010476 semapv:LexicalMatching Coronary artery fistula coronary fistula -HP:0030882 skos:exactMatch MP:0010477 semapv:LexicalMatching Coronary artery aneurysm coronary artery aneurysm -HP:0006548 skos:exactMatch MP:0010480 semapv:LexicalMatching Pulmonary arteriovenous malformation pulmonary arteriovenous malformation -HP:0031932 skos:exactMatch MP:0010481 semapv:LexicalMatching Aorto-left ventricular tunnel left ventricle to aorta tunnel -HP:0011645 skos:exactMatch MP:0010483 semapv:LexicalMatching Dilatation of the sinus of Valsalva aortic sinus aneurysm -HP:0003115 skos:exactMatch MP:0010508 semapv:LexicalMatching Abnormal EKG abnormal heart electrocardiography waveform feature -HP:0005165 skos:exactMatch MP:0010511 semapv:LexicalMatching Shortened PR interval shortened PR interval -HP:0001678 skos:exactMatch MP:0010519 semapv:LexicalMatching Atrioventricular block atrioventricular block -HP:0012723 skos:exactMatch MP:0010520 semapv:LexicalMatching Sinoatrial block sinoatrial block -HP:0004974 skos:exactMatch MP:0010525 semapv:LexicalMatching Coarctation of abdominal aorta abdominal aorta coarctation -HP:0006574 skos:exactMatch MP:0010529 semapv:LexicalMatching Hepatic arteriovenous malformation hepatic arteriovenous malformation -HP:0002408 skos:exactMatch MP:0010530 semapv:LexicalMatching Cerebral arteriovenous malformation cerebral arteriovenous malformation -HP:0002629 skos:exactMatch MP:0010531 semapv:LexicalMatching Gastrointestinal arteriovenous malformation gastrointestinal arteriovenous malformation -HP:0010316 skos:exactMatch MP:0010536 semapv:LexicalMatching Ebstein anomaly of the tricuspid valve Ebstein's malformation of tricuspid valve -HP:0012722 skos:exactMatch MP:0010559 semapv:LexicalMatching Heart block heart block -HP:0012561 skos:exactMatch MP:0010596 semapv:LexicalMatching Unicuspid aortic valve unicuspid aortic valve -HP:0031569 skos:exactMatch MP:0010597 semapv:LexicalMatching Absent aortic valve cusps absent aortic valve cusps -HP:0031566 skos:exactMatch MP:0010602 semapv:LexicalMatching Abnormal pulmonary valve cusp morphology abnormal pulmonary valve cusp morphology -HP:0001691 skos:exactMatch MP:0010612 semapv:LexicalMatching Muscular subvalvular aortic stenosis muscular subaortic stenosis -HP:0031480 skos:exactMatch MP:0010614 semapv:LexicalMatching Abnormal mitral valve leaflet morphology abnormal mitral valve cusp morphology -HP:0031443 skos:exactMatch MP:0010622 semapv:LexicalMatching Abnormal tricuspid valve leaflet morphology abnormal tricuspid valve cusp morphology -HP:0031834 skos:exactMatch MP:0010635 semapv:LexicalMatching Aortopulmonary collateral arteries aorta pulmonary collateral arteries -HP:0011710 skos:exactMatch MP:0010636 semapv:LexicalMatching Bundle branch block bundle branch block -HP:0001688 skos:exactMatch MP:0010637 semapv:LexicalMatching Sinus bradycardia sinus bradycardia -HP:0004959 skos:exactMatch MP:0010660 semapv:LexicalMatching Descending thoracic aorta aneurysm descending thoracic aorta aneurysm -HP:0007968 skos:exactMatch MP:0010711 semapv:LexicalMatching Remnants of the hyaloid vascular system persistent hyperplastic primary vitreous -HP:0000612 skos:exactMatch MP:0010714 semapv:LexicalMatching Iris coloboma iris coloboma -HP:0000480 skos:exactMatch MP:0010715 semapv:LexicalMatching Retinal coloboma retina coloboma -HP:0000588 skos:exactMatch MP:0010716 semapv:LexicalMatching Optic nerve coloboma optic disk coloboma -HP:0000588 skos:exactMatch MP:0010717 semapv:LexicalMatching Optic nerve coloboma optic nerve coloboma -HP:0020006 skos:exactMatch MP:0010719 semapv:LexicalMatching Ciliary body coloboma ciliary body coloboma -HP:0000270 skos:exactMatch MP:0010743 semapv:LexicalMatching Delayed cranial suture closure delayed cranial suture closure -HP:0000649 skos:exactMatch MP:0010748 semapv:LexicalMatching Abnormality of visual evoked potentials abnormal visual evoked potential -HP:0001172 skos:exactMatch MP:0010772 semapv:LexicalMatching Abnormal thumb morphology abnormal pollex morphology -HP:0002107 skos:exactMatch MP:0010822 semapv:LexicalMatching Pneumothorax pneumothorax -HP:0011616 skos:exactMatch MP:0010854 semapv:LexicalMatching Pulmonary situs inversus lung situs inversus -HP:0001511 skos:exactMatch MP:0010865 semapv:LexicalMatching Intrauterine growth retardation prenatal growth retardation -HP:0010450 skos:exactMatch MP:0010884 semapv:LexicalMatching Esophageal stenosis esophagus stenosis -HP:0012253 skos:exactMatch MP:0010942 semapv:LexicalMatching Abnormal respiratory epithelium morphology abnormal respiratory epithelium morphology -HP:0006517 skos:exactMatch MP:0010998 semapv:LexicalMatching Alveolar proteinosis pulmonary alveolar proteinosis -HP:0002110 skos:exactMatch MP:0011012 semapv:LexicalMatching Bronchiectasis bronchiectasis -HP:0410397 skos:exactMatch MP:0011013 semapv:LexicalMatching Bronchiolectasis bronchiolectasis -HP:0005938 skos:exactMatch MP:0011050 semapv:LexicalMatching Abnormal respiratory motile cilium morphology abnormal respiratory motile cilium morphology -HP:0012261 skos:exactMatch MP:0011055 semapv:LexicalMatching Abnormal respiratory motile cilium physiology abnormal respiratory motile cilium physiology -HP:0030895 skos:exactMatch MP:0011082 semapv:LexicalMatching Abnormal gastrointestinal motility abnormal gastrointestinal motility -HP:0031538 skos:exactMatch MP:0011159 semapv:LexicalMatching Abnormal dermoepidermal junction morphology abnormal epidermal-dermal junction morphology -HP:0012490 skos:exactMatch MP:0011164 semapv:LexicalMatching Panniculitis panniculitis -HP:0009125 skos:exactMatch MP:0011174 semapv:LexicalMatching Lipodystrophy lipodystrophy -HP:0000926 skos:exactMatch MP:0011175 semapv:LexicalMatching Platyspondyly platyspondylia -HP:0040126 skos:exactMatch MP:0011227 semapv:LexicalMatching Abnormal vitamin B12 level abnormal vitamin B12 level -HP:0003363 skos:exactMatch MP:0011249 semapv:LexicalMatching Abdominal situs inversus abdominal situs inversus -HP:0031565 skos:exactMatch MP:0011250 semapv:LexicalMatching Abdominal situs ambiguus abdominal situs ambiguus -HP:0001696 skos:exactMatch MP:0011252 semapv:LexicalMatching Situs inversus totalis situs inversus totalis -HP:0031592 skos:exactMatch MP:0011253 semapv:LexicalMatching Situs inversus with levocardia situs inversus with levocardia -HP:0032464 skos:exactMatch MP:0011298 semapv:LexicalMatching Ureteral hypoplasia ureter hypoplasia -HP:0000108 skos:exactMatch MP:0011308 semapv:LexicalMatching Renal corticomedullary cysts kidney corticomedullary cysts -HP:0008776 skos:exactMatch MP:0011317 semapv:LexicalMatching Abnormal renal artery morphology abnormal renal artery morphology -HP:0001967 skos:exactMatch MP:0011353 semapv:LexicalMatching Diffuse mesangial sclerosis expanded mesangial matrix -HP:0000125 skos:exactMatch MP:0011361 semapv:LexicalMatching Pelvic kidney pelvic kidney -HP:0012330 skos:exactMatch MP:0011403 semapv:LexicalMatching Pyelonephritis pyelonephritis -HP:0001970 skos:exactMatch MP:0011405 semapv:LexicalMatching Tubulointerstitial nephritis tubulointerstitial nephritis -HP:0012085 skos:exactMatch MP:0011420 semapv:LexicalMatching Pyuria pyuria -HP:0012615 skos:exactMatch MP:0011421 semapv:LexicalMatching Cylindruria cylindruria -HP:0012574 skos:exactMatch MP:0011427 semapv:LexicalMatching Mesangial hypercellularity mesangial cell hyperplasia -HP:0030762 skos:exactMatch MP:0011430 semapv:LexicalMatching Mesangiolysis mesangiolysis -HP:0031811 skos:exactMatch MP:0011464 semapv:LexicalMatching Bilirubinuria bilirubinuria -HP:0008155 skos:exactMatch MP:0011473 semapv:LexicalMatching Mucopolysacchariduria increased urine glycosaminoglycan level -HP:0011483 skos:exactMatch MP:0011481 semapv:LexicalMatching Anterior synechiae of the anterior chamber anterior iris synechia -HP:0000074 skos:exactMatch MP:0011491 semapv:LexicalMatching Ureteropelvic junction obstruction ureteropelvic junction obstruction -HP:0030735 skos:exactMatch MP:0011492 semapv:LexicalMatching Ureterovesical junction obstruction ureterovesical junction obstruction -HP:0000073 skos:exactMatch MP:0011493 semapv:LexicalMatching Ureteral duplication double ureter -HP:0006487 skos:exactMatch MP:0011505 semapv:LexicalMatching Bowing of the long bones camptomelia -HP:0000979 skos:exactMatch MP:0011515 semapv:LexicalMatching Purpura purpura -HP:0012068 skos:exactMatch MP:0011516 semapv:LexicalMatching Aspartylglucosaminuria aspartylglucosaminuria -HP:0100515 skos:exactMatch MP:0011535 semapv:LexicalMatching Pollakisuria increased urination frequency -HP:0031591 skos:exactMatch MP:0011571 semapv:LexicalMatching Enlarged Eustachian valve enlarged inferior vena cava valve -HP:0031209 skos:exactMatch MP:0011579 semapv:LexicalMatching Decreased lipoprotein lipase activity decreased lipoprotein lipase activity -HP:0000176 skos:exactMatch MP:0011615 semapv:LexicalMatching Submucous cleft hard palate submucous cleft palate -HP:0012087 skos:exactMatch MP:0011633 semapv:LexicalMatching Abnormal mitochondrial shape abnormal mitochondrial shape -HP:0011004 skos:exactMatch MP:0011655 semapv:LexicalMatching Abnormal systemic arterial morphology abnormal systemic artery morphology -HP:0031563 skos:exactMatch MP:0011656 semapv:LexicalMatching Coronary arteriovenous fistula coronary arterio-venous fistula -HP:0011612 skos:exactMatch MP:0011658 semapv:LexicalMatching Interrupted aortic arch type A "interrupted aortic arch type a" -HP:0011613 skos:exactMatch MP:0011659 semapv:LexicalMatching Interrupted aortic arch type B "interrupted aortic arch type b" -HP:0001683 skos:exactMatch MP:0011660 semapv:LexicalMatching Ectopia cordis ectopia cordis -HP:0004384 skos:exactMatch MP:0011661 semapv:LexicalMatching Type I truncus arteriosus persistent truncus arteriosus type i -HP:0011608 skos:exactMatch MP:0011662 semapv:LexicalMatching Type II truncus arteriosus persistent truncus arteriosus type ii -HP:0011609 skos:exactMatch MP:0011663 semapv:LexicalMatching Type III truncus arteriosus persistent truncus arteriosus type iii -HP:0011610 skos:exactMatch MP:0011664 semapv:LexicalMatching Type IV truncus arteriosus persistent truncus arteriosus type iv -HP:0031348 skos:exactMatch MP:0011665 semapv:LexicalMatching Dextrotransposition of the great arteries d-loop transposition of the great arteries -HP:0011652 skos:exactMatch MP:0011669 semapv:LexicalMatching Double outlet right ventricle with doubly committed ventricular septal defect without pulmonary stenosis "double outlet right ventricle doubly committed ventricular septal defect" -HP:0011654 skos:exactMatch MP:0011670 semapv:LexicalMatching Double outlet right ventricle with non-committed ventricular septal defect without pulmonary stenosis "double outlet right ventricle noncommitted ventricular septal defect" -HP:0011573 skos:exactMatch MP:0011680 semapv:LexicalMatching Hypoplastic tricuspid valve tricuspid valve hypoplasia -HP:0002282 skos:exactMatch MP:0011723 semapv:LexicalMatching Gray matter heterotopia ectopic neuron -HP:0031086 skos:exactMatch MP:0011727 semapv:LexicalMatching Ectopic ovary ectopic ovary -HP:0025382 skos:exactMatch MP:0011737 semapv:LexicalMatching Hypodipsia hypodipsia -HP:0012050 skos:exactMatch MP:0011738 semapv:LexicalMatching Anasarca anasarca -HP:0031812 skos:exactMatch MP:0011741 semapv:LexicalMatching Nitrituria increased urine nitrite level -HP:0031633 skos:exactMatch MP:0011745 semapv:LexicalMatching Isolation of the left subclavian artery isolation of the left subclavian artery -HP:0011974 skos:exactMatch MP:0011747 semapv:LexicalMatching Myelofibrosis myelofibrosis -HP:0032200 skos:exactMatch MP:0011749 semapv:LexicalMatching Perivascular fibrosis perivascular fibrosis -HP:0500006 skos:exactMatch MP:0011763 semapv:LexicalMatching Urethritis urethritis -HP:0000070 skos:exactMatch MP:0011767 semapv:LexicalMatching Ureterocele ureterocele -HP:0025023 skos:exactMatch MP:0011775 semapv:LexicalMatching Rectal atresia rectal atresia -HP:0025407 skos:exactMatch MP:0011786 semapv:LexicalMatching Rectourethral fistula rectourethral fistula -HP:0000796 skos:exactMatch MP:0011801 semapv:LexicalMatching Urethral obstruction urethra obstruction -HP:0005580 skos:exactMatch MP:0011803 semapv:LexicalMatching Duplication of renal pelvis double kidney pelvis -HP:0001586 skos:exactMatch MP:0011829 semapv:LexicalMatching Vesicovaginal fistula vesicovaginal fistula -HP:0010479 skos:exactMatch MP:0011852 semapv:LexicalMatching Patent urachus patent urachus -HP:0002181 skos:exactMatch MP:0011854 semapv:LexicalMatching Cerebral edema cerebral edema -HP:0020133 skos:exactMatch MP:0011871 semapv:LexicalMatching Podocyte hypertrophy podocyte hypertrophy -HP:0030261 skos:exactMatch MP:0011876 semapv:LexicalMatching Absent penis absent penis -HP:0008986 skos:exactMatch MP:0011883 semapv:LexicalMatching Agenesis of the diaphragm absent diaphragm -HP:0032385 skos:exactMatch MP:0011892 semapv:LexicalMatching Abnormal circulating transferrin level abnormal circulating transferrin level -HP:0032195 skos:exactMatch MP:0011920 semapv:LexicalMatching Abnormal S wave abnormal S wave -HP:0031427 skos:exactMatch MP:0011922 semapv:LexicalMatching Abnormal circulating osteocalcin level abnormal circulating osteocalcin level -HP:0030329 skos:exactMatch MP:0011965 semapv:LexicalMatching Retinal thinning decreased total retina thickness -HP:0031795 skos:exactMatch MP:0011973 semapv:LexicalMatching Abnormal circulating glycerol level abnormal circulating glycerol level -HP:0002373 skos:exactMatch MP:0012011 semapv:LexicalMatching Febrile seizures febrile seizures -HP:0001257 skos:exactMatch MP:0012051 semapv:LexicalMatching Spasticity spasticity -HP:0001276 skos:exactMatch MP:0012052 semapv:LexicalMatching Hypertonia hypertonicity -HP:0002509 skos:exactMatch MP:0012053 semapv:LexicalMatching Limb hypertonia limb hypertonicity -HP:0000465 skos:exactMatch MP:0012077 semapv:LexicalMatching Webbed neck webbed neck -HP:0012281 skos:exactMatch MP:0012080 semapv:LexicalMatching Chylous ascites chylous ascites -HP:0000647 skos:exactMatch MP:0012121 semapv:LexicalMatching Sclerocornea sclerocornea -HP:0001562 skos:exactMatch MP:0012171 semapv:LexicalMatching Oligohydramnios oligohydramnios -HP:0031821 skos:exactMatch MP:0012208 semapv:LexicalMatching Abnormal hypoxanthine-guanine phosphoribosyltransferase level abnormal hypoxanthine-guanine phosphoribosyltransferase level -HP:0031823 skos:exactMatch MP:0012209 semapv:LexicalMatching Reduced hypoxanthine-guanine phosphoribosyltransferase level decreased hypoxanthine-guanine phosphoribosyltransferase level -HP:0005326 skos:exactMatch MP:0012258 semapv:LexicalMatching Hypoplastic philtrum philtrum hypoplasia -HP:0002435 skos:exactMatch MP:0012259 semapv:LexicalMatching Meningocele meningocele -HP:0002084 skos:exactMatch MP:0012260 semapv:LexicalMatching Encephalocele encephalomeningocele -HP:0032463 skos:exactMatch MP:0012332 semapv:LexicalMatching Reduced circulating fibronectin level decreased circulating fibronectin level -HP:0002153 skos:exactMatch MP:0012339 semapv:LexicalMatching Hyperkalemia hyperkalemia -HP:0032199 skos:exactMatch MP:0012354 semapv:LexicalMatching Abnormal prothrombin time abnormal prothrombin time -HP:0032198 skos:exactMatch MP:0012355 semapv:LexicalMatching Decreased prothrombin time decreased prothrombin time -HP:0008151 skos:exactMatch MP:0012356 semapv:LexicalMatching Prolonged prothrombin time increased prothrombin time -HP:0003645 skos:exactMatch MP:0012357 semapv:LexicalMatching Prolonged partial thromboplastin time abnormal partial thromboplastin time -HP:0003645 skos:exactMatch MP:0012359 semapv:LexicalMatching Prolonged partial thromboplastin time increased partial thromboplastin time -HP:0000767 skos:exactMatch MP:0012514 semapv:LexicalMatching Pectus excavatum pectus excavatum -HP:0009922 skos:exactMatch MP:0012538 semapv:LexicalMatching Vascular remnant arising from the disc persistent hyaloid artery -HP:0003396 skos:exactMatch MP:0012545 semapv:LexicalMatching Syringomyelia syringomyelia -HP:0000325 skos:exactMatch MP:0012546 semapv:LexicalMatching Triangular face triangular face -HP:0002475 skos:exactMatch MP:0012547 semapv:LexicalMatching Myelomeningocele spina bifida cystica -HP:0012418 skos:exactMatch MP:0012549 semapv:LexicalMatching Hypoxemia hypoxemia -HP:0005972 skos:exactMatch MP:0012550 semapv:LexicalMatching Respiratory acidosis respiratory acidosis -HP:0001942 skos:exactMatch MP:0012551 semapv:LexicalMatching Metabolic acidosis metabolic acidosis -HP:0003128 skos:exactMatch MP:0012552 semapv:LexicalMatching Lactic acidosis lactic acidosis -HP:0004336 skos:exactMatch MP:0012674 semapv:LexicalMatching Myelin outfoldings tomacula -HP:0030175 skos:exactMatch MP:0012674 semapv:LexicalMatching Myelin tomacula tomacula -HP:0100562 skos:exactMatch MP:0012711 semapv:LexicalMatching Diplomyelia diplomyelia -HP:0430021 skos:exactMatch MP:0012729 semapv:LexicalMatching Abnormal common carotid artery morphology abnormal common carotid artery morphology -HP:0000421 skos:exactMatch MP:0013127 semapv:LexicalMatching Epistaxis epistaxis -HP:0004099 skos:exactMatch MP:0013149 semapv:LexicalMatching Macrodactyly macrodactyly -HP:0005268 skos:exactMatch MP:0013172 semapv:LexicalMatching Spontaneous abortion miscarriage -HP:0020179 skos:exactMatch MP:0013215 semapv:LexicalMatching Abnormal haptoglobin level abnormal haptoglobin level -HP:0410012 skos:exactMatch MP:0013262 semapv:LexicalMatching Abnormal mouth floor morphology abnormal mouth floor morphology -HP:0010296 skos:exactMatch MP:0013264 semapv:LexicalMatching Ankyloglossia tongue ankylosis -HP:0002836 skos:exactMatch MP:0013282 semapv:LexicalMatching Bladder exstrophy urinary bladder exstrophy -HP:0004727 skos:exactMatch MP:0013305 semapv:LexicalMatching Impaired renal concentrating ability isosthenuria -HP:0003271 skos:exactMatch MP:0013328 semapv:LexicalMatching Visceromegaly visceromegaly -HP:0010799 skos:exactMatch MP:0013365 semapv:LexicalMatching Pinealoma increased pineal gland tumor incidence -HP:0011850 skos:exactMatch MP:0013367 semapv:LexicalMatching Parotitis parotid gland inflammation -HP:0000970 skos:exactMatch MP:0013368 semapv:LexicalMatching Anhidrosis abnormal sweat gland physiology -HP:0000970 skos:exactMatch MP:0013370 semapv:LexicalMatching Anhidrosis anhidrosis -HP:0000966 skos:exactMatch MP:0013371 semapv:LexicalMatching Hypohidrosis hypohidrosis -HP:0000975 skos:exactMatch MP:0013372 semapv:LexicalMatching Hyperhidrosis hyperhidrosis -HP:0009720 skos:exactMatch MP:0013383 semapv:LexicalMatching Adenoma sebaceum increased sebaceous gland adenoma incidence -HP:0010605 skos:exactMatch MP:0013390 semapv:LexicalMatching Chalazion Meibomian gland cyst -HP:0025610 skos:exactMatch MP:0013391 semapv:LexicalMatching Posterior blepharitis abnormal Meibomian gland physiology -HP:0025610 skos:exactMatch MP:0013392 semapv:LexicalMatching Posterior blepharitis Meibomian gland inflammation -HP:0430007 skos:exactMatch MP:0013393 semapv:LexicalMatching Symblepharon symblepharon -HP:0000579 skos:exactMatch MP:0013451 semapv:LexicalMatching Nasolacrimal duct obstruction nasolacrimal duct obstruction -HP:0001097 skos:exactMatch MP:0013466 semapv:LexicalMatching Keratoconjunctivitis sicca keratoconjunctivitis sicca -HP:0100532 skos:exactMatch MP:0013479 semapv:LexicalMatching Scleritis scleritis -HP:0030934 skos:exactMatch MP:0013492 semapv:LexicalMatching Oral erythroplakia oral erythroplakia -HP:0000029 skos:exactMatch MP:0013600 semapv:LexicalMatching Testicular atrophy testis degeneration -HP:0012130 skos:exactMatch MP:0013659 semapv:LexicalMatching Abnormal erythroid lineage cell morphology abnormal erythroid lineage cell morphology -HP:0010307 skos:exactMatch MP:0013752 semapv:LexicalMatching Stridor stridor -HP:0002779 skos:exactMatch MP:0013753 semapv:LexicalMatching Tracheomalacia tracheomalacia -HP:0005528 skos:exactMatch MP:0013776 semapv:LexicalMatching Bone marrow hypocellularity bone marrow failure -HP:0009933 skos:exactMatch MP:0013789 semapv:LexicalMatching Narrow naris small external nares -HP:0009932 skos:exactMatch MP:0013790 semapv:LexicalMatching Single naris single external naris -HP:0001298 skos:exactMatch MP:0013806 semapv:LexicalMatching Encephalopathy encephalopathy -HP:0007430 skos:exactMatch MP:0013807 semapv:LexicalMatching Generalized edema generalized edema -HP:0012327 skos:exactMatch MP:0013856 semapv:LexicalMatching Celiac artery compression celiac artery compression -HP:0000499 skos:exactMatch MP:0013895 semapv:LexicalMatching Abnormal eyelash morphology abnormal eyelid cilium morphology -HP:0100686 skos:exactMatch MP:0013942 semapv:LexicalMatching Enthesitis enthesitis -HP:0004401 skos:exactMatch MP:0014036 semapv:LexicalMatching Meconium ileus meconium ileus -HP:0011359 skos:exactMatch MP:0014053 semapv:LexicalMatching Dry hair dry hair -HP:0030779 skos:exactMatch MP:0014061 semapv:LexicalMatching Ethmocephaly ethmocephaly -HP:0100318 skos:exactMatch MP:0014063 semapv:LexicalMatching Lafora bodies Lafora bodies -HP:0100317 skos:exactMatch MP:0014064 semapv:LexicalMatching Argyrophilic inclusion bodies argyrophilic inclusion bodies -HP:0100315 skos:exactMatch MP:0014065 semapv:LexicalMatching Lewy bodies Lewy bodies -HP:0100316 skos:exactMatch MP:0014067 semapv:LexicalMatching Hirano bodies Hirano bodies -HP:0001028 skos:exactMatch MP:0014086 semapv:LexicalMatching Hemangioma hemangioma -HP:0007359 skos:exactMatch MP:0014120 semapv:LexicalMatching Focal-onset seizure focal seizures -HP:0100522 skos:exactMatch MP:0014127 semapv:LexicalMatching Thymoma increased thymoma incidence -HP:0000522 skos:exactMatch MP:0014157 semapv:LexicalMatching Alacrima alacrima -HP:0003118 skos:exactMatch MP:0014161 semapv:LexicalMatching Increased circulating cortisol level increased circulating cortisol level -HP:0008163 skos:exactMatch MP:0014162 semapv:LexicalMatching Decreased circulating cortisol level decreased circulating cortisol level -HP:0012628 skos:exactMatch MP:0014176 semapv:LexicalMatching Abnormal suspensory ligament of lens morphology abnormal cilary zonule morphology -HP:0012860 skos:exactMatch MP:0014189 semapv:LexicalMatching Testicular fibrosis testis fibrosis -HP:0400005 skos:exactMatch MP:0020084 semapv:LexicalMatching Short ear short ears -HP:0400004 skos:exactMatch MP:0020085 semapv:LexicalMatching Long ear long ears -HP:0045081 skos:exactMatch MP:0020182 semapv:LexicalMatching Abnormality of body mass index abnormal body mass index -HP:0000632 skos:exactMatch MP:0020218 semapv:LexicalMatching Lacrimation abnormality abnormal tear production -HP:0009926 skos:exactMatch MP:0020219 semapv:LexicalMatching Epiphora increased tear production -HP:0031731 skos:exactMatch MP:0020219 semapv:LexicalMatching Increased tear production increased tear production -HP:0000633 skos:exactMatch MP:0020220 semapv:LexicalMatching Decreased lacrimation decreased tear production -HP:0020037 skos:exactMatch MP:0020289 semapv:LexicalMatching Astasia astasia -HP:0011958 skos:exactMatch MP:0020441 semapv:LexicalMatching Retinal perforation rhegmatogenous retinal detachment -HP:0012230 skos:exactMatch MP:0020441 semapv:LexicalMatching Rhegmatogenous retinal detachment rhegmatogenous retinal detachment -HP:0012231 skos:exactMatch MP:0020442 semapv:LexicalMatching Exudative retinal detachment serous retinal detachment -HP:0007917 skos:exactMatch MP:0020443 semapv:LexicalMatching Tractional retinal detachment tractional retinal detachment -HP:0011966 skos:exactMatch MP:0020836 semapv:LexicalMatching Elevated plasma citrulline increased circulating citrulline level -HP:0001607 skos:exactMatch MP:0030001 semapv:LexicalMatching Subglottic stenosis subglottis stenosis -HP:0410170 skos:exactMatch MP:0030003 semapv:LexicalMatching Hippocampal atrophy hippocampus atrophy -HP:0025517 skos:exactMatch MP:0030004 semapv:LexicalMatching Hypoplastic hippocampus hippocampus hypoplasia -HP:0002645 skos:exactMatch MP:0030030 semapv:LexicalMatching Wormian bones Wormian bones -HP:0000290 skos:exactMatch MP:0030031 semapv:LexicalMatching Abnormality of the forehead abnormal forehead morphology -HP:0005281 skos:exactMatch MP:0030035 semapv:LexicalMatching Hypoplastic nasal bridge small nasal bridge -HP:0003194 skos:exactMatch MP:0030036 semapv:LexicalMatching Short nasal bridge short nasal bridge -HP:0011220 skos:exactMatch MP:0030049 semapv:LexicalMatching Prominent forehead prominent forehead -HP:0000303 skos:exactMatch MP:0030050 semapv:LexicalMatching Mandibular prognathia large mandible -HP:0030756 skos:exactMatch MP:0030058 semapv:LexicalMatching Erythrodontia erythrodontia -HP:0000274 skos:exactMatch MP:0030065 semapv:LexicalMatching Small face face hypoplasia -HP:0001999 skos:exactMatch MP:0030071 semapv:LexicalMatching Abnormal facial shape abnormal face shape -HP:0100663 skos:exactMatch MP:0030078 semapv:LexicalMatching Synotia synotia -HP:0002677 skos:exactMatch MP:0030094 semapv:LexicalMatching Small foramen magnum foramen magnum stenosis -HP:0004467 skos:exactMatch MP:0030097 semapv:LexicalMatching Preauricular pit preauricular pit -HP:0000629 skos:exactMatch MP:0030098 semapv:LexicalMatching Periorbital fullness periorbital fullness -HP:0011332 skos:exactMatch MP:0030100 semapv:LexicalMatching Hemifacial hypoplasia hemifacial hypoplasia -HP:0000670 skos:exactMatch MP:0030101 semapv:LexicalMatching Carious teeth carious teeth -HP:0000473 skos:exactMatch MP:0030126 semapv:LexicalMatching Torticollis torticollis -HP:0000206 skos:exactMatch MP:0030129 semapv:LexicalMatching Glossitis tongue inflammation -HP:0000230 skos:exactMatch MP:0030130 semapv:LexicalMatching Gingivitis gum inflammation -HP:0000704 skos:exactMatch MP:0030132 semapv:LexicalMatching Periodontitis periodontium inflammation -HP:0011468 skos:exactMatch MP:0030143 semapv:LexicalMatching Facial tics facial muscle spasm -HP:0000215 skos:exactMatch MP:0030169 semapv:LexicalMatching Thick upper lip vermilion thick upper lip -HP:0005104 skos:exactMatch MP:0030197 semapv:LexicalMatching Hypoplastic nasal septum small nasal septum -HP:0004411 skos:exactMatch MP:0030199 semapv:LexicalMatching Deviated nasal septum deviated nasal septum -HP:0009746 skos:exactMatch MP:0030205 semapv:LexicalMatching Thick nasal septum thick nasal septum -HP:3000051 skos:exactMatch MP:0030212 semapv:LexicalMatching Abnormal hyoglossus muscle morphology abnormal hyoglossus muscle morphology -HP:0002380 skos:exactMatch MP:0030214 semapv:LexicalMatching Fasciculations muscle fasciculation -HP:0001308 skos:exactMatch MP:0030216 semapv:LexicalMatching Tongue fasciculations tongue muscle fasciculation -HP:0025011 skos:exactMatch MP:0030218 semapv:LexicalMatching Pyriform aperture stenosis piriform aperture stenosis -HP:0004472 skos:exactMatch MP:0030223 semapv:LexicalMatching Mandibular hyperostosis mandibular hyperostosis -HP:0002010 skos:exactMatch MP:0030248 semapv:LexicalMatching Narrow maxilla narrow maxilla -HP:0030867 skos:exactMatch MP:0030253 semapv:LexicalMatching Vertical orbital dystopia vertical orbital dystopia -HP:0002007 skos:exactMatch MP:0030262 semapv:LexicalMatching Frontal bossing frontal bossing -HP:0002007 skos:exactMatch MP:0030263 semapv:LexicalMatching Frontal bossing cranial bossing -HP:0000242 skos:exactMatch MP:0030265 semapv:LexicalMatching Parietal bossing parietal bossing -HP:0000278 skos:exactMatch MP:0030270 semapv:LexicalMatching Retrognathia retrogenia -HP:0000347 skos:exactMatch MP:0030273 semapv:LexicalMatching Micrognathia mandibular retrognathia -HP:0000327 skos:exactMatch MP:0030274 semapv:LexicalMatching Hypoplasia of the maxilla maxillary retrognathia -HP:0002684 skos:exactMatch MP:0030278 semapv:LexicalMatching Thickened calvaria thick neurocranium -HP:0010539 skos:exactMatch MP:0030279 semapv:LexicalMatching Thin calvarium thin neurocranium -HP:0031046 skos:exactMatch MP:0030290 semapv:LexicalMatching Absent soft palate absent soft palate -HP:0000252 skos:exactMatch MP:0030315 semapv:LexicalMatching Microcephaly small neurocranium -HP:0012478 skos:exactMatch MP:0030327 semapv:LexicalMatching Temporomandibular joint ankylosis temporomandibular joint ankylosis -HP:0004440 skos:exactMatch MP:0030350 semapv:LexicalMatching Coronal craniosynostosis premature coronal suture closure -HP:0004442 skos:exactMatch MP:0030354 semapv:LexicalMatching Sagittal craniosynostosis premature sagittal suture closure -HP:0004443 skos:exactMatch MP:0030356 semapv:LexicalMatching Lambdoidal craniosynostosis premature lambdoid suture closure -HP:0005441 skos:exactMatch MP:0030359 semapv:LexicalMatching Sclerotic cranial sutures cranial suture sclerosis -HP:0011330 skos:exactMatch MP:0030367 semapv:LexicalMatching Metopic synostosis premature metopic suture closure -HP:0002692 skos:exactMatch MP:0030386 semapv:LexicalMatching Hypoplastic facial bones facial bone hypoplasia -HP:0001363 skos:exactMatch MP:0030392 semapv:LexicalMatching Craniosynostosis premature fontanelle closure -HP:0005458 skos:exactMatch MP:0030392 semapv:LexicalMatching Premature closure of fontanelles premature fontanelle closure -HP:0200111 skos:exactMatch MP:0030403 semapv:LexicalMatching Absent stapes head absent stapes head -HP:0004493 skos:exactMatch MP:0030417 semapv:LexicalMatching Craniofacial hyperostosis craniofacial hyperostosis -HP:0005465 skos:exactMatch MP:0030418 semapv:LexicalMatching Facial hyperostosis facial hyperostosis -HP:0030789 skos:exactMatch MP:0030419 semapv:LexicalMatching Excessive cerumen excessive cerumen -HP:0001363 skos:exactMatch MP:0030435 semapv:LexicalMatching Craniosynostosis premature craniofacial suture closure -HP:0009722 skos:exactMatch MP:0030460 semapv:LexicalMatching Dental enamel pits enamel pits -HP:0030757 skos:exactMatch MP:0030462 semapv:LexicalMatching Tooth abscess tooth abscess -HP:0030758 skos:exactMatch MP:0030463 semapv:LexicalMatching Periapical tooth abscess apical tooth abscess -HP:0011090 skos:exactMatch MP:0030472 semapv:LexicalMatching Fused teeth fused teeth -HP:0003771 skos:exactMatch MP:0030491 semapv:LexicalMatching Pulp stones dental pulp stones -HP:0011072 skos:exactMatch MP:0030495 semapv:LexicalMatching Rootless teeth absent tooth root -HP:0000679 skos:exactMatch MP:0030496 semapv:LexicalMatching Taurodontia taurodontia -HP:0000698 skos:exactMatch MP:0030499 semapv:LexicalMatching Conical tooth conical tooth -HP:0001571 skos:exactMatch MP:0030505 semapv:LexicalMatching Multiple impacted teeth tooth impaction -HP:0011079 skos:exactMatch MP:0030505 semapv:LexicalMatching Impacted tooth tooth impaction -HP:0100656 skos:exactMatch MP:0030579 semapv:LexicalMatching Thoracoabdominal wall defect thoracoabdominoschisis -HP:0004334 skos:exactMatch MP:0030584 semapv:LexicalMatching Dermal atrophy skin atrophy -HP:0006349 skos:exactMatch MP:0030608 semapv:LexicalMatching Agenesis of permanent teeth decreased tooth number -HP:0000674 skos:exactMatch MP:0030610 semapv:LexicalMatching Anodontia absent teeth -HP:0003260 skos:exactMatch MP:0030681 semapv:LexicalMatching Hydroxyprolinemia increased circulating hydroxyproline level -HP:0003080 skos:exactMatch MP:0030682 semapv:LexicalMatching Hydroxyprolinuria hydroxyprolinuria -HP:0025441 skos:exactMatch MP:0030776 semapv:LexicalMatching Achilles tendon calcification calcified calcaneal tendon -HP:0003368 skos:exactMatch MP:0030788 semapv:LexicalMatching Abnormality of the femoral head abnormal femur head morphology -HP:0003367 skos:exactMatch MP:0030789 semapv:LexicalMatching Abnormality of the femoral neck abnormal femur neck morphology -HP:0100864 skos:exactMatch MP:0030793 semapv:LexicalMatching Short femoral neck short femur neck -HP:0002827 skos:exactMatch MP:0030796 semapv:LexicalMatching Hip dislocation hip dislocation -HP:0001388 skos:exactMatch MP:0030797 semapv:LexicalMatching Joint laxity joint laxity -HP:0001371 skos:exactMatch MP:0030798 semapv:LexicalMatching Flexion contracture joint contracture -HP:0025230 skos:exactMatch MP:0030801 semapv:LexicalMatching Tendonitis tendonitis -HP:0012317 skos:exactMatch MP:0030822 semapv:LexicalMatching Sacroiliac arthritis sacroiliac joint inflammation -HP:0031846 skos:exactMatch MP:0030827 semapv:LexicalMatching Femur fracture femur fracture -HP:0003042 skos:exactMatch MP:0030843 semapv:LexicalMatching Elbow dislocation elbow dislocation -HP:0003994 skos:exactMatch MP:0030864 semapv:LexicalMatching Dislocated wrist wrist dislocation -HP:0000897 skos:exactMatch MP:0030884 semapv:LexicalMatching Rachitic rosary rachitic rosary -HP:0000923 skos:exactMatch MP:0030884 semapv:LexicalMatching Beaded ribs rachitic rosary -HP:0007384 skos:exactMatch MP:0030915 semapv:LexicalMatching Aberrant melanosome maturation abnormal melanosome maturation -HP:0005592 skos:exactMatch MP:0030917 semapv:LexicalMatching Giant melanosomes in melanocytes enlarged melanosome -HP:0031615 skos:exactMatch MP:0030932 semapv:LexicalMatching Hypopyon hypopyon -HP:0011886 skos:exactMatch MP:0030933 semapv:LexicalMatching Hyphema hyphema -HP:0001993 skos:exactMatch MP:0030971 semapv:LexicalMatching Ketoacidosis ketoacidosis -HP:0031428 skos:exactMatch MP:0030984 semapv:LexicalMatching Increased circulating osteocalcin level increased circulating osteocalcin level -HP:0031429 skos:exactMatch MP:0030985 semapv:LexicalMatching Decreased circulating osteocalcin level decreased circulating osteocalcin level -HP:0012486 skos:exactMatch MP:0030987 semapv:LexicalMatching Myelitis spinal cord inflammation -HP:0031002 skos:exactMatch MP:0030990 semapv:LexicalMatching Neuritis nerve inflammation -HP:0100653 skos:exactMatch MP:0030991 semapv:LexicalMatching Optic neuritis optic nerve inflammation -HP:0009894 skos:exactMatch MP:0000019 semapv:LogicalReasoning Thickened ears thick ears -HP:0000377 skos:exactMatch MP:0000022 semapv:LogicalReasoning Abnormality of the pinna abnormal ear shape -HP:0000369 skos:exactMatch MP:0000024 semapv:LogicalReasoning Low-set ears lowered ear position -HP:0011390 skos:exactMatch MP:0000026 semapv:LogicalReasoning Morphological abnormality of the inner ear abnormal inner ear morphology -HP:0011376 skos:exactMatch MP:0000034 semapv:LogicalReasoning Morphological abnormality of the vestibule of the inner ear abnormal inner ear vestibule morphology -HP:0008609 skos:exactMatch MP:0000049 semapv:LogicalReasoning Morphological abnormality of the middle ear abnormal middle ear morphology -HP:0002696 skos:exactMatch MP:0000109 semapv:LogicalReasoning Abnormal parietal bone morphology abnormal parietal bone morphology -HP:0011323 skos:exactMatch MP:0000114 semapv:LogicalReasoning Cleft of chin cleft chin -HP:0002753 skos:exactMatch MP:0000135 semapv:LogicalReasoning Thin bony cortex decreased compact bone thickness -HP:0000782 skos:exactMatch MP:0000149 semapv:LogicalReasoning Abnormality of the scapula abnormal scapula morphology -HP:0003141 skos:exactMatch MP:0000182 semapv:LogicalReasoning Increased LDL cholesterol concentration increased circulating LDL cholesterol level -HP:0003233 skos:exactMatch MP:0000186 semapv:LogicalReasoning Decreased HDL cholesterol concentration decreased circulating HDL cholesterol level -HP:0001640 skos:exactMatch MP:0000274 semapv:LogicalReasoning Cardiomegaly enlarged heart -HP:0011994 skos:exactMatch MP:0000282 semapv:LogicalReasoning Abnormal atrial septum morphology abnormal interatrial septum morphology -HP:0100495 skos:exactMatch MP:0000324 semapv:LogicalReasoning Mastocytosis increased mast cell number -HP:0001006 skos:exactMatch MP:0000414 semapv:LogicalReasoning Hypotrichosis alopecia -HP:0040194 skos:exactMatch MP:0000434 semapv:LogicalReasoning Increased head circumference megacephaly -HP:0000248 skos:exactMatch MP:0000435 semapv:LogicalReasoning Brachycephaly shortened head -HP:0000327 skos:exactMatch MP:0000457 semapv:LogicalReasoning Hypoplasia of the maxilla maxilla hypoplasia -HP:0005815 skos:exactMatch MP:0000480 semapv:LogicalReasoning Supernumerary ribs increased rib number -HP:0010946 skos:exactMatch MP:0000519 semapv:LogicalReasoning Dilatation of the renal pelvis hydronephrosis -HP:0008873 skos:exactMatch MP:0000547 semapv:LogicalReasoning Disproportionate short-limb short stature short limbs -HP:0045009 skos:exactMatch MP:0000552 semapv:LogicalReasoning Abnormal morphology of the radius abnormal radius morphology -HP:0002992 skos:exactMatch MP:0000558 semapv:LogicalReasoning Abnormality of tibia morphology abnormal tibia morphology -HP:0002823 skos:exactMatch MP:0000559 semapv:LogicalReasoning Abnormality of femur morphology abnormal femur morphology -HP:0001883 skos:exactMatch MP:0000576 semapv:LogicalReasoning Talipes clubfoot -HP:0012681 skos:exactMatch MP:0000632 semapv:LogicalReasoning Abnormality of pineal morphology abnormal pineal gland morphology -HP:0011732 skos:exactMatch MP:0000639 semapv:LogicalReasoning Abnormality of adrenal morphology abnormal adrenal gland morphology -HP:0008711 skos:exactMatch MP:0000659 semapv:LogicalReasoning Benign prostatic hyperplasia prostate gland hyperplasia -HP:0040088 skos:exactMatch MP:0000717 semapv:LogicalReasoning Abnormal lymphocyte count abnormal lymphocyte cell number -HP:0005422 skos:exactMatch MP:0000727 semapv:LogicalReasoning Absence of CD8-positive T cells "absent CD8-positive alpha-beta T cells" -HP:0001322 skos:exactMatch MP:0000774 semapv:LogicalReasoning obsolete Brain very small decreased brain size -HP:0100547 skos:exactMatch MP:0000783 semapv:LogicalReasoning Abnormality of forebrain morphology abnormal forebrain morphology -HP:0006872 skos:exactMatch MP:0000785 semapv:LogicalReasoning Cerebral hypoplasia telencephalon hypoplasia -HP:0006891 skos:exactMatch MP:0000789 semapv:LogicalReasoning Thick cerebral cortex thickened cerebral cortex -HP:0025100 skos:exactMatch MP:0000807 semapv:LogicalReasoning Abnormal morphology of the hippocampus abnormal hippocampus morphology -HP:0040327 skos:exactMatch MP:0000819 semapv:LogicalReasoning Abnormal morphology of the olfactory bulb abnormal olfactory bulb morphology -HP:0006956 skos:exactMatch MP:0000825 semapv:LogicalReasoning Dilation of lateral ventricles dilated lateral ventricles -HP:0011282 skos:exactMatch MP:0000841 semapv:LogicalReasoning Abnormality of hindbrain morphology abnormal hindbrain morphology -HP:0007027 skos:exactMatch MP:0000847 semapv:LogicalReasoning Poorly formed metencephalon abnormal metencephalon morphology -HP:0002335 skos:exactMatch MP:0000865 semapv:LogicalReasoning Agenesis of cerebellar vermis absent cerebellum vermis -HP:0001320 skos:exactMatch MP:0000866 semapv:LogicalReasoning Cerebellar vermis hypoplasia cerebellum vermis hypoplasia -HP:0002450 skos:exactMatch MP:0000937 semapv:LogicalReasoning Abnormal motor neuron morphology abnormal motor neuron morphology -HP:0002398 skos:exactMatch MP:0000938 semapv:LogicalReasoning Degeneration of anterior horn cells motor neuron degeneration -HP:0025028 skos:exactMatch MP:0001044 semapv:LogicalReasoning Abnormality of enteric nervous system morphology abnormal enteric nervous system morphology -HP:0010824 skos:exactMatch MP:0001065 semapv:LogicalReasoning Abnormal fifth cranial nerve morphology abnormal trigeminal nerve morphology -HP:3000047 skos:exactMatch MP:0001073 semapv:LogicalReasoning Abnormal glossopharyngeal nerve morphology abnormal glossopharyngeal nerve morphology -HP:0010791 skos:exactMatch MP:0001152 semapv:LogicalReasoning Hyperplasia of the Leydig cells Leydig cell hyperplasia -HP:0011124 skos:exactMatch MP:0001216 semapv:LogicalReasoning Abnormality of epidermal morphology abnormal epidermal layer morphology -HP:0000962 skos:exactMatch MP:0001219 semapv:LogicalReasoning Hyperkeratosis thick epidermis -HP:0000002 skos:exactMatch MP:0001253 semapv:LogicalReasoning Abnormality of body height abnormal body height -HP:0004323 skos:exactMatch MP:0001259 semapv:LogicalReasoning Abnormality of body weight abnormal body weight -HP:0100625 skos:exactMatch MP:0001267 semapv:LogicalReasoning Enlarged thorax enlarged chest -HP:0000525 skos:exactMatch MP:0001322 semapv:LogicalReasoning Abnormality iris morphology abnormal iris morphology -HP:0010999 skos:exactMatch MP:0001334 semapv:LogicalReasoning Aplasia of the optic tract absent optic tract -HP:0000733 skos:exactMatch MP:0001409 semapv:LogicalReasoning Stereotypy increased stereotypic behavior -HP:0011843 skos:exactMatch MP:0001533 semapv:LogicalReasoning Abnormality of skeletal physiology abnormal skeleton physiology -HP:0002155 skos:exactMatch MP:0001552 semapv:LogicalReasoning Hypertriglyceridemia increased circulating triglyceride level -HP:0012184 skos:exactMatch MP:0001556 semapv:LogicalReasoning Increased HDL cholesterol concentration increased circulating HDL cholesterol level -HP:0025032 skos:exactMatch MP:0001663 semapv:LogicalReasoning Abnormality of digestive system physiology abnormal digestive system physiology -HP:0001508 skos:exactMatch MP:0001732 semapv:LogicalReasoning Failure to thrive postnatal growth retardation -HP:0003154 skos:exactMatch MP:0001748 semapv:LogicalReasoning Increased circulating ACTH level increased circulating adrenocorticotropin level -HP:0010978 skos:exactMatch MP:0001790 semapv:LogicalReasoning Abnormality of immune system physiology abnormal immune system physiology -HP:0002720 skos:exactMatch MP:0001807 semapv:LogicalReasoning Decreased circulating IgA level decreased IgA level -HP:0001892 skos:exactMatch MP:0001914 semapv:LogicalReasoning Abnormal bleeding hemorrhage -HP:0000080 skos:exactMatch MP:0001919 semapv:LogicalReasoning Abnormality of reproductive system physiology abnormal reproductive system physiology -HP:0000823 skos:exactMatch MP:0001938 semapv:LogicalReasoning Delayed puberty delayed sexual maturation -HP:0012090 skos:exactMatch MP:0001944 semapv:LogicalReasoning Abnormal pancreas morphology abnormal pancreas morphology -HP:0002093 skos:exactMatch MP:0001953 semapv:LogicalReasoning Respiratory insufficiency respiratory failure -HP:0000138 skos:exactMatch MP:0002016 semapv:LogicalReasoning Ovarian cyst ovary cysts -HP:0010719 skos:exactMatch MP:0002074 semapv:LogicalReasoning Abnormality of hair texture abnormal hair texture -HP:0006482 skos:exactMatch MP:0002100 semapv:LogicalReasoning Abnormality of dental morphology abnormal tooth morphology -HP:0012252 skos:exactMatch MP:0002132 semapv:LogicalReasoning Abnormal respiratory system morphology abnormal respiratory system morphology -HP:0002795 skos:exactMatch MP:0002133 semapv:LogicalReasoning Functional respiratory abnormality abnormal respiratory system physiology -HP:0410043 skos:exactMatch MP:0002151 semapv:LogicalReasoning Abnormal neural tube morphology abnormal neural tube morphology -HP:0002991 skos:exactMatch MP:0002187 semapv:LogicalReasoning Abnormality of fibula morphology abnormal fibula morphology -HP:0002718 skos:exactMatch MP:0002412 semapv:LogicalReasoning Recurrent bacterial infections increased susceptibility to bacterial infection -HP:0011840 skos:exactMatch MP:0002444 semapv:LogicalReasoning Abnormality of T cell physiology abnormal T cell physiology -HP:0010975 skos:exactMatch MP:0002458 semapv:LogicalReasoning Abnormal B cell count abnormal B cell number -HP:0005372 skos:exactMatch MP:0002459 semapv:LogicalReasoning Abnormality of B cell physiology abnormal B cell physiology -HP:0011990 skos:exactMatch MP:0002463 semapv:LogicalReasoning Abnormality of neutrophil physiology abnormal neutrophil physiology -HP:0410245 skos:exactMatch MP:0002491 semapv:LogicalReasoning Decreased circulating total IgD decreased IgD level -HP:0005479 skos:exactMatch MP:0002492 semapv:LogicalReasoning Decreased circulating total IgE decreased IgE level -HP:0003496 skos:exactMatch MP:0002494 semapv:LogicalReasoning Increased circulating IgM level increased IgM level -HP:0003261 skos:exactMatch MP:0002495 semapv:LogicalReasoning Increased circulating IgA level increased IgA level -HP:0003212 skos:exactMatch MP:0002497 semapv:LogicalReasoning Increased circulating total IgE level increased IgE level -HP:0011927 skos:exactMatch MP:0002544 semapv:LogicalReasoning Short digit brachydactyly -HP:0012153 skos:exactMatch MP:0002644 semapv:LogicalReasoning Hypotriglyceridemia decreased circulating triglyceride level -HP:0002920 skos:exactMatch MP:0002664 semapv:LogicalReasoning Decreased circulating ACTH level decreased circulating adrenocorticotropin level -HP:0011070 skos:exactMatch MP:0002689 semapv:LogicalReasoning Abnormality of molar morphology abnormal molar morphology -HP:0012091 skos:exactMatch MP:0002693 semapv:LogicalReasoning Abnormality of pancreas physiology abnormal pancreas physiology -HP:0002624 skos:exactMatch MP:0002725 semapv:LogicalReasoning Abnormal venous morphology abnormal vein morphology -HP:0030968 skos:exactMatch MP:0002726 semapv:LogicalReasoning Abnormal pulmonary vein morphology abnormal pulmonary vein morphology -HP:0006426 skos:exactMatch MP:0002728 semapv:LogicalReasoning Rudimentary to absent tibiae absent tibia -HP:0006436 skos:exactMatch MP:0002764 semapv:LogicalReasoning Shortening of the tibia short tibia -HP:0040171 skos:exactMatch MP:0002780 semapv:LogicalReasoning Decreased serum testosterone level decreased circulating testosterone level -HP:0030088 skos:exactMatch MP:0002781 semapv:LogicalReasoning Increased serum testosterone level increased circulating testosterone level -HP:0001098 skos:exactMatch MP:0002864 semapv:LogicalReasoning Abnormal fundus morphology abnormal ocular fundus morphology -HP:0012757 skos:exactMatch MP:0002882 semapv:LogicalReasoning Abnormal neuron morphology abnormal neuron morphology -HP:0012365 skos:exactMatch MP:0002901 semapv:LogicalReasoning Hypophosphaturia increased urine phosphate level -HP:0003109 skos:exactMatch MP:0002902 semapv:LogicalReasoning Hyperphosphaturia decreased urine phosphate level -HP:0011733 skos:exactMatch MP:0002909 semapv:LogicalReasoning Abnormality of adrenal physiology abnormal adrenal gland physiology -HP:0007770 skos:exactMatch MP:0002984 semapv:LogicalReasoning Hypoplasia of the retina retina hypoplasia -HP:0100957 skos:exactMatch MP:0003014 semapv:LogicalReasoning Abnormal renal medulla morphology abnormal kidney medulla morphology -HP:3000052 skos:exactMatch MP:0003056 semapv:LogicalReasoning Abnormality of hyoid bone abnormal hyoid bone morphology -HP:0025321 skos:exactMatch MP:0003066 semapv:LogicalReasoning Copper accumulation in liver increased liver copper level -HP:0000105 skos:exactMatch MP:0003068 semapv:LogicalReasoning Enlarged kidney enlarged kidney -HP:0010048 skos:exactMatch MP:0003074 semapv:LogicalReasoning Aplasia of metacarpal bones absent metacarpal bones -HP:0005237 skos:exactMatch MP:0003103 semapv:LogicalReasoning Degenerative liver disease liver degeneration -HP:0005120 skos:exactMatch MP:0003105 semapv:LogicalReasoning Abnormal cardiac atrium morphology abnormal heart atrium morphology -HP:0012132 skos:exactMatch MP:0003135 semapv:LogicalReasoning Erythroid hyperplasia increased erythroid progenitor cell number -HP:0011373 skos:exactMatch MP:0003148 semapv:LogicalReasoning Incomplete partition of the cochlea decreased cochlear coiling -HP:0003107 skos:exactMatch MP:0003191 semapv:LogicalReasoning Abnormal circulating cholesterol concentration abnormal cellular cholesterol metabolism -HP:0005222 skos:exactMatch MP:0003262 semapv:LogicalReasoning Bowel diverticulosis intestinal/bowel diverticulum -HP:0004398 skos:exactMatch MP:0003300 semapv:LogicalReasoning Peptic ulcer gastrointestinal ulcer -HP:3000002 skos:exactMatch MP:0003308 semapv:LogicalReasoning Abnormal inner ear epithelium morphology abnormal cochlear sensory epithelium morphology -HP:0006274 skos:exactMatch MP:0003339 semapv:LogicalReasoning Reduced pancreatic beta cells decreased pancreatic beta cell number -HP:0009799 skos:exactMatch MP:0003342 semapv:LogicalReasoning Supernumerary spleens accessory spleen -HP:0012569 skos:exactMatch MP:0003377 semapv:LogicalReasoning Delayed menarche late onset of menarche -HP:0011767 skos:exactMatch MP:0003431 semapv:LogicalReasoning Abnormality of the parathyroid physiology abnormal parathyroid gland physiology -HP:0008208 skos:exactMatch MP:0003493 semapv:LogicalReasoning Parathyroid hyperplasia parathyroid gland hyperplasia -HP:0008249 skos:exactMatch MP:0003498 semapv:LogicalReasoning Thyroid hyperplasia thyroid gland hyperplasia -HP:0040253 skos:exactMatch MP:0003529 semapv:LogicalReasoning Increased size of the clitoris enlarged clitoris -HP:0040254 skos:exactMatch MP:0003530 semapv:LogicalReasoning Decreased size of the clitoris small clitoris -HP:0008697 skos:exactMatch MP:0003576 semapv:LogicalReasoning Hypoplasia of the fallopian tube oviduct hypoplasia -HP:0000068 skos:exactMatch MP:0003591 semapv:LogicalReasoning Urethral atresia urethra atresia -HP:0008661 skos:exactMatch MP:0003592 semapv:LogicalReasoning Urethral stenosis urethra stricture -HP:0005343 skos:exactMatch MP:0003617 semapv:LogicalReasoning Hypoplasia of the bladder urinary bladder hypoplasia -HP:0012639 skos:exactMatch MP:0003632 semapv:LogicalReasoning Abnormality of nervous system morphology abnormal nervous system morphology -HP:0012638 skos:exactMatch MP:0003633 semapv:LogicalReasoning Abnormality of nervous system physiology abnormal nervous system physiology -HP:0003750 skos:exactMatch MP:0003646 semapv:LogicalReasoning Increased muscle fatiguability muscle fatigue -HP:0200007 skos:exactMatch MP:0003671 semapv:LogicalReasoning Abnormal size of the palpebral fissures abnormal eyelid aperture -HP:0000107 skos:exactMatch MP:0003675 semapv:LogicalReasoning Renal cyst kidney cysts -HP:0000385 skos:exactMatch MP:0003679 semapv:LogicalReasoning Small earlobe ear lobe hypoplasia -HP:0011314 skos:exactMatch MP:0003723 semapv:LogicalReasoning Abnormality of long bone morphology abnormal long bone morphology -HP:0008544 skos:exactMatch MP:0003736 semapv:LogicalReasoning Abnormally folded helix folded helix -HP:0001999 skos:exactMatch MP:0003743 semapv:LogicalReasoning Abnormal facial shape abnormal facial morphology -HP:0002707 skos:exactMatch MP:0003768 semapv:LogicalReasoning Palate telangiectasia palatal telangiectases -HP:0002298 skos:exactMatch MP:0003815 semapv:LogicalReasoning Absent hair hairless -HP:0001711 skos:exactMatch MP:0003921 semapv:LogicalReasoning Abnormal left ventricle morphology abnormal heart left ventricle morphology -HP:0025580 skos:exactMatch MP:0003922 semapv:LogicalReasoning Abnormal right atrium morphology abnormal heart right atrium morphology -HP:0025579 skos:exactMatch MP:0003923 semapv:LogicalReasoning Abnormal left atrium morphology abnormal heart left atrium morphology -HP:0003234 skos:exactMatch MP:0003978 semapv:LogicalReasoning Decreased plasma carnitine decreased circulating carnitine level -HP:0010994 skos:exactMatch MP:0004077 semapv:LogicalReasoning Abnormal corpus striatum morphology abnormal striatum morphology -HP:0007343 skos:exactMatch MP:0004166 semapv:LogicalReasoning Abnormal morphology of the limbic system abnormal limbic system morphology -HP:0009893 skos:exactMatch MP:0004176 semapv:LogicalReasoning Telangiectasia of the ear ear telangiectases -HP:0011456 skos:exactMatch MP:0004204 semapv:LogicalReasoning Absent stapes absent stapes -HP:0001655 skos:exactMatch MP:0004225 semapv:LogicalReasoning Patent foramen ovale patent cardiac foramen ovale -HP:0012767 skos:exactMatch MP:0004258 semapv:LogicalReasoning Abnormal placental size abnormal placenta size -HP:0006267 skos:exactMatch MP:0004260 semapv:LogicalReasoning Large placenta enlarged placenta -HP:0011377 skos:exactMatch MP:0004314 semapv:LogicalReasoning Aplasia of the vestibule absent inner ear vestibule -HP:0000882 skos:exactMatch MP:0004344 semapv:LogicalReasoning Hypoplastic scapulae scapular bone hypoplasia -HP:0012744 skos:exactMatch MP:0004349 semapv:LogicalReasoning Femoral aplasia absent femur -HP:0005792 skos:exactMatch MP:0004351 semapv:LogicalReasoning Short humerus short humerus -HP:0002984 skos:exactMatch MP:0004356 semapv:LogicalReasoning Hypoplasia of the radius radius hypoplasia -HP:0010504 skos:exactMatch MP:0004357 semapv:LogicalReasoning Increased length of the tibia long tibia -HP:0003194 skos:exactMatch MP:0004471 semapv:LogicalReasoning Short nasal bridge short nasal bone -HP:0040163 skos:exactMatch MP:0004509 semapv:LogicalReasoning Abnormal pelvis bone morphology abnormal pelvic girdle bone morphology -HP:0004791 skos:exactMatch MP:0004547 semapv:LogicalReasoning Esophageal ulceration esophageal ulcer -HP:0009555 skos:exactMatch MP:0004555 semapv:LogicalReasoning Hypoplasia of the pharynx pharynx hypoplasia -HP:3000078 skos:exactMatch MP:0004594 semapv:LogicalReasoning Abnormal mandible coronoid process morphology abnormal mandibular coronoid process morphology -HP:3000077 skos:exactMatch MP:0004595 semapv:LogicalReasoning Abnormal mandible condylar process morphology abnormal mandibular condyloid process morphology -HP:0030040 skos:exactMatch MP:0004621 semapv:LogicalReasoning Fused lumbar vertebrae lumbar vertebral fusion -HP:0030039 skos:exactMatch MP:0004623 semapv:LogicalReasoning Fused thoracic vertebrae thoracic vertebral fusion -HP:0001547 skos:exactMatch MP:0004624 semapv:LogicalReasoning Abnormality of the rib cage abnormal thoracic cage morphology -HP:0010049 skos:exactMatch MP:0004634 semapv:LogicalReasoning Short metacarpal short metacarpal bones -HP:0010493 skos:exactMatch MP:0004638 semapv:LogicalReasoning Long metacarpals elongated metacarpal bones -HP:0009701 skos:exactMatch MP:0004639 semapv:LogicalReasoning Metacarpal synostosis fused metacarpal bones -HP:0001440 skos:exactMatch MP:0004642 semapv:LogicalReasoning Metatarsal synostosis fused metatarsal bones -HP:0008479 skos:exactMatch MP:0004667 semapv:LogicalReasoning Hypoplastic vertebral bodies vertebral body hypoplasia -HP:0005645 skos:exactMatch MP:0004685 semapv:LogicalReasoning Intervertebral disk calcification calcified intervertebral disk -HP:0003026 skos:exactMatch MP:0004686 semapv:LogicalReasoning Short long bone decreased length of long bones -HP:0008428 skos:exactMatch MP:0004687 semapv:LogicalReasoning Vertebral clefting split vertebrae -HP:0003175 skos:exactMatch MP:0004690 semapv:LogicalReasoning Hypoplastic ischia ischium hypoplasia -HP:0003173 skos:exactMatch MP:0004693 semapv:LogicalReasoning Hypoplastic pubic bone pubis hypoplasia -HP:0002766 skos:exactMatch MP:0004704 semapv:LogicalReasoning Relatively short spine short vertebral column -HP:0011393 skos:exactMatch MP:0004719 semapv:LogicalReasoning Aplasia of the vestibular nerve. absent vestibular nerve -HP:0100879 skos:exactMatch MP:0004832 semapv:LogicalReasoning Enlarged ovaries enlarged ovary -HP:0005466 skos:exactMatch MP:0004869 semapv:LogicalReasoning Hypoplasia of the frontal bone frontal bone hypoplasia -HP:0010650 skos:exactMatch MP:0004871 semapv:LogicalReasoning Hypoplasia of the premaxilla premaxilla hypoplasia -HP:0002797 skos:exactMatch MP:0004993 semapv:LogicalReasoning Osteolysis decreased bone resorption -HP:0010976 skos:exactMatch MP:0005017 semapv:LogicalReasoning B lymphocytopenia decreased B cell number -HP:0005403 skos:exactMatch MP:0005018 semapv:LogicalReasoning Decrease in T cell count decreased T cell number -HP:0012176 skos:exactMatch MP:0005068 semapv:LogicalReasoning Abnormal natural killer cell morphology abnormal NK cell morphology -HP:0040071 skos:exactMatch MP:0005108 semapv:LogicalReasoning Abnormal morphology of ulna abnormal ulna morphology -HP:0000870 skos:exactMatch MP:0005139 semapv:LogicalReasoning Increased circulating prolactin concentration increased prolactin level -HP:0003362 skos:exactMatch MP:0005145 semapv:LogicalReasoning Increased VLDL cholesterol concentration increased circulating VLDL cholesterol level -HP:0031243 skos:exactMatch MP:0005146 semapv:LogicalReasoning Decreased VLDL cholesterol concentration decreased circulating VLDL cholesterol level -HP:0008687 skos:exactMatch MP:0005147 semapv:LogicalReasoning Hypoplasia of the prostate prostate gland hypoplasia -HP:0008724 skos:exactMatch MP:0005158 semapv:LogicalReasoning Hypoplasia of the ovary ovary hypoplasia -HP:0000593 skos:exactMatch MP:0005205 semapv:LogicalReasoning Abnormal anterior chamber morphology abnormal eye anterior chamber morphology -HP:0001939 skos:exactMatch MP:0005266 semapv:LogicalReasoning Abnormality of metabolism/homeostasis abnormal metabolism -HP:0001713 skos:exactMatch MP:0005294 semapv:LogicalReasoning Abnormal cardiac ventricle morphology abnormal heart ventricle morphology -HP:0011488 skos:exactMatch MP:0005301 semapv:LogicalReasoning Abnormal corneal endothelium morphology abnormal corneal endothelium morphology -HP:0008191 skos:exactMatch MP:0005314 semapv:LogicalReasoning Thyroid agenesis absent thyroid gland -HP:0002904 skos:exactMatch MP:0005344 semapv:LogicalReasoning Hyperbilirubinemia increased circulating bilirubin level -HP:0000853 skos:exactMatch MP:0005355 semapv:LogicalReasoning Goiter enlarged thyroid gland -HP:0011063 skos:exactMatch MP:0005358 semapv:LogicalReasoning Abnormality of incisor morphology abnormal incisor morphology -HP:0002990 skos:exactMatch MP:0005430 semapv:LogicalReasoning Fibular aplasia absent fibula -HP:0008247 skos:exactMatch MP:0005477 semapv:LogicalReasoning Euthyroid hyperthyroxinemia increased circulating thyroxine level -HP:0011788 skos:exactMatch MP:0005480 semapv:LogicalReasoning Increased circulating free T3 increased circulating triiodothyronine level -HP:0011277 skos:exactMatch MP:0005502 semapv:LogicalReasoning Abnormality of the urinary system physiology abnormal renal/urinary system physiology -HP:0100261 skos:exactMatch MP:0005503 semapv:LogicalReasoning Abnormal tendon morphology abnormal tendon morphology -HP:0011842 skos:exactMatch MP:0005508 semapv:LogicalReasoning Abnormality of skeletal morphology abnormal skeleton morphology -HP:0010790 skos:exactMatch MP:0005536 semapv:LogicalReasoning Hyoplasia of the Leydig cells Leydig cell hypoplasia -HP:0012101 skos:exactMatch MP:0005554 semapv:LogicalReasoning Decreased serum creatinine decreased circulating creatinine level -HP:0001900 skos:exactMatch MP:0005564 semapv:LogicalReasoning Increased hemoglobin increased hemoglobin content -HP:0000139 skos:exactMatch MP:0005577 semapv:LogicalReasoning Uterine prolapse uterus prolapse -HP:0009892 skos:exactMatch MP:0005579 semapv:LogicalReasoning Anotia absent outer ear -HP:0012364 skos:exactMatch MP:0005618 semapv:LogicalReasoning Decreased urinary potassium decreased urine potassium level -HP:0003081 skos:exactMatch MP:0005619 semapv:LogicalReasoning Increased urinary potassium increased urine potassium level -HP:0011017 skos:exactMatch MP:0005621 semapv:LogicalReasoning Abnormal cellular physiology abnormal cell physiology -HP:0002153 skos:exactMatch MP:0005627 semapv:LogicalReasoning Hyperkalemia increased circulating potassium level -HP:0002900 skos:exactMatch MP:0005628 semapv:LogicalReasoning Hypokalemia decreased circulating potassium level -HP:0031793 skos:exactMatch MP:0005669 semapv:LogicalReasoning Increased serum leptin increased circulating leptin level -HP:0008322 skos:exactMatch MP:0006035 semapv:LogicalReasoning Abnormal mitochondrial morphology abnormal mitochondrion morphology -HP:0010444 skos:exactMatch MP:0006048 semapv:LogicalReasoning Pulmonary insufficiency pulmonary valve regurgitation -HP:0001671 skos:exactMatch MP:0006113 semapv:LogicalReasoning Abnormal cardiac septum morphology abnormal heart septum morphology -HP:0004380 skos:exactMatch MP:0006116 semapv:LogicalReasoning Aortic valve calcification calcified aortic valve -HP:0004382 skos:exactMatch MP:0006121 semapv:LogicalReasoning Mitral valve calcification calcified mitral valve -HP:0003207 skos:exactMatch MP:0006133 semapv:LogicalReasoning Arterial calcification calcified artery -HP:0100545 skos:exactMatch MP:0006135 semapv:LogicalReasoning Arterial stenosis artery stenosis -HP:0007862 skos:exactMatch MP:0006188 semapv:LogicalReasoning Retinal calcification calcified retina -HP:0011885 skos:exactMatch MP:0006203 semapv:LogicalReasoning Hemorrhage of the eye eye hemorrhage -HP:0007990 skos:exactMatch MP:0006230 semapv:LogicalReasoning Hypoplastic iris stroma iris stroma hypoplasia -HP:0011372 skos:exactMatch MP:0006285 semapv:LogicalReasoning Aplasia of the inner ear absent inner ear -HP:0011839 skos:exactMatch MP:0006387 semapv:LogicalReasoning Abnormal T cell count abnormal T cell number -HP:0002843 skos:exactMatch MP:0008037 semapv:LogicalReasoning Abnormal T cell morphology abnormal T cell morphology -HP:0040089 skos:exactMatch MP:0008043 semapv:LogicalReasoning Abnormal natural killer cell count abnormal NK cell number -HP:0005415 skos:exactMatch MP:0008079 semapv:LogicalReasoning Decreased proportion of CD8-positive T cells "decreased CD8-positive alpha-beta T cell number" -HP:0011472 skos:exactMatch MP:0008108 semapv:LogicalReasoning Abnormality of small intestinal villus morphology abnormal small intestinal villus morphology -HP:0005513 skos:exactMatch MP:0008254 semapv:LogicalReasoning Increased megakaryocyte count increased megakaryocyte cell number -HP:0005548 skos:exactMatch MP:0008255 semapv:LogicalReasoning Megakaryocytopenia decreased megakaryocyte cell number -HP:0008239 skos:exactMatch MP:0008301 semapv:LogicalReasoning Adrenal medullary hypoplasia adrenal medulla hyperplasia -HP:0010627 skos:exactMatch MP:0008365 semapv:LogicalReasoning Anterior pituitary hypoplasia adenohypophysis hypoplasia -HP:0002849 skos:exactMatch MP:0008523 semapv:LogicalReasoning Absence of lymph node germinal center absent lymph node germinal center -HP:0000113 skos:exactMatch MP:0008528 semapv:LogicalReasoning Polycystic kidney dysplasia polycystic kidney -HP:0007485 skos:exactMatch MP:0008843 semapv:LogicalReasoning Absence of subcutaneous fat absent subcutaneous adipose tissue -HP:0003758 skos:exactMatch MP:0008844 semapv:LogicalReasoning Reduced subcutaneous adipose tissue decreased subcutaneous adipose tissue amount -HP:0012081 skos:exactMatch MP:0008914 semapv:LogicalReasoning Enlarged cerebellum enlarged cerebellum -HP:0012504 skos:exactMatch MP:0008936 semapv:LogicalReasoning Abnormal size of pituitary gland abnormal pituitary gland size -HP:0006424 skos:exactMatch MP:0008951 semapv:LogicalReasoning Elongated radius long radius -HP:0012133 skos:exactMatch MP:0008973 semapv:LogicalReasoning Erythroid hypoplasia decreased erythroid progenitor cell number -HP:0010303 skos:exactMatch MP:0009023 semapv:LogicalReasoning Abnormal spinal meningeal morphology abnormal spinal cord meninges morphology -HP:0040252 skos:exactMatch MP:0009100 semapv:LogicalReasoning Abnormal size of the clitoris abnormal clitoris size -HP:0004510 skos:exactMatch MP:0009171 semapv:LogicalReasoning Pancreatic islet-cell hyperplasia enlarged pancreatic islets -HP:0000978 skos:exactMatch MP:0009276 semapv:LogicalReasoning Bruising susceptibility ecchymosis -HP:0012613 skos:exactMatch MP:0009472 semapv:LogicalReasoning Increased urinary sulfate increased urine sulfate level -HP:0025057 skos:exactMatch MP:0009944 semapv:LogicalReasoning Abnormality of olfactory lobe morphology abnormal olfactory lobe morphology -HP:0008887 skos:exactMatch MP:0010025 semapv:LogicalReasoning Adipose tissue loss decreased total body fat amount -HP:0040326 skos:exactMatch MP:0010059 semapv:LogicalReasoning Hypoplasia of the olfactory bulb olfactory bulb hypoplasia -HP:0040081 skos:exactMatch MP:0010089 semapv:LogicalReasoning Abnormal circulating creatine kinase concentration abnormal circulating creatine kinase level -HP:0003236 skos:exactMatch MP:0010090 semapv:LogicalReasoning Elevated serum creatine kinase increased circulating creatine kinase level -HP:0004348 skos:exactMatch MP:0010119 semapv:LogicalReasoning Abnormality of bone mineral density abnormal bone mineral density -HP:0012093 skos:exactMatch MP:0010147 semapv:LogicalReasoning Abnormality of endocrine pancreas physiology abnormal endocrine pancreas physiology -HP:0012092 skos:exactMatch MP:0010148 semapv:LogicalReasoning Abnormality of exocrine pancreas physiology abnormal exocrine pancreas physiology -HP:0011068 skos:exactMatch MP:0010353 semapv:LogicalReasoning Odontoma increased odontoma incidence -HP:0006568 skos:exactMatch MP:0010400 semapv:LogicalReasoning Increased hepatic glycogen content increased liver glycogen level -HP:0011103 skos:exactMatch MP:0010429 semapv:LogicalReasoning Abnormal left ventricular outflow tract morphology abnormal heart left ventricle outflow tract morphology -HP:0001680 skos:exactMatch MP:0010463 semapv:LogicalReasoning Coarctation of aorta aorta stenosis -HP:0004963 skos:exactMatch MP:0010522 semapv:LogicalReasoning Calcification of the aorta calcified aorta -HP:0004962 skos:exactMatch MP:0010523 semapv:LogicalReasoning Thoracic aorta calcification calcified thoracic aorta -HP:0005303 skos:exactMatch MP:0010524 semapv:LogicalReasoning Aortic arch calcification calcified aortic arch -HP:0005304 skos:exactMatch MP:0010528 semapv:LogicalReasoning Hypoplastic pulmonary veins pulmonary vein hypoplasia -HP:0011138 skos:exactMatch MP:0010678 semapv:LogicalReasoning Abnormality of skin adnexa morphology abnormal skin adnexa morphology -HP:0100671 skos:exactMatch MP:0010867 semapv:LogicalReasoning Abnormal trabecular bone morphology abnormal bone trabecula morphology -HP:0002043 skos:exactMatch MP:0010884 semapv:LogicalReasoning Esophageal stricture esophagus stenosis -HP:0012676 skos:exactMatch MP:0011214 semapv:LogicalReasoning Copper accumulation in brain increased brain copper level -HP:0000092 skos:exactMatch MP:0011346 semapv:LogicalReasoning Tubular atrophy renal tubule atrophy -HP:0002119 skos:exactMatch MP:0011380 semapv:LogicalReasoning Ventriculomegaly enlarged brain ventricles -HP:0000028 skos:exactMatch MP:0011410 semapv:LogicalReasoning Cryptorchidism ectopic testis -HP:0011935 skos:exactMatch MP:0011424 semapv:LogicalReasoning Decreased urinary urate decreased urine uric acid level -HP:0012601 skos:exactMatch MP:0011460 semapv:LogicalReasoning Hypochloriduria decreased urine chloride ion level -HP:0045011 skos:exactMatch MP:0011463 semapv:LogicalReasoning Decreased urine bicarbonate concentration decreased urine bicarbonate level -HP:0003541 skos:exactMatch MP:0011473 semapv:LogicalReasoning Urinary glycosaminoglycan excretion increased urine glycosaminoglycan level -HP:0030321 skos:exactMatch MP:0011513 semapv:LogicalReasoning Abnormal vertebral artery morphology abnormal vertebral artery morphology -HP:0012611 skos:exactMatch MP:0011537 semapv:LogicalReasoning Increased urinary urate uraturia -HP:0012517 skos:exactMatch MP:0011594 semapv:LogicalReasoning Reduced catalase activity decreased catalase activity -HP:0001010 skos:exactMatch MP:0011627 semapv:LogicalReasoning Hypopigmentation of the skin decreased skin pigmentation -HP:0040014 skos:exactMatch MP:0011628 semapv:LogicalReasoning Increased mitochondrial number increased mitochondria number -HP:0040013 skos:exactMatch MP:0011629 semapv:LogicalReasoning Decreased mitochondrial number decreased mitochondria number -HP:0010906 skos:exactMatch MP:0011652 semapv:LogicalReasoning Hyperhistidinemia increased circulating histidine level -HP:0500145 skos:exactMatch MP:0011653 semapv:LogicalReasoning Hypohistidinemia decreased circulating histidine level -HP:0012688 skos:exactMatch MP:0011728 semapv:LogicalReasoning Abnormality of pineal physiology abnormal pineal gland physiology -HP:0005235 skos:exactMatch MP:0011878 semapv:LogicalReasoning Jejunal atresia jejunum atresia -HP:0011102 skos:exactMatch MP:0011879 semapv:LogicalReasoning Ileal atresia ileum atresia -HP:0011486 skos:exactMatch MP:0011961 semapv:LogicalReasoning Abnormality of corneal thickness abnormal cornea thickness -HP:0011487 skos:exactMatch MP:0011962 semapv:LogicalReasoning Increased corneal thickness increased cornea thickness -HP:0100512 skos:exactMatch MP:0012336 semapv:LogicalReasoning Low levels of vitamin D decreased vitamin D level -HP:0007705 skos:exactMatch MP:0012351 semapv:LogicalReasoning Corneal degeneration cornea degeneration -HP:0012310 skos:exactMatch MP:0012441 semapv:LogicalReasoning Abnormal monocyte count abnormal monocyte cell number -HP:0031806 skos:exactMatch MP:0012442 semapv:LogicalReasoning Abnormal basophil count abnormal basophil cell number -HP:3000062 skos:exactMatch MP:0012730 semapv:LogicalReasoning Abnormal internal carotid artery morphology abnormal internal carotid artery morphology -HP:0011073 skos:exactMatch MP:0013129 semapv:LogicalReasoning Abnormality of dental color abnormal tooth color -HP:0000190 skos:exactMatch MP:0013263 semapv:LogicalReasoning Abnormal oral frenulum morphology abnormal tongue frenulum morphology -HP:0430009 skos:exactMatch MP:0013395 semapv:LogicalReasoning Hypoplasia of eyelid eyelid hypoplasia -HP:0007734 skos:exactMatch MP:0013453 semapv:LogicalReasoning Enlarged lacrimal glands enlarged lacrimal gland -HP:0020047 skos:exactMatch MP:0013658 semapv:LogicalReasoning Abnormal myeloid cell morphology abnormal myeloid cell morphology -HP:0500133 skos:exactMatch MP:0013724 semapv:LogicalReasoning Hypotyrosinemia decreased circulating tyrosine level -HP:0007774 skos:exactMatch MP:0013743 semapv:LogicalReasoning Hypoplasia of the ciliary body ciliary body hypoplasia -HP:0008165 skos:exactMatch MP:0013764 semapv:LogicalReasoning Decreased proportion circulating T-helper cells decreased T-helper cell number -HP:0100596 skos:exactMatch MP:0013791 semapv:LogicalReasoning Absent nares absent external nares -HP:0009145 skos:exactMatch MP:0013821 semapv:LogicalReasoning Abnormal cerebral artery morphology abnormal cerebral artery morphology -HP:0010764 skos:exactMatch MP:0013898 semapv:LogicalReasoning Short eyelashes short eyelid cilia -HP:0011756 skos:exactMatch MP:0013926 semapv:LogicalReasoning Posterior pituitary agenesis absent neurohypophysis -HP:0011473 skos:exactMatch MP:0014078 semapv:LogicalReasoning Villous atrophy small intestinal villus atrophy -HP:0030326 skos:exactMatch MP:0020202 semapv:LogicalReasoning Abnormal macrophage count abnormal macrophage cell number -HP:0012675 skos:exactMatch MP:0020365 semapv:LogicalReasoning Iron accumulation in brain increased brain iron level -HP:0003166 skos:exactMatch MP:0020405 semapv:LogicalReasoning Increased urinary taurine taurinuria -HP:0003572 skos:exactMatch MP:0020837 semapv:LogicalReasoning Low plasma citrulline decreased circulating citrulline level -HP:0002007 skos:exactMatch MP:0030049 semapv:LogicalReasoning Frontal bossing prominent forehead -HP:0040309 skos:exactMatch MP:0030050 semapv:LogicalReasoning Increased size of the mandible large mandible -HP:0001593 skos:exactMatch MP:0030080 semapv:LogicalReasoning Maxillary lateral incisor microdontia small lower incisors -HP:0010669 skos:exactMatch MP:0030112 semapv:LogicalReasoning Hypoplasia of the zygomatic bone zygomatic bone hypoplasia -HP:0007628 skos:exactMatch MP:0030259 semapv:LogicalReasoning Mandibular condyle hypoplasia mandibular condyloid process hypoplasia -HP:0000278 skos:exactMatch MP:0030273 semapv:LogicalReasoning Retrognathia mandibular retrognathia -HP:0005469 skos:exactMatch MP:0030289 semapv:LogicalReasoning Flat occiput flat occipital bone -HP:0008551 skos:exactMatch MP:0030297 semapv:LogicalReasoning Microtia outer ear hypoplasia -HP:0000272 skos:exactMatch MP:0030377 semapv:LogicalReasoning Malar flattening zygomatic arch hypoplasia -HP:0006308 skos:exactMatch MP:0030466 semapv:LogicalReasoning Atrophy of alveolar ridges alveolar process atrophy -HP:0500181 skos:exactMatch MP:0030638 semapv:LogicalReasoning Hypertaurinemia increased circulating taurine level -HP:0500182 skos:exactMatch MP:0030639 semapv:LogicalReasoning Hypotaurinemia decreased circulating taurine level -HP:0500136 skos:exactMatch MP:0030704 semapv:LogicalReasoning Hypothreoninemia decreased circulating threonine level -HP:0500132 skos:exactMatch MP:0030728 semapv:LogicalReasoning Hypovalinemia decreased circulating valine level -HP:0500253 skos:exactMatch MP:0030734 semapv:LogicalReasoning Increased level of gamma-aminobutyric acid in urine increased urine gamma-aminobutyric acid level -HP:0003345 skos:exactMatch MP:0030772 semapv:LogicalReasoning Elevated urinary norepinephrine increased urine noradrenaline level -HP:0006261 skos:exactMatch MP:0030813 semapv:LogicalReasoning Abnormal phalangeal joint morphology of the hand abnormal hand interphalangeal joint morphology +# curie_map: +# HP: http://purl.obolibrary.org/obo/HP_ +# MP: http://purl.obolibrary.org/obo/MP_ +# owl: http://www.w3.org/2002/07/owl# +# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# +# rdfs: http://www.w3.org/2000/01/rdf-schema# +# semapv: https://w3id.org/semapv/vocab/ +# skos: http://www.w3.org/2004/02/skos/core# +# sssom: https://w3id.org/sssom/ +# license: https://creativecommons.org/publicdomain/zero/1.0/ +# mapping_provider: http://purl.obolibrary.org/obo/upheno.owl +# mapping_set_id: https://w3id.org/sssom/mappings/27f85fe9-8a72-4e76-909b-7ba4244d9ede +subject_id subject_label predicate_id object_id object_label mapping_justification +HP:0000175 Cleft palate skos:exactMatch MP:0000111 cleft palate semapv:LexicalMatching +HP:0000252 Microcephaly skos:exactMatch MP:0000433 microcephaly semapv:LexicalMatching +HP:0000260 Wide anterior fontanel skos:exactMatch MP:0000085 large anterior fontanelle semapv:LexicalMatching +HP:0000375 Abnormal cochlea morphology skos:exactMatch MP:0000031 abnormal cochlea morphology semapv:LexicalMatching +HP:0000411 Protruding ear skos:exactMatch MP:0000021 prominent ears semapv:LexicalMatching +HP:0000822 Hypertension skos:exactMatch MP:0000231 hypertension semapv:LexicalMatching +HP:0001336 Myoclonus skos:exactMatch MP:0000243 myoclonus semapv:LexicalMatching +HP:0001363 Craniosynostosis skos:exactMatch MP:0000081 premature cranial suture closure semapv:LexicalMatching +HP:0001596 Alopecia skos:exactMatch MP:0000414 alopecia semapv:LexicalMatching +HP:0001627 Abnormal heart morphology skos:exactMatch MP:0000266 abnormal heart morphology semapv:LexicalMatching +HP:0001633 Abnormal mitral valve morphology skos:exactMatch MP:0000286 abnormal mitral valve morphology semapv:LexicalMatching +HP:0001667 Right ventricular hypertrophy skos:exactMatch MP:0000276 heart right ventricle hypertrophy semapv:LexicalMatching +HP:0001679 Abnormal aortic morphology skos:exactMatch MP:0000272 abnormal aorta morphology semapv:LexicalMatching +HP:0001719 Double outlet right ventricle skos:exactMatch MP:0000284 double outlet right ventricle semapv:LexicalMatching +HP:0001882 Leukopenia skos:exactMatch MP:0000221 decreased leukocyte cell number semapv:LexicalMatching +HP:0001913 Granulocytopenia skos:exactMatch MP:0000334 decreased granulocyte number semapv:LexicalMatching +HP:0001974 Leukocytosis skos:exactMatch MP:0000218 increased leukocyte cell number semapv:LexicalMatching +HP:0001978 Extramedullary hematopoiesis skos:exactMatch MP:0000240 extramedullary hematopoiesis semapv:LexicalMatching +HP:0001981 Schistocytosis skos:exactMatch MP:0000314 schistocytosis semapv:LexicalMatching +HP:0002212 Curly hair skos:exactMatch MP:0000410 waved hair semapv:LexicalMatching +HP:0002659 Increased susceptibility to fractures skos:exactMatch MP:0000061 fragile skeleton semapv:LexicalMatching +HP:0002763 Abnormal cartilage morphology skos:exactMatch MP:0000163 abnormal cartilage morphology semapv:LexicalMatching +HP:0003307 Hyperlordosis skos:exactMatch MP:0000162 lordosis semapv:LexicalMatching +HP:0004349 Reduced bone mineral density skos:exactMatch MP:0000063 decreased bone mineral density semapv:LexicalMatching +HP:0006288 Advanced eruption of teeth skos:exactMatch MP:0000122 premature tooth eruption semapv:LexicalMatching +HP:0008551 Microtia skos:exactMatch MP:0000018 small ears semapv:LexicalMatching +HP:0009124 Abnormal adipose tissue morphology skos:exactMatch MP:0000003 abnormal adipose tissue morphology semapv:LexicalMatching +HP:0009910 Aplasia of the middle ear ossicles skos:exactMatch MP:0000040 absent middle ear ossicles semapv:LexicalMatching +HP:0009939 Mandibular aplasia skos:exactMatch MP:0000087 absent mandible semapv:LexicalMatching +HP:0011002 Osteopetrosis skos:exactMatch MP:0000067 osteopetrosis semapv:LexicalMatching +HP:0011457 Loss of eyelashes skos:exactMatch MP:0000425 loss of eyelid cilia semapv:LexicalMatching +HP:0011897 Neutrophilia skos:exactMatch MP:0000219 increased neutrophil cell number semapv:LexicalMatching +HP:0012234 Agranulocytosis skos:exactMatch MP:0000334 decreased granulocyte number semapv:LexicalMatching +HP:0012543 Hemosiderinuria skos:exactMatch MP:0000327 hemosiderinuria semapv:LexicalMatching +HP:0025065 Abnormal mean corpuscular volume skos:exactMatch MP:0000226 abnormal mean corpuscular volume semapv:LexicalMatching +HP:0025084 Folliculitis skos:exactMatch MP:0000376 folliculitis semapv:LexicalMatching +HP:0031377 Abnormal cell proliferation skos:exactMatch MP:0000350 abnormal cell proliferation semapv:LexicalMatching +HP:0031851 Reduced hematocrit skos:exactMatch MP:0000208 decreased hematocrit semapv:LexicalMatching +HP:0032310 Granulocytosis skos:exactMatch MP:0000322 increased granulocyte number semapv:LexicalMatching +HP:0100629 Midline facial cleft skos:exactMatch MP:0000108 midline facial cleft semapv:LexicalMatching +HP:0100671 Abnormal trabecular bone morphology skos:exactMatch MP:0000130 abnormal trabecular bone morphology semapv:LexicalMatching +HP:0400001 Chin with vertical crease skos:exactMatch MP:0000114 cleft chin semapv:LexicalMatching + diff --git a/examples/external/example1.sssom.tsv b/examples/external/example1.sssom.tsv index f67f5542..9abfcc11 100644 --- a/examples/external/example1.sssom.tsv +++ b/examples/external/example1.sssom.tsv @@ -1,6 +1,6 @@ -subject_id subject_label predicate_id object_id object_label confidence comment mapping_justification mapping_date author_id subject_source_version object_source_version -KF_FOOD:F001 apple skos:exactMatch FOODON:00002473 apple (whole) 0.95 We could map to FOODON:03310788 instead to cover sliced apples, but only "whole" apple types exist. semapv:ManualMappingCuration 2022-05-02 orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl -KF_FOOD:F002 gala skos:exactMatch FOODON:00003348 Gala apple (whole) 1 semapv:ManualMappingCuration 2022-05-02 orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl -KF_FOOD:F003 pink skos:exactMatch FOODON:00004186 Pink apple (whole) 0.9 We could map to FOODON:00004187 instead which more specifically refers to "raw" Pink apples. Decided against to be consistent with other mapping choices. semapv:ManualMappingCuration 2022-05-02 orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl -KF_FOOD:F004 braeburn skos:exactMatch sssom:NoMapping 1 semapv:ManualMappingCuration 2022-05-02 orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl -KF_FOOD:F004 braeburn skos:broadMatch FOODON:00002473 apple (whole) 1 semapv:ManualMappingCuration 2022-05-02 orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl \ No newline at end of file +subject_id subject_label predicate_id object_id object_label mapping_justification author_id object_source_version mapping_date confidence comment +KF_FOOD:F001 apple skos:exactMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.95 "We could map to FOODON:03310788 instead to cover sliced apples, but only ""whole"" apple types exist." +KF_FOOD:F002 gala skos:exactMatch FOODON:00003348 Gala apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0 +KF_FOOD:F003 pink skos:exactMatch FOODON:00004187 Pink apple (whole, raw) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 0.9 "We could map to FOODON:00004187 instead which more specifically refers to ""raw"" Pink apples. Decided against to be consistent with other mapping choices." +KF_FOOD:F004 braeburn skos:exactMatch sssom:NoMapping semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0 +KF_FOOD:F004 braeburn skos:broadMatch FOODON:00002473 apple (whole) semapv:ManualMappingCuration orcid:0000-0002-7356-1779 http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl 2022-05-02 1.0 diff --git a/examples/external/example1.sssom.yml b/examples/external/example1.sssom.yml index 93e1fb60..cea3eb78 100644 --- a/examples/external/example1.sssom.yml +++ b/examples/external/example1.sssom.yml @@ -1,13 +1,23 @@ -mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv -license: https://creativecommons.org/licenses/by/4.0/ -mapping_set_version: "2022-06-01" -mapping_set_description: "Manually curated alignment of KEWL FOODIE INC internal food and nutrition database with Food Ontology (FOODON). Intended to be used for ontological analysis and grouping of KEWL FOODIE INC related data." -object_source: wikidata:Q55118395 -subject_source: KF_FOOD:DB +comment: We could map to FOODON:00004187 instead which more specifically refers to + 'raw' Pink apples. Decided against to be consistent with other mapping choices. curie_map: - KF_FOOD: https://kewl-foodie.inc/food/ - wikidata: http://www.wikidata.org/entity/ FOODON: http://purl.obolibrary.org/obo/FOODON_ - sempav: https://w3id.org/semapv/ - skos: "http://www.w3.org/2004/02/skos/core#" - sssom: https://w3id.org/sssom/ \ No newline at end of file + KF_FOOD: https://kewl-foodie.inc/food/ + orcid: https://orcid.org/ + owl: http://www.w3.org/2002/07/owl# + rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# + rdfs: http://www.w3.org/2000/01/rdf-schema# + semapv: https://w3id.org/semapv/vocab/ + skos: http://www.w3.org/2004/02/skos/core# + sssom: https://w3id.org/sssom/ + wikidata: https://www.wikidata.org/wiki/ +license: https://creativecommons.org/licenses/by/4.0/ +mapping_date: '2022-05-02' +mapping_set_description: Manually curated alignment of KEWL FOODIE INC internal food + and nutrition database with Food Ontology (FOODON). Intended to be used for ontological + analysis and grouping of KEWL FOODIE INC related data. +mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv +mapping_set_version: '2022-05-01' +object_source: wikidata:Q55118395 +object_source_version: http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl +subject_source: KF_FOOD:DB \ No newline at end of file diff --git a/examples/external/mp-hp-exact-0.0.1.sssom.tsv b/examples/external/mp-hp-exact-0.0.1.sssom.tsv index a08d0008..aec846e0 100644 --- a/examples/external/mp-hp-exact-0.0.1.sssom.tsv +++ b/examples/external/mp-hp-exact-0.0.1.sssom.tsv @@ -1,1485 +1,43 @@ -subject_id predicate_id object_id mapping_justification subject_label object_label -HP:0009124 skos:exactMatch MP:0000003 semapv:LexicalMatching Abnormal adipose tissue morphology abnormal adipose tissue morphology -HP:0008551 skos:exactMatch MP:0000018 semapv:LexicalMatching Microtia small ears -HP:0000411 skos:exactMatch MP:0000021 semapv:LexicalMatching Protruding ear prominent ears -HP:0000375 skos:exactMatch MP:0000031 semapv:LexicalMatching Abnormal cochlea morphology abnormal cochlea morphology -HP:0009910 skos:exactMatch MP:0000040 semapv:LexicalMatching Aplasia of the middle ear ossicles absent middle ear ossicles -HP:0002659 skos:exactMatch MP:0000061 semapv:LexicalMatching Increased susceptibility to fractures fragile skeleton -HP:0004349 skos:exactMatch MP:0000063 semapv:LexicalMatching Reduced bone mineral density decreased bone mineral density -HP:0011002 skos:exactMatch MP:0000067 semapv:LexicalMatching Osteopetrosis osteopetrosis -HP:0001363 skos:exactMatch MP:0000081 semapv:LexicalMatching Craniosynostosis premature cranial suture closure -HP:0000260 skos:exactMatch MP:0000085 semapv:LexicalMatching Wide anterior fontanel large anterior fontanelle -HP:0009939 skos:exactMatch MP:0000087 semapv:LexicalMatching Mandibular aplasia absent mandible -HP:0100629 skos:exactMatch MP:0000108 semapv:LexicalMatching Midline facial cleft midline facial cleft -HP:0000175 skos:exactMatch MP:0000111 semapv:LexicalMatching Cleft palate cleft palate -HP:0400001 skos:exactMatch MP:0000114 semapv:LexicalMatching Chin with vertical crease cleft chin -HP:0006288 skos:exactMatch MP:0000122 semapv:LexicalMatching Advanced eruption of teeth premature tooth eruption -HP:0100671 skos:exactMatch MP:0000130 semapv:LexicalMatching Abnormal trabecular bone morphology abnormal trabecular bone morphology -HP:0003307 skos:exactMatch MP:0000162 semapv:LexicalMatching Hyperlordosis lordosis -HP:0002763 skos:exactMatch MP:0000163 semapv:LexicalMatching Abnormal cartilage morphology abnormal cartilage morphology -HP:0031851 skos:exactMatch MP:0000208 semapv:LexicalMatching Reduced hematocrit decreased hematocrit -HP:0001974 skos:exactMatch MP:0000218 semapv:LexicalMatching Leukocytosis increased leukocyte cell number -HP:0011897 skos:exactMatch MP:0000219 semapv:LexicalMatching Neutrophilia increased neutrophil cell number -HP:0001882 skos:exactMatch MP:0000221 semapv:LexicalMatching Leukopenia decreased leukocyte cell number -HP:0025065 skos:exactMatch MP:0000226 semapv:LexicalMatching Abnormal mean corpuscular volume abnormal mean corpuscular volume -HP:0000822 skos:exactMatch MP:0000231 semapv:LexicalMatching Hypertension hypertension -HP:0001978 skos:exactMatch MP:0000240 semapv:LexicalMatching Extramedullary hematopoiesis extramedullary hematopoiesis -HP:0001336 skos:exactMatch MP:0000243 semapv:LexicalMatching Myoclonus myoclonus -HP:0001627 skos:exactMatch MP:0000266 semapv:LexicalMatching Abnormal heart morphology abnormal heart morphology -HP:0001679 skos:exactMatch MP:0000272 semapv:LexicalMatching Abnormal aortic morphology abnormal aorta morphology -HP:0001667 skos:exactMatch MP:0000276 semapv:LexicalMatching Right ventricular hypertrophy heart right ventricle hypertrophy -HP:0001719 skos:exactMatch MP:0000284 semapv:LexicalMatching Double outlet right ventricle double outlet right ventricle -HP:0001633 skos:exactMatch MP:0000286 semapv:LexicalMatching Abnormal mitral valve morphology abnormal mitral valve morphology -HP:0001981 skos:exactMatch MP:0000314 semapv:LexicalMatching Schistocytosis schistocytosis -HP:0032310 skos:exactMatch MP:0000322 semapv:LexicalMatching Granulocytosis increased granulocyte number -HP:0012543 skos:exactMatch MP:0000327 semapv:LexicalMatching Hemosiderinuria hemosiderinuria -HP:0001913 skos:exactMatch MP:0000334 semapv:LexicalMatching Granulocytopenia decreased granulocyte number -HP:0012234 skos:exactMatch MP:0000334 semapv:LexicalMatching Agranulocytosis decreased granulocyte number -HP:0031377 skos:exactMatch MP:0000350 semapv:LexicalMatching Abnormal cell proliferation abnormal cell proliferation -HP:0025084 skos:exactMatch MP:0000376 semapv:LexicalMatching Folliculitis folliculitis -HP:0002212 skos:exactMatch MP:0000410 semapv:LexicalMatching Curly hair waved hair -HP:0001596 skos:exactMatch MP:0000414 semapv:LexicalMatching Alopecia alopecia -HP:0011457 skos:exactMatch MP:0000425 semapv:LexicalMatching Loss of eyelashes loss of eyelid cilia -HP:0000252 skos:exactMatch MP:0000433 semapv:LexicalMatching Microcephaly microcephaly -HP:0000256 skos:exactMatch MP:0000434 semapv:LexicalMatching Macrocephaly megacephaly -HP:0002457 skos:exactMatch MP:0000436 semapv:LexicalMatching Abnormal head movements abnormal head movements -HP:0030791 skos:exactMatch MP:0000454 semapv:LexicalMatching Abnormal jaw morphology abnormal jaw morphology -HP:0000347 skos:exactMatch MP:0000460 semapv:LexicalMatching Micrognathia mandible hypoplasia -HP:0002031 skos:exactMatch MP:0000467 semapv:LexicalMatching Abnormal esophagus morphology abnormal esophagus morphology -HP:0002242 skos:exactMatch MP:0000477 semapv:LexicalMatching Abnormal intestine morphology abnormal intestine morphology -HP:0031855 skos:exactMatch MP:0000508 semapv:LexicalMatching Right isomerism right-sided isomerism -HP:0000126 skos:exactMatch MP:0000519 semapv:LexicalMatching Hydronephrosis hydronephrosis -HP:0010958 skos:exactMatch MP:0000520 semapv:LexicalMatching Bilateral renal agenesis absent kidney -HP:0000803 skos:exactMatch MP:0000522 semapv:LexicalMatching Renal cortical cysts kidney cortex cysts -HP:0001947 skos:exactMatch MP:0000525 semapv:LexicalMatching Renal tubular acidosis renal tubular acidosis -HP:0000072 skos:exactMatch MP:0000536 semapv:LexicalMatching Hydroureter hydroureter -HP:0000021 skos:exactMatch MP:0000539 semapv:LexicalMatching Megacystis distended urinary bladder -HP:0031854 skos:exactMatch MP:0000542 semapv:LexicalMatching Left Isomerism left-sided isomerism -HP:0009826 skos:exactMatch MP:0000547 semapv:LexicalMatching Limb undergrowth short limbs -HP:0004231 skos:exactMatch MP:0000555 semapv:LexicalMatching Carpal bone aplasia absent carpal bone -HP:0009776 skos:exactMatch MP:0000561 semapv:LexicalMatching Adactyly adactyly -HP:0001159 skos:exactMatch MP:0000564 semapv:LexicalMatching Syndactyly syndactyly -HP:0001762 skos:exactMatch MP:0000576 semapv:LexicalMatching Talipes equinovarus clubfoot -HP:0002164 skos:exactMatch MP:0000579 semapv:LexicalMatching Nail dysplasia abnormal nail morphology -HP:0008404 skos:exactMatch MP:0000579 semapv:LexicalMatching Nail dystrophy abnormal nail morphology -HP:0002910 skos:exactMatch MP:0000609 semapv:LexicalMatching Elevated hepatic transaminase abnormal liver physiology -HP:0031865 skos:exactMatch MP:0000609 semapv:LexicalMatching Abnormal liver physiology abnormal liver physiology -HP:0001396 skos:exactMatch MP:0000610 semapv:LexicalMatching Cholestasis cholestasis -HP:0000952 skos:exactMatch MP:0000611 semapv:LexicalMatching Jaundice jaundice -HP:0010286 skos:exactMatch MP:0000613 semapv:LexicalMatching Abnormal salivary gland morphology abnormal salivary gland morphology -HP:0002307 skos:exactMatch MP:0000622 semapv:LexicalMatching Drooling increased salivation -HP:0003781 skos:exactMatch MP:0000622 semapv:LexicalMatching Excessive salivation increased salivation -HP:0000217 skos:exactMatch MP:0000623 semapv:LexicalMatching Xerostomia decreased salivation -HP:0100783 skos:exactMatch MP:0000629 semapv:LexicalMatching Breast aplasia absent mammary gland -HP:0008216 skos:exactMatch MP:0000639 semapv:LexicalMatching Adrenal gland dysgenesis abnormal adrenal gland morphology -HP:0001651 skos:exactMatch MP:0000644 semapv:LexicalMatching Dextrocardia dextrocardia -HP:0032226 skos:exactMatch MP:0000647 semapv:LexicalMatching Abnormal sebaceous gland morphology abnormal sebaceous gland morphology -HP:0410400 skos:exactMatch MP:0000648 semapv:LexicalMatching Absent sebaceous glands absent sebaceous gland -HP:0011599 skos:exactMatch MP:0000650 semapv:LexicalMatching Mesocardia mesocardia -HP:0000971 skos:exactMatch MP:0000674 semapv:LexicalMatching Abnormal sweat gland morphology abnormal sweat gland morphology -HP:0008188 skos:exactMatch MP:0000681 semapv:LexicalMatching Thyroid dysgenesis abnormal thyroid gland morphology -HP:0025408 skos:exactMatch MP:0000689 semapv:LexicalMatching Abnormal spleen morphology abnormal spleen morphology -HP:0002716 skos:exactMatch MP:0000702 semapv:LexicalMatching Lymphadenopathy enlarged lymph nodes -HP:0000778 skos:exactMatch MP:0000706 semapv:LexicalMatching Hypoplasia of the thymus small thymus -HP:0002487 skos:exactMatch MP:0000743 semapv:LexicalMatching Hyperkinetic movements muscle spasm -HP:0003394 skos:exactMatch MP:0000743 semapv:LexicalMatching Muscle spasm muscle spasm -HP:0001337 skos:exactMatch MP:0000745 semapv:LexicalMatching Tremor tremors -HP:0003202 skos:exactMatch MP:0000749 semapv:LexicalMatching Skeletal muscle atrophy muscle degeneration -HP:0003470 skos:exactMatch MP:0000753 semapv:LexicalMatching Paralysis paralysis -HP:0001543 skos:exactMatch MP:0000757 semapv:LexicalMatching Gastroschisis herniated abdominal wall -HP:0011805 skos:exactMatch MP:0000759 semapv:LexicalMatching Abnormal skeletal muscle morphology abnormal skeletal muscle morphology -HP:0030809 skos:exactMatch MP:0000762 semapv:LexicalMatching Abnormal tongue morphology abnormal tongue morphology -HP:0001273 skos:exactMatch MP:0000780 semapv:LexicalMatching Abnormal corpus callosum morphology abnormal corpus callosum morphology -HP:0025101 skos:exactMatch MP:0000808 semapv:LexicalMatching Dysgenesis of the hippocampus abnormal hippocampus development -HP:0001317 skos:exactMatch MP:0000849 semapv:LexicalMatching Abnormal cerebellum morphology abnormal cerebellum morphology -HP:0007033 skos:exactMatch MP:0000849 semapv:LexicalMatching Cerebellar dysplasia abnormal cerebellum morphology -HP:0001321 skos:exactMatch MP:0000852 semapv:LexicalMatching Cerebellar hypoplasia small cerebellum -HP:0030769 skos:exactMatch MP:0000914 semapv:LexicalMatching Exencephaly exencephaly -HP:0012447 skos:exactMatch MP:0000920 semapv:LexicalMatching Abnormal myelination abnormal myelination -HP:0011096 skos:exactMatch MP:0000921 semapv:LexicalMatching Peripheral demyelination demyelination -HP:0007373 skos:exactMatch MP:0000938 semapv:LexicalMatching Motor neuron atrophy motor neuron degeneration -HP:0001291 skos:exactMatch MP:0001056 semapv:LexicalMatching Abnormal cranial nerve morphology abnormal cranial nerve morphology -HP:0000135 skos:exactMatch MP:0001116 semapv:LexicalMatching Hypogonadism small gonad -HP:0031105 skos:exactMatch MP:0001120 semapv:LexicalMatching Abnormal uterus morphology abnormal uterus morphology -HP:0000142 skos:exactMatch MP:0001139 semapv:LexicalMatching Abnormal vagina morphology abnormal vagina morphology -HP:0000035 skos:exactMatch MP:0001146 semapv:LexicalMatching Abnormal testis morphology abnormal testis morphology -HP:0000053 skos:exactMatch MP:0001148 semapv:LexicalMatching Macroorchidism enlarged testis -HP:0008669 skos:exactMatch MP:0001156 semapv:LexicalMatching Abnormal spermatogenesis abnormal spermatogenesis -HP:0008775 skos:exactMatch MP:0001158 semapv:LexicalMatching Abnormal prostate morphology abnormal prostate gland morphology -HP:0002088 skos:exactMatch MP:0001175 semapv:LexicalMatching Abnormal lung morphology abnormal lung morphology -HP:0100750 skos:exactMatch MP:0001177 semapv:LexicalMatching Atelectasis atelectasis -HP:0005944 skos:exactMatch MP:0001181 semapv:LexicalMatching Bilateral lung agenesis absent lungs -HP:0040223 skos:exactMatch MP:0001182 semapv:LexicalMatching Pulmonary hemorrhage lung hemorrhage -HP:0010783 skos:exactMatch MP:0001190 semapv:LexicalMatching Erythema reddish skin -HP:0040189 skos:exactMatch MP:0001192 semapv:LexicalMatching Scaling skin scaly skin -HP:0000963 skos:exactMatch MP:0001199 semapv:LexicalMatching Thin skin thin skin -HP:0001072 skos:exactMatch MP:0001200 semapv:LexicalMatching Thickened skin thick skin -HP:0010648 skos:exactMatch MP:0001201 semapv:LexicalMatching Dermal translucency translucent skin -HP:0000992 skos:exactMatch MP:0001202 semapv:LexicalMatching Cutaneous photosensitivity skin photosensitivity -HP:0200037 skos:exactMatch MP:0001208 semapv:LexicalMatching Skin vesicle blistering -HP:0000962 skos:exactMatch MP:0001242 semapv:LexicalMatching Hyperkeratosis hyperkeratosis -HP:0001552 skos:exactMatch MP:0001268 semapv:LexicalMatching Barrel-shaped chest barrel chest -HP:0000528 skos:exactMatch MP:0001293 semapv:LexicalMatching Anophthalmia anophthalmia -HP:0000568 skos:exactMatch MP:0001297 semapv:LexicalMatching Microphthalmia microphthalmia -HP:0012376 skos:exactMatch MP:0001306 semapv:LexicalMatching Microphakia small lens -HP:0007957 skos:exactMatch MP:0001314 semapv:LexicalMatching Corneal opacity corneal opacity -HP:0007973 skos:exactMatch MP:0001325 semapv:LexicalMatching Retinal dysplasia abnormal retina morphology -HP:0000546 skos:exactMatch MP:0001326 semapv:LexicalMatching Retinal degeneration retinal degeneration -HP:0001093 skos:exactMatch MP:0001330 semapv:LexicalMatching Optic nerve dysplasia abnormal optic nerve morphology -HP:0001097 skos:exactMatch MP:0001337 semapv:LexicalMatching Keratoconjunctivitis sicca dry eyes -HP:0000492 skos:exactMatch MP:0001340 semapv:LexicalMatching Abnormal eyelid morphology abnormal eyelid morphology -HP:0011224 skos:exactMatch MP:0001341 semapv:LexicalMatching Ablepharon absent eyelids -HP:0000508 skos:exactMatch MP:0001344 semapv:LexicalMatching Ptosis blepharoptosis -HP:0007656 skos:exactMatch MP:0001347 semapv:LexicalMatching Lacrimal gland aplasia absent lacrimal glands -HP:0009926 skos:exactMatch MP:0001349 semapv:LexicalMatching Epiphora excessive tearing -HP:0012875 skos:exactMatch MP:0001378 semapv:LexicalMatching Abnormal ejaculation abnormal ejaculation -HP:0000496 skos:exactMatch MP:0001389 semapv:LexicalMatching Abnormality of eye movement abnormal eye movement -HP:0001251 skos:exactMatch MP:0001393 semapv:LexicalMatching Ataxia ataxia -HP:0000752 skos:exactMatch MP:0001399 semapv:LexicalMatching Hyperactivity hyperactivity -HP:0001288 skos:exactMatch MP:0001406 semapv:LexicalMatching Gait disturbance abnormal gait -HP:0000733 skos:exactMatch MP:0001408 semapv:LexicalMatching Stereotypy stereotypic behavior -HP:0030082 skos:exactMatch MP:0001422 semapv:LexicalMatching Abnormal drinking behavior abnormal drinking behavior -HP:0001959 skos:exactMatch MP:0001426 semapv:LexicalMatching Polydipsia polydipsia -HP:0001944 skos:exactMatch MP:0001429 semapv:LexicalMatching Dehydration dehydration -HP:0100738 skos:exactMatch MP:0001431 semapv:LexicalMatching Abnormal eating behavior abnormal eating behavior -HP:0010831 skos:exactMatch MP:0001516 semapv:LexicalMatching Impaired proprioception abnormal motor coordination/balance -HP:0002305 skos:exactMatch MP:0001527 semapv:LexicalMatching Athetosis athetotic walking movements -HP:0030781 skos:exactMatch MP:0001554 semapv:LexicalMatching Increased circulating free fatty acid level increased circulating free fatty acid level -HP:0040214 skos:exactMatch MP:0001560 semapv:LexicalMatching Abnormal insulin level abnormal circulating insulin level -HP:0040215 skos:exactMatch MP:0001560 semapv:LexicalMatching Abnormal circulating insulin level abnormal circulating insulin level -HP:0000961 skos:exactMatch MP:0001575 semapv:LexicalMatching Cyanosis cyanosis -HP:0001903 skos:exactMatch MP:0001577 semapv:LexicalMatching Anemia anemia -HP:0001878 skos:exactMatch MP:0001585 semapv:LexicalMatching Hemolytic anemia hemolytic anemia -HP:0020058 skos:exactMatch MP:0001586 semapv:LexicalMatching Abnormal red blood cell count abnormal erythrocyte cell number -HP:0011902 skos:exactMatch MP:0001588 semapv:LexicalMatching Abnormal hemoglobin abnormal hemoglobin -HP:0025546 skos:exactMatch MP:0001589 semapv:LexicalMatching Abnormal mean corpuscular hemoglobin concentration abnormal mean corpuscular hemoglobin -HP:0002615 skos:exactMatch MP:0001596 semapv:LexicalMatching Hypotension hypotension -HP:0011675 skos:exactMatch MP:0001629 semapv:LexicalMatching Arrhythmia abnormal heart rate -HP:0011675 skos:exactMatch MP:0001636 semapv:LexicalMatching Arrhythmia irregular heartbeat -HP:0002605 skos:exactMatch MP:0001654 semapv:LexicalMatching Hepatic necrosis hepatic necrosis -HP:0002028 skos:exactMatch MP:0001665 semapv:LexicalMatching Chronic diarrhea chronic diarrhea -HP:0008897 skos:exactMatch MP:0001732 semapv:LexicalMatching Postnatal growth retardation postnatal growth retardation -HP:0008232 skos:exactMatch MP:0001750 semapv:LexicalMatching Elevated circulating follicle stimulating hormone level increased circulating follicle stimulating hormone level -HP:0012337 skos:exactMatch MP:0001764 semapv:LexicalMatching Abnormal homeostasis abnormal homeostasis -HP:0000777 skos:exactMatch MP:0001823 semapv:LexicalMatching Abnormality of the thymus thymus hypoplasia -HP:0410035 skos:exactMatch MP:0001828 semapv:LexicalMatching Abnormal T cell activation abnormal T cell activation -HP:0012647 skos:exactMatch MP:0001845 semapv:LexicalMatching Abnormal inflammatory response abnormal inflammatory response -HP:0002383 skos:exactMatch MP:0001847 semapv:LexicalMatching Encephalitis brain inflammation -HP:0012123 skos:exactMatch MP:0001848 semapv:LexicalMatching Posterior uveitis choroid inflammation -HP:0000509 skos:exactMatch MP:0001852 semapv:LexicalMatching Conjunctivitis conjunctivitis -HP:0012819 skos:exactMatch MP:0001856 semapv:LexicalMatching Myocarditis myocarditis -HP:0001701 skos:exactMatch MP:0001857 semapv:LexicalMatching Pericarditis pericarditis -HP:0000123 skos:exactMatch MP:0001859 semapv:LexicalMatching Nephritis kidney inflammation -HP:0012115 skos:exactMatch MP:0001860 semapv:LexicalMatching Hepatitis liver inflammation -HP:0002090 skos:exactMatch MP:0001861 semapv:LexicalMatching Pneumonia lung inflammation -HP:0006515 skos:exactMatch MP:0001862 semapv:LexicalMatching Interstitial pneumonitis interstitial pneumonia -HP:0012384 skos:exactMatch MP:0001866 semapv:LexicalMatching Rhinitis nasal inflammation -HP:0012384 skos:exactMatch MP:0001867 semapv:LexicalMatching Rhinitis rhinitis -HP:0031259 skos:exactMatch MP:0001868 semapv:LexicalMatching Oophoritis ovary inflammation -HP:0001733 skos:exactMatch MP:0001869 semapv:LexicalMatching Pancreatitis pancreas inflammation -HP:0031281 skos:exactMatch MP:0001870 semapv:LexicalMatching Sialadenitis salivary gland inflammation -HP:0000246 skos:exactMatch MP:0001872 semapv:LexicalMatching Sinusitis sinus inflammation -HP:0005263 skos:exactMatch MP:0001873 semapv:LexicalMatching Gastritis stomach inflammation -HP:0025092 skos:exactMatch MP:0001874 semapv:LexicalMatching Epidermal acanthosis acanthosis -HP:0100796 skos:exactMatch MP:0001875 semapv:LexicalMatching Orchitis testis inflammation -HP:0031094 skos:exactMatch MP:0001881 semapv:LexicalMatching Abnormal breast physiology abnormal mammary gland physiology -HP:0002323 skos:exactMatch MP:0001890 semapv:LexicalMatching Anencephaly anencephaly -HP:0000238 skos:exactMatch MP:0001891 semapv:LexicalMatching Hydrocephalus hydrocephaly -HP:0001334 skos:exactMatch MP:0001893 semapv:LexicalMatching Communicating hydrocephalus non-obstructive hydrocephaly -HP:0001342 skos:exactMatch MP:0001916 semapv:LexicalMatching Cerebral hemorrhage intracerebral hemorrhage -HP:0030746 skos:exactMatch MP:0001917 semapv:LexicalMatching Intraventricular hemorrhage intraventricular hemorrhage -HP:0008734 skos:exactMatch MP:0001940 semapv:LexicalMatching Decreased testicular size testis hypoplasia -HP:0002795 skos:exactMatch MP:0001943 semapv:LexicalMatching Functional respiratory abnormality abnormal respiration -HP:0005232 skos:exactMatch MP:0001944 semapv:LexicalMatching Pancreatic dysplasia abnormal pancreas morphology -HP:0031602 skos:exactMatch MP:0001947 semapv:LexicalMatching Abnormal mucociliary clearance abnormal mucociliary clearance -HP:0000076 skos:exactMatch MP:0001948 semapv:LexicalMatching Vesicoureteral reflux vesicoureteral reflux -HP:0002878 skos:exactMatch MP:0001953 semapv:LexicalMatching Respiratory failure respiratory failure -HP:0002094 skos:exactMatch MP:0001954 semapv:LexicalMatching Dyspnea respiratory distress -HP:0002098 skos:exactMatch MP:0001954 semapv:LexicalMatching Respiratory distress respiratory distress -HP:0040213 skos:exactMatch MP:0001956 semapv:LexicalMatching Hypopnea hypopnea -HP:0031826 skos:exactMatch MP:0001961 semapv:LexicalMatching Abnormal reflex abnormal reflex -HP:0000992 skos:exactMatch MP:0001999 semapv:LexicalMatching Cutaneous photosensitivity photosensitivity -HP:0002664 skos:exactMatch MP:0002006 semapv:LexicalMatching Neoplasm neoplasm -HP:0030434 skos:exactMatch MP:0002013 semapv:LexicalMatching Pilomatrixoma increased pilomatricoma incidence -HP:0100243 skos:exactMatch MP:0002035 semapv:LexicalMatching Leiomyosarcoma increased leiomyosarcoma incidence -HP:0002859 skos:exactMatch MP:0002036 semapv:LexicalMatching Rhabdomyosarcoma increased rhabdomyosarcoma incidence -HP:0001250 skos:exactMatch MP:0002064 semapv:LexicalMatching Seizures seizures -HP:0100852 skos:exactMatch MP:0002065 semapv:LexicalMatching Abnormal fear/anxiety-related behavior abnormal fear/anxiety-related behavior -HP:0040202 skos:exactMatch MP:0002069 semapv:LexicalMatching Abnormal consumption behavior abnormal consumption behavior -HP:0011014 skos:exactMatch MP:0002078 semapv:LexicalMatching Abnormal glucose homeostasis abnormal glucose homeostasis -HP:0001000 skos:exactMatch MP:0002095 semapv:LexicalMatching Abnormality of skin pigmentation abnormal skin pigmentation -HP:0031703 skos:exactMatch MP:0002102 semapv:LexicalMatching Abnormal ear morphology abnormal ear morphology -HP:0011805 skos:exactMatch MP:0002108 semapv:LexicalMatching Abnormal skeletal muscle morphology abnormal muscle morphology -HP:0011297 skos:exactMatch MP:0002110 semapv:LexicalMatching Abnormal digit morphology abnormal digit morphology -HP:0000110 skos:exactMatch MP:0002135 semapv:LexicalMatching Renal dysplasia abnormal kidney morphology -HP:0012210 skos:exactMatch MP:0002135 semapv:LexicalMatching Abnormal renal morphology abnormal kidney morphology -HP:0002171 skos:exactMatch MP:0002183 semapv:LexicalMatching Gliosis gliosis -HP:0001961 skos:exactMatch MP:0002188 semapv:LexicalMatching Hypoplastic heart small heart -HP:0012244 skos:exactMatch MP:0002210 semapv:LexicalMatching Abnormal sex determination abnormal sex determination -HP:0010459 skos:exactMatch MP:0002213 semapv:LexicalMatching True hermaphroditism true hermaphroditism -HP:0002180 skos:exactMatch MP:0002229 semapv:LexicalMatching Neurodegeneration neurodegeneration -HP:0025423 skos:exactMatch MP:0002249 semapv:LexicalMatching Abnormal larynx morphology abnormal larynx morphology -HP:0025426 skos:exactMatch MP:0002264 semapv:LexicalMatching Abnormal bronchus morphology abnormal bronchus morphology -HP:0003202 skos:exactMatch MP:0002269 semapv:LexicalMatching Skeletal muscle atrophy muscular atrophy -HP:0001311 skos:exactMatch MP:0002272 semapv:LexicalMatching Abnormal nervous system electrophysiology abnormal nervous system electrophysiology -HP:0002778 skos:exactMatch MP:0002282 semapv:LexicalMatching Abnormal trachea morphology abnormal trachea morphology -HP:0000028 skos:exactMatch MP:0002286 semapv:LexicalMatching Cryptorchidism cryptorchism -HP:0030875 skos:exactMatch MP:0002295 semapv:LexicalMatching Abnormality of pulmonary circulation abnormal pulmonary circulation -HP:0002835 skos:exactMatch MP:0002296 semapv:LexicalMatching Aspiration aspiration -HP:0012416 skos:exactMatch MP:0002318 semapv:LexicalMatching Hypercapnia hypercapnia -HP:0012415 skos:exactMatch MP:0002329 semapv:LexicalMatching Abnormal blood gas level abnormal blood gas level -HP:0025035 skos:exactMatch MP:0002416 semapv:LexicalMatching Abnormal proerythroblast morphology abnormal proerythroblast morphology -HP:0012143 skos:exactMatch MP:0002417 semapv:LexicalMatching Abnormal megakaryocyte morphology abnormal megakaryocyte morphology -HP:0001912 skos:exactMatch MP:0002422 semapv:LexicalMatching Abnormal basophil morphology abnormal basophil morphology -HP:0004312 skos:exactMatch MP:0002424 semapv:LexicalMatching Abnormal reticulocyte morphology abnormal reticulocyte morphology -HP:0001911 skos:exactMatch MP:0002441 semapv:LexicalMatching Abnormal granulocyte morphology abnormal granulocyte morphology -HP:0001877 skos:exactMatch MP:0002447 semapv:LexicalMatching Abnormal erythrocyte morphology abnormal erythrocyte morphology -HP:0100845 skos:exactMatch MP:0002531 semapv:LexicalMatching Anaphylactic shock abnormal type I hypersensitivity reaction -HP:0009803 skos:exactMatch MP:0002543 semapv:LexicalMatching Short phalanx of finger brachyphalangia -HP:0001156 skos:exactMatch MP:0002544 semapv:LexicalMatching Brachydactyly brachydactyly -HP:0011499 skos:exactMatch MP:0002546 semapv:LexicalMatching Mydriasis mydriasis -HP:0012433 skos:exactMatch MP:0002557 semapv:LexicalMatching Abnormal social behavior abnormal social/conspecific interaction -HP:0100851 skos:exactMatch MP:0002572 semapv:LexicalMatching Abnormal emotion/affect behavior abnormal emotion/affect behavior -HP:0410175 skos:exactMatch MP:0002575 semapv:LexicalMatching Hyperketonemia increased circulating ketone body level -HP:0005518 skos:exactMatch MP:0002590 semapv:LexicalMatching Increased mean corpuscular volume increased mean corpuscular volume -HP:0025066 skos:exactMatch MP:0002591 semapv:LexicalMatching Decreased mean corpuscular volume decreased mean corpuscular volume -HP:0031850 skos:exactMatch MP:0002596 semapv:LexicalMatching Abnormal hematocrit abnormal hematocrit -HP:0020064 skos:exactMatch MP:0002602 semapv:LexicalMatching Abnormal eosinophil count abnormal eosinophil cell number -HP:0001899 skos:exactMatch MP:0002608 semapv:LexicalMatching Increased hematocrit increased hematocrit -HP:0004332 skos:exactMatch MP:0002619 semapv:LexicalMatching Abnormal lymphocyte morphology abnormal lymphocyte morphology -HP:0001702 skos:exactMatch MP:0002624 semapv:LexicalMatching Abnormal tricuspid valve morphology abnormal tricuspid valve morphology -HP:0030732 skos:exactMatch MP:0002624 semapv:LexicalMatching Dysplastic tricuspid valve abnormal tricuspid valve morphology -HP:0001712 skos:exactMatch MP:0002625 semapv:LexicalMatching Left ventricular hypertrophy heart left ventricle hypertrophy -HP:0001649 skos:exactMatch MP:0002626 semapv:LexicalMatching Tachycardia increased heart rate -HP:0001397 skos:exactMatch MP:0002628 semapv:LexicalMatching Hepatic steatosis hepatic steatosis -HP:0001660 skos:exactMatch MP:0002633 semapv:LexicalMatching Truncus arteriosus persistent truncus arteriosis -HP:0000013 skos:exactMatch MP:0002637 semapv:LexicalMatching Hypoplasia of the uterus small uterus -HP:0000347 skos:exactMatch MP:0002639 semapv:LexicalMatching Micrognathia micrognathia -HP:0011273 skos:exactMatch MP:0002642 semapv:LexicalMatching Anisocytosis anisocytosis -HP:0008707 skos:exactMatch MP:0002670 semapv:LexicalMatching Absent scrotum absent scrotum -HP:0012206 skos:exactMatch MP:0002674 semapv:LexicalMatching Abnormal sperm motility abnormal sperm motility -HP:0012207 skos:exactMatch MP:0002675 semapv:LexicalMatching Reduced sperm motility asthenozoospermia -HP:0012205 skos:exactMatch MP:0002686 semapv:LexicalMatching Globozoospermia globozoospermia -HP:0000798 skos:exactMatch MP:0002687 semapv:LexicalMatching Oligospermia oligozoospermia -HP:0002304 skos:exactMatch MP:0002690 semapv:LexicalMatching Akinesia akinesia -HP:0030687 skos:exactMatch MP:0002695 semapv:LexicalMatching Abnormal glucagon level abnormal circulating glucagon level -HP:0040299 skos:exactMatch MP:0002702 semapv:LexicalMatching Decreased circulating free fatty acid level decreased circulating free fatty acid level -HP:0000787 skos:exactMatch MP:0002708 semapv:LexicalMatching Nephrolithiasis nephrolithiasis -HP:0009556 skos:exactMatch MP:0002728 semapv:LexicalMatching Absent tibia absent tibia -HP:0002251 skos:exactMatch MP:0002731 semapv:LexicalMatching Aganglionic megacolon megacolon -HP:0025367 skos:exactMatch MP:0002732 semapv:LexicalMatching Trichoepithelioma increased trichoepithelioma incidence -HP:0000099 skos:exactMatch MP:0002743 semapv:LexicalMatching Glomerulonephritis glomerulonephritis -HP:0001646 skos:exactMatch MP:0002747 semapv:LexicalMatching Abnormal aortic valve morphology abnormal aortic valve morphology -HP:0001641 skos:exactMatch MP:0002748 semapv:LexicalMatching Abnormal pulmonary valve morphology abnormal pulmonary valve morphology -HP:0005164 skos:exactMatch MP:0002748 semapv:LexicalMatching Dysplastic pulmonary valve abnormal pulmonary valve morphology -HP:0000520 skos:exactMatch MP:0002750 semapv:LexicalMatching Proptosis exophthalmos -HP:0005133 skos:exactMatch MP:0002754 semapv:LexicalMatching Right ventricular dilatation dilated heart right ventricle -HP:0005736 skos:exactMatch MP:0002764 semapv:LexicalMatching Short tibia short tibia -HP:0003038 skos:exactMatch MP:0002765 semapv:LexicalMatching Fibular hypoplasia short fibula -HP:0003363 skos:exactMatch MP:0002766 semapv:LexicalMatching Abdominal situs inversus situs inversus -HP:0000835 skos:exactMatch MP:0002768 semapv:LexicalMatching Adrenal hypoplasia small adrenal glands -HP:0012872 skos:exactMatch MP:0002769 semapv:LexicalMatching Abnormal vas deferens morphology abnormal vas deferens morphology -HP:0030341 skos:exactMatch MP:0002790 semapv:LexicalMatching Decreased circulating follicle stimulating hormone level decreased circulating follicle stimulating hormone level -HP:0002570 skos:exactMatch MP:0002791 semapv:LexicalMatching Steatorrhea steatorrhea -HP:0001142 skos:exactMatch MP:0002794 semapv:LexicalMatching Lenticonus lenticonus -HP:0001644 skos:exactMatch MP:0002795 semapv:LexicalMatching Dilated cardiomyopathy dilated cardiomyopathy -HP:0001935 skos:exactMatch MP:0002810 semapv:LexicalMatching Microcytic anemia microcytic anemia -HP:0001972 skos:exactMatch MP:0002811 semapv:LexicalMatching Macrocytic anemia macrocytic anemia -HP:0025066 skos:exactMatch MP:0002813 semapv:LexicalMatching Decreased mean corpuscular volume microcytosis -HP:0002583 skos:exactMatch MP:0002816 semapv:LexicalMatching Colitis colitis -HP:0031263 skos:exactMatch MP:0002827 semapv:LexicalMatching Abnormal renal corpuscle morphology abnormal renal corpuscle morphology -HP:0031264 skos:exactMatch MP:0002828 semapv:LexicalMatching Abnormal morphology of Bowman capsule abnormal renal glomerular capsule morphology -HP:0001081 skos:exactMatch MP:0002830 semapv:LexicalMatching Cholelithiasis gallstones -HP:0002615 skos:exactMatch MP:0002843 semapv:LexicalMatching Hypotension decreased systemic arterial blood pressure -HP:0012212 skos:exactMatch MP:0002847 semapv:LexicalMatching Abnormal glomerular filtration rate abnormal renal glomerular filtration rate -HP:0012592 skos:exactMatch MP:0002871 semapv:LexicalMatching Albuminuria albuminuria -HP:0020060 skos:exactMatch MP:0002875 semapv:LexicalMatching Decreased red blood cell count decreased erythrocyte cell number -HP:0002179 skos:exactMatch MP:0002880 semapv:LexicalMatching Opisthotonus opisthotonus -HP:0002919 skos:exactMatch MP:0002893 semapv:LexicalMatching Ketonuria ketoaciduria -HP:0012378 skos:exactMatch MP:0002899 semapv:LexicalMatching Fatigue fatigue -HP:0003109 skos:exactMatch MP:0002901 semapv:LexicalMatching Hyperphosphaturia increased urine phosphate level -HP:0012365 skos:exactMatch MP:0002902 semapv:LexicalMatching Hypophosphaturia decreased urine phosphate level -HP:0031817 skos:exactMatch MP:0002905 semapv:LexicalMatching Decreased circulating parathyroid hormone level decreased circulating parathyroid hormone level -HP:0030191 skos:exactMatch MP:0002913 semapv:LexicalMatching Abnormal peripheral nervous system synaptic transmission abnormal PNS synaptic transmission -HP:0002251 skos:exactMatch MP:0002926 semapv:LexicalMatching Aganglionic megacolon aganglionic megacolon -HP:0001367 skos:exactMatch MP:0002932 semapv:LexicalMatching Abnormal joint morphology abnormal joint morphology -HP:0100769 skos:exactMatch MP:0002933 semapv:LexicalMatching Synovitis joint inflammation -HP:0012594 skos:exactMatch MP:0002959 semapv:LexicalMatching Microalbuminuria increased urine microalbumin level -HP:0012117 skos:exactMatch MP:0002965 semapv:LexicalMatching Hyperalbuminemia increased circulating serum albumin level -HP:0012861 skos:exactMatch MP:0002996 semapv:LexicalMatching Ovotestis ovotestis -HP:0001948 skos:exactMatch MP:0003028 semapv:LexicalMatching Alkalosis alkalosis -HP:0032369 skos:exactMatch MP:0003029 semapv:LexicalMatching Alkalemia alkalemia -HP:0032368 skos:exactMatch MP:0003030 semapv:LexicalMatching Acidemia acidemia -HP:0012417 skos:exactMatch MP:0003032 semapv:LexicalMatching Hypocapnia hypocapnia -HP:0005317 skos:exactMatch MP:0003034 semapv:LexicalMatching Increased pulmonary vascular resistance increased pulmonary vascular resistance -HP:0001394 skos:exactMatch MP:0003046 semapv:LexicalMatching Cirrhosis liver cirrhosis -HP:0001539 skos:exactMatch MP:0003052 semapv:LexicalMatching Omphalocele omphalocele -HP:0000684 skos:exactMatch MP:0003053 semapv:LexicalMatching Delayed eruption of teeth delayed tooth eruption -HP:0002414 skos:exactMatch MP:0003054 semapv:LexicalMatching Spina bifida spina bifida -HP:0010301 skos:exactMatch MP:0003054 semapv:LexicalMatching Spinal dysraphism spina bifida -HP:0004303 skos:exactMatch MP:0003084 semapv:LexicalMatching Abnormal muscle fiber morphology abnormal skeletal muscle fiber morphology -HP:0100565 skos:exactMatch MP:0003086 semapv:LexicalMatching Hydromyelia hydromyelia -HP:0000541 skos:exactMatch MP:0003099 semapv:LexicalMatching Retinal detachment retinal detachment -HP:0000545 skos:exactMatch MP:0003100 semapv:LexicalMatching Myopia myopia -HP:0011003 skos:exactMatch MP:0003101 semapv:LexicalMatching High myopia high myopia -HP:0030716 skos:exactMatch MP:0003104 semapv:LexicalMatching Acrania acrania -HP:0002748 skos:exactMatch MP:0003116 semapv:LexicalMatching Rickets rickets -HP:0000047 skos:exactMatch MP:0003124 semapv:LexicalMatching Hypospadias hypospadia -HP:0012621 skos:exactMatch MP:0003129 semapv:LexicalMatching Persistent cloaca persistent cloaca -HP:0009892 skos:exactMatch MP:0003142 semapv:LexicalMatching Anotia anotia -HP:0100736 skos:exactMatch MP:0003154 semapv:LexicalMatching Abnormal soft palate morphology abnormal soft palate morphology -HP:0002015 skos:exactMatch MP:0003158 semapv:LexicalMatching Dysphagia dysphagia -HP:0012533 skos:exactMatch MP:0003177 semapv:LexicalMatching Allodynia allodynia -HP:0003761 skos:exactMatch MP:0003195 semapv:LexicalMatching Calcinosis calcinosis -HP:0000121 skos:exactMatch MP:0003197 semapv:LexicalMatching Nephrocalcinosis nephrocalcinosis -HP:0002185 skos:exactMatch MP:0003214 semapv:LexicalMatching Neurofibrillary tangles neurofibrillary tangles -HP:0005576 skos:exactMatch MP:0003215 semapv:LexicalMatching Tubulointerstitial fibrosis renal interstitial fibrosis -HP:0002121 skos:exactMatch MP:0003216 semapv:LexicalMatching Absence seizure absence seizures -HP:0001657 skos:exactMatch MP:0003233 semapv:LexicalMatching Prolonged QT interval prolonged QT interval -HP:0011467 skos:exactMatch MP:0003250 semapv:LexicalMatching Absent gallbladder absent gallbladder -HP:0001082 skos:exactMatch MP:0003251 semapv:LexicalMatching Cholecystitis gallbladder inflammation -HP:0030151 skos:exactMatch MP:0003254 semapv:LexicalMatching Cholangitis bile duct inflammation -HP:0001408 skos:exactMatch MP:0003255 semapv:LexicalMatching Bile duct proliferation bile duct proliferation -HP:0002613 skos:exactMatch MP:0003256 semapv:LexicalMatching Biliary cirrhosis biliary cirrhosis -HP:0002036 skos:exactMatch MP:0003258 semapv:LexicalMatching Hiatus hernia hiatal hernia -HP:0002018 skos:exactMatch MP:0003259 semapv:LexicalMatching Nausea nausea -HP:0002013 skos:exactMatch MP:0003260 semapv:LexicalMatching Vomiting vomiting -HP:0002248 skos:exactMatch MP:0003261 semapv:LexicalMatching Hematemesis hematemesis -HP:0100890 skos:exactMatch MP:0003266 semapv:LexicalMatching Cyst of the ductus choledochus biliary cyst -HP:0012450 skos:exactMatch MP:0003268 semapv:LexicalMatching Chronic constipation chronic constipation -HP:0100633 skos:exactMatch MP:0003278 semapv:LexicalMatching Esophagitis esophageal inflammation -HP:0000020 skos:exactMatch MP:0003280 semapv:LexicalMatching Urinary incontinence urinary incontinence -HP:0002607 skos:exactMatch MP:0003281 semapv:LexicalMatching Bowel incontinence fecal incontinence -HP:0002020 skos:exactMatch MP:0003286 semapv:LexicalMatching Gastroesophageal reflux gastroesophageal reflux -HP:0002573 skos:exactMatch MP:0003293 semapv:LexicalMatching Hematochezia rectal hemorrhage -HP:0002576 skos:exactMatch MP:0003294 semapv:LexicalMatching Intussusception intussusception -HP:0004398 skos:exactMatch MP:0003301 semapv:LexicalMatching Peptic ulcer peptic ulcer -HP:0002021 skos:exactMatch MP:0003307 semapv:LexicalMatching Pyloric stenosis pyloric stenosis -HP:0001310 skos:exactMatch MP:0003314 semapv:LexicalMatching Dysmetria dysmetria -HP:0005218 skos:exactMatch MP:0003317 semapv:LexicalMatching Anoperineal fistula anoperineal fistula -HP:0004792 skos:exactMatch MP:0003318 semapv:LexicalMatching Rectoperineal fistula rectoperineal fistula -HP:0000143 skos:exactMatch MP:0003320 semapv:LexicalMatching Rectovaginal fistula rectovaginal fistula -HP:0001395 skos:exactMatch MP:0003333 semapv:LexicalMatching Hepatic fibrosis liver fibrosis -HP:0100732 skos:exactMatch MP:0003334 semapv:LexicalMatching Pancreatic fibrosis pancreas fibrosis -HP:0006280 skos:exactMatch MP:0003341 semapv:LexicalMatching Chronic pancreatitis chronic pancreas inflammation -HP:0001747 skos:exactMatch MP:0003342 semapv:LexicalMatching Accessory spleen accessory spleen -HP:0001748 skos:exactMatch MP:0003342 semapv:LexicalMatching Polysplenia accessory spleen -HP:0003187 skos:exactMatch MP:0003344 semapv:LexicalMatching Breast hypoplasia mammary gland hypoplasia -HP:0011957 skos:exactMatch MP:0003346 semapv:LexicalMatching Abnormal pectoral muscle morphology abnormal pectoral muscle morphology -HP:0002446 skos:exactMatch MP:0003354 semapv:LexicalMatching Astrocytosis astrocytosis -HP:0030338 skos:exactMatch MP:0003361 semapv:LexicalMatching Abnormal circulating gonadotropin level abnormal circulating gonadotropin level -HP:0000837 skos:exactMatch MP:0003362 semapv:LexicalMatching Increased circulating gonadotropin level increased circulating gonadotropin level -HP:0030339 skos:exactMatch MP:0003363 semapv:LexicalMatching Decreased circulating gonadotropin level decreased circulating gonadotropin level -HP:0025132 skos:exactMatch MP:0003369 semapv:LexicalMatching Abnormal circulating estrogen level abnormal circulating estrogen level -HP:0000826 skos:exactMatch MP:0003378 semapv:LexicalMatching Precocious puberty early sexual maturation -HP:0001680 skos:exactMatch MP:0003387 semapv:LexicalMatching Coarctation of aorta aorta coarctation -HP:0001004 skos:exactMatch MP:0003390 semapv:LexicalMatching Lymphedema lymphedema -HP:0031251 skos:exactMatch MP:0003395 semapv:LexicalMatching Abnormal subclavian artery morphology abnormal subclavian artery morphology -HP:0200040 skos:exactMatch MP:0003414 semapv:LexicalMatching Epidermoid cyst epidermal cyst -HP:0001036 skos:exactMatch MP:0003427 semapv:LexicalMatching Parakeratosis parakeratosis -HP:0000843 skos:exactMatch MP:0003432 semapv:LexicalMatching Hyperparathyroidism increased activity of parathyroid -HP:0000829 skos:exactMatch MP:0003433 semapv:LexicalMatching Hypoparathyroidism decreased activity of parathyroid -HP:0031794 skos:exactMatch MP:0003442 semapv:LexicalMatching Decreased circulating glycerol level decreased circulating glycerol level -HP:0010497 skos:exactMatch MP:0003445 semapv:LexicalMatching Sirenomelia sirenomelia -HP:0000197 skos:exactMatch MP:0003452 semapv:LexicalMatching Abnormal parotid gland morphology abnormal parotid gland morphology -HP:0001019 skos:exactMatch MP:0003454 semapv:LexicalMatching Erythroderma erythroderma -HP:0100646 skos:exactMatch MP:0003504 semapv:LexicalMatching Thyroiditis thyroid gland inflammation -HP:0012882 skos:exactMatch MP:0003517 semapv:LexicalMatching Hyperplastic labia majora enlarged labia majora -HP:0000059 skos:exactMatch MP:0003518 semapv:LexicalMatching Hypoplastic labia majora small labia majora -HP:0008665 skos:exactMatch MP:0003529 semapv:LexicalMatching Clitoral hypertrophy enlarged clitoris -HP:0000060 skos:exactMatch MP:0003530 semapv:LexicalMatching Clitoral hypoplasia small clitoris -HP:0001153 skos:exactMatch MP:0003533 semapv:LexicalMatching Septate vagina bifid vagina -HP:0040314 skos:exactMatch MP:0003534 semapv:LexicalMatching Blind vagina blind vagina -HP:0031088 skos:exactMatch MP:0003536 semapv:LexicalMatching Vaginal dryness vagina dryness -HP:0030010 skos:exactMatch MP:0003537 semapv:LexicalMatching Hydrometrocolpos hydrometrocolpos -HP:0030011 skos:exactMatch MP:0003540 semapv:LexicalMatching Imperforate hymen imperforate hymen -HP:0030683 skos:exactMatch MP:0003541 semapv:LexicalMatching Vaginitis vaginal inflammation -HP:0001741 skos:exactMatch MP:0003554 semapv:LexicalMatching Phimosis phimosis -HP:0000041 skos:exactMatch MP:0003555 semapv:LexicalMatching Chordee chordee -HP:0012873 skos:exactMatch MP:0003557 semapv:LexicalMatching Absent vas deferens absent vas deferens -HP:0002758 skos:exactMatch MP:0003560 semapv:LexicalMatching Osteoarthritis osteoarthritis -HP:0001370 skos:exactMatch MP:0003561 semapv:LexicalMatching Rheumatoid arthritis rheumatoid arthritis -HP:0010463 skos:exactMatch MP:0003578 semapv:LexicalMatching Aplasia of the ovary absent ovary -HP:0025318 skos:exactMatch MP:0003579 semapv:LexicalMatching Ovarian carcinoma increased ovarian carcinoma incidence -HP:0000072 skos:exactMatch MP:0003585 semapv:LexicalMatching Hydroureter large ureter -HP:0025634 skos:exactMatch MP:0003589 semapv:LexicalMatching Abnormal ureter physiology abnormal ureter physiology -HP:0000076 skos:exactMatch MP:0003590 semapv:LexicalMatching Vesicoureteral reflux ureteral reflux -HP:0008716 skos:exactMatch MP:0003593 semapv:LexicalMatching Urethrovaginal fistula urethrovaginal fistula -HP:0030424 skos:exactMatch MP:0003595 semapv:LexicalMatching Epididymal cyst epididymal cyst -HP:0000039 skos:exactMatch MP:0003598 semapv:LexicalMatching Epispadias epispadia -HP:0008696 skos:exactMatch MP:0003602 semapv:LexicalMatching Renal hamartoma increased renal hamartoma incidence -HP:0000122 skos:exactMatch MP:0003604 semapv:LexicalMatching Unilateral renal agenesis single kidney -HP:0000024 skos:exactMatch MP:0003608 semapv:LexicalMatching Prostatitis prostate gland inflammation -HP:0030276 skos:exactMatch MP:0003609 semapv:LexicalMatching Small scrotum small scrotum -HP:0100645 skos:exactMatch MP:0003614 semapv:LexicalMatching Cystocele urinary bladder prolapse -HP:0000015 skos:exactMatch MP:0003615 semapv:LexicalMatching Bladder diverticulum urinary bladder diverticulum -HP:0100520 skos:exactMatch MP:0003620 semapv:LexicalMatching Oliguria oliguria -HP:0100518 skos:exactMatch MP:0003621 semapv:LexicalMatching Dysuria dysuria -HP:0000016 skos:exactMatch MP:0003622 semapv:LexicalMatching Urinary retention ischuria -HP:0012535 skos:exactMatch MP:0003635 semapv:LexicalMatching Abnormal synaptic transmission abnormal synaptic transmission -HP:0002089 skos:exactMatch MP:0003641 semapv:LexicalMatching Pulmonary hypoplasia small lung -HP:0010310 skos:exactMatch MP:0003660 semapv:LexicalMatching Chylothorax chylothorax -HP:0200058 skos:exactMatch MP:0003667 semapv:LexicalMatching Angiosarcoma increased hemangiosarcoma incidence -HP:0000387 skos:exactMatch MP:0003678 semapv:LexicalMatching Absent earlobe absent ear lobes -HP:0009748 skos:exactMatch MP:0003680 semapv:LexicalMatching Large earlobe thick ear lobes -HP:0009748 skos:exactMatch MP:0003683 semapv:LexicalMatching Large earlobe prominent ear lobes -HP:0000597 skos:exactMatch MP:0003688 semapv:LexicalMatching Ophthalmoparesis ophthalmoparesis -HP:0001114 skos:exactMatch MP:0003692 semapv:LexicalMatching Xanthelasma xanthoma -HP:0020156 skos:exactMatch MP:0003696 semapv:LexicalMatching Abnormal zona pellucida morphology abnormal zona pellucida morphology -HP:0000980 skos:exactMatch MP:0003717 semapv:LexicalMatching Pallor pallor -HP:0000378 skos:exactMatch MP:0003735 semapv:LexicalMatching Cupped ear cup-shaped ears -HP:0005103 skos:exactMatch MP:0003737 semapv:LexicalMatching Calcification of the auricular cartilage ossification of pinnae -HP:0005473 skos:exactMatch MP:0003740 semapv:LexicalMatching Fusion of middle ear ossicles fusion of middle ear ossicles -HP:0000360 skos:exactMatch MP:0003741 semapv:LexicalMatching Tinnitus tinnitus -HP:0000268 skos:exactMatch MP:0003742 semapv:LexicalMatching Dolichocephaly narrow head -HP:0010280 skos:exactMatch MP:0003746 semapv:LexicalMatching Stomatitis stomatitis -HP:0002714 skos:exactMatch MP:0003749 semapv:LexicalMatching Downturned corners of mouth down-turned corners of mouth -HP:0002745 skos:exactMatch MP:0003751 semapv:LexicalMatching Oral leukoplakia oral leukoplakia -HP:0000174 skos:exactMatch MP:0003755 semapv:LexicalMatching Abnormal palate morphology abnormal palate morphology -HP:0012472 skos:exactMatch MP:0003773 semapv:LexicalMatching Eclabion eclabion -HP:0012471 skos:exactMatch MP:0003774 semapv:LexicalMatching Thick vermilion border thick lip -HP:0100825 skos:exactMatch MP:0003777 semapv:LexicalMatching Cheilitis lip inflammation -HP:0003103 skos:exactMatch MP:0003797 semapv:LexicalMatching Abnormal cortical bone morphology abnormal compact bone morphology -HP:0012385 skos:exactMatch MP:0003807 semapv:LexicalMatching Camptodactyly camptodactyly -HP:0002299 skos:exactMatch MP:0003848 semapv:LexicalMatching Brittle hair brittle hair -HP:0000958 skos:exactMatch MP:0003853 semapv:LexicalMatching Dry skin dry skin -HP:0002840 skos:exactMatch MP:0003865 semapv:LexicalMatching Lymphadenitis lymph node inflammation -HP:0031685 skos:exactMatch MP:0003868 semapv:LexicalMatching Abnormal stool composition abnormal feces composition -HP:0012575 skos:exactMatch MP:0003881 semapv:LexicalMatching Abnormal nephron morphology abnormal nephron morphology -HP:0030850 skos:exactMatch MP:0003882 semapv:LexicalMatching Abnormal pulse pressure abnormal pulse pressure -HP:0012248 skos:exactMatch MP:0003896 semapv:LexicalMatching Prolonged PR interval prolonged PR interval -HP:0012249 skos:exactMatch MP:0003897 semapv:LexicalMatching Abnormal ST segment abnormal ST segment -HP:0025074 skos:exactMatch MP:0003898 semapv:LexicalMatching Abnormal QRS complex abnormal QRS complex -HP:0031547 skos:exactMatch MP:0003899 semapv:LexicalMatching Abnormal QT interval abnormal QT interval -HP:0012232 skos:exactMatch MP:0003900 semapv:LexicalMatching Shortened QT interval shortened QT interval -HP:0031593 skos:exactMatch MP:0003901 semapv:LexicalMatching Abnormal PR interval abnormal PR interval -HP:0000776 skos:exactMatch MP:0003924 semapv:LexicalMatching Congenital diaphragmatic hernia diaphragmatic hernia -HP:0031862 skos:exactMatch MP:0003928 semapv:LexicalMatching Increased heart rate variability increased heart rate variability -HP:0031861 skos:exactMatch MP:0003929 semapv:LexicalMatching Decreased heart rate variability decreased heart rate variability -HP:0011054 skos:exactMatch MP:0003931 semapv:LexicalMatching Agenesis of molar absent molars -HP:0031409 skos:exactMatch MP:0003945 semapv:LexicalMatching Abnormal lymphocyte physiology abnormal lymphocyte physiology -HP:0032367 skos:exactMatch MP:0003968 semapv:LexicalMatching Abnormal growth hormone level abnormal growth hormone level -HP:0030345 skos:exactMatch MP:0003969 semapv:LexicalMatching Abnormal circulating luteinizing hormone level abnormal luteinizing hormone level -HP:0040086 skos:exactMatch MP:0003970 semapv:LexicalMatching Abnormal prolactin level abnormal prolactin level -HP:0031097 skos:exactMatch MP:0003971 semapv:LexicalMatching Abnormal thyroid-stimulating hormone level abnormal thyroid-stimulating hormone level -HP:0030760 skos:exactMatch MP:0003985 semapv:LexicalMatching Renal fibrosis renal fibrosis -HP:0002634 skos:exactMatch MP:0003991 semapv:LexicalMatching Arteriosclerosis arteriosclerosis -HP:0002069 skos:exactMatch MP:0003997 semapv:LexicalMatching Generalized tonic-clonic seizures tonic-clonic seizures -HP:0004890 skos:exactMatch MP:0004012 semapv:LexicalMatching Elevated pulmonary artery pressure increased pulmonary artery pressure -HP:0001561 skos:exactMatch MP:0004020 semapv:LexicalMatching Polyhydramnios polyhydramnios -HP:0040012 skos:exactMatch MP:0004028 semapv:LexicalMatching Chromosome breakage chromosome breakage -HP:0002647 skos:exactMatch MP:0004044 semapv:LexicalMatching Aortic dissection aortic dissection -HP:0031196 skos:exactMatch MP:0004057 semapv:LexicalMatching Thin myocardium compact layer thin myocardium compact layer -HP:0030718 skos:exactMatch MP:0004062 semapv:LexicalMatching Right atrial enlargement dilated heart right atrium -HP:0031595 skos:exactMatch MP:0004070 semapv:LexicalMatching Abnormal P wave abnormal P wave -HP:0002339 skos:exactMatch MP:0004078 semapv:LexicalMatching Abnormal caudate nucleus morphology abnormal caudate nucleus morphology -HP:0031982 skos:exactMatch MP:0004079 semapv:LexicalMatching Abnormal putamen morphology abnormal putamen morphology -HP:0002453 skos:exactMatch MP:0004081 semapv:LexicalMatching Abnormal globus pallidus morphology abnormal globus pallidus morphology -HP:0004303 skos:exactMatch MP:0004087 semapv:LexicalMatching Abnormal muscle fiber morphology abnormal muscle fiber morphology -HP:0006704 skos:exactMatch MP:0004111 semapv:LexicalMatching Abnormal coronary artery morphology abnormal coronary artery morphology -HP:0002900 skos:exactMatch MP:0004119 semapv:LexicalMatching Hypokalemia hypokalemia -HP:0030853 skos:exactMatch MP:0004133 semapv:LexicalMatching Heterotaxy heterotaxia -HP:0001257 skos:exactMatch MP:0004143 semapv:LexicalMatching Spasticity muscle hypertonia -HP:0008682 skos:exactMatch MP:0004154 semapv:LexicalMatching Acute tubular necrosis renal tubular necrosis -HP:0011611 skos:exactMatch MP:0004157 semapv:LexicalMatching Interrupted aortic arch interrupted aortic arch -HP:0012020 skos:exactMatch MP:0004158 semapv:LexicalMatching Right aortic arch right aortic arch -HP:0011590 skos:exactMatch MP:0004159 semapv:LexicalMatching Double aortic arch double aortic arch -HP:0011588 skos:exactMatch MP:0004161 semapv:LexicalMatching Cervical aortic arch cervical aortic arch -HP:0005344 skos:exactMatch MP:0004181 semapv:LexicalMatching Abnormal carotid artery morphology abnormal carotid artery morphology -HP:0010944 skos:exactMatch MP:0004194 semapv:LexicalMatching Abnormal renal pelvis morphology abnormal kidney pelvis morphology -HP:0100792 skos:exactMatch MP:0004241 semapv:LexicalMatching Acantholysis acantholysis -HP:0011970 skos:exactMatch MP:0004254 semapv:LexicalMatching Cerebral amyloid angiopathy cerebral amyloid angiopathy -HP:0000278 skos:exactMatch MP:0004282 semapv:LexicalMatching Retrognathia retrognathia -HP:0031000 skos:exactMatch MP:0004329 semapv:LexicalMatching Vestibular saccular degeneration vestibular saccular degeneration -HP:0000894 skos:exactMatch MP:0004337 semapv:LexicalMatching Short clavicles clavicle hypoplasia -HP:0010317 skos:exactMatch MP:0004341 semapv:LexicalMatching Scapular aplasia absent scapula -HP:0000882 skos:exactMatch MP:0004343 semapv:LexicalMatching Hypoplastic scapulae small scapula -HP:0002984 skos:exactMatch MP:0004355 semapv:LexicalMatching Hypoplasia of the radius short radius -HP:0003022 skos:exactMatch MP:0004359 semapv:LexicalMatching Hypoplasia of the ulna short ulna -HP:0100616 skos:exactMatch MP:0004478 semapv:LexicalMatching Testicular teratoma increased testicular teratoma incidence -HP:0100614 skos:exactMatch MP:0004510 semapv:LexicalMatching Myositis myositis -HP:0000458 skos:exactMatch MP:0004512 semapv:LexicalMatching Anosmia anosmia -HP:0010667 skos:exactMatch MP:0004539 semapv:LexicalMatching Aplasia of the maxilla absent maxilla -HP:0000327 skos:exactMatch MP:0004540 semapv:LexicalMatching Hypoplasia of the maxilla small maxilla -HP:0040116 skos:exactMatch MP:0004541 semapv:LexicalMatching Aplasia of the Eustachian tube absent auditory tube -HP:0000347 skos:exactMatch MP:0004592 semapv:LexicalMatching Micrognathia small mandible -HP:0002948 skos:exactMatch MP:0004609 semapv:LexicalMatching Vertebral fusion vertebral fusion -HP:0008479 skos:exactMatch MP:0004610 semapv:LexicalMatching Hypoplastic vertebral bodies small vertebrae -HP:0002948 skos:exactMatch MP:0004612 semapv:LexicalMatching Vertebral fusion fusion of vertebral bodies -HP:0002953 skos:exactMatch MP:0004626 semapv:LexicalMatching Vertebral compression fractures vertebral compression -HP:0030304 skos:exactMatch MP:0004643 semapv:LexicalMatching Abnormal number of vertebrae abnormal vertebrae number -HP:0100891 skos:exactMatch MP:0004678 semapv:LexicalMatching Bifid xiphoid process split xiphoid process -HP:0009900 skos:exactMatch MP:0004699 semapv:LexicalMatching Unilateral deafness unilateral deafness -HP:0500166 skos:exactMatch MP:0004730 semapv:LexicalMatching Abnormal circulating gastrin level abnormal circulating gastrin level -HP:0000405 skos:exactMatch MP:0004739 semapv:LexicalMatching Conductive hearing impairment conductive hearing loss -HP:0000407 skos:exactMatch MP:0004740 semapv:LexicalMatching Sensorineural hearing impairment sensorineural hearing loss -HP:0000410 skos:exactMatch MP:0004741 semapv:LexicalMatching Mixed hearing impairment mixed hearing loss -HP:0006560 skos:exactMatch MP:0004839 semapv:LexicalMatching Biliary hyperplasia bile duct hyperplasia -HP:0007670 skos:exactMatch MP:0004844 semapv:LexicalMatching Abnormal vestibulo-ocular reflex abnormal vestibuloocular reflex -HP:0012114 skos:exactMatch MP:0004868 semapv:LexicalMatching Endometrial carcinoma increased endometrial carcinoma incidence -HP:0010650 skos:exactMatch MP:0004870 semapv:LexicalMatching Hypoplasia of the premaxilla small premaxilla -HP:0005273 skos:exactMatch MP:0004872 semapv:LexicalMatching Absent nasal septal cartilage absent nasal septum -HP:0030684 skos:exactMatch MP:0004891 semapv:LexicalMatching Abnormal adiponectin level abnormal adiponectin level -HP:0030686 skos:exactMatch MP:0004892 semapv:LexicalMatching Increased adiponectin level increased adiponectin level -HP:0030685 skos:exactMatch MP:0004893 semapv:LexicalMatching Decreased adiponectin level decreased adiponectin level -HP:0000362 skos:exactMatch MP:0004897 semapv:LexicalMatching Otosclerosis otosclerosis -HP:0011123 skos:exactMatch MP:0004947 semapv:LexicalMatching Inflammatory abnormality of the skin skin inflammation -HP:0002797 skos:exactMatch MP:0004992 semapv:LexicalMatching Osteolysis increased bone resorption -HP:0001880 skos:exactMatch MP:0005011 semapv:LexicalMatching Eosinophilia increased eosinophil cell number -HP:0031891 skos:exactMatch MP:0005012 semapv:LexicalMatching Decreased eosinophil count decreased eosinophil cell number -HP:0100827 skos:exactMatch MP:0005013 semapv:LexicalMatching Lymphocytosis increased lymphocyte cell number -HP:0001888 skos:exactMatch MP:0005016 semapv:LexicalMatching Lymphopenia decreased lymphocyte cell number -HP:0100806 skos:exactMatch MP:0005044 semapv:LexicalMatching Sepsis sepsis -HP:0001977 skos:exactMatch MP:0005048 semapv:LexicalMatching Abnormal thrombosis abnormal thrombosis -HP:0001879 skos:exactMatch MP:0005061 semapv:LexicalMatching Abnormal eosinophil morphology abnormal eosinophil morphology -HP:0012437 skos:exactMatch MP:0005084 semapv:LexicalMatching Abnormal gallbladder morphology abnormal gallbladder morphology -HP:0031379 skos:exactMatch MP:0005094 semapv:LexicalMatching Abnormal T cell proliferation abnormal T cell proliferation -HP:0000610 skos:exactMatch MP:0005098 semapv:LexicalMatching Abnormal choroid morphology abnormal optic choroid morphology -HP:0008034 skos:exactMatch MP:0005102 semapv:LexicalMatching Abnormal iris pigmentation abnormal iris pigmentation -HP:0000870 skos:exactMatch MP:0005124 semapv:LexicalMatching Increased circulating prolactin concentration increased circulating prolactin level -HP:0031098 skos:exactMatch MP:0005134 semapv:LexicalMatching Decreased thyroid-stimulating hormone level decreased thyroid-stimulating hormone level -HP:0002925 skos:exactMatch MP:0005135 semapv:LexicalMatching Increased thyroid-stimulating hormone level increased thyroid-stimulating hormone level -HP:0031380 skos:exactMatch MP:0005153 semapv:LexicalMatching Abnormal B cell proliferation abnormal B cell proliferation -HP:0002067 skos:exactMatch MP:0005156 semapv:LexicalMatching Bradykinesia bradykinesia -HP:0001360 skos:exactMatch MP:0005157 semapv:LexicalMatching Holoprosencephaly holoprosencephaly -HP:0000027 skos:exactMatch MP:0005159 semapv:LexicalMatching Azoospermia azoospermia -HP:0000790 skos:exactMatch MP:0005161 semapv:LexicalMatching Hematuria hematuria -HP:0031189 skos:exactMatch MP:0005162 semapv:LexicalMatching Wrist drop carpoptosis -HP:0009914 skos:exactMatch MP:0005163 semapv:LexicalMatching Cyclopia cyclopia -HP:0000204 skos:exactMatch MP:0005170 semapv:LexicalMatching Cleft upper lip cleft upper lip -HP:0031212 skos:exactMatch MP:0005184 semapv:LexicalMatching Abnormal circulating progesterone level abnormal circulating progesterone level -HP:0000054 skos:exactMatch MP:0005188 semapv:LexicalMatching Micropenis small penis -HP:0030260 skos:exactMatch MP:0005188 semapv:LexicalMatching Microphallus small penis -HP:0002754 skos:exactMatch MP:0005190 semapv:LexicalMatching Osteomyelitis osteomyelitis -HP:0000553 skos:exactMatch MP:0005197 semapv:LexicalMatching Abnormal uvea morphology abnormal uvea morphology -HP:0001254 skos:exactMatch MP:0005202 semapv:LexicalMatching Lethargy lethargy -HP:0012630 skos:exactMatch MP:0005203 semapv:LexicalMatching Abnormal trabecular meshwork morphology abnormal trabecular meshwork morphology -HP:0100257 skos:exactMatch MP:0005230 semapv:LexicalMatching Ectrodactyly ectrodactyly -HP:0001126 skos:exactMatch MP:0005242 semapv:LexicalMatching Cryptophthalmos cryptophthalmos -HP:0012151 skos:exactMatch MP:0005243 semapv:LexicalMatching Hemothorax hemothorax -HP:0011851 skos:exactMatch MP:0005244 semapv:LexicalMatching Hemopericardium hemopericardium -HP:0000498 skos:exactMatch MP:0005251 semapv:LexicalMatching Blepharitis blepharitis -HP:0000486 skos:exactMatch MP:0005254 semapv:LexicalMatching Strabismus strabismus -HP:0000577 skos:exactMatch MP:0005255 semapv:LexicalMatching Exotropia exotropia -HP:0000565 skos:exactMatch MP:0005256 semapv:LexicalMatching Esotropia esotropia -HP:0012632 skos:exactMatch MP:0005257 semapv:LexicalMatching Abnormal intraocular pressure abnormal intraocular pressure -HP:0007906 skos:exactMatch MP:0005258 semapv:LexicalMatching Ocular hypertension ocular hypertension -HP:0000589 skos:exactMatch MP:0005262 semapv:LexicalMatching Coloboma coloboma -HP:0000096 skos:exactMatch MP:0005264 semapv:LexicalMatching Glomerulosclerosis glomerulosclerosis -HP:0009911 skos:exactMatch MP:0005272 semapv:LexicalMatching Abnormal temporal bone morphology abnormal temporal bone morphology -HP:0002508 skos:exactMatch MP:0005277 semapv:LexicalMatching Brainstem dysplasia abnormal brainstem morphology -HP:0003107 skos:exactMatch MP:0005278 semapv:LexicalMatching Abnormal circulating cholesterol concentration abnormal cholesterol homeostasis -HP:0030050 skos:exactMatch MP:0005279 semapv:LexicalMatching Narcolepsy narcolepsy -HP:0000581 skos:exactMatch MP:0005287 semapv:LexicalMatching Blepharophimosis narrow eye opening -HP:0001952 skos:exactMatch MP:0005293 semapv:LexicalMatching Glucose intolerance impaired glucose tolerance -HP:0040270 skos:exactMatch MP:0005293 semapv:LexicalMatching Impaired glucose tolerance impaired glucose tolerance -HP:0031095 skos:exactMatch MP:0005296 semapv:LexicalMatching Abnormal humerus morphology abnormal humerus morphology -HP:0003298 skos:exactMatch MP:0005297 semapv:LexicalMatching Spina bifida occulta spina bifida occulta -HP:0000011 skos:exactMatch MP:0005302 semapv:LexicalMatching Neurogenic bladder neurogenic bladder -HP:0001698 skos:exactMatch MP:0005312 semapv:LexicalMatching Pericardial effusion pericardial effusion -HP:0010626 skos:exactMatch MP:0005315 semapv:LexicalMatching Anterior pituitary agenesis absent pituitary gland -HP:0001332 skos:exactMatch MP:0005323 semapv:LexicalMatching Dystonia dystonia -HP:0001541 skos:exactMatch MP:0005324 semapv:LexicalMatching Ascites ascites -HP:0012100 skos:exactMatch MP:0005328 semapv:LexicalMatching Abnormal circulating creatinine level abnormal circulating creatinine level -HP:0001662 skos:exactMatch MP:0005333 semapv:LexicalMatching Bradycardia decreased heart rate -HP:0012112 skos:exactMatch MP:0005345 semapv:LexicalMatching Abnormal circulating corticosterone level abnormal circulating corticosterone level -HP:0000252 skos:exactMatch MP:0005352 semapv:LexicalMatching Microcephaly small cranium -HP:0003045 skos:exactMatch MP:0005353 semapv:LexicalMatching Abnormal patella morphology abnormal patella morphology -HP:0040129 skos:exactMatch MP:0005403 semapv:LexicalMatching Abnormal nerve conduction velocity abnormal nerve conduction -HP:0040078 skos:exactMatch MP:0005405 semapv:LexicalMatching Axonal degeneration axon degeneration -HP:0031005 skos:exactMatch MP:0005407 semapv:LexicalMatching Hyperalgesia hyperalgesia -HP:0001010 skos:exactMatch MP:0005408 semapv:LexicalMatching Hypopigmentation of the skin hypopigmentation -HP:0012334 skos:exactMatch MP:0005414 semapv:LexicalMatching Extrahepatic cholestasis extrahepatic cholestasis -HP:0001406 skos:exactMatch MP:0005415 semapv:LexicalMatching Intrahepatic cholestasis intrahepatic cholestasis -HP:0010876 skos:exactMatch MP:0005416 semapv:LexicalMatching Abnormal circulating protein level abnormal circulating protein level -HP:0000973 skos:exactMatch MP:0005421 semapv:LexicalMatching Cutis laxa loose skin -HP:0011001 skos:exactMatch MP:0005422 semapv:LexicalMatching Increased bone mineral density osteosclerosis -HP:0002789 skos:exactMatch MP:0005426 semapv:LexicalMatching Tachypnea tachypnea -HP:0011854 skos:exactMatch MP:0005435 semapv:LexicalMatching Hemoperitoneum hemoperitoneum -HP:0031508 skos:exactMatch MP:0005468 semapv:LexicalMatching Abnormal thyroid hormone level abnormal thyroid hormone level -HP:0031505 skos:exactMatch MP:0005475 semapv:LexicalMatching Abnormal circulating thyroxine level abnormal circulating thyroxine level -HP:0031506 skos:exactMatch MP:0005477 semapv:LexicalMatching Increased circulating thyroxine level increased circulating thyroxine level -HP:0031507 skos:exactMatch MP:0005478 semapv:LexicalMatching Decreased circulating thyroxine level decreased circulating thyroxine level -HP:0005506 skos:exactMatch MP:0005481 semapv:LexicalMatching Chronic myelogenous leukemia increased chronic myelocytic leukemia incidence -HP:0001894 skos:exactMatch MP:0005505 semapv:LexicalMatching Thrombocytosis thrombocytosis -HP:0000554 skos:exactMatch MP:0005515 semapv:LexicalMatching Uveitis uveitis -HP:0012214 skos:exactMatch MP:0005527 semapv:LexicalMatching Increased glomerular filtration rate increased renal glomerular filtration rate -HP:0012213 skos:exactMatch MP:0005528 semapv:LexicalMatching Decreased glomerular filtration rate decreased renal glomerular filtration rate -HP:0002045 skos:exactMatch MP:0005534 semapv:LexicalMatching Hypothermia decreased body temperature -HP:0011496 skos:exactMatch MP:0005542 semapv:LexicalMatching Corneal neovascularization corneal vascularization -HP:0000531 skos:exactMatch MP:0005544 semapv:LexicalMatching Corneal crystals corneal deposits -HP:0011506 skos:exactMatch MP:0005546 semapv:LexicalMatching Choroidal neovascularization choroidal neovascularization -HP:0012213 skos:exactMatch MP:0005558 semapv:LexicalMatching Decreased glomerular filtration rate decreased creatinine clearance -HP:0025548 skos:exactMatch MP:0005561 semapv:LexicalMatching Increased mean corpuscular hemoglobin concentration increased mean corpuscular hemoglobin -HP:0032231 skos:exactMatch MP:0005562 semapv:LexicalMatching Hypochromia decreased mean corpuscular hemoglobin -HP:0031969 skos:exactMatch MP:0005566 semapv:LexicalMatching Reduced blood urea nitrogen decreased blood urea nitrogen level -HP:0002152 skos:exactMatch MP:0005568 semapv:LexicalMatching Hyperproteinemia increased circulating total protein level -HP:0012864 skos:exactMatch MP:0005578 semapv:LexicalMatching Abnormal sperm morphology teratozoospermia -HP:0012379 skos:exactMatch MP:0005584 semapv:LexicalMatching Abnormal enzyme/coenzyme activity abnormal enzyme/coenzyme activity -HP:0003010 skos:exactMatch MP:0005606 semapv:LexicalMatching Prolonged bleeding time increased bleeding time -HP:0025546 skos:exactMatch MP:0005640 semapv:LexicalMatching Abnormal mean corpuscular hemoglobin concentration abnormal mean corpuscular hemoglobin concentration -HP:0025548 skos:exactMatch MP:0005641 semapv:LexicalMatching Increased mean corpuscular hemoglobin concentration increased mean corpuscular hemoglobin concentration -HP:0025547 skos:exactMatch MP:0005642 semapv:LexicalMatching Decreased mean corpuscular hemoglobin concentration decreased mean corpuscular hemoglobin concentration -HP:0012245 skos:exactMatch MP:0005652 semapv:LexicalMatching Sex reversal sex reversal -HP:0002269 skos:exactMatch MP:0006009 semapv:LexicalMatching Abnormality of neuronal migration abnormal neuronal migration -HP:0002206 skos:exactMatch MP:0006050 semapv:LexicalMatching Pulmonary fibrosis pulmonary fibrosis -HP:0011536 skos:exactMatch MP:0006061 semapv:LexicalMatching Right atrial isomerism right atrial isomerism -HP:0000023 skos:exactMatch MP:0006077 semapv:LexicalMatching Inguinal hernia inguinal hernia -HP:0004404 skos:exactMatch MP:0006078 semapv:LexicalMatching Abnormal nipple morphology abnormal nipple morphology -HP:0001700 skos:exactMatch MP:0006085 semapv:LexicalMatching Myocardial necrosis myocardium necrosis -HP:0045082 skos:exactMatch MP:0006086 semapv:LexicalMatching Decreased body mass index decreased body mass index -HP:0031418 skos:exactMatch MP:0006087 semapv:LexicalMatching Increased body mass index increased body mass index -HP:0030999 skos:exactMatch MP:0006089 semapv:LexicalMatching Abnormal vestibular saccule morphology abnormal vestibular saccule morphology -HP:0004947 skos:exactMatch MP:0006093 semapv:LexicalMatching Arteriovenous fistula arteriovenous malformation -HP:0030759 skos:exactMatch MP:0006094 semapv:LexicalMatching Adipocyte hypertrophy increased fat cell size -HP:0001663 skos:exactMatch MP:0006110 semapv:LexicalMatching Ventricular fibrillation ventricular fibrillation -HP:0001681 skos:exactMatch MP:0006112 semapv:LexicalMatching Angina pectoris angina -HP:0030148 skos:exactMatch MP:0006114 semapv:LexicalMatching Heart murmur cardiac murmur -HP:0025578 skos:exactMatch MP:0006118 semapv:LexicalMatching Aortic valve prolapse aortic valve prolapse -HP:0011560 skos:exactMatch MP:0006119 semapv:LexicalMatching Mitral atresia mitral valve atresia -HP:0011662 skos:exactMatch MP:0006123 semapv:LexicalMatching Tricuspid atresia tricuspid valve atresia -HP:0010446 skos:exactMatch MP:0006124 semapv:LexicalMatching Tricuspid stenosis tricuspid valve stenosis -HP:0025324 skos:exactMatch MP:0006134 semapv:LexicalMatching Arterial occlusion artery occlusion -HP:0002619 skos:exactMatch MP:0006136 semapv:LexicalMatching Varicose veins varicose veins -HP:0001635 skos:exactMatch MP:0006138 semapv:LexicalMatching Congestive heart failure congestive heart failure -HP:0000622 skos:exactMatch MP:0006149 semapv:LexicalMatching Blurred vision decreased visual acuity -HP:0007663 skos:exactMatch MP:0006149 semapv:LexicalMatching Reduced visual acuity decreased visual acuity -HP:0000651 skos:exactMatch MP:0006150 semapv:LexicalMatching Diplopia double vision -HP:0000540 skos:exactMatch MP:0006153 semapv:LexicalMatching Hypermetropia hypermetropia -HP:0001107 skos:exactMatch MP:0006159 semapv:LexicalMatching Ocular albinism ocular albinism -HP:0030939 skos:exactMatch MP:0006162 semapv:LexicalMatching Palpebral thickening thick eyelids -HP:0000621 skos:exactMatch MP:0006165 semapv:LexicalMatching Entropion entropion -HP:0500043 skos:exactMatch MP:0006166 semapv:LexicalMatching Eyelid retraction eyelid retraction -HP:0000537 skos:exactMatch MP:0006168 semapv:LexicalMatching Epicanthus inversus epicanthus inversus -HP:0001096 skos:exactMatch MP:0006194 semapv:LexicalMatching Keratoconjunctivitis keratoconjunctivitis -HP:0000490 skos:exactMatch MP:0006198 semapv:LexicalMatching Deeply set eye enophthalmos -HP:0025586 skos:exactMatch MP:0006199 semapv:LexicalMatching Hypertropia hypertropia -HP:0032479 skos:exactMatch MP:0006204 semapv:LexicalMatching Preimplantation lethality embryonic lethality before implantation -HP:0007807 skos:exactMatch MP:0006220 semapv:LexicalMatching Optic nerve compression optic nerve compression -HP:0000538 skos:exactMatch MP:0006223 semapv:LexicalMatching Pseudopapilledema optic nerve swelling -HP:0001085 skos:exactMatch MP:0006223 semapv:LexicalMatching Papilledema optic nerve swelling -HP:0000657 skos:exactMatch MP:0006224 semapv:LexicalMatching Oculomotor apraxia oculomotor apraxia -HP:0011500 skos:exactMatch MP:0006235 semapv:LexicalMatching Polycoria polycoria -HP:0009916 skos:exactMatch MP:0006240 semapv:LexicalMatching Anisocoria anisocoria -HP:0009918 skos:exactMatch MP:0006241 semapv:LexicalMatching Ectopia pupillae abnormal placement of pupils -HP:0000555 skos:exactMatch MP:0006242 semapv:LexicalMatching Leukocoria white pupil -HP:0000643 skos:exactMatch MP:0006244 semapv:LexicalMatching Blepharospasm eyelid muscle spasm -HP:0031786 skos:exactMatch MP:0006244 semapv:LexicalMatching Cogan lid twitch eyelid muscle spasm -HP:0012019 skos:exactMatch MP:0006245 semapv:LexicalMatching Lens luxation dislocated lens -HP:0000667 skos:exactMatch MP:0006249 semapv:LexicalMatching Phthisis bulbi phthisis bulbi -HP:0030084 skos:exactMatch MP:0006253 semapv:LexicalMatching Clinodactyly clinodactyly -HP:0001734 skos:exactMatch MP:0006261 semapv:LexicalMatching Annular pancreas annular pancreas -HP:0500104 skos:exactMatch MP:0006263 semapv:LexicalMatching Decreased diastolic blood pressure decreased systemic arterial diastolic blood pressure -HP:0500105 skos:exactMatch MP:0006264 semapv:LexicalMatching Decreased systolic blood pressure decreased systemic arterial systolic blood pressure -HP:0004942 skos:exactMatch MP:0006278 semapv:LexicalMatching Aortic aneurysm aortic aneurysm -HP:0012806 skos:exactMatch MP:0006290 semapv:LexicalMatching Proboscis proboscis -HP:0007268 skos:exactMatch MP:0006291 semapv:LexicalMatching Aprosencephaly aprosencephaly -HP:0001166 skos:exactMatch MP:0006296 semapv:LexicalMatching Arachnodactyly arachnodactyly -HP:0020119 skos:exactMatch MP:0006303 semapv:LexicalMatching Abnormal retinal nerve fiber layer morphology abnormal retinal nerve fiber layer morphology -HP:0020129 skos:exactMatch MP:0006315 semapv:LexicalMatching Abnormal urine protein level abnormal urine protein level -HP:0000405 skos:exactMatch MP:0006326 semapv:LexicalMatching Conductive hearing impairment conductive hearing impairment -HP:0000410 skos:exactMatch MP:0006327 semapv:LexicalMatching Mixed hearing impairment mixed hearing impairment -HP:0000407 skos:exactMatch MP:0006329 semapv:LexicalMatching Sensorineural hearing impairment sensorineural hearing impairment -HP:0030869 skos:exactMatch MP:0006415 semapv:LexicalMatching Anorchism absent testes -HP:0100615 skos:exactMatch MP:0008000 semapv:LexicalMatching Ovarian neoplasm increased ovary tumor incidence -HP:0032448 skos:exactMatch MP:0008003 semapv:LexicalMatching Achlorhydria achlorhydria -HP:0200008 skos:exactMatch MP:0008011 semapv:LexicalMatching Intestinal polyposis intestine polyps -HP:0004783 skos:exactMatch MP:0008012 semapv:LexicalMatching Duodenal polyposis duodenum polyps -HP:0031871 skos:exactMatch MP:0008117 semapv:LexicalMatching Abnormal Langerhans cell morphology abnormal Langerhans cell morphology -HP:0031266 skos:exactMatch MP:0008140 semapv:LexicalMatching Podocyte foot process effacement podocyte foot process effacement -HP:0000662 skos:exactMatch MP:0008144 semapv:LexicalMatching Nyctalopia nyctalopia -HP:0012047 skos:exactMatch MP:0008145 semapv:LexicalMatching Hemeralopia hemeralopia -HP:0003100 skos:exactMatch MP:0008150 semapv:LexicalMatching Slender long bone decreased diameter of long bones -HP:0031107 skos:exactMatch MP:0008153 semapv:LexicalMatching Decreased fibular diameter decreased diameter of fibula -HP:0012107 skos:exactMatch MP:0008159 semapv:LexicalMatching Increased fibular diameter increased diameter of fibula -HP:0001881 skos:exactMatch MP:0008246 semapv:LexicalMatching Abnormal leukocyte morphology abnormal leukocyte morphology -HP:0011849 skos:exactMatch MP:0008271 semapv:LexicalMatching Abnormal bone ossification abnormal bone ossification -HP:0012790 skos:exactMatch MP:0008273 semapv:LexicalMatching Abnormal intramembranous ossification abnormal intramembranous bone ossification -HP:0100961 skos:exactMatch MP:0008282 semapv:LexicalMatching Enlarged hippocampus enlarged hippocampus -HP:0025517 skos:exactMatch MP:0008283 semapv:LexicalMatching Hypoplastic hippocampus small hippocampus -HP:0001931 skos:exactMatch MP:0008387 semapv:LexicalMatching Hypochromic anemia hypochromic anemia -HP:0004840 skos:exactMatch MP:0008388 semapv:LexicalMatching Hypochromic microcytic anemia hypochromic microcytic anemia -HP:0030334 skos:exactMatch MP:0008397 semapv:LexicalMatching "Abnormal CD4-positive CD25-positive alpha-beta regulatory T cell morphology" "abnormal CD4-positive CD25-positive alpha-beta regulatory T cell morphology" -HP:0025082 skos:exactMatch MP:0008418 semapv:LexicalMatching Abnormal cutaneous elastic fiber morphology abnormal cutaneous elastic fiber morphology -HP:0031512 skos:exactMatch MP:0008438 semapv:LexicalMatching Abnormal cutaneous collagen fibril morphology abnormal cutaneous collagen fibril morphology -HP:0011537 skos:exactMatch MP:0008461 semapv:LexicalMatching Left atrial isomerism left atrial isomerism -HP:0006956 skos:exactMatch MP:0008535 semapv:LexicalMatching Dilation of lateral ventricles enlarged lateral ventricles -HP:0005110 skos:exactMatch MP:0008543 semapv:LexicalMatching Atrial fibrillation atrial fibrillation -HP:0004409 skos:exactMatch MP:0008544 semapv:LexicalMatching Hyposmia impaired olfaction -HP:0010633 skos:exactMatch MP:0008544 semapv:LexicalMatching Partial anosmia impaired olfaction -HP:0032558 skos:exactMatch MP:0008545 semapv:LexicalMatching Absent sperm flagella absent sperm flagellum -HP:0040238 skos:exactMatch MP:0008720 semapv:LexicalMatching Impaired neutrophil chemotaxis impaired neutrophil chemotaxis -HP:0002983 skos:exactMatch MP:0008736 semapv:LexicalMatching Micromelia micromelia -HP:0040134 skos:exactMatch MP:0008738 semapv:LexicalMatching Abnormal hepatic iron concentration abnormal liver iron level -HP:0030770 skos:exactMatch MP:0008784 semapv:LexicalMatching Craniorachischisis craniorachischisis -HP:0100731 skos:exactMatch MP:0008798 semapv:LexicalMatching Transverse facial cleft lateral facial cleft -HP:0410282 skos:exactMatch MP:0008804 semapv:LexicalMatching Abnormal circulating amylase level abnormal circulating amylase level -HP:0410289 skos:exactMatch MP:0008805 semapv:LexicalMatching Hypoamylasemia decreased circulating amylase level -HP:0410288 skos:exactMatch MP:0008806 semapv:LexicalMatching Hyperamylasemia increased circulating amylase level -HP:0000762 skos:exactMatch MP:0008814 semapv:LexicalMatching Decreased nerve conduction velocity decreased nerve conduction velocity -HP:0030855 skos:exactMatch MP:0008815 semapv:LexicalMatching Anterior staphyloma anterior staphyloma -HP:0000967 skos:exactMatch MP:0008816 semapv:LexicalMatching Petechiae petechiae -HP:0002937 skos:exactMatch MP:0008832 semapv:LexicalMatching Hemivertebrae hemivertebra -HP:0030666 skos:exactMatch MP:0008852 semapv:LexicalMatching Retinal neovascularization retinal neovascularization -HP:0004484 skos:exactMatch MP:0008863 semapv:LexicalMatching Craniofacial asymmetry craniofacial asymmetry -HP:0009702 skos:exactMatch MP:0008915 semapv:LexicalMatching Carpal synostosis fused carpal bones -HP:0005537 skos:exactMatch MP:0008935 semapv:LexicalMatching Decreased mean platelet volume decreased mean platelet volume -HP:0004857 skos:exactMatch MP:0008945 semapv:LexicalMatching Hyperchromic macrocytic anemia hyperchromic macrocytic anemia -HP:0004756 skos:exactMatch MP:0008950 semapv:LexicalMatching Ventricular tachycardia ventricular tachycardia -HP:0030146 skos:exactMatch MP:0008986 semapv:LexicalMatching Abnormal liver parenchyma morphology abnormal liver parenchyma morphology -HP:0002023 skos:exactMatch MP:0008999 semapv:LexicalMatching Anal atresia absent anus -HP:0012386 skos:exactMatch MP:0009001 semapv:LexicalMatching Absent hallux absent hallux -HP:0012703 skos:exactMatch MP:0009027 semapv:LexicalMatching Abnormal subarachnoid space morphology abnormal subarachnoid space morphology -HP:0025246 skos:exactMatch MP:0009042 semapv:LexicalMatching Trichilemmal cyst pilar cyst -HP:0002380 skos:exactMatch MP:0009046 semapv:LexicalMatching Fasciculations muscle twitch -HP:0012673 skos:exactMatch MP:0009072 semapv:LexicalMatching Aplasia of the upper vagina absent cranial vagina -HP:0012094 skos:exactMatch MP:0009106 semapv:LexicalMatching Abnormal pancreas size abnormal pancreas size -HP:0002894 skos:exactMatch MP:0009153 semapv:LexicalMatching Neoplasm of the pancreas increased pancreas tumor incidence -HP:0010461 skos:exactMatch MP:0009198 semapv:LexicalMatching Abnormality of the male genitalia abnormal male genitalia morphology -HP:0010784 skos:exactMatch MP:0009222 semapv:LexicalMatching Uterine neoplasm increased uterus tumor incidence -HP:0030160 skos:exactMatch MP:0009228 semapv:LexicalMatching Cervicitis uterine cervix inflammation -HP:0003270 skos:exactMatch MP:0009247 semapv:LexicalMatching Abdominal distention meteorism -HP:0000557 skos:exactMatch MP:0009274 semapv:LexicalMatching Buphthalmos buphthalmos -HP:0031364 skos:exactMatch MP:0009276 semapv:LexicalMatching Ecchymosis ecchymosis -HP:0006771 skos:exactMatch MP:0009311 semapv:LexicalMatching Duodenal adenocarcinoma increased duodenum adenocarcinoma incidence -HP:0030439 skos:exactMatch MP:0009316 semapv:LexicalMatching Anal canal adenocarcinoma increased anal adenocarcinoma incidence -HP:0002213 skos:exactMatch MP:0009351 semapv:LexicalMatching Fine hair thin hair shaft -HP:0025636 skos:exactMatch MP:0009360 semapv:LexicalMatching Endometritis endometrium inflammation -HP:0020157 skos:exactMatch MP:0009375 semapv:LexicalMatching Thin zona pellucida thin zona pellucida -HP:0003687 skos:exactMatch MP:0009404 semapv:LexicalMatching Centrally nucleated skeletal muscle fibers centrally nucleated skeletal muscle fibers -HP:0003202 skos:exactMatch MP:0009417 semapv:LexicalMatching Skeletal muscle atrophy skeletal muscle atrophy -HP:0030951 skos:exactMatch MP:0009419 semapv:LexicalMatching Skeletal muscle fibrosis skeletal muscle fibrosis -HP:0002385 skos:exactMatch MP:0009434 semapv:LexicalMatching Paraparesis paraparesis -HP:0025274 skos:exactMatch MP:0009442 semapv:LexicalMatching Ovarian dermoid cyst increased ovarian teratoma incidence -HP:0003712 skos:exactMatch MP:0009461 semapv:LexicalMatching Skeletal muscle hypertrophy skeletal muscle hypertrophy -HP:0031111 skos:exactMatch MP:0009469 semapv:LexicalMatching Cutaneous hamartoma increased skin hamartoma incidence -HP:0032564 skos:exactMatch MP:0009482 semapv:LexicalMatching Ileitis ileum inflammation -HP:0030075 skos:exactMatch MP:0009508 semapv:LexicalMatching Ductal carcinoma in situ increased mammary gland ductal carcinoma incidence -HP:0030187 skos:exactMatch MP:0009514 semapv:LexicalMatching Titubation titubation -HP:0004445 skos:exactMatch MP:0009547 semapv:LexicalMatching Elliptocytosis elliptocytosis -HP:0030402 skos:exactMatch MP:0009548 semapv:LexicalMatching Abnormal platelet aggregation abnormal platelet aggregation -HP:0003540 skos:exactMatch MP:0009549 semapv:LexicalMatching Impaired platelet aggregation decreased platelet aggregation -HP:0025114 skos:exactMatch MP:0009600 semapv:LexicalMatching Hypergranulosis hypergranulosis -HP:0012585 skos:exactMatch MP:0009641 semapv:LexicalMatching Renal atrophy kidney degeneration -HP:0002157 skos:exactMatch MP:0009644 semapv:LexicalMatching Azotemia uremia -HP:0020074 skos:exactMatch MP:0009645 semapv:LexicalMatching Crystalluria crystalluria -HP:0100577 skos:exactMatch MP:0009646 semapv:LexicalMatching Urinary bladder inflammation urinary bladder inflammation -HP:0031456 skos:exactMatch MP:0009668 semapv:LexicalMatching Ectopic pregnancy ectopic pregnancy -HP:0025080 skos:exactMatch MP:0009675 semapv:LexicalMatching Orthokeratotic hyperkeratosis orthokeratosis -HP:0040162 skos:exactMatch MP:0009675 semapv:LexicalMatching Orthokeratosis orthokeratosis -HP:0012238 skos:exactMatch MP:0009699 semapv:LexicalMatching Increased circulating chylomicron concentration hyperchylomicronemia -HP:0000413 skos:exactMatch MP:0009707 semapv:LexicalMatching Atresia of the external auditory canal absent external auditory canal -HP:0012154 skos:exactMatch MP:0009710 semapv:LexicalMatching Anhedonia anhedonia -HP:0100258 skos:exactMatch MP:0009743 semapv:LexicalMatching Preaxial polydactyly preaxial polydactyly -HP:0100259 skos:exactMatch MP:0009744 semapv:LexicalMatching Postaxial polydactyly postaxial polydactyly -HP:0001051 skos:exactMatch MP:0009792 semapv:LexicalMatching Seborrheic dermatitis seborrheic dermatitis -HP:0012804 skos:exactMatch MP:0009825 semapv:LexicalMatching Corneal ulceration cornea ulcer -HP:0032156 skos:exactMatch MP:0009827 semapv:LexicalMatching Skin detachment skin detachment -HP:0002578 skos:exactMatch MP:0009854 semapv:LexicalMatching Gastroparesis impaired gastric peristalsis -HP:0011800 skos:exactMatch MP:0009855 semapv:LexicalMatching Midface retrusion midface retrusion -HP:0009741 skos:exactMatch MP:0009860 semapv:LexicalMatching Nephrosclerosis nephrosclerosis -HP:0031784 skos:exactMatch MP:0009867 semapv:LexicalMatching Abnormal ascending aorta morphology abnormal ascending aorta morphology -HP:0031934 skos:exactMatch MP:0009869 semapv:LexicalMatching Abnormal descending aorta morphology abnormal descending aorta morphology -HP:0000160 skos:exactMatch MP:0009880 semapv:LexicalMatching Narrow mouth microstomia -HP:0000154 skos:exactMatch MP:0009881 semapv:LexicalMatching Wide mouth macrostomia -HP:0000171 skos:exactMatch MP:0009904 semapv:LexicalMatching Microglossia tongue hypoplasia -HP:0012730 skos:exactMatch MP:0009905 semapv:LexicalMatching Aglossia absent tongue -HP:0010297 skos:exactMatch MP:0009910 semapv:LexicalMatching Bifid tongue bifurcated tongue -HP:0002475 skos:exactMatch MP:0009929 semapv:LexicalMatching Myelomeningocele meningomyelocele -HP:0002213 skos:exactMatch MP:0009930 semapv:LexicalMatching Fine hair fuzzy hair -HP:0001045 skos:exactMatch MP:0010016 semapv:LexicalMatching Vitiligo variable depigmentation -HP:0012072 skos:exactMatch MP:0010028 semapv:LexicalMatching Aciduria aciduria -HP:0100588 skos:exactMatch MP:0010033 semapv:LexicalMatching Paraphimosis paraphimosis -HP:0012113 skos:exactMatch MP:0010063 semapv:LexicalMatching Abnormal circulating creatine concentration abnormal circulating creatine level -HP:0031965 skos:exactMatch MP:0010067 semapv:LexicalMatching Increased RBC distribution width increased red blood cell distribution width -HP:0004446 skos:exactMatch MP:0010074 semapv:LexicalMatching Stomatocytosis stomatocytosis -HP:0030431 skos:exactMatch MP:0010079 semapv:LexicalMatching Osteochondroma increased osteochondroma incidence -HP:0005107 skos:exactMatch MP:0010113 semapv:LexicalMatching Abnormal sacrum morphology abnormal sacrum morphology -HP:0011105 skos:exactMatch MP:0010127 semapv:LexicalMatching Hypervolemia hypervolemia -HP:0011106 skos:exactMatch MP:0010128 semapv:LexicalMatching Hypovolemia hypovolemia -HP:0012089 skos:exactMatch MP:0010138 semapv:LexicalMatching Arteritis arteritis -HP:0001537 skos:exactMatch MP:0010146 semapv:LexicalMatching Umbilical hernia umbilical hernia -HP:0001878 skos:exactMatch MP:0010163 semapv:LexicalMatching Hemolytic anemia hemolysis -HP:0032563 skos:exactMatch MP:0010176 semapv:LexicalMatching Dacryocytosis dacryocytosis -HP:0001927 skos:exactMatch MP:0010177 semapv:LexicalMatching Acanthocytosis acanthocytosis -HP:0045006 skos:exactMatch MP:0010194 semapv:LexicalMatching Aplasia of lymphatic vessels absent lymphatic vessels -HP:0031109 skos:exactMatch MP:0010249 semapv:LexicalMatching Agalactia lactation failure -HP:0000523 skos:exactMatch MP:0010251 semapv:LexicalMatching Subcapsular cataract subcapsular cataracts -HP:0025201 skos:exactMatch MP:0010331 semapv:LexicalMatching Abnormal apolipoprotein level abnormal apolipoprotein level -HP:0002202 skos:exactMatch MP:0010334 semapv:LexicalMatching Pleural effusion pleural effusion -HP:0005483 skos:exactMatch MP:0010371 semapv:LexicalMatching Abnormal epiglottis morphology abnormal epiglottis morphology -HP:0010445 skos:exactMatch MP:0010404 semapv:LexicalMatching Primum atrial septal defect ostium primum atrial septal defect -HP:0001684 skos:exactMatch MP:0010405 semapv:LexicalMatching Secundum atrial septal defect ostium secundum atrial septal defect -HP:0011565 skos:exactMatch MP:0010406 semapv:LexicalMatching Common atrium common atrium -HP:0011643 skos:exactMatch MP:0010407 semapv:LexicalMatching Coronary sinus atrial septal defect coronary sinus atrial septal defect -HP:0011567 skos:exactMatch MP:0010408 semapv:LexicalMatching Sinus venosus atrial septal defect sinus venosus atrial septal defect -HP:0010774 skos:exactMatch MP:0010409 semapv:LexicalMatching Cor triatriatum cor triatriatum -HP:0011566 skos:exactMatch MP:0010411 semapv:LexicalMatching Cor triatriatum dexter cor triatriatum dextrum -HP:0006695 skos:exactMatch MP:0010412 semapv:LexicalMatching Atrioventricular canal defect atrioventricular septal defect -HP:0001674 skos:exactMatch MP:0010413 semapv:LexicalMatching Complete atrioventricular canal defect complete atrioventricular septal defect -HP:0011577 skos:exactMatch MP:0010414 semapv:LexicalMatching Partial atrioventricular canal defect partial atrioventricular septal defect -HP:0011576 skos:exactMatch MP:0010415 semapv:LexicalMatching Intermediate atrioventricular canal defect intermediate atrioventricular septal defect -HP:0030958 skos:exactMatch MP:0010416 semapv:LexicalMatching Membranous ventricular septal aneurysm interventricular septum membranous part aneurysm -HP:0011681 skos:exactMatch MP:0010417 semapv:LexicalMatching Subarterial ventricular septal defect subarterial ventricular septal defect -HP:0011682 skos:exactMatch MP:0010418 semapv:LexicalMatching Perimembranous ventricular septal defect perimembraneous ventricular septal defect -HP:0011622 skos:exactMatch MP:0010419 semapv:LexicalMatching Inlet ventricular septal defect inlet ventricular septal defect -HP:0011623 skos:exactMatch MP:0010420 semapv:LexicalMatching Muscular ventricular septal defect muscular ventricular septal defect -HP:0011581 skos:exactMatch MP:0010427 semapv:LexicalMatching Double outlet left ventricle double outlet left ventricle -HP:0011719 skos:exactMatch MP:0010430 semapv:LexicalMatching Supracardiac total anomalous pulmonary venous connection "total anomalous pulmonary venous connection supracardiac" -HP:0011538 skos:exactMatch MP:0010431 semapv:LexicalMatching Atrial situs inversus atrial situs inversus -HP:0001750 skos:exactMatch MP:0010432 semapv:LexicalMatching Single ventricle common ventricle -HP:0011555 skos:exactMatch MP:0010433 semapv:LexicalMatching Double inlet left ventricle double inlet heart left ventricle -HP:0011556 skos:exactMatch MP:0010434 semapv:LexicalMatching Double inlet right ventricle double inlet heart right ventricle -HP:0005160 skos:exactMatch MP:0010441 semapv:LexicalMatching Total anomalous pulmonary venous return total anomalous pulmonary venous connection -HP:0010773 skos:exactMatch MP:0010442 semapv:LexicalMatching Partial anomalous pulmonary venous return partial anomalous pulmonary venous connection -HP:0011720 skos:exactMatch MP:0010443 semapv:LexicalMatching Cardiac total anomalous pulmonary venous connection "total anomalous pulmonary venous connection intracardiac" -HP:0011722 skos:exactMatch MP:0010445 semapv:LexicalMatching Mixed total anomalous pulmonary venous connection "total anomalous pulmonary venous connection mixed" -HP:0004383 skos:exactMatch MP:0010446 semapv:LexicalMatching Hypoplastic left heart heart left ventricle hypoplasia -HP:0011604 skos:exactMatch MP:0010455 semapv:LexicalMatching Aortopulmonary window aortopulmonary window -HP:0011660 skos:exactMatch MP:0010456 semapv:LexicalMatching Anomalous origin of one pulmonary artery from ascending aorta hemitruncus -HP:0004937 skos:exactMatch MP:0010462 semapv:LexicalMatching Pulmonary artery aneurysm pulmonary artery aneurysm -HP:0010775 skos:exactMatch MP:0010466 semapv:LexicalMatching Vascular ring vascular ring -HP:0004961 skos:exactMatch MP:0010467 semapv:LexicalMatching Pulmonary artery sling pulmonary artery sling -HP:0031935 skos:exactMatch MP:0010469 semapv:LexicalMatching Ascending aorta hypoplasia ascending aorta hypoplasia -HP:0004381 skos:exactMatch MP:0010471 semapv:LexicalMatching Supravalvular aortic stenosis supravalvar aortic stenosis -HP:0025495 skos:exactMatch MP:0010474 semapv:LexicalMatching Descending aorta hypoplasia descending aorta hypoplasia -HP:0011638 skos:exactMatch MP:0010475 semapv:LexicalMatching Anomalous origin of left coronary artery from the pulmonary artery anomalous pulmonary origin of left coronary artery -HP:0011641 skos:exactMatch MP:0010476 semapv:LexicalMatching Coronary artery fistula coronary fistula -HP:0030882 skos:exactMatch MP:0010477 semapv:LexicalMatching Coronary artery aneurysm coronary artery aneurysm -HP:0006548 skos:exactMatch MP:0010480 semapv:LexicalMatching Pulmonary arteriovenous malformation pulmonary arteriovenous malformation -HP:0031932 skos:exactMatch MP:0010481 semapv:LexicalMatching Aorto-left ventricular tunnel left ventricle to aorta tunnel -HP:0011645 skos:exactMatch MP:0010483 semapv:LexicalMatching Dilatation of the sinus of Valsalva aortic sinus aneurysm -HP:0003115 skos:exactMatch MP:0010508 semapv:LexicalMatching Abnormal EKG abnormal heart electrocardiography waveform feature -HP:0005165 skos:exactMatch MP:0010511 semapv:LexicalMatching Shortened PR interval shortened PR interval -HP:0001678 skos:exactMatch MP:0010519 semapv:LexicalMatching Atrioventricular block atrioventricular block -HP:0012723 skos:exactMatch MP:0010520 semapv:LexicalMatching Sinoatrial block sinoatrial block -HP:0004974 skos:exactMatch MP:0010525 semapv:LexicalMatching Coarctation of abdominal aorta abdominal aorta coarctation -HP:0006574 skos:exactMatch MP:0010529 semapv:LexicalMatching Hepatic arteriovenous malformation hepatic arteriovenous malformation -HP:0002408 skos:exactMatch MP:0010530 semapv:LexicalMatching Cerebral arteriovenous malformation cerebral arteriovenous malformation -HP:0002629 skos:exactMatch MP:0010531 semapv:LexicalMatching Gastrointestinal arteriovenous malformation gastrointestinal arteriovenous malformation -HP:0010316 skos:exactMatch MP:0010536 semapv:LexicalMatching Ebstein anomaly of the tricuspid valve Ebstein's malformation of tricuspid valve -HP:0012722 skos:exactMatch MP:0010559 semapv:LexicalMatching Heart block heart block -HP:0012561 skos:exactMatch MP:0010596 semapv:LexicalMatching Unicuspid aortic valve unicuspid aortic valve -HP:0031569 skos:exactMatch MP:0010597 semapv:LexicalMatching Absent aortic valve cusps absent aortic valve cusps -HP:0031566 skos:exactMatch MP:0010602 semapv:LexicalMatching Abnormal pulmonary valve cusp morphology abnormal pulmonary valve cusp morphology -HP:0001691 skos:exactMatch MP:0010612 semapv:LexicalMatching Muscular subvalvular aortic stenosis muscular subaortic stenosis -HP:0031480 skos:exactMatch MP:0010614 semapv:LexicalMatching Abnormal mitral valve leaflet morphology abnormal mitral valve cusp morphology -HP:0031443 skos:exactMatch MP:0010622 semapv:LexicalMatching Abnormal tricuspid valve leaflet morphology abnormal tricuspid valve cusp morphology -HP:0031834 skos:exactMatch MP:0010635 semapv:LexicalMatching Aortopulmonary collateral arteries aorta pulmonary collateral arteries -HP:0011710 skos:exactMatch MP:0010636 semapv:LexicalMatching Bundle branch block bundle branch block -HP:0001688 skos:exactMatch MP:0010637 semapv:LexicalMatching Sinus bradycardia sinus bradycardia -HP:0004959 skos:exactMatch MP:0010660 semapv:LexicalMatching Descending thoracic aorta aneurysm descending thoracic aorta aneurysm -HP:0007968 skos:exactMatch MP:0010711 semapv:LexicalMatching Remnants of the hyaloid vascular system persistent hyperplastic primary vitreous -HP:0000612 skos:exactMatch MP:0010714 semapv:LexicalMatching Iris coloboma iris coloboma -HP:0000480 skos:exactMatch MP:0010715 semapv:LexicalMatching Retinal coloboma retina coloboma -HP:0000588 skos:exactMatch MP:0010716 semapv:LexicalMatching Optic nerve coloboma optic disk coloboma -HP:0000588 skos:exactMatch MP:0010717 semapv:LexicalMatching Optic nerve coloboma optic nerve coloboma -HP:0020006 skos:exactMatch MP:0010719 semapv:LexicalMatching Ciliary body coloboma ciliary body coloboma -HP:0000270 skos:exactMatch MP:0010743 semapv:LexicalMatching Delayed cranial suture closure delayed cranial suture closure -HP:0000649 skos:exactMatch MP:0010748 semapv:LexicalMatching Abnormality of visual evoked potentials abnormal visual evoked potential -HP:0001172 skos:exactMatch MP:0010772 semapv:LexicalMatching Abnormal thumb morphology abnormal pollex morphology -HP:0002107 skos:exactMatch MP:0010822 semapv:LexicalMatching Pneumothorax pneumothorax -HP:0011616 skos:exactMatch MP:0010854 semapv:LexicalMatching Pulmonary situs inversus lung situs inversus -HP:0001511 skos:exactMatch MP:0010865 semapv:LexicalMatching Intrauterine growth retardation prenatal growth retardation -HP:0010450 skos:exactMatch MP:0010884 semapv:LexicalMatching Esophageal stenosis esophagus stenosis -HP:0012253 skos:exactMatch MP:0010942 semapv:LexicalMatching Abnormal respiratory epithelium morphology abnormal respiratory epithelium morphology -HP:0006517 skos:exactMatch MP:0010998 semapv:LexicalMatching Alveolar proteinosis pulmonary alveolar proteinosis -HP:0002110 skos:exactMatch MP:0011012 semapv:LexicalMatching Bronchiectasis bronchiectasis -HP:0410397 skos:exactMatch MP:0011013 semapv:LexicalMatching Bronchiolectasis bronchiolectasis -HP:0005938 skos:exactMatch MP:0011050 semapv:LexicalMatching Abnormal respiratory motile cilium morphology abnormal respiratory motile cilium morphology -HP:0012261 skos:exactMatch MP:0011055 semapv:LexicalMatching Abnormal respiratory motile cilium physiology abnormal respiratory motile cilium physiology -HP:0030895 skos:exactMatch MP:0011082 semapv:LexicalMatching Abnormal gastrointestinal motility abnormal gastrointestinal motility -HP:0031538 skos:exactMatch MP:0011159 semapv:LexicalMatching Abnormal dermoepidermal junction morphology abnormal epidermal-dermal junction morphology -HP:0012490 skos:exactMatch MP:0011164 semapv:LexicalMatching Panniculitis panniculitis -HP:0009125 skos:exactMatch MP:0011174 semapv:LexicalMatching Lipodystrophy lipodystrophy -HP:0000926 skos:exactMatch MP:0011175 semapv:LexicalMatching Platyspondyly platyspondylia -HP:0040126 skos:exactMatch MP:0011227 semapv:LexicalMatching Abnormal vitamin B12 level abnormal vitamin B12 level -HP:0003363 skos:exactMatch MP:0011249 semapv:LexicalMatching Abdominal situs inversus abdominal situs inversus -HP:0031565 skos:exactMatch MP:0011250 semapv:LexicalMatching Abdominal situs ambiguus abdominal situs ambiguus -HP:0001696 skos:exactMatch MP:0011252 semapv:LexicalMatching Situs inversus totalis situs inversus totalis -HP:0031592 skos:exactMatch MP:0011253 semapv:LexicalMatching Situs inversus with levocardia situs inversus with levocardia -HP:0032464 skos:exactMatch MP:0011298 semapv:LexicalMatching Ureteral hypoplasia ureter hypoplasia -HP:0000108 skos:exactMatch MP:0011308 semapv:LexicalMatching Renal corticomedullary cysts kidney corticomedullary cysts -HP:0008776 skos:exactMatch MP:0011317 semapv:LexicalMatching Abnormal renal artery morphology abnormal renal artery morphology -HP:0001967 skos:exactMatch MP:0011353 semapv:LexicalMatching Diffuse mesangial sclerosis expanded mesangial matrix -HP:0000125 skos:exactMatch MP:0011361 semapv:LexicalMatching Pelvic kidney pelvic kidney -HP:0012330 skos:exactMatch MP:0011403 semapv:LexicalMatching Pyelonephritis pyelonephritis -HP:0001970 skos:exactMatch MP:0011405 semapv:LexicalMatching Tubulointerstitial nephritis tubulointerstitial nephritis -HP:0012085 skos:exactMatch MP:0011420 semapv:LexicalMatching Pyuria pyuria -HP:0012615 skos:exactMatch MP:0011421 semapv:LexicalMatching Cylindruria cylindruria -HP:0012574 skos:exactMatch MP:0011427 semapv:LexicalMatching Mesangial hypercellularity mesangial cell hyperplasia -HP:0030762 skos:exactMatch MP:0011430 semapv:LexicalMatching Mesangiolysis mesangiolysis -HP:0031811 skos:exactMatch MP:0011464 semapv:LexicalMatching Bilirubinuria bilirubinuria -HP:0008155 skos:exactMatch MP:0011473 semapv:LexicalMatching Mucopolysacchariduria increased urine glycosaminoglycan level -HP:0011483 skos:exactMatch MP:0011481 semapv:LexicalMatching Anterior synechiae of the anterior chamber anterior iris synechia -HP:0000074 skos:exactMatch MP:0011491 semapv:LexicalMatching Ureteropelvic junction obstruction ureteropelvic junction obstruction -HP:0030735 skos:exactMatch MP:0011492 semapv:LexicalMatching Ureterovesical junction obstruction ureterovesical junction obstruction -HP:0000073 skos:exactMatch MP:0011493 semapv:LexicalMatching Ureteral duplication double ureter -HP:0006487 skos:exactMatch MP:0011505 semapv:LexicalMatching Bowing of the long bones camptomelia -HP:0000979 skos:exactMatch MP:0011515 semapv:LexicalMatching Purpura purpura -HP:0012068 skos:exactMatch MP:0011516 semapv:LexicalMatching Aspartylglucosaminuria aspartylglucosaminuria -HP:0100515 skos:exactMatch MP:0011535 semapv:LexicalMatching Pollakisuria increased urination frequency -HP:0031591 skos:exactMatch MP:0011571 semapv:LexicalMatching Enlarged Eustachian valve enlarged inferior vena cava valve -HP:0031209 skos:exactMatch MP:0011579 semapv:LexicalMatching Decreased lipoprotein lipase activity decreased lipoprotein lipase activity -HP:0000176 skos:exactMatch MP:0011615 semapv:LexicalMatching Submucous cleft hard palate submucous cleft palate -HP:0012087 skos:exactMatch MP:0011633 semapv:LexicalMatching Abnormal mitochondrial shape abnormal mitochondrial shape -HP:0011004 skos:exactMatch MP:0011655 semapv:LexicalMatching Abnormal systemic arterial morphology abnormal systemic artery morphology -HP:0031563 skos:exactMatch MP:0011656 semapv:LexicalMatching Coronary arteriovenous fistula coronary arterio-venous fistula -HP:0011612 skos:exactMatch MP:0011658 semapv:LexicalMatching Interrupted aortic arch type A "interrupted aortic arch type a" -HP:0011613 skos:exactMatch MP:0011659 semapv:LexicalMatching Interrupted aortic arch type B "interrupted aortic arch type b" -HP:0001683 skos:exactMatch MP:0011660 semapv:LexicalMatching Ectopia cordis ectopia cordis -HP:0004384 skos:exactMatch MP:0011661 semapv:LexicalMatching Type I truncus arteriosus persistent truncus arteriosus type i -HP:0011608 skos:exactMatch MP:0011662 semapv:LexicalMatching Type II truncus arteriosus persistent truncus arteriosus type ii -HP:0011609 skos:exactMatch MP:0011663 semapv:LexicalMatching Type III truncus arteriosus persistent truncus arteriosus type iii -HP:0011610 skos:exactMatch MP:0011664 semapv:LexicalMatching Type IV truncus arteriosus persistent truncus arteriosus type iv -HP:0031348 skos:exactMatch MP:0011665 semapv:LexicalMatching Dextrotransposition of the great arteries d-loop transposition of the great arteries -HP:0011652 skos:exactMatch MP:0011669 semapv:LexicalMatching Double outlet right ventricle with doubly committed ventricular septal defect without pulmonary stenosis "double outlet right ventricle doubly committed ventricular septal defect" -HP:0011654 skos:exactMatch MP:0011670 semapv:LexicalMatching Double outlet right ventricle with non-committed ventricular septal defect without pulmonary stenosis "double outlet right ventricle noncommitted ventricular septal defect" -HP:0011573 skos:exactMatch MP:0011680 semapv:LexicalMatching Hypoplastic tricuspid valve tricuspid valve hypoplasia -HP:0002282 skos:exactMatch MP:0011723 semapv:LexicalMatching Gray matter heterotopia ectopic neuron -HP:0031086 skos:exactMatch MP:0011727 semapv:LexicalMatching Ectopic ovary ectopic ovary -HP:0025382 skos:exactMatch MP:0011737 semapv:LexicalMatching Hypodipsia hypodipsia -HP:0012050 skos:exactMatch MP:0011738 semapv:LexicalMatching Anasarca anasarca -HP:0031812 skos:exactMatch MP:0011741 semapv:LexicalMatching Nitrituria increased urine nitrite level -HP:0031633 skos:exactMatch MP:0011745 semapv:LexicalMatching Isolation of the left subclavian artery isolation of the left subclavian artery -HP:0011974 skos:exactMatch MP:0011747 semapv:LexicalMatching Myelofibrosis myelofibrosis -HP:0032200 skos:exactMatch MP:0011749 semapv:LexicalMatching Perivascular fibrosis perivascular fibrosis -HP:0500006 skos:exactMatch MP:0011763 semapv:LexicalMatching Urethritis urethritis -HP:0000070 skos:exactMatch MP:0011767 semapv:LexicalMatching Ureterocele ureterocele -HP:0025023 skos:exactMatch MP:0011775 semapv:LexicalMatching Rectal atresia rectal atresia -HP:0025407 skos:exactMatch MP:0011786 semapv:LexicalMatching Rectourethral fistula rectourethral fistula -HP:0000796 skos:exactMatch MP:0011801 semapv:LexicalMatching Urethral obstruction urethra obstruction -HP:0005580 skos:exactMatch MP:0011803 semapv:LexicalMatching Duplication of renal pelvis double kidney pelvis -HP:0001586 skos:exactMatch MP:0011829 semapv:LexicalMatching Vesicovaginal fistula vesicovaginal fistula -HP:0010479 skos:exactMatch MP:0011852 semapv:LexicalMatching Patent urachus patent urachus -HP:0002181 skos:exactMatch MP:0011854 semapv:LexicalMatching Cerebral edema cerebral edema -HP:0020133 skos:exactMatch MP:0011871 semapv:LexicalMatching Podocyte hypertrophy podocyte hypertrophy -HP:0030261 skos:exactMatch MP:0011876 semapv:LexicalMatching Absent penis absent penis -HP:0008986 skos:exactMatch MP:0011883 semapv:LexicalMatching Agenesis of the diaphragm absent diaphragm -HP:0032385 skos:exactMatch MP:0011892 semapv:LexicalMatching Abnormal circulating transferrin level abnormal circulating transferrin level -HP:0032195 skos:exactMatch MP:0011920 semapv:LexicalMatching Abnormal S wave abnormal S wave -HP:0031427 skos:exactMatch MP:0011922 semapv:LexicalMatching Abnormal circulating osteocalcin level abnormal circulating osteocalcin level -HP:0030329 skos:exactMatch MP:0011965 semapv:LexicalMatching Retinal thinning decreased total retina thickness -HP:0031795 skos:exactMatch MP:0011973 semapv:LexicalMatching Abnormal circulating glycerol level abnormal circulating glycerol level -HP:0002373 skos:exactMatch MP:0012011 semapv:LexicalMatching Febrile seizures febrile seizures -HP:0001257 skos:exactMatch MP:0012051 semapv:LexicalMatching Spasticity spasticity -HP:0001276 skos:exactMatch MP:0012052 semapv:LexicalMatching Hypertonia hypertonicity -HP:0002509 skos:exactMatch MP:0012053 semapv:LexicalMatching Limb hypertonia limb hypertonicity -HP:0000465 skos:exactMatch MP:0012077 semapv:LexicalMatching Webbed neck webbed neck -HP:0012281 skos:exactMatch MP:0012080 semapv:LexicalMatching Chylous ascites chylous ascites -HP:0000647 skos:exactMatch MP:0012121 semapv:LexicalMatching Sclerocornea sclerocornea -HP:0001562 skos:exactMatch MP:0012171 semapv:LexicalMatching Oligohydramnios oligohydramnios -HP:0031821 skos:exactMatch MP:0012208 semapv:LexicalMatching Abnormal hypoxanthine-guanine phosphoribosyltransferase level abnormal hypoxanthine-guanine phosphoribosyltransferase level -HP:0031823 skos:exactMatch MP:0012209 semapv:LexicalMatching Reduced hypoxanthine-guanine phosphoribosyltransferase level decreased hypoxanthine-guanine phosphoribosyltransferase level -HP:0005326 skos:exactMatch MP:0012258 semapv:LexicalMatching Hypoplastic philtrum philtrum hypoplasia -HP:0002435 skos:exactMatch MP:0012259 semapv:LexicalMatching Meningocele meningocele -HP:0002084 skos:exactMatch MP:0012260 semapv:LexicalMatching Encephalocele encephalomeningocele -HP:0032463 skos:exactMatch MP:0012332 semapv:LexicalMatching Reduced circulating fibronectin level decreased circulating fibronectin level -HP:0002153 skos:exactMatch MP:0012339 semapv:LexicalMatching Hyperkalemia hyperkalemia -HP:0032199 skos:exactMatch MP:0012354 semapv:LexicalMatching Abnormal prothrombin time abnormal prothrombin time -HP:0032198 skos:exactMatch MP:0012355 semapv:LexicalMatching Decreased prothrombin time decreased prothrombin time -HP:0008151 skos:exactMatch MP:0012356 semapv:LexicalMatching Prolonged prothrombin time increased prothrombin time -HP:0003645 skos:exactMatch MP:0012357 semapv:LexicalMatching Prolonged partial thromboplastin time abnormal partial thromboplastin time -HP:0003645 skos:exactMatch MP:0012359 semapv:LexicalMatching Prolonged partial thromboplastin time increased partial thromboplastin time -HP:0000767 skos:exactMatch MP:0012514 semapv:LexicalMatching Pectus excavatum pectus excavatum -HP:0009922 skos:exactMatch MP:0012538 semapv:LexicalMatching Vascular remnant arising from the disc persistent hyaloid artery -HP:0003396 skos:exactMatch MP:0012545 semapv:LexicalMatching Syringomyelia syringomyelia -HP:0000325 skos:exactMatch MP:0012546 semapv:LexicalMatching Triangular face triangular face -HP:0002475 skos:exactMatch MP:0012547 semapv:LexicalMatching Myelomeningocele spina bifida cystica -HP:0012418 skos:exactMatch MP:0012549 semapv:LexicalMatching Hypoxemia hypoxemia -HP:0005972 skos:exactMatch MP:0012550 semapv:LexicalMatching Respiratory acidosis respiratory acidosis -HP:0001942 skos:exactMatch MP:0012551 semapv:LexicalMatching Metabolic acidosis metabolic acidosis -HP:0003128 skos:exactMatch MP:0012552 semapv:LexicalMatching Lactic acidosis lactic acidosis -HP:0004336 skos:exactMatch MP:0012674 semapv:LexicalMatching Myelin outfoldings tomacula -HP:0030175 skos:exactMatch MP:0012674 semapv:LexicalMatching Myelin tomacula tomacula -HP:0100562 skos:exactMatch MP:0012711 semapv:LexicalMatching Diplomyelia diplomyelia -HP:0430021 skos:exactMatch MP:0012729 semapv:LexicalMatching Abnormal common carotid artery morphology abnormal common carotid artery morphology -HP:0000421 skos:exactMatch MP:0013127 semapv:LexicalMatching Epistaxis epistaxis -HP:0004099 skos:exactMatch MP:0013149 semapv:LexicalMatching Macrodactyly macrodactyly -HP:0005268 skos:exactMatch MP:0013172 semapv:LexicalMatching Spontaneous abortion miscarriage -HP:0020179 skos:exactMatch MP:0013215 semapv:LexicalMatching Abnormal haptoglobin level abnormal haptoglobin level -HP:0410012 skos:exactMatch MP:0013262 semapv:LexicalMatching Abnormal mouth floor morphology abnormal mouth floor morphology -HP:0010296 skos:exactMatch MP:0013264 semapv:LexicalMatching Ankyloglossia tongue ankylosis -HP:0002836 skos:exactMatch MP:0013282 semapv:LexicalMatching Bladder exstrophy urinary bladder exstrophy -HP:0004727 skos:exactMatch MP:0013305 semapv:LexicalMatching Impaired renal concentrating ability isosthenuria -HP:0003271 skos:exactMatch MP:0013328 semapv:LexicalMatching Visceromegaly visceromegaly -HP:0010799 skos:exactMatch MP:0013365 semapv:LexicalMatching Pinealoma increased pineal gland tumor incidence -HP:0011850 skos:exactMatch MP:0013367 semapv:LexicalMatching Parotitis parotid gland inflammation -HP:0000970 skos:exactMatch MP:0013368 semapv:LexicalMatching Anhidrosis abnormal sweat gland physiology -HP:0000970 skos:exactMatch MP:0013370 semapv:LexicalMatching Anhidrosis anhidrosis -HP:0000966 skos:exactMatch MP:0013371 semapv:LexicalMatching Hypohidrosis hypohidrosis -HP:0000975 skos:exactMatch MP:0013372 semapv:LexicalMatching Hyperhidrosis hyperhidrosis -HP:0009720 skos:exactMatch MP:0013383 semapv:LexicalMatching Adenoma sebaceum increased sebaceous gland adenoma incidence -HP:0010605 skos:exactMatch MP:0013390 semapv:LexicalMatching Chalazion Meibomian gland cyst -HP:0025610 skos:exactMatch MP:0013391 semapv:LexicalMatching Posterior blepharitis abnormal Meibomian gland physiology -HP:0025610 skos:exactMatch MP:0013392 semapv:LexicalMatching Posterior blepharitis Meibomian gland inflammation -HP:0430007 skos:exactMatch MP:0013393 semapv:LexicalMatching Symblepharon symblepharon -HP:0000579 skos:exactMatch MP:0013451 semapv:LexicalMatching Nasolacrimal duct obstruction nasolacrimal duct obstruction -HP:0001097 skos:exactMatch MP:0013466 semapv:LexicalMatching Keratoconjunctivitis sicca keratoconjunctivitis sicca -HP:0100532 skos:exactMatch MP:0013479 semapv:LexicalMatching Scleritis scleritis -HP:0030934 skos:exactMatch MP:0013492 semapv:LexicalMatching Oral erythroplakia oral erythroplakia -HP:0000029 skos:exactMatch MP:0013600 semapv:LexicalMatching Testicular atrophy testis degeneration -HP:0012130 skos:exactMatch MP:0013659 semapv:LexicalMatching Abnormal erythroid lineage cell morphology abnormal erythroid lineage cell morphology -HP:0010307 skos:exactMatch MP:0013752 semapv:LexicalMatching Stridor stridor -HP:0002779 skos:exactMatch MP:0013753 semapv:LexicalMatching Tracheomalacia tracheomalacia -HP:0005528 skos:exactMatch MP:0013776 semapv:LexicalMatching Bone marrow hypocellularity bone marrow failure -HP:0009933 skos:exactMatch MP:0013789 semapv:LexicalMatching Narrow naris small external nares -HP:0009932 skos:exactMatch MP:0013790 semapv:LexicalMatching Single naris single external naris -HP:0001298 skos:exactMatch MP:0013806 semapv:LexicalMatching Encephalopathy encephalopathy -HP:0007430 skos:exactMatch MP:0013807 semapv:LexicalMatching Generalized edema generalized edema -HP:0012327 skos:exactMatch MP:0013856 semapv:LexicalMatching Celiac artery compression celiac artery compression -HP:0000499 skos:exactMatch MP:0013895 semapv:LexicalMatching Abnormal eyelash morphology abnormal eyelid cilium morphology -HP:0100686 skos:exactMatch MP:0013942 semapv:LexicalMatching Enthesitis enthesitis -HP:0004401 skos:exactMatch MP:0014036 semapv:LexicalMatching Meconium ileus meconium ileus -HP:0011359 skos:exactMatch MP:0014053 semapv:LexicalMatching Dry hair dry hair -HP:0030779 skos:exactMatch MP:0014061 semapv:LexicalMatching Ethmocephaly ethmocephaly -HP:0100318 skos:exactMatch MP:0014063 semapv:LexicalMatching Lafora bodies Lafora bodies -HP:0100317 skos:exactMatch MP:0014064 semapv:LexicalMatching Argyrophilic inclusion bodies argyrophilic inclusion bodies -HP:0100315 skos:exactMatch MP:0014065 semapv:LexicalMatching Lewy bodies Lewy bodies -HP:0100316 skos:exactMatch MP:0014067 semapv:LexicalMatching Hirano bodies Hirano bodies -HP:0001028 skos:exactMatch MP:0014086 semapv:LexicalMatching Hemangioma hemangioma -HP:0007359 skos:exactMatch MP:0014120 semapv:LexicalMatching Focal-onset seizure focal seizures -HP:0100522 skos:exactMatch MP:0014127 semapv:LexicalMatching Thymoma increased thymoma incidence -HP:0000522 skos:exactMatch MP:0014157 semapv:LexicalMatching Alacrima alacrima -HP:0003118 skos:exactMatch MP:0014161 semapv:LexicalMatching Increased circulating cortisol level increased circulating cortisol level -HP:0008163 skos:exactMatch MP:0014162 semapv:LexicalMatching Decreased circulating cortisol level decreased circulating cortisol level -HP:0012628 skos:exactMatch MP:0014176 semapv:LexicalMatching Abnormal suspensory ligament of lens morphology abnormal cilary zonule morphology -HP:0012860 skos:exactMatch MP:0014189 semapv:LexicalMatching Testicular fibrosis testis fibrosis -HP:0400005 skos:exactMatch MP:0020084 semapv:LexicalMatching Short ear short ears -HP:0400004 skos:exactMatch MP:0020085 semapv:LexicalMatching Long ear long ears -HP:0045081 skos:exactMatch MP:0020182 semapv:LexicalMatching Abnormality of body mass index abnormal body mass index -HP:0000632 skos:exactMatch MP:0020218 semapv:LexicalMatching Lacrimation abnormality abnormal tear production -HP:0009926 skos:exactMatch MP:0020219 semapv:LexicalMatching Epiphora increased tear production -HP:0031731 skos:exactMatch MP:0020219 semapv:LexicalMatching Increased tear production increased tear production -HP:0000633 skos:exactMatch MP:0020220 semapv:LexicalMatching Decreased lacrimation decreased tear production -HP:0020037 skos:exactMatch MP:0020289 semapv:LexicalMatching Astasia astasia -HP:0011958 skos:exactMatch MP:0020441 semapv:LexicalMatching Retinal perforation rhegmatogenous retinal detachment -HP:0012230 skos:exactMatch MP:0020441 semapv:LexicalMatching Rhegmatogenous retinal detachment rhegmatogenous retinal detachment -HP:0012231 skos:exactMatch MP:0020442 semapv:LexicalMatching Exudative retinal detachment serous retinal detachment -HP:0007917 skos:exactMatch MP:0020443 semapv:LexicalMatching Tractional retinal detachment tractional retinal detachment -HP:0011966 skos:exactMatch MP:0020836 semapv:LexicalMatching Elevated plasma citrulline increased circulating citrulline level -HP:0001607 skos:exactMatch MP:0030001 semapv:LexicalMatching Subglottic stenosis subglottis stenosis -HP:0410170 skos:exactMatch MP:0030003 semapv:LexicalMatching Hippocampal atrophy hippocampus atrophy -HP:0025517 skos:exactMatch MP:0030004 semapv:LexicalMatching Hypoplastic hippocampus hippocampus hypoplasia -HP:0002645 skos:exactMatch MP:0030030 semapv:LexicalMatching Wormian bones Wormian bones -HP:0000290 skos:exactMatch MP:0030031 semapv:LexicalMatching Abnormality of the forehead abnormal forehead morphology -HP:0005281 skos:exactMatch MP:0030035 semapv:LexicalMatching Hypoplastic nasal bridge small nasal bridge -HP:0003194 skos:exactMatch MP:0030036 semapv:LexicalMatching Short nasal bridge short nasal bridge -HP:0011220 skos:exactMatch MP:0030049 semapv:LexicalMatching Prominent forehead prominent forehead -HP:0000303 skos:exactMatch MP:0030050 semapv:LexicalMatching Mandibular prognathia large mandible -HP:0030756 skos:exactMatch MP:0030058 semapv:LexicalMatching Erythrodontia erythrodontia -HP:0000274 skos:exactMatch MP:0030065 semapv:LexicalMatching Small face face hypoplasia -HP:0001999 skos:exactMatch MP:0030071 semapv:LexicalMatching Abnormal facial shape abnormal face shape -HP:0100663 skos:exactMatch MP:0030078 semapv:LexicalMatching Synotia synotia -HP:0002677 skos:exactMatch MP:0030094 semapv:LexicalMatching Small foramen magnum foramen magnum stenosis -HP:0004467 skos:exactMatch MP:0030097 semapv:LexicalMatching Preauricular pit preauricular pit -HP:0000629 skos:exactMatch MP:0030098 semapv:LexicalMatching Periorbital fullness periorbital fullness -HP:0011332 skos:exactMatch MP:0030100 semapv:LexicalMatching Hemifacial hypoplasia hemifacial hypoplasia -HP:0000670 skos:exactMatch MP:0030101 semapv:LexicalMatching Carious teeth carious teeth -HP:0000473 skos:exactMatch MP:0030126 semapv:LexicalMatching Torticollis torticollis -HP:0000206 skos:exactMatch MP:0030129 semapv:LexicalMatching Glossitis tongue inflammation -HP:0000230 skos:exactMatch MP:0030130 semapv:LexicalMatching Gingivitis gum inflammation -HP:0000704 skos:exactMatch MP:0030132 semapv:LexicalMatching Periodontitis periodontium inflammation -HP:0011468 skos:exactMatch MP:0030143 semapv:LexicalMatching Facial tics facial muscle spasm -HP:0000215 skos:exactMatch MP:0030169 semapv:LexicalMatching Thick upper lip vermilion thick upper lip -HP:0005104 skos:exactMatch MP:0030197 semapv:LexicalMatching Hypoplastic nasal septum small nasal septum -HP:0004411 skos:exactMatch MP:0030199 semapv:LexicalMatching Deviated nasal septum deviated nasal septum -HP:0009746 skos:exactMatch MP:0030205 semapv:LexicalMatching Thick nasal septum thick nasal septum -HP:3000051 skos:exactMatch MP:0030212 semapv:LexicalMatching Abnormal hyoglossus muscle morphology abnormal hyoglossus muscle morphology -HP:0002380 skos:exactMatch MP:0030214 semapv:LexicalMatching Fasciculations muscle fasciculation -HP:0001308 skos:exactMatch MP:0030216 semapv:LexicalMatching Tongue fasciculations tongue muscle fasciculation -HP:0025011 skos:exactMatch MP:0030218 semapv:LexicalMatching Pyriform aperture stenosis piriform aperture stenosis -HP:0004472 skos:exactMatch MP:0030223 semapv:LexicalMatching Mandibular hyperostosis mandibular hyperostosis -HP:0002010 skos:exactMatch MP:0030248 semapv:LexicalMatching Narrow maxilla narrow maxilla -HP:0030867 skos:exactMatch MP:0030253 semapv:LexicalMatching Vertical orbital dystopia vertical orbital dystopia -HP:0002007 skos:exactMatch MP:0030262 semapv:LexicalMatching Frontal bossing frontal bossing -HP:0002007 skos:exactMatch MP:0030263 semapv:LexicalMatching Frontal bossing cranial bossing -HP:0000242 skos:exactMatch MP:0030265 semapv:LexicalMatching Parietal bossing parietal bossing -HP:0000278 skos:exactMatch MP:0030270 semapv:LexicalMatching Retrognathia retrogenia -HP:0000347 skos:exactMatch MP:0030273 semapv:LexicalMatching Micrognathia mandibular retrognathia -HP:0000327 skos:exactMatch MP:0030274 semapv:LexicalMatching Hypoplasia of the maxilla maxillary retrognathia -HP:0002684 skos:exactMatch MP:0030278 semapv:LexicalMatching Thickened calvaria thick neurocranium -HP:0010539 skos:exactMatch MP:0030279 semapv:LexicalMatching Thin calvarium thin neurocranium -HP:0031046 skos:exactMatch MP:0030290 semapv:LexicalMatching Absent soft palate absent soft palate -HP:0000252 skos:exactMatch MP:0030315 semapv:LexicalMatching Microcephaly small neurocranium -HP:0012478 skos:exactMatch MP:0030327 semapv:LexicalMatching Temporomandibular joint ankylosis temporomandibular joint ankylosis -HP:0004440 skos:exactMatch MP:0030350 semapv:LexicalMatching Coronal craniosynostosis premature coronal suture closure -HP:0004442 skos:exactMatch MP:0030354 semapv:LexicalMatching Sagittal craniosynostosis premature sagittal suture closure -HP:0004443 skos:exactMatch MP:0030356 semapv:LexicalMatching Lambdoidal craniosynostosis premature lambdoid suture closure -HP:0005441 skos:exactMatch MP:0030359 semapv:LexicalMatching Sclerotic cranial sutures cranial suture sclerosis -HP:0011330 skos:exactMatch MP:0030367 semapv:LexicalMatching Metopic synostosis premature metopic suture closure -HP:0002692 skos:exactMatch MP:0030386 semapv:LexicalMatching Hypoplastic facial bones facial bone hypoplasia -HP:0001363 skos:exactMatch MP:0030392 semapv:LexicalMatching Craniosynostosis premature fontanelle closure -HP:0005458 skos:exactMatch MP:0030392 semapv:LexicalMatching Premature closure of fontanelles premature fontanelle closure -HP:0200111 skos:exactMatch MP:0030403 semapv:LexicalMatching Absent stapes head absent stapes head -HP:0004493 skos:exactMatch MP:0030417 semapv:LexicalMatching Craniofacial hyperostosis craniofacial hyperostosis -HP:0005465 skos:exactMatch MP:0030418 semapv:LexicalMatching Facial hyperostosis facial hyperostosis -HP:0030789 skos:exactMatch MP:0030419 semapv:LexicalMatching Excessive cerumen excessive cerumen -HP:0001363 skos:exactMatch MP:0030435 semapv:LexicalMatching Craniosynostosis premature craniofacial suture closure -HP:0009722 skos:exactMatch MP:0030460 semapv:LexicalMatching Dental enamel pits enamel pits -HP:0030757 skos:exactMatch MP:0030462 semapv:LexicalMatching Tooth abscess tooth abscess -HP:0030758 skos:exactMatch MP:0030463 semapv:LexicalMatching Periapical tooth abscess apical tooth abscess -HP:0011090 skos:exactMatch MP:0030472 semapv:LexicalMatching Fused teeth fused teeth -HP:0003771 skos:exactMatch MP:0030491 semapv:LexicalMatching Pulp stones dental pulp stones -HP:0011072 skos:exactMatch MP:0030495 semapv:LexicalMatching Rootless teeth absent tooth root -HP:0000679 skos:exactMatch MP:0030496 semapv:LexicalMatching Taurodontia taurodontia -HP:0000698 skos:exactMatch MP:0030499 semapv:LexicalMatching Conical tooth conical tooth -HP:0001571 skos:exactMatch MP:0030505 semapv:LexicalMatching Multiple impacted teeth tooth impaction -HP:0011079 skos:exactMatch MP:0030505 semapv:LexicalMatching Impacted tooth tooth impaction -HP:0100656 skos:exactMatch MP:0030579 semapv:LexicalMatching Thoracoabdominal wall defect thoracoabdominoschisis -HP:0004334 skos:exactMatch MP:0030584 semapv:LexicalMatching Dermal atrophy skin atrophy -HP:0006349 skos:exactMatch MP:0030608 semapv:LexicalMatching Agenesis of permanent teeth decreased tooth number -HP:0000674 skos:exactMatch MP:0030610 semapv:LexicalMatching Anodontia absent teeth -HP:0003260 skos:exactMatch MP:0030681 semapv:LexicalMatching Hydroxyprolinemia increased circulating hydroxyproline level -HP:0003080 skos:exactMatch MP:0030682 semapv:LexicalMatching Hydroxyprolinuria hydroxyprolinuria -HP:0025441 skos:exactMatch MP:0030776 semapv:LexicalMatching Achilles tendon calcification calcified calcaneal tendon -HP:0003368 skos:exactMatch MP:0030788 semapv:LexicalMatching Abnormality of the femoral head abnormal femur head morphology -HP:0003367 skos:exactMatch MP:0030789 semapv:LexicalMatching Abnormality of the femoral neck abnormal femur neck morphology -HP:0100864 skos:exactMatch MP:0030793 semapv:LexicalMatching Short femoral neck short femur neck -HP:0002827 skos:exactMatch MP:0030796 semapv:LexicalMatching Hip dislocation hip dislocation -HP:0001388 skos:exactMatch MP:0030797 semapv:LexicalMatching Joint laxity joint laxity -HP:0001371 skos:exactMatch MP:0030798 semapv:LexicalMatching Flexion contracture joint contracture -HP:0025230 skos:exactMatch MP:0030801 semapv:LexicalMatching Tendonitis tendonitis -HP:0012317 skos:exactMatch MP:0030822 semapv:LexicalMatching Sacroiliac arthritis sacroiliac joint inflammation -HP:0031846 skos:exactMatch MP:0030827 semapv:LexicalMatching Femur fracture femur fracture -HP:0003042 skos:exactMatch MP:0030843 semapv:LexicalMatching Elbow dislocation elbow dislocation -HP:0003994 skos:exactMatch MP:0030864 semapv:LexicalMatching Dislocated wrist wrist dislocation -HP:0000897 skos:exactMatch MP:0030884 semapv:LexicalMatching Rachitic rosary rachitic rosary -HP:0000923 skos:exactMatch MP:0030884 semapv:LexicalMatching Beaded ribs rachitic rosary -HP:0007384 skos:exactMatch MP:0030915 semapv:LexicalMatching Aberrant melanosome maturation abnormal melanosome maturation -HP:0005592 skos:exactMatch MP:0030917 semapv:LexicalMatching Giant melanosomes in melanocytes enlarged melanosome -HP:0031615 skos:exactMatch MP:0030932 semapv:LexicalMatching Hypopyon hypopyon -HP:0011886 skos:exactMatch MP:0030933 semapv:LexicalMatching Hyphema hyphema -HP:0001993 skos:exactMatch MP:0030971 semapv:LexicalMatching Ketoacidosis ketoacidosis -HP:0031428 skos:exactMatch MP:0030984 semapv:LexicalMatching Increased circulating osteocalcin level increased circulating osteocalcin level -HP:0031429 skos:exactMatch MP:0030985 semapv:LexicalMatching Decreased circulating osteocalcin level decreased circulating osteocalcin level -HP:0012486 skos:exactMatch MP:0030987 semapv:LexicalMatching Myelitis spinal cord inflammation -HP:0031002 skos:exactMatch MP:0030990 semapv:LexicalMatching Neuritis nerve inflammation -HP:0100653 skos:exactMatch MP:0030991 semapv:LexicalMatching Optic neuritis optic nerve inflammation -HP:0009894 skos:exactMatch MP:0000019 semapv:LogicalReasoning Thickened ears thick ears -HP:0000377 skos:exactMatch MP:0000022 semapv:LogicalReasoning Abnormality of the pinna abnormal ear shape -HP:0000369 skos:exactMatch MP:0000024 semapv:LogicalReasoning Low-set ears lowered ear position -HP:0011390 skos:exactMatch MP:0000026 semapv:LogicalReasoning Morphological abnormality of the inner ear abnormal inner ear morphology -HP:0011376 skos:exactMatch MP:0000034 semapv:LogicalReasoning Morphological abnormality of the vestibule of the inner ear abnormal inner ear vestibule morphology -HP:0008609 skos:exactMatch MP:0000049 semapv:LogicalReasoning Morphological abnormality of the middle ear abnormal middle ear morphology -HP:0002696 skos:exactMatch MP:0000109 semapv:LogicalReasoning Abnormal parietal bone morphology abnormal parietal bone morphology -HP:0011323 skos:exactMatch MP:0000114 semapv:LogicalReasoning Cleft of chin cleft chin -HP:0002753 skos:exactMatch MP:0000135 semapv:LogicalReasoning Thin bony cortex decreased compact bone thickness -HP:0000782 skos:exactMatch MP:0000149 semapv:LogicalReasoning Abnormality of the scapula abnormal scapula morphology -HP:0003141 skos:exactMatch MP:0000182 semapv:LogicalReasoning Increased LDL cholesterol concentration increased circulating LDL cholesterol level -HP:0003233 skos:exactMatch MP:0000186 semapv:LogicalReasoning Decreased HDL cholesterol concentration decreased circulating HDL cholesterol level -HP:0001640 skos:exactMatch MP:0000274 semapv:LogicalReasoning Cardiomegaly enlarged heart -HP:0011994 skos:exactMatch MP:0000282 semapv:LogicalReasoning Abnormal atrial septum morphology abnormal interatrial septum morphology -HP:0100495 skos:exactMatch MP:0000324 semapv:LogicalReasoning Mastocytosis increased mast cell number -HP:0001006 skos:exactMatch MP:0000414 semapv:LogicalReasoning Hypotrichosis alopecia -HP:0040194 skos:exactMatch MP:0000434 semapv:LogicalReasoning Increased head circumference megacephaly -HP:0000248 skos:exactMatch MP:0000435 semapv:LogicalReasoning Brachycephaly shortened head -HP:0000327 skos:exactMatch MP:0000457 semapv:LogicalReasoning Hypoplasia of the maxilla maxilla hypoplasia -HP:0005815 skos:exactMatch MP:0000480 semapv:LogicalReasoning Supernumerary ribs increased rib number -HP:0010946 skos:exactMatch MP:0000519 semapv:LogicalReasoning Dilatation of the renal pelvis hydronephrosis -HP:0008873 skos:exactMatch MP:0000547 semapv:LogicalReasoning Disproportionate short-limb short stature short limbs -HP:0045009 skos:exactMatch MP:0000552 semapv:LogicalReasoning Abnormal morphology of the radius abnormal radius morphology -HP:0002992 skos:exactMatch MP:0000558 semapv:LogicalReasoning Abnormality of tibia morphology abnormal tibia morphology -HP:0002823 skos:exactMatch MP:0000559 semapv:LogicalReasoning Abnormality of femur morphology abnormal femur morphology -HP:0001883 skos:exactMatch MP:0000576 semapv:LogicalReasoning Talipes clubfoot -HP:0012681 skos:exactMatch MP:0000632 semapv:LogicalReasoning Abnormality of pineal morphology abnormal pineal gland morphology -HP:0011732 skos:exactMatch MP:0000639 semapv:LogicalReasoning Abnormality of adrenal morphology abnormal adrenal gland morphology -HP:0008711 skos:exactMatch MP:0000659 semapv:LogicalReasoning Benign prostatic hyperplasia prostate gland hyperplasia -HP:0040088 skos:exactMatch MP:0000717 semapv:LogicalReasoning Abnormal lymphocyte count abnormal lymphocyte cell number -HP:0005422 skos:exactMatch MP:0000727 semapv:LogicalReasoning Absence of CD8-positive T cells "absent CD8-positive alpha-beta T cells" -HP:0001322 skos:exactMatch MP:0000774 semapv:LogicalReasoning obsolete Brain very small decreased brain size -HP:0100547 skos:exactMatch MP:0000783 semapv:LogicalReasoning Abnormality of forebrain morphology abnormal forebrain morphology -HP:0006872 skos:exactMatch MP:0000785 semapv:LogicalReasoning Cerebral hypoplasia telencephalon hypoplasia -HP:0006891 skos:exactMatch MP:0000789 semapv:LogicalReasoning Thick cerebral cortex thickened cerebral cortex -HP:0025100 skos:exactMatch MP:0000807 semapv:LogicalReasoning Abnormal morphology of the hippocampus abnormal hippocampus morphology -HP:0040327 skos:exactMatch MP:0000819 semapv:LogicalReasoning Abnormal morphology of the olfactory bulb abnormal olfactory bulb morphology -HP:0006956 skos:exactMatch MP:0000825 semapv:LogicalReasoning Dilation of lateral ventricles dilated lateral ventricles -HP:0011282 skos:exactMatch MP:0000841 semapv:LogicalReasoning Abnormality of hindbrain morphology abnormal hindbrain morphology -HP:0007027 skos:exactMatch MP:0000847 semapv:LogicalReasoning Poorly formed metencephalon abnormal metencephalon morphology -HP:0002335 skos:exactMatch MP:0000865 semapv:LogicalReasoning Agenesis of cerebellar vermis absent cerebellum vermis -HP:0001320 skos:exactMatch MP:0000866 semapv:LogicalReasoning Cerebellar vermis hypoplasia cerebellum vermis hypoplasia -HP:0002450 skos:exactMatch MP:0000937 semapv:LogicalReasoning Abnormal motor neuron morphology abnormal motor neuron morphology -HP:0002398 skos:exactMatch MP:0000938 semapv:LogicalReasoning Degeneration of anterior horn cells motor neuron degeneration -HP:0025028 skos:exactMatch MP:0001044 semapv:LogicalReasoning Abnormality of enteric nervous system morphology abnormal enteric nervous system morphology -HP:0010824 skos:exactMatch MP:0001065 semapv:LogicalReasoning Abnormal fifth cranial nerve morphology abnormal trigeminal nerve morphology -HP:3000047 skos:exactMatch MP:0001073 semapv:LogicalReasoning Abnormal glossopharyngeal nerve morphology abnormal glossopharyngeal nerve morphology -HP:0010791 skos:exactMatch MP:0001152 semapv:LogicalReasoning Hyperplasia of the Leydig cells Leydig cell hyperplasia -HP:0011124 skos:exactMatch MP:0001216 semapv:LogicalReasoning Abnormality of epidermal morphology abnormal epidermal layer morphology -HP:0000962 skos:exactMatch MP:0001219 semapv:LogicalReasoning Hyperkeratosis thick epidermis -HP:0000002 skos:exactMatch MP:0001253 semapv:LogicalReasoning Abnormality of body height abnormal body height -HP:0004323 skos:exactMatch MP:0001259 semapv:LogicalReasoning Abnormality of body weight abnormal body weight -HP:0100625 skos:exactMatch MP:0001267 semapv:LogicalReasoning Enlarged thorax enlarged chest -HP:0000525 skos:exactMatch MP:0001322 semapv:LogicalReasoning Abnormality iris morphology abnormal iris morphology -HP:0010999 skos:exactMatch MP:0001334 semapv:LogicalReasoning Aplasia of the optic tract absent optic tract -HP:0000733 skos:exactMatch MP:0001409 semapv:LogicalReasoning Stereotypy increased stereotypic behavior -HP:0011843 skos:exactMatch MP:0001533 semapv:LogicalReasoning Abnormality of skeletal physiology abnormal skeleton physiology -HP:0002155 skos:exactMatch MP:0001552 semapv:LogicalReasoning Hypertriglyceridemia increased circulating triglyceride level -HP:0012184 skos:exactMatch MP:0001556 semapv:LogicalReasoning Increased HDL cholesterol concentration increased circulating HDL cholesterol level -HP:0025032 skos:exactMatch MP:0001663 semapv:LogicalReasoning Abnormality of digestive system physiology abnormal digestive system physiology -HP:0001508 skos:exactMatch MP:0001732 semapv:LogicalReasoning Failure to thrive postnatal growth retardation -HP:0003154 skos:exactMatch MP:0001748 semapv:LogicalReasoning Increased circulating ACTH level increased circulating adrenocorticotropin level -HP:0010978 skos:exactMatch MP:0001790 semapv:LogicalReasoning Abnormality of immune system physiology abnormal immune system physiology -HP:0002720 skos:exactMatch MP:0001807 semapv:LogicalReasoning Decreased circulating IgA level decreased IgA level -HP:0001892 skos:exactMatch MP:0001914 semapv:LogicalReasoning Abnormal bleeding hemorrhage -HP:0000080 skos:exactMatch MP:0001919 semapv:LogicalReasoning Abnormality of reproductive system physiology abnormal reproductive system physiology -HP:0000823 skos:exactMatch MP:0001938 semapv:LogicalReasoning Delayed puberty delayed sexual maturation -HP:0012090 skos:exactMatch MP:0001944 semapv:LogicalReasoning Abnormal pancreas morphology abnormal pancreas morphology -HP:0002093 skos:exactMatch MP:0001953 semapv:LogicalReasoning Respiratory insufficiency respiratory failure -HP:0000138 skos:exactMatch MP:0002016 semapv:LogicalReasoning Ovarian cyst ovary cysts -HP:0010719 skos:exactMatch MP:0002074 semapv:LogicalReasoning Abnormality of hair texture abnormal hair texture -HP:0006482 skos:exactMatch MP:0002100 semapv:LogicalReasoning Abnormality of dental morphology abnormal tooth morphology -HP:0012252 skos:exactMatch MP:0002132 semapv:LogicalReasoning Abnormal respiratory system morphology abnormal respiratory system morphology -HP:0002795 skos:exactMatch MP:0002133 semapv:LogicalReasoning Functional respiratory abnormality abnormal respiratory system physiology -HP:0410043 skos:exactMatch MP:0002151 semapv:LogicalReasoning Abnormal neural tube morphology abnormal neural tube morphology -HP:0002991 skos:exactMatch MP:0002187 semapv:LogicalReasoning Abnormality of fibula morphology abnormal fibula morphology -HP:0002718 skos:exactMatch MP:0002412 semapv:LogicalReasoning Recurrent bacterial infections increased susceptibility to bacterial infection -HP:0011840 skos:exactMatch MP:0002444 semapv:LogicalReasoning Abnormality of T cell physiology abnormal T cell physiology -HP:0010975 skos:exactMatch MP:0002458 semapv:LogicalReasoning Abnormal B cell count abnormal B cell number -HP:0005372 skos:exactMatch MP:0002459 semapv:LogicalReasoning Abnormality of B cell physiology abnormal B cell physiology -HP:0011990 skos:exactMatch MP:0002463 semapv:LogicalReasoning Abnormality of neutrophil physiology abnormal neutrophil physiology -HP:0410245 skos:exactMatch MP:0002491 semapv:LogicalReasoning Decreased circulating total IgD decreased IgD level -HP:0005479 skos:exactMatch MP:0002492 semapv:LogicalReasoning Decreased circulating total IgE decreased IgE level -HP:0003496 skos:exactMatch MP:0002494 semapv:LogicalReasoning Increased circulating IgM level increased IgM level -HP:0003261 skos:exactMatch MP:0002495 semapv:LogicalReasoning Increased circulating IgA level increased IgA level -HP:0003212 skos:exactMatch MP:0002497 semapv:LogicalReasoning Increased circulating total IgE level increased IgE level -HP:0011927 skos:exactMatch MP:0002544 semapv:LogicalReasoning Short digit brachydactyly -HP:0012153 skos:exactMatch MP:0002644 semapv:LogicalReasoning Hypotriglyceridemia decreased circulating triglyceride level -HP:0002920 skos:exactMatch MP:0002664 semapv:LogicalReasoning Decreased circulating ACTH level decreased circulating adrenocorticotropin level -HP:0011070 skos:exactMatch MP:0002689 semapv:LogicalReasoning Abnormality of molar morphology abnormal molar morphology -HP:0012091 skos:exactMatch MP:0002693 semapv:LogicalReasoning Abnormality of pancreas physiology abnormal pancreas physiology -HP:0002624 skos:exactMatch MP:0002725 semapv:LogicalReasoning Abnormal venous morphology abnormal vein morphology -HP:0030968 skos:exactMatch MP:0002726 semapv:LogicalReasoning Abnormal pulmonary vein morphology abnormal pulmonary vein morphology -HP:0006426 skos:exactMatch MP:0002728 semapv:LogicalReasoning Rudimentary to absent tibiae absent tibia -HP:0006436 skos:exactMatch MP:0002764 semapv:LogicalReasoning Shortening of the tibia short tibia -HP:0040171 skos:exactMatch MP:0002780 semapv:LogicalReasoning Decreased serum testosterone level decreased circulating testosterone level -HP:0030088 skos:exactMatch MP:0002781 semapv:LogicalReasoning Increased serum testosterone level increased circulating testosterone level -HP:0001098 skos:exactMatch MP:0002864 semapv:LogicalReasoning Abnormal fundus morphology abnormal ocular fundus morphology -HP:0012757 skos:exactMatch MP:0002882 semapv:LogicalReasoning Abnormal neuron morphology abnormal neuron morphology -HP:0012365 skos:exactMatch MP:0002901 semapv:LogicalReasoning Hypophosphaturia increased urine phosphate level -HP:0003109 skos:exactMatch MP:0002902 semapv:LogicalReasoning Hyperphosphaturia decreased urine phosphate level -HP:0011733 skos:exactMatch MP:0002909 semapv:LogicalReasoning Abnormality of adrenal physiology abnormal adrenal gland physiology -HP:0007770 skos:exactMatch MP:0002984 semapv:LogicalReasoning Hypoplasia of the retina retina hypoplasia -HP:0100957 skos:exactMatch MP:0003014 semapv:LogicalReasoning Abnormal renal medulla morphology abnormal kidney medulla morphology -HP:3000052 skos:exactMatch MP:0003056 semapv:LogicalReasoning Abnormality of hyoid bone abnormal hyoid bone morphology -HP:0025321 skos:exactMatch MP:0003066 semapv:LogicalReasoning Copper accumulation in liver increased liver copper level -HP:0000105 skos:exactMatch MP:0003068 semapv:LogicalReasoning Enlarged kidney enlarged kidney -HP:0010048 skos:exactMatch MP:0003074 semapv:LogicalReasoning Aplasia of metacarpal bones absent metacarpal bones -HP:0005237 skos:exactMatch MP:0003103 semapv:LogicalReasoning Degenerative liver disease liver degeneration -HP:0005120 skos:exactMatch MP:0003105 semapv:LogicalReasoning Abnormal cardiac atrium morphology abnormal heart atrium morphology -HP:0012132 skos:exactMatch MP:0003135 semapv:LogicalReasoning Erythroid hyperplasia increased erythroid progenitor cell number -HP:0011373 skos:exactMatch MP:0003148 semapv:LogicalReasoning Incomplete partition of the cochlea decreased cochlear coiling -HP:0003107 skos:exactMatch MP:0003191 semapv:LogicalReasoning Abnormal circulating cholesterol concentration abnormal cellular cholesterol metabolism -HP:0005222 skos:exactMatch MP:0003262 semapv:LogicalReasoning Bowel diverticulosis intestinal/bowel diverticulum -HP:0004398 skos:exactMatch MP:0003300 semapv:LogicalReasoning Peptic ulcer gastrointestinal ulcer -HP:3000002 skos:exactMatch MP:0003308 semapv:LogicalReasoning Abnormal inner ear epithelium morphology abnormal cochlear sensory epithelium morphology -HP:0006274 skos:exactMatch MP:0003339 semapv:LogicalReasoning Reduced pancreatic beta cells decreased pancreatic beta cell number -HP:0009799 skos:exactMatch MP:0003342 semapv:LogicalReasoning Supernumerary spleens accessory spleen -HP:0012569 skos:exactMatch MP:0003377 semapv:LogicalReasoning Delayed menarche late onset of menarche -HP:0011767 skos:exactMatch MP:0003431 semapv:LogicalReasoning Abnormality of the parathyroid physiology abnormal parathyroid gland physiology -HP:0008208 skos:exactMatch MP:0003493 semapv:LogicalReasoning Parathyroid hyperplasia parathyroid gland hyperplasia -HP:0008249 skos:exactMatch MP:0003498 semapv:LogicalReasoning Thyroid hyperplasia thyroid gland hyperplasia -HP:0040253 skos:exactMatch MP:0003529 semapv:LogicalReasoning Increased size of the clitoris enlarged clitoris -HP:0040254 skos:exactMatch MP:0003530 semapv:LogicalReasoning Decreased size of the clitoris small clitoris -HP:0008697 skos:exactMatch MP:0003576 semapv:LogicalReasoning Hypoplasia of the fallopian tube oviduct hypoplasia -HP:0000068 skos:exactMatch MP:0003591 semapv:LogicalReasoning Urethral atresia urethra atresia -HP:0008661 skos:exactMatch MP:0003592 semapv:LogicalReasoning Urethral stenosis urethra stricture -HP:0005343 skos:exactMatch MP:0003617 semapv:LogicalReasoning Hypoplasia of the bladder urinary bladder hypoplasia -HP:0012639 skos:exactMatch MP:0003632 semapv:LogicalReasoning Abnormality of nervous system morphology abnormal nervous system morphology -HP:0012638 skos:exactMatch MP:0003633 semapv:LogicalReasoning Abnormality of nervous system physiology abnormal nervous system physiology -HP:0003750 skos:exactMatch MP:0003646 semapv:LogicalReasoning Increased muscle fatiguability muscle fatigue -HP:0200007 skos:exactMatch MP:0003671 semapv:LogicalReasoning Abnormal size of the palpebral fissures abnormal eyelid aperture -HP:0000107 skos:exactMatch MP:0003675 semapv:LogicalReasoning Renal cyst kidney cysts -HP:0000385 skos:exactMatch MP:0003679 semapv:LogicalReasoning Small earlobe ear lobe hypoplasia -HP:0011314 skos:exactMatch MP:0003723 semapv:LogicalReasoning Abnormality of long bone morphology abnormal long bone morphology -HP:0008544 skos:exactMatch MP:0003736 semapv:LogicalReasoning Abnormally folded helix folded helix -HP:0001999 skos:exactMatch MP:0003743 semapv:LogicalReasoning Abnormal facial shape abnormal facial morphology -HP:0002707 skos:exactMatch MP:0003768 semapv:LogicalReasoning Palate telangiectasia palatal telangiectases -HP:0002298 skos:exactMatch MP:0003815 semapv:LogicalReasoning Absent hair hairless -HP:0001711 skos:exactMatch MP:0003921 semapv:LogicalReasoning Abnormal left ventricle morphology abnormal heart left ventricle morphology -HP:0025580 skos:exactMatch MP:0003922 semapv:LogicalReasoning Abnormal right atrium morphology abnormal heart right atrium morphology -HP:0025579 skos:exactMatch MP:0003923 semapv:LogicalReasoning Abnormal left atrium morphology abnormal heart left atrium morphology -HP:0003234 skos:exactMatch MP:0003978 semapv:LogicalReasoning Decreased plasma carnitine decreased circulating carnitine level -HP:0010994 skos:exactMatch MP:0004077 semapv:LogicalReasoning Abnormal corpus striatum morphology abnormal striatum morphology -HP:0007343 skos:exactMatch MP:0004166 semapv:LogicalReasoning Abnormal morphology of the limbic system abnormal limbic system morphology -HP:0009893 skos:exactMatch MP:0004176 semapv:LogicalReasoning Telangiectasia of the ear ear telangiectases -HP:0011456 skos:exactMatch MP:0004204 semapv:LogicalReasoning Absent stapes absent stapes -HP:0001655 skos:exactMatch MP:0004225 semapv:LogicalReasoning Patent foramen ovale patent cardiac foramen ovale -HP:0012767 skos:exactMatch MP:0004258 semapv:LogicalReasoning Abnormal placental size abnormal placenta size -HP:0006267 skos:exactMatch MP:0004260 semapv:LogicalReasoning Large placenta enlarged placenta -HP:0011377 skos:exactMatch MP:0004314 semapv:LogicalReasoning Aplasia of the vestibule absent inner ear vestibule -HP:0000882 skos:exactMatch MP:0004344 semapv:LogicalReasoning Hypoplastic scapulae scapular bone hypoplasia -HP:0012744 skos:exactMatch MP:0004349 semapv:LogicalReasoning Femoral aplasia absent femur -HP:0005792 skos:exactMatch MP:0004351 semapv:LogicalReasoning Short humerus short humerus -HP:0002984 skos:exactMatch MP:0004356 semapv:LogicalReasoning Hypoplasia of the radius radius hypoplasia -HP:0010504 skos:exactMatch MP:0004357 semapv:LogicalReasoning Increased length of the tibia long tibia -HP:0003194 skos:exactMatch MP:0004471 semapv:LogicalReasoning Short nasal bridge short nasal bone -HP:0040163 skos:exactMatch MP:0004509 semapv:LogicalReasoning Abnormal pelvis bone morphology abnormal pelvic girdle bone morphology -HP:0004791 skos:exactMatch MP:0004547 semapv:LogicalReasoning Esophageal ulceration esophageal ulcer -HP:0009555 skos:exactMatch MP:0004555 semapv:LogicalReasoning Hypoplasia of the pharynx pharynx hypoplasia -HP:3000078 skos:exactMatch MP:0004594 semapv:LogicalReasoning Abnormal mandible coronoid process morphology abnormal mandibular coronoid process morphology -HP:3000077 skos:exactMatch MP:0004595 semapv:LogicalReasoning Abnormal mandible condylar process morphology abnormal mandibular condyloid process morphology -HP:0030040 skos:exactMatch MP:0004621 semapv:LogicalReasoning Fused lumbar vertebrae lumbar vertebral fusion -HP:0030039 skos:exactMatch MP:0004623 semapv:LogicalReasoning Fused thoracic vertebrae thoracic vertebral fusion -HP:0001547 skos:exactMatch MP:0004624 semapv:LogicalReasoning Abnormality of the rib cage abnormal thoracic cage morphology -HP:0010049 skos:exactMatch MP:0004634 semapv:LogicalReasoning Short metacarpal short metacarpal bones -HP:0010493 skos:exactMatch MP:0004638 semapv:LogicalReasoning Long metacarpals elongated metacarpal bones -HP:0009701 skos:exactMatch MP:0004639 semapv:LogicalReasoning Metacarpal synostosis fused metacarpal bones -HP:0001440 skos:exactMatch MP:0004642 semapv:LogicalReasoning Metatarsal synostosis fused metatarsal bones -HP:0008479 skos:exactMatch MP:0004667 semapv:LogicalReasoning Hypoplastic vertebral bodies vertebral body hypoplasia -HP:0005645 skos:exactMatch MP:0004685 semapv:LogicalReasoning Intervertebral disk calcification calcified intervertebral disk -HP:0003026 skos:exactMatch MP:0004686 semapv:LogicalReasoning Short long bone decreased length of long bones -HP:0008428 skos:exactMatch MP:0004687 semapv:LogicalReasoning Vertebral clefting split vertebrae -HP:0003175 skos:exactMatch MP:0004690 semapv:LogicalReasoning Hypoplastic ischia ischium hypoplasia -HP:0003173 skos:exactMatch MP:0004693 semapv:LogicalReasoning Hypoplastic pubic bone pubis hypoplasia -HP:0002766 skos:exactMatch MP:0004704 semapv:LogicalReasoning Relatively short spine short vertebral column -HP:0011393 skos:exactMatch MP:0004719 semapv:LogicalReasoning Aplasia of the vestibular nerve. absent vestibular nerve -HP:0100879 skos:exactMatch MP:0004832 semapv:LogicalReasoning Enlarged ovaries enlarged ovary -HP:0005466 skos:exactMatch MP:0004869 semapv:LogicalReasoning Hypoplasia of the frontal bone frontal bone hypoplasia -HP:0010650 skos:exactMatch MP:0004871 semapv:LogicalReasoning Hypoplasia of the premaxilla premaxilla hypoplasia -HP:0002797 skos:exactMatch MP:0004993 semapv:LogicalReasoning Osteolysis decreased bone resorption -HP:0010976 skos:exactMatch MP:0005017 semapv:LogicalReasoning B lymphocytopenia decreased B cell number -HP:0005403 skos:exactMatch MP:0005018 semapv:LogicalReasoning Decrease in T cell count decreased T cell number -HP:0012176 skos:exactMatch MP:0005068 semapv:LogicalReasoning Abnormal natural killer cell morphology abnormal NK cell morphology -HP:0040071 skos:exactMatch MP:0005108 semapv:LogicalReasoning Abnormal morphology of ulna abnormal ulna morphology -HP:0000870 skos:exactMatch MP:0005139 semapv:LogicalReasoning Increased circulating prolactin concentration increased prolactin level -HP:0003362 skos:exactMatch MP:0005145 semapv:LogicalReasoning Increased VLDL cholesterol concentration increased circulating VLDL cholesterol level -HP:0031243 skos:exactMatch MP:0005146 semapv:LogicalReasoning Decreased VLDL cholesterol concentration decreased circulating VLDL cholesterol level -HP:0008687 skos:exactMatch MP:0005147 semapv:LogicalReasoning Hypoplasia of the prostate prostate gland hypoplasia -HP:0008724 skos:exactMatch MP:0005158 semapv:LogicalReasoning Hypoplasia of the ovary ovary hypoplasia -HP:0000593 skos:exactMatch MP:0005205 semapv:LogicalReasoning Abnormal anterior chamber morphology abnormal eye anterior chamber morphology -HP:0001939 skos:exactMatch MP:0005266 semapv:LogicalReasoning Abnormality of metabolism/homeostasis abnormal metabolism -HP:0001713 skos:exactMatch MP:0005294 semapv:LogicalReasoning Abnormal cardiac ventricle morphology abnormal heart ventricle morphology -HP:0011488 skos:exactMatch MP:0005301 semapv:LogicalReasoning Abnormal corneal endothelium morphology abnormal corneal endothelium morphology -HP:0008191 skos:exactMatch MP:0005314 semapv:LogicalReasoning Thyroid agenesis absent thyroid gland -HP:0002904 skos:exactMatch MP:0005344 semapv:LogicalReasoning Hyperbilirubinemia increased circulating bilirubin level -HP:0000853 skos:exactMatch MP:0005355 semapv:LogicalReasoning Goiter enlarged thyroid gland -HP:0011063 skos:exactMatch MP:0005358 semapv:LogicalReasoning Abnormality of incisor morphology abnormal incisor morphology -HP:0002990 skos:exactMatch MP:0005430 semapv:LogicalReasoning Fibular aplasia absent fibula -HP:0008247 skos:exactMatch MP:0005477 semapv:LogicalReasoning Euthyroid hyperthyroxinemia increased circulating thyroxine level -HP:0011788 skos:exactMatch MP:0005480 semapv:LogicalReasoning Increased circulating free T3 increased circulating triiodothyronine level -HP:0011277 skos:exactMatch MP:0005502 semapv:LogicalReasoning Abnormality of the urinary system physiology abnormal renal/urinary system physiology -HP:0100261 skos:exactMatch MP:0005503 semapv:LogicalReasoning Abnormal tendon morphology abnormal tendon morphology -HP:0011842 skos:exactMatch MP:0005508 semapv:LogicalReasoning Abnormality of skeletal morphology abnormal skeleton morphology -HP:0010790 skos:exactMatch MP:0005536 semapv:LogicalReasoning Hyoplasia of the Leydig cells Leydig cell hypoplasia -HP:0012101 skos:exactMatch MP:0005554 semapv:LogicalReasoning Decreased serum creatinine decreased circulating creatinine level -HP:0001900 skos:exactMatch MP:0005564 semapv:LogicalReasoning Increased hemoglobin increased hemoglobin content -HP:0000139 skos:exactMatch MP:0005577 semapv:LogicalReasoning Uterine prolapse uterus prolapse -HP:0009892 skos:exactMatch MP:0005579 semapv:LogicalReasoning Anotia absent outer ear -HP:0012364 skos:exactMatch MP:0005618 semapv:LogicalReasoning Decreased urinary potassium decreased urine potassium level -HP:0003081 skos:exactMatch MP:0005619 semapv:LogicalReasoning Increased urinary potassium increased urine potassium level -HP:0011017 skos:exactMatch MP:0005621 semapv:LogicalReasoning Abnormal cellular physiology abnormal cell physiology -HP:0002153 skos:exactMatch MP:0005627 semapv:LogicalReasoning Hyperkalemia increased circulating potassium level -HP:0002900 skos:exactMatch MP:0005628 semapv:LogicalReasoning Hypokalemia decreased circulating potassium level -HP:0031793 skos:exactMatch MP:0005669 semapv:LogicalReasoning Increased serum leptin increased circulating leptin level -HP:0008322 skos:exactMatch MP:0006035 semapv:LogicalReasoning Abnormal mitochondrial morphology abnormal mitochondrion morphology -HP:0010444 skos:exactMatch MP:0006048 semapv:LogicalReasoning Pulmonary insufficiency pulmonary valve regurgitation -HP:0001671 skos:exactMatch MP:0006113 semapv:LogicalReasoning Abnormal cardiac septum morphology abnormal heart septum morphology -HP:0004380 skos:exactMatch MP:0006116 semapv:LogicalReasoning Aortic valve calcification calcified aortic valve -HP:0004382 skos:exactMatch MP:0006121 semapv:LogicalReasoning Mitral valve calcification calcified mitral valve -HP:0003207 skos:exactMatch MP:0006133 semapv:LogicalReasoning Arterial calcification calcified artery -HP:0100545 skos:exactMatch MP:0006135 semapv:LogicalReasoning Arterial stenosis artery stenosis -HP:0007862 skos:exactMatch MP:0006188 semapv:LogicalReasoning Retinal calcification calcified retina -HP:0011885 skos:exactMatch MP:0006203 semapv:LogicalReasoning Hemorrhage of the eye eye hemorrhage -HP:0007990 skos:exactMatch MP:0006230 semapv:LogicalReasoning Hypoplastic iris stroma iris stroma hypoplasia -HP:0011372 skos:exactMatch MP:0006285 semapv:LogicalReasoning Aplasia of the inner ear absent inner ear -HP:0011839 skos:exactMatch MP:0006387 semapv:LogicalReasoning Abnormal T cell count abnormal T cell number -HP:0002843 skos:exactMatch MP:0008037 semapv:LogicalReasoning Abnormal T cell morphology abnormal T cell morphology -HP:0040089 skos:exactMatch MP:0008043 semapv:LogicalReasoning Abnormal natural killer cell count abnormal NK cell number -HP:0005415 skos:exactMatch MP:0008079 semapv:LogicalReasoning Decreased proportion of CD8-positive T cells "decreased CD8-positive alpha-beta T cell number" -HP:0011472 skos:exactMatch MP:0008108 semapv:LogicalReasoning Abnormality of small intestinal villus morphology abnormal small intestinal villus morphology -HP:0005513 skos:exactMatch MP:0008254 semapv:LogicalReasoning Increased megakaryocyte count increased megakaryocyte cell number -HP:0005548 skos:exactMatch MP:0008255 semapv:LogicalReasoning Megakaryocytopenia decreased megakaryocyte cell number -HP:0008239 skos:exactMatch MP:0008301 semapv:LogicalReasoning Adrenal medullary hypoplasia adrenal medulla hyperplasia -HP:0010627 skos:exactMatch MP:0008365 semapv:LogicalReasoning Anterior pituitary hypoplasia adenohypophysis hypoplasia -HP:0002849 skos:exactMatch MP:0008523 semapv:LogicalReasoning Absence of lymph node germinal center absent lymph node germinal center -HP:0000113 skos:exactMatch MP:0008528 semapv:LogicalReasoning Polycystic kidney dysplasia polycystic kidney -HP:0007485 skos:exactMatch MP:0008843 semapv:LogicalReasoning Absence of subcutaneous fat absent subcutaneous adipose tissue -HP:0003758 skos:exactMatch MP:0008844 semapv:LogicalReasoning Reduced subcutaneous adipose tissue decreased subcutaneous adipose tissue amount -HP:0012081 skos:exactMatch MP:0008914 semapv:LogicalReasoning Enlarged cerebellum enlarged cerebellum -HP:0012504 skos:exactMatch MP:0008936 semapv:LogicalReasoning Abnormal size of pituitary gland abnormal pituitary gland size -HP:0006424 skos:exactMatch MP:0008951 semapv:LogicalReasoning Elongated radius long radius -HP:0012133 skos:exactMatch MP:0008973 semapv:LogicalReasoning Erythroid hypoplasia decreased erythroid progenitor cell number -HP:0010303 skos:exactMatch MP:0009023 semapv:LogicalReasoning Abnormal spinal meningeal morphology abnormal spinal cord meninges morphology -HP:0040252 skos:exactMatch MP:0009100 semapv:LogicalReasoning Abnormal size of the clitoris abnormal clitoris size -HP:0004510 skos:exactMatch MP:0009171 semapv:LogicalReasoning Pancreatic islet-cell hyperplasia enlarged pancreatic islets -HP:0000978 skos:exactMatch MP:0009276 semapv:LogicalReasoning Bruising susceptibility ecchymosis -HP:0012613 skos:exactMatch MP:0009472 semapv:LogicalReasoning Increased urinary sulfate increased urine sulfate level -HP:0025057 skos:exactMatch MP:0009944 semapv:LogicalReasoning Abnormality of olfactory lobe morphology abnormal olfactory lobe morphology -HP:0008887 skos:exactMatch MP:0010025 semapv:LogicalReasoning Adipose tissue loss decreased total body fat amount -HP:0040326 skos:exactMatch MP:0010059 semapv:LogicalReasoning Hypoplasia of the olfactory bulb olfactory bulb hypoplasia -HP:0040081 skos:exactMatch MP:0010089 semapv:LogicalReasoning Abnormal circulating creatine kinase concentration abnormal circulating creatine kinase level -HP:0003236 skos:exactMatch MP:0010090 semapv:LogicalReasoning Elevated serum creatine kinase increased circulating creatine kinase level -HP:0004348 skos:exactMatch MP:0010119 semapv:LogicalReasoning Abnormality of bone mineral density abnormal bone mineral density -HP:0012093 skos:exactMatch MP:0010147 semapv:LogicalReasoning Abnormality of endocrine pancreas physiology abnormal endocrine pancreas physiology -HP:0012092 skos:exactMatch MP:0010148 semapv:LogicalReasoning Abnormality of exocrine pancreas physiology abnormal exocrine pancreas physiology -HP:0011068 skos:exactMatch MP:0010353 semapv:LogicalReasoning Odontoma increased odontoma incidence -HP:0006568 skos:exactMatch MP:0010400 semapv:LogicalReasoning Increased hepatic glycogen content increased liver glycogen level -HP:0011103 skos:exactMatch MP:0010429 semapv:LogicalReasoning Abnormal left ventricular outflow tract morphology abnormal heart left ventricle outflow tract morphology -HP:0001680 skos:exactMatch MP:0010463 semapv:LogicalReasoning Coarctation of aorta aorta stenosis -HP:0004963 skos:exactMatch MP:0010522 semapv:LogicalReasoning Calcification of the aorta calcified aorta -HP:0004962 skos:exactMatch MP:0010523 semapv:LogicalReasoning Thoracic aorta calcification calcified thoracic aorta -HP:0005303 skos:exactMatch MP:0010524 semapv:LogicalReasoning Aortic arch calcification calcified aortic arch -HP:0005304 skos:exactMatch MP:0010528 semapv:LogicalReasoning Hypoplastic pulmonary veins pulmonary vein hypoplasia -HP:0011138 skos:exactMatch MP:0010678 semapv:LogicalReasoning Abnormality of skin adnexa morphology abnormal skin adnexa morphology -HP:0100671 skos:exactMatch MP:0010867 semapv:LogicalReasoning Abnormal trabecular bone morphology abnormal bone trabecula morphology -HP:0002043 skos:exactMatch MP:0010884 semapv:LogicalReasoning Esophageal stricture esophagus stenosis -HP:0012676 skos:exactMatch MP:0011214 semapv:LogicalReasoning Copper accumulation in brain increased brain copper level -HP:0000092 skos:exactMatch MP:0011346 semapv:LogicalReasoning Tubular atrophy renal tubule atrophy -HP:0002119 skos:exactMatch MP:0011380 semapv:LogicalReasoning Ventriculomegaly enlarged brain ventricles -HP:0000028 skos:exactMatch MP:0011410 semapv:LogicalReasoning Cryptorchidism ectopic testis -HP:0011935 skos:exactMatch MP:0011424 semapv:LogicalReasoning Decreased urinary urate decreased urine uric acid level -HP:0012601 skos:exactMatch MP:0011460 semapv:LogicalReasoning Hypochloriduria decreased urine chloride ion level -HP:0045011 skos:exactMatch MP:0011463 semapv:LogicalReasoning Decreased urine bicarbonate concentration decreased urine bicarbonate level -HP:0003541 skos:exactMatch MP:0011473 semapv:LogicalReasoning Urinary glycosaminoglycan excretion increased urine glycosaminoglycan level -HP:0030321 skos:exactMatch MP:0011513 semapv:LogicalReasoning Abnormal vertebral artery morphology abnormal vertebral artery morphology -HP:0012611 skos:exactMatch MP:0011537 semapv:LogicalReasoning Increased urinary urate uraturia -HP:0012517 skos:exactMatch MP:0011594 semapv:LogicalReasoning Reduced catalase activity decreased catalase activity -HP:0001010 skos:exactMatch MP:0011627 semapv:LogicalReasoning Hypopigmentation of the skin decreased skin pigmentation -HP:0040014 skos:exactMatch MP:0011628 semapv:LogicalReasoning Increased mitochondrial number increased mitochondria number -HP:0040013 skos:exactMatch MP:0011629 semapv:LogicalReasoning Decreased mitochondrial number decreased mitochondria number -HP:0010906 skos:exactMatch MP:0011652 semapv:LogicalReasoning Hyperhistidinemia increased circulating histidine level -HP:0500145 skos:exactMatch MP:0011653 semapv:LogicalReasoning Hypohistidinemia decreased circulating histidine level -HP:0012688 skos:exactMatch MP:0011728 semapv:LogicalReasoning Abnormality of pineal physiology abnormal pineal gland physiology -HP:0005235 skos:exactMatch MP:0011878 semapv:LogicalReasoning Jejunal atresia jejunum atresia -HP:0011102 skos:exactMatch MP:0011879 semapv:LogicalReasoning Ileal atresia ileum atresia -HP:0011486 skos:exactMatch MP:0011961 semapv:LogicalReasoning Abnormality of corneal thickness abnormal cornea thickness -HP:0011487 skos:exactMatch MP:0011962 semapv:LogicalReasoning Increased corneal thickness increased cornea thickness -HP:0100512 skos:exactMatch MP:0012336 semapv:LogicalReasoning Low levels of vitamin D decreased vitamin D level -HP:0007705 skos:exactMatch MP:0012351 semapv:LogicalReasoning Corneal degeneration cornea degeneration -HP:0012310 skos:exactMatch MP:0012441 semapv:LogicalReasoning Abnormal monocyte count abnormal monocyte cell number -HP:0031806 skos:exactMatch MP:0012442 semapv:LogicalReasoning Abnormal basophil count abnormal basophil cell number -HP:3000062 skos:exactMatch MP:0012730 semapv:LogicalReasoning Abnormal internal carotid artery morphology abnormal internal carotid artery morphology -HP:0011073 skos:exactMatch MP:0013129 semapv:LogicalReasoning Abnormality of dental color abnormal tooth color -HP:0000190 skos:exactMatch MP:0013263 semapv:LogicalReasoning Abnormal oral frenulum morphology abnormal tongue frenulum morphology -HP:0430009 skos:exactMatch MP:0013395 semapv:LogicalReasoning Hypoplasia of eyelid eyelid hypoplasia -HP:0007734 skos:exactMatch MP:0013453 semapv:LogicalReasoning Enlarged lacrimal glands enlarged lacrimal gland -HP:0020047 skos:exactMatch MP:0013658 semapv:LogicalReasoning Abnormal myeloid cell morphology abnormal myeloid cell morphology -HP:0500133 skos:exactMatch MP:0013724 semapv:LogicalReasoning Hypotyrosinemia decreased circulating tyrosine level -HP:0007774 skos:exactMatch MP:0013743 semapv:LogicalReasoning Hypoplasia of the ciliary body ciliary body hypoplasia -HP:0008165 skos:exactMatch MP:0013764 semapv:LogicalReasoning Decreased proportion circulating T-helper cells decreased T-helper cell number -HP:0100596 skos:exactMatch MP:0013791 semapv:LogicalReasoning Absent nares absent external nares -HP:0009145 skos:exactMatch MP:0013821 semapv:LogicalReasoning Abnormal cerebral artery morphology abnormal cerebral artery morphology -HP:0010764 skos:exactMatch MP:0013898 semapv:LogicalReasoning Short eyelashes short eyelid cilia -HP:0011756 skos:exactMatch MP:0013926 semapv:LogicalReasoning Posterior pituitary agenesis absent neurohypophysis -HP:0011473 skos:exactMatch MP:0014078 semapv:LogicalReasoning Villous atrophy small intestinal villus atrophy -HP:0030326 skos:exactMatch MP:0020202 semapv:LogicalReasoning Abnormal macrophage count abnormal macrophage cell number -HP:0012675 skos:exactMatch MP:0020365 semapv:LogicalReasoning Iron accumulation in brain increased brain iron level -HP:0003166 skos:exactMatch MP:0020405 semapv:LogicalReasoning Increased urinary taurine taurinuria -HP:0003572 skos:exactMatch MP:0020837 semapv:LogicalReasoning Low plasma citrulline decreased circulating citrulline level -HP:0002007 skos:exactMatch MP:0030049 semapv:LogicalReasoning Frontal bossing prominent forehead -HP:0040309 skos:exactMatch MP:0030050 semapv:LogicalReasoning Increased size of the mandible large mandible -HP:0001593 skos:exactMatch MP:0030080 semapv:LogicalReasoning Maxillary lateral incisor microdontia small lower incisors -HP:0010669 skos:exactMatch MP:0030112 semapv:LogicalReasoning Hypoplasia of the zygomatic bone zygomatic bone hypoplasia -HP:0007628 skos:exactMatch MP:0030259 semapv:LogicalReasoning Mandibular condyle hypoplasia mandibular condyloid process hypoplasia -HP:0000278 skos:exactMatch MP:0030273 semapv:LogicalReasoning Retrognathia mandibular retrognathia -HP:0005469 skos:exactMatch MP:0030289 semapv:LogicalReasoning Flat occiput flat occipital bone -HP:0008551 skos:exactMatch MP:0030297 semapv:LogicalReasoning Microtia outer ear hypoplasia -HP:0000272 skos:exactMatch MP:0030377 semapv:LogicalReasoning Malar flattening zygomatic arch hypoplasia -HP:0006308 skos:exactMatch MP:0030466 semapv:LogicalReasoning Atrophy of alveolar ridges alveolar process atrophy -HP:0500181 skos:exactMatch MP:0030638 semapv:LogicalReasoning Hypertaurinemia increased circulating taurine level -HP:0500182 skos:exactMatch MP:0030639 semapv:LogicalReasoning Hypotaurinemia decreased circulating taurine level -HP:0500136 skos:exactMatch MP:0030704 semapv:LogicalReasoning Hypothreoninemia decreased circulating threonine level -HP:0500132 skos:exactMatch MP:0030728 semapv:LogicalReasoning Hypovalinemia decreased circulating valine level -HP:0500253 skos:exactMatch MP:0030734 semapv:LogicalReasoning Increased level of gamma-aminobutyric acid in urine increased urine gamma-aminobutyric acid level -HP:0003345 skos:exactMatch MP:0030772 semapv:LogicalReasoning Elevated urinary norepinephrine increased urine noradrenaline level -HP:0006261 skos:exactMatch MP:0030813 semapv:LogicalReasoning Abnormal phalangeal joint morphology of the hand abnormal hand interphalangeal joint morphology +subject_id subject_label predicate_id object_id object_label mapping_justification +HP:0000175 Cleft palate skos:exactMatch MP:0000111 cleft palate semapv:LexicalMatching +HP:0000252 Microcephaly skos:exactMatch MP:0000433 microcephaly semapv:LexicalMatching +HP:0000260 Wide anterior fontanel skos:exactMatch MP:0000085 large anterior fontanelle semapv:LexicalMatching +HP:0000375 Abnormal cochlea morphology skos:exactMatch MP:0000031 abnormal cochlea morphology semapv:LexicalMatching +HP:0000411 Protruding ear skos:exactMatch MP:0000021 prominent ears semapv:LexicalMatching +HP:0000822 Hypertension skos:exactMatch MP:0000231 hypertension semapv:LexicalMatching +HP:0001336 Myoclonus skos:exactMatch MP:0000243 myoclonus semapv:LexicalMatching +HP:0001363 Craniosynostosis skos:exactMatch MP:0000081 premature cranial suture closure semapv:LexicalMatching +HP:0001596 Alopecia skos:exactMatch MP:0000414 alopecia semapv:LexicalMatching +HP:0001627 Abnormal heart morphology skos:exactMatch MP:0000266 abnormal heart morphology semapv:LexicalMatching +HP:0001633 Abnormal mitral valve morphology skos:exactMatch MP:0000286 abnormal mitral valve morphology semapv:LexicalMatching +HP:0001667 Right ventricular hypertrophy skos:exactMatch MP:0000276 heart right ventricle hypertrophy semapv:LexicalMatching +HP:0001679 Abnormal aortic morphology skos:exactMatch MP:0000272 abnormal aorta morphology semapv:LexicalMatching +HP:0001719 Double outlet right ventricle skos:exactMatch MP:0000284 double outlet right ventricle semapv:LexicalMatching +HP:0001882 Leukopenia skos:exactMatch MP:0000221 decreased leukocyte cell number semapv:LexicalMatching +HP:0001913 Granulocytopenia skos:exactMatch MP:0000334 decreased granulocyte number semapv:LexicalMatching +HP:0001974 Leukocytosis skos:exactMatch MP:0000218 increased leukocyte cell number semapv:LexicalMatching +HP:0001978 Extramedullary hematopoiesis skos:exactMatch MP:0000240 extramedullary hematopoiesis semapv:LexicalMatching +HP:0001981 Schistocytosis skos:exactMatch MP:0000314 schistocytosis semapv:LexicalMatching +HP:0002212 Curly hair skos:exactMatch MP:0000410 waved hair semapv:LexicalMatching +HP:0002659 Increased susceptibility to fractures skos:exactMatch MP:0000061 fragile skeleton semapv:LexicalMatching +HP:0002763 Abnormal cartilage morphology skos:exactMatch MP:0000163 abnormal cartilage morphology semapv:LexicalMatching +HP:0003307 Hyperlordosis skos:exactMatch MP:0000162 lordosis semapv:LexicalMatching +HP:0004349 Reduced bone mineral density skos:exactMatch MP:0000063 decreased bone mineral density semapv:LexicalMatching +HP:0006288 Advanced eruption of teeth skos:exactMatch MP:0000122 premature tooth eruption semapv:LexicalMatching +HP:0008551 Microtia skos:exactMatch MP:0000018 small ears semapv:LexicalMatching +HP:0009124 Abnormal adipose tissue morphology skos:exactMatch MP:0000003 abnormal adipose tissue morphology semapv:LexicalMatching +HP:0009910 Aplasia of the middle ear ossicles skos:exactMatch MP:0000040 absent middle ear ossicles semapv:LexicalMatching +HP:0009939 Mandibular aplasia skos:exactMatch MP:0000087 absent mandible semapv:LexicalMatching +HP:0011002 Osteopetrosis skos:exactMatch MP:0000067 osteopetrosis semapv:LexicalMatching +HP:0011457 Loss of eyelashes skos:exactMatch MP:0000425 loss of eyelid cilia semapv:LexicalMatching +HP:0011897 Neutrophilia skos:exactMatch MP:0000219 increased neutrophil cell number semapv:LexicalMatching +HP:0012234 Agranulocytosis skos:exactMatch MP:0000334 decreased granulocyte number semapv:LexicalMatching +HP:0012543 Hemosiderinuria skos:exactMatch MP:0000327 hemosiderinuria semapv:LexicalMatching +HP:0025065 Abnormal mean corpuscular volume skos:exactMatch MP:0000226 abnormal mean corpuscular volume semapv:LexicalMatching +HP:0025084 Folliculitis skos:exactMatch MP:0000376 folliculitis semapv:LexicalMatching +HP:0031377 Abnormal cell proliferation skos:exactMatch MP:0000350 abnormal cell proliferation semapv:LexicalMatching +HP:0031851 Reduced hematocrit skos:exactMatch MP:0000208 decreased hematocrit semapv:LexicalMatching +HP:0032310 Granulocytosis skos:exactMatch MP:0000322 increased granulocyte number semapv:LexicalMatching +HP:0100629 Midline facial cleft skos:exactMatch MP:0000108 midline facial cleft semapv:LexicalMatching +HP:0100671 Abnormal trabecular bone morphology skos:exactMatch MP:0000130 abnormal trabecular bone morphology semapv:LexicalMatching +HP:0400001 Chin with vertical crease skos:exactMatch MP:0000114 cleft chin semapv:LexicalMatching diff --git a/examples/external/mp-hp-exact-0.0.1.sssom.yml b/examples/external/mp-hp-exact-0.0.1.sssom.yml index f5f7e01c..97eee82e 100644 --- a/examples/external/mp-hp-exact-0.0.1.sssom.yml +++ b/examples/external/mp-hp-exact-0.0.1.sssom.yml @@ -1,7 +1,12 @@ -creator_id: "https://orcid.org/0000-0002-7356-1779" -curie_map: - HP: "http://purl.obolibrary.org/obo/HP_" - MP: "http://purl.obolibrary.org/obo/MP_" - skos: "http://www.w3.org/2004/02/skos/core" -license: "https://creativecommons.org/publicdomain/zero/1.0/" -mapping_provider: "http://purl.obolibrary.org/obo/upheno.owl" +curie_map: + HP: http://purl.obolibrary.org/obo/HP_ + MP: http://purl.obolibrary.org/obo/MP_ + owl: http://www.w3.org/2002/07/owl# + rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# + rdfs: http://www.w3.org/2000/01/rdf-schema# + semapv: https://w3id.org/semapv/vocab/ + skos: http://www.w3.org/2004/02/skos/core# + sssom: https://w3id.org/sssom/ +license: https://creativecommons.org/publicdomain/zero/1.0/ +mapping_provider: http://purl.obolibrary.org/obo/upheno.owl +mapping_set_id: https://w3id.org/sssom/mappings/27f85fe9-8a72-4e76-909b-7ba4244d9ede \ No newline at end of file diff --git a/examples/schema/curation_rule.sssom.tsv b/examples/schema/curation_rule.sssom.tsv new file mode 100644 index 00000000..3e9d7b7e --- /dev/null +++ b/examples/schema/curation_rule.sssom.tsv @@ -0,0 +1,14 @@ +#curie_map: +# HP: http://purl.obolibrary.org/obo/HP_ +# MP: http://purl.obolibrary.org/obo/MP_ +# orcid: https://orcid.org/ +# DISEASE_MAPPING_COMMONS_RULES: https://w3id.org/sssom/commons/disease/curation-rules/ +#mapping_set_id: https://w3id.org/sssom/commons/examples/curation_rule.sssom.tsv +#license: "https://creativecommons.org/publicdomain/zero/1.0/" +#creator_id: orcid:0000-0002-7356-1779 +#mapping_provider: "https://w3id.org/sssom/core_team" +#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated. +subject_id predicate_id object_id mapping_justification curation_rule see_also +HP:0009124 skos:exactMatch MP:0000003 semapv:ManualMappingCuration DISEASE_MAPPING_COMMONS_RULES:MPR2 https://github.com/mapping-commons/disease-mappings/issues/16 +HP:0008551 skos:exactMatch MP:0000018 semapv:ManualMappingCuration DISEASE_MAPPING_COMMONS_RULES:MPR3 https://github.com/mapping-commons/disease-mappings/issues/16 +HP:0000411 skos:exactMatch MP:0000021 semapv:ManualMappingCuration DISEASE_MAPPING_COMMONS_RULES:MPR3 https://github.com/mapping-commons/disease-mappings/issues/16 diff --git a/examples/schema/curation_rule_text.sssom.tsv b/examples/schema/curation_rule_text.sssom.tsv new file mode 100644 index 00000000..2a2fc60f --- /dev/null +++ b/examples/schema/curation_rule_text.sssom.tsv @@ -0,0 +1,14 @@ +#curie_map: +# HP: http://purl.obolibrary.org/obo/HP_ +# MP: http://purl.obolibrary.org/obo/MP_ +# orcid: https://orcid.org/ +# DISEASE_MAPPING_COMMONS_RULES: https://w3id.org/sssom/commons/disease/curation-rules/ +#mapping_set_id: https://w3id.org/sssom/commons/examples/curation_rule_text.sssom.tsv +#license: "https://creativecommons.org/publicdomain/zero/1.0/" +#creator_id: orcid:0000-0002-7356-1779 +#mapping_provider: "https://w3id.org/sssom/core_team" +#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated. +subject_id predicate_id object_id mapping_justification curation_rule_text see_also +HP:0009124 skos:exactMatch MP:0000003 semapv:ManualMappingCuration The two phenotypes inhere in homologous structures and exhibit the same phenotypic quality https://github.com/mapping-commons/disease-mappings/issues/16 +HP:0008551 skos:exactMatch MP:0000018 semapv:ManualMappingCuration The two phenotypes inhere in homologous structures and exhibit the same phenotypic quality https://github.com/mapping-commons/disease-mappings/issues/16 +HP:0000411 skos:exactMatch MP:0000021 semapv:ManualMappingCuration The two phenotypes are associated with the exact same set of diseases https://github.com/mapping-commons/disease-mappings/issues/16 diff --git a/examples/schema/curation_rule_text2.sssom.tsv b/examples/schema/curation_rule_text2.sssom.tsv new file mode 100644 index 00000000..3c5777ea --- /dev/null +++ b/examples/schema/curation_rule_text2.sssom.tsv @@ -0,0 +1,18 @@ +#curie_map: +# WTO: http://purl.obolibrary.org/obo/WTO_ +# CO321: "http://www.cropontology.org/rdf/CO_321:" +# ror: https://ror.org/ +#mapping_set_id: https://w3id.org/sssom/commons/examples/curation_rule_text2.sssom.tsv +#license: "https://www.etalab.gouv.fr/licence-ouverte-open-licence/" +#comment: This is an example file for the SSSOM for illustration only. This example was extracted from a real mapping set where the subject source (WTO) is an ontology used to annotate text (e.g. scientific literature) and the object source (CO321) is an ontology used to annotate the traits evaluated from observational data. The objective of the alignment is to allow information retrieval from both textual and experimental phenotypic dataset. +#creator_id: ror:02kvxyf05 +#creator_label: "INRAE" +subject_id subject_label predicate_id object_id object_label mapping_justification curation_rule_text comment +WTO:0000304 cold resistance skos:closeMatch CO321:0000080 Cold tolerance semapv:ManualMappingCuration Rule 4: We consider that "tolerance" and "resistance" are almost equivalent when applied to abiotic environmental conditions. +WTO:0000450 aluminium toxicity skos:closeMatch CO321:0000079 Aluminum tolerance semapv:ManualMappingCuration Rule 3: We consider that the user of the information retrieval function interested in plant traits related to metal toxicity (WTO) also wants to retrieve observational data measuring the plant tolerance to the same metal (CO_321). The rule metal + toxicity (WTO) <-> metal + tolerance (CO321) is valid for any kind of metal. +WTO:0000065 anther extrusion skos:exactMatch CO321:0000982 Anther extrusion semapv:ManualMappingCuration +WTO:0000296 aphid resistance skos:closeMatch CO321:0000085 Aphid damage semapv:ManualMappingCuration Rule 2: We consider that the user of the information retrieval function interested in plant traits related to damages caused by some animal, insect, nematode, etc. also wants to retrieve observational data mentioning resistance to the same living organism. +WTO:0000281 Armyworm resistance skos:closeMatch CO321:0000086 Armyworm damage semapv:ManualMappingCuration Rule 2: We consider that the user of the information retrieval function interested in plant traits related to damages caused by some animal, insect, nematode, etc. also wants to retrieve observational data mentioning resistance to the same living organism. +WTO:0000125 awn color skos:exactMatch CO321:0000960 Awn color semapv:ManualMappingCuration +WTO:0000126 awn length skos:exactMatch CO321:0000026 Awn length semapv:ManualMappingCuration +WTO:0000452 bacterial leaf blight resistance skos:closeMatch CO321:0000932 Bacterial leaf blight severity semapv:ManualMappingCuration Rule 1.3: We consider that the user of the information retrieval function, given a pathogen or a disease, would like to retrieve all data, independently of the way the affection is observed. In observational data, a severity score is represented by two digits representing the vertical disease progress and an estimate of severity. The capacity of resistance to a disease would be deduced from the severity of this one on the plant. \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 623a96f2..0f0fe992 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -36,14 +36,21 @@ nav: - How to contribute?: contributing.md - Code of Conduct: code_of_conduct.md - Resources for users: - - Use cases: usecases.md + - Use cases: + - Overview: usecases.md + - How to gradually enrich OMOP mappings with SSSOM: tutorials/omop-mappings.md - Workshops: workshops.md - Presentations: presentations.md - Basic Tutorial: tutorial.md + - Mapping Justifications: mapping-justifications.md - How to use mapping predicates: mapping-predicates.md + - Set up a mapping registry/commons: mapping-commons.md - Overview of Chaining Rules: chaining_rules.md - A basic guide for the SSSOM toolkit: toolkit.md - 5-Star Entity Mappings - Cheatsheet: 5star-mappings.md + - Update schema/context and release: update.md + - Matching tool implementation guide: matching-tool-implementation-guide.md + - Glossary: glossary.md site_url: https://mapping-commons.github.io/sssom/ repo_url: https://github.com/mapping-commons/sssom/ diff --git a/project.Makefile b/project.Makefile index 48602770..b7bcee13 100644 --- a/project.Makefile +++ b/project.Makefile @@ -10,4 +10,34 @@ build: poetry build pypi: - poetry publish \ No newline at end of file + poetry publish + +####################################### +##### Mapping validation ############# +####################################### + +MAPPING_DIR_SCHEMA=examples/schema +MAPPING_DIR_EMBEDDED=examples/embedded +TMPDIR = tmp + +validate-example-schema-%: + mkdir -p $(TMPDIR) + tsvalid $(MAPPING_DIR_SCHEMA)/$*.sssom.tsv --comment "#" --skip E1 + sssom validate $(MAPPING_DIR_SCHEMA)/$*.sssom.tsv + sssom convert $(MAPPING_DIR_SCHEMA)/$*.sssom.tsv -o $(TMPDIR)/schema-$*.sssom.ttl + +validate-example-embedded-%: + mkdir -p $(TMPDIR) + tsvalid $(MAPPING_DIR_EMBEDDED)/$*.sssom.tsv --comment "#" --skip E1 + sssom validate $(MAPPING_DIR_EMBEDDED)/$*.sssom.tsv + sssom convert $(MAPPING_DIR_EMBEDDED)/$*.sssom.tsv -o $(TMPDIR)/embedded-$*.sssom.ttl + +MAPPINGS_SCHEMA=$(notdir $(wildcard $(MAPPING_DIR_SCHEMA)/*.sssom.tsv)) +VALIDATE_MAPPINGS_SCHEMA=$(patsubst %.sssom.tsv, validate-example-schema-%, $(notdir $(wildcard $(MAPPING_DIR_SCHEMA)/*.sssom.tsv))) + +MAPPINGS_EMBEDDED=$(notdir $(wildcard $(MAPPING_DIR_EMBEDDED)/*.sssom.tsv)) +VALIDATE_MAPPINGS_EMBEDDED=$(patsubst %.sssom.tsv, validate-example-embedded-%, $(notdir $(wildcard $(MAPPING_DIR_EMBEDDED)/*.sssom.tsv))) + +validate_mappings: + $(MAKE) $(VALIDATE_MAPPINGS_SCHEMA) + $(MAKE) $(VALIDATE_MAPPINGS_EMBEDDED) diff --git a/project/excel/sssom_schema.xlsx b/project/excel/sssom_schema.xlsx index 46402f7f..4a9e10fc 100644 Binary files a/project/excel/sssom_schema.xlsx and b/project/excel/sssom_schema.xlsx differ diff --git a/project/graphql/sssom_schema.graphql b/project/graphql/sssom_schema.graphql index 981c1a59..d7c283ad 100644 --- a/project/graphql/sssom_schema.graphql +++ b/project/graphql/sssom_schema.graphql @@ -24,11 +24,14 @@ type Mapping objectSource: EntityReference objectSourceVersion: String mappingProvider: Uri + mappingSource: EntityReference mappingCardinality: MappingCardinalityEnum mappingTool: String mappingToolVersion: String mappingDate: Date confidence: Double + curationRule: [EntityReference] + curationRuleText: [String] subjectMatchField: [EntityReference] objectMatchField: [EntityReference] matchString: [String] @@ -44,6 +47,8 @@ type Mapping type MappingRegistry { mappingRegistryId: EntityReference! + mappingRegistryTitle: String + mappingRegistryDescription: String imports: [Uri] mappingSetReferences: [MappingSetReference] documentation: Uri @@ -56,6 +61,7 @@ type MappingSet mappingSetId: Uri! mappingSetVersion: String mappingSetSource: [Uri] + mappingSetTitle: String mappingSetDescription: String creatorId: [EntityReference] creatorLabel: [String] @@ -68,6 +74,7 @@ type MappingSet objectSourceVersion: String mappingProvider: Uri mappingTool: String + mappingToolVersion: String mappingDate: Date subjectMatchField: [EntityReference] objectMatchField: [EntityReference] diff --git a/project/jsonld/sssom_schema.context.jsonld b/project/jsonld/sssom_schema.context.jsonld index 9085b824..50efb3c2 100644 --- a/project/jsonld/sssom_schema.context.jsonld +++ b/project/jsonld/sssom_schema.context.jsonld @@ -1,7 +1,10 @@ { - "_comments": "Auto generated from sssom_schema.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-06-07T11:23:12\n Schema: sssom\n metamodel version: 1.7.0\n model version: None\n \n id: https://w3id.org/sssom/schema/\n description: Datamodel for Simple Standard for Sharing Ontological Mappings (SSSOM)\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "comments": { + "description": "Auto generated by LinkML jsonld context generator", + "generation_date": "2023-07-25T10:05:02", + "source": "sssom_schema.yaml" + }, "@context": { - "dc": "http://purl.org/dc/terms/", "dcterms": "http://purl.org/dc/terms/", "linkml": "https://w3id.org/linkml/", "oboInOwl": "http://www.geneontology.org/formats/oboInOwl#", @@ -10,7 +13,7 @@ "prov": "http://www.w3.org/ns/prov#", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "semapv": "https://w3id.org/semapv/", + "semapv": "https://w3id.org/semapv/vocab/", "skos": "http://www.w3.org/2004/02/skos/core#", "sssom": "https://w3id.org/sssom/", "@vocab": "https://w3id.org/sssom/", @@ -26,7 +29,10 @@ }, "creator_id": { "@type": "rdfs:Resource", - "@id": "dc:creator" + "@id": "dcterms:creator" + }, + "curation_rule": { + "@type": "rdfs:Resource" }, "documentation": { "@type": "@id" @@ -66,7 +72,7 @@ "@type": "rdfs:Resource" }, "mapping_set_description": { - "@id": "dc:description" + "@id": "dcterms:description" }, "mapping_set_id": { "@type": "@id" @@ -78,6 +84,9 @@ "@type": "@id", "@id": "prov:wasDerivedFrom" }, + "mapping_set_title": { + "@id": "dcterms:title" + }, "mapping_set_version": { "@id": "owl:versionInfo" }, @@ -133,7 +142,7 @@ }, "publication_date": { "@type": "xsd:date", - "@id": "dc:created" + "@id": "dcterms:created" }, "registry_confidence": { "@type": "xsd:double" diff --git a/project/jsonld/sssom_schema.jsonld b/project/jsonld/sssom_schema.jsonld index 40a65d5d..27148822 100644 --- a/project/jsonld/sssom_schema.jsonld +++ b/project/jsonld/sssom_schema.jsonld @@ -11,6 +11,10 @@ ], "license": "https://creativecommons.org/publicdomain/zero/1.0/", "prefixes": [ + { + "prefix_prefix": "dcterms", + "prefix_reference": "http://purl.org/dc/terms/" + }, { "prefix_prefix": "linkml", "prefix_reference": "https://w3id.org/linkml/" @@ -45,7 +49,7 @@ }, { "prefix_prefix": "semapv", - "prefix_reference": "https://w3id.org/semapv/" + "prefix_reference": "https://w3id.org/semapv/vocab/" } ], "default_curi_maps": [ @@ -72,6 +76,9 @@ "description": "A character string", "from_schema": "https://w3id.org/linkml/types", "imported_from": "linkml:types", + "exact_mappings": [ + "schema:Text" + ], "base": "str", "uri": "http://www.w3.org/2001/XMLSchema#string", "@type": "TypeDefinition" @@ -82,6 +89,9 @@ "description": "An integer", "from_schema": "https://w3id.org/linkml/types", "imported_from": "linkml:types", + "exact_mappings": [ + "schema:Integer" + ], "base": "int", "uri": "http://www.w3.org/2001/XMLSchema#integer", "@type": "TypeDefinition" @@ -92,6 +102,9 @@ "description": "A binary (true or false) value", "from_schema": "https://w3id.org/linkml/types", "imported_from": "linkml:types", + "exact_mappings": [ + "schema:Boolean" + ], "base": "Bool", "uri": "http://www.w3.org/2001/XMLSchema#boolean", "repr": "bool", @@ -103,6 +116,9 @@ "description": "A real number that conforms to the xsd:float specification", "from_schema": "https://w3id.org/linkml/types", "imported_from": "linkml:types", + "exact_mappings": [ + "schema:Float" + ], "base": "float", "uri": "http://www.w3.org/2001/XMLSchema#float", "@type": "TypeDefinition" @@ -113,6 +129,9 @@ "description": "A real number that conforms to the xsd:double specification", "from_schema": "https://w3id.org/linkml/types", "imported_from": "linkml:types", + "close_mappings": [ + "schema:Float" + ], "base": "float", "uri": "http://www.w3.org/2001/XMLSchema#double", "@type": "TypeDefinition" @@ -123,6 +142,9 @@ "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", "from_schema": "https://w3id.org/linkml/types", "imported_from": "linkml:types", + "broad_mappings": [ + "schema:Number" + ], "base": "Decimal", "uri": "http://www.w3.org/2001/XMLSchema#decimal", "@type": "TypeDefinition" @@ -132,12 +154,15 @@ "definition_uri": "https://w3id.org/linkml/Time", "description": "A time object represents a (local) time of day, independent of any particular day", "notes": [ - "URI is dateTime because OWL reasoners don't work with straight date or time" + "URI is dateTime because OWL reasoners do not work with straight date or time" ], "from_schema": "https://w3id.org/linkml/types", "imported_from": "linkml:types", + "exact_mappings": [ + "schema:Time" + ], "base": "XSDTime", - "uri": "http://www.w3.org/2001/XMLSchema#dateTime", + "uri": "http://www.w3.org/2001/XMLSchema#time", "repr": "str", "@type": "TypeDefinition" }, @@ -150,6 +175,9 @@ ], "from_schema": "https://w3id.org/linkml/types", "imported_from": "linkml:types", + "exact_mappings": [ + "schema:Date" + ], "base": "XSDDate", "uri": "http://www.w3.org/2001/XMLSchema#date", "repr": "str", @@ -161,11 +189,25 @@ "description": "The combination of a date and time", "from_schema": "https://w3id.org/linkml/types", "imported_from": "linkml:types", + "exact_mappings": [ + "schema:DateTime" + ], "base": "XSDDateTime", "uri": "http://www.w3.org/2001/XMLSchema#dateTime", "repr": "str", "@type": "TypeDefinition" }, + { + "name": "date_or_datetime", + "definition_uri": "https://w3id.org/linkml/DateOrDatetime", + "description": "Either a date or a datetime", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "str", + "uri": "https://w3id.org/linkml/DateOrDatetime", + "repr": "str", + "@type": "TypeDefinition" + }, { "name": "uriorcurie", "definition_uri": "https://w3id.org/linkml/Uriorcurie", @@ -177,12 +219,35 @@ "repr": "str", "@type": "TypeDefinition" }, + { + "name": "curie", + "definition_uri": "https://w3id.org/linkml/Curie", + "conforms_to": "https://www.w3.org/TR/curie/", + "description": "a compact URI", + "comments": [ + "in RDF serializations this MUST be expanded to a URI", + "in non-RDF serializations MAY be serialized as the compact representation" + ], + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "Curie", + "uri": "http://www.w3.org/2001/XMLSchema#string", + "repr": "str", + "@type": "TypeDefinition" + }, { "name": "uri", "definition_uri": "https://w3id.org/linkml/Uri", + "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", "description": "a complete URI", + "comments": [ + "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" + ], "from_schema": "https://w3id.org/linkml/types", "imported_from": "linkml:types", + "close_mappings": [ + "schema:URL" + ], "base": "URI", "uri": "http://www.w3.org/2001/XMLSchema#anyURI", "repr": "str", @@ -204,7 +269,7 @@ "definition_uri": "https://w3id.org/linkml/Objectidentifier", "description": "A URI or CURIE that represents an object in the model.", "comments": [ - "Used for inheritence and type checking" + "Used for inheritance and type checking" ], "from_schema": "https://w3id.org/linkml/types", "imported_from": "linkml:types", @@ -223,6 +288,42 @@ "uri": "http://www.w3.org/ns/shex#nonLiteral", "repr": "str", "@type": "TypeDefinition" + }, + { + "name": "jsonpointer", + "definition_uri": "https://w3id.org/linkml/Jsonpointer", + "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", + "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "str", + "uri": "http://www.w3.org/2001/XMLSchema#string", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "jsonpath", + "definition_uri": "https://w3id.org/linkml/Jsonpath", + "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", + "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "str", + "uri": "http://www.w3.org/2001/XMLSchema#string", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "sparqlpath", + "definition_uri": "https://w3id.org/linkml/Sparqlpath", + "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", + "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "str", + "uri": "http://www.w3.org/2001/XMLSchema#string", + "repr": "str", + "@type": "TypeDefinition" } ], "enums": [ @@ -403,6 +504,32 @@ "required": true, "@type": "SlotDefinition" }, + { + "name": "mapping_registry_title", + "definition_uri": "https://w3id.org/sssom/mapping_registry_title", + "description": "The title of a mapping registry.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_registry_title", + "owner": "MappingRegistry", + "domain_of": [ + "MappingRegistry" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "mapping_registry_description", + "definition_uri": "https://w3id.org/sssom/mapping_registry_description", + "description": "The description of a mapping registry.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_registry_description", + "owner": "MappingRegistry", + "domain_of": [ + "MappingRegistry" + ], + "range": "string", + "@type": "SlotDefinition" + }, { "name": "imports", "definition_uri": "https://w3id.org/sssom/imports", @@ -508,13 +635,18 @@ { "name": "subject_category", "definition_uri": "https://w3id.org/sssom/subject_category", - "description": "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary.", + "description": "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases.", "examples": [ { "value": "UBERON:0001062", "description": "(The CURIE of the Uberon term for \"anatomical entity\".)", "@type": "Example" }, + { + "value": "anatomical entity", + "description": "(A string, rather than ID, describing the \"anatomical entity\" category. This is possible, but less preferred than using an ID.)", + "@type": "Example" + }, { "value": "biolink:Gene", "description": "(The CURIE of the biolink class for genes.)", @@ -522,6 +654,10 @@ } ], "from_schema": "https://w3id.org/sssom/schema/", + "see_also": [ + "https://github.com/mapping-commons/sssom/issues/13", + "https://github.com/mapping-commons/sssom/issues/256" + ], "slot_uri": "https://w3id.org/sssom/subject_category", "owner": "Mapping", "domain_of": [ @@ -586,6 +722,9 @@ } ], "from_schema": "https://w3id.org/sssom/schema/", + "see_also": [ + "https://github.com/mapping-commons/sssom/issues/107" + ], "slot_uri": "https://w3id.org/sssom/predicate_modifier", "owner": "Mapping", "domain_of": [ @@ -650,7 +789,7 @@ "@type": "Example" }, { - "value": "oboInOwl:database_cross_reference", + "value": "oboInOwl:hasDbXref", "description": "Two terms are related in some way. The meaning is frequently consistent across a single set of mappings. Note this property is often overloaded even where the terms are of a different nature (e.g. interpro2go)", "@type": "Example" }, @@ -736,13 +875,18 @@ { "name": "object_category", "definition_uri": "https://w3id.org/sssom/object_category", - "description": "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary.", + "description": "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases.", "examples": [ { "value": "UBERON:0001062", "description": "(The CURIE of the Uberon term for \"anatomical entity\".)", "@type": "Example" }, + { + "value": "anatomical entity", + "description": "(A string, rather than ID, describing the \"anatomical entity\" category. This is possible, but less preferred than using an ID.)", + "@type": "Example" + }, { "value": "biolink:Gene", "description": "(The CURIE of the biolink class for genes.)", @@ -750,6 +894,10 @@ } ], "from_schema": "https://w3id.org/sssom/schema/", + "see_also": [ + "https://github.com/mapping-commons/sssom/issues/13", + "https://github.com/mapping-commons/sssom/issues/256" + ], "slot_uri": "https://w3id.org/sssom/object_category", "owner": "Mapping", "domain_of": [ @@ -904,6 +1052,28 @@ "range": "string", "@type": "SlotDefinition" }, + { + "name": "mapping_set_title", + "definition_uri": "https://w3id.org/sssom/mapping_set_title", + "description": "The display name of a mapping set.", + "examples": [ + { + "value": "The Mondo-OMIM mappings by Monarch Initiative.", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://purl.org/dc/terms/title" + ], + "slot_uri": "http://purl.org/dc/terms/title", + "owner": "MappingSet", + "domain_of": [ + "MappingSet" + ], + "range": "string", + "@type": "SlotDefinition" + }, { "name": "mapping_set_description", "definition_uri": "https://w3id.org/sssom/mapping_set_description", @@ -1007,7 +1177,7 @@ { "name": "reviewer_label", "definition_uri": "https://w3id.org/sssom/reviewer_label", - "description": "A string identifying the reviewer of this mapping. In the spirit of provenance, consider to use author_id instead.", + "description": "A string identifying the reviewer of this mapping. In the spirit of provenance, consider to use reviewer_id instead.", "from_schema": "https://w3id.org/sssom/schema/", "slot_uri": "https://w3id.org/sssom/reviewer_label", "multivalued": true, @@ -1179,6 +1349,10 @@ ], "from_schema": "https://w3id.org/sssom/schema/", "slot_uri": "https://w3id.org/sssom/mapping_source", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], "range": "EntityReference", "@type": "SlotDefinition" }, @@ -1229,6 +1403,7 @@ "slot_uri": "https://w3id.org/sssom/mapping_tool_version", "owner": "Mapping", "domain_of": [ + "MappingSet", "Mapping" ], "range": "string", @@ -1370,6 +1545,44 @@ "range": "EntityReference", "@type": "SlotDefinition" }, + { + "name": "curation_rule", + "definition_uri": "https://w3id.org/sssom/curation_rule", + "description": "A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation rule is captured as a resource rather than a string, which enables higher levels of transparency and sharing across mapping sets. The URI representation of the curation rule is expected to be a resolvable identifier which provides details about the nature of the curation rule.", + "from_schema": "https://w3id.org/sssom/schema/", + "see_also": [ + "https://github.com/mapping-commons/sssom/issues/166", + "https://github.com/mapping-commons/sssom/pull/258", + "https://github.com/mapping-commons/sssom/blob/master/examples/schema/curation_rule.sssom.tsv" + ], + "slot_uri": "https://w3id.org/sssom/curation_rule", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "EntityReference", + "@type": "SlotDefinition" + }, + { + "name": "curation_rule_text", + "definition_uri": "https://w3id.org/sssom/curation_rule_text", + "description": "A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation rule should be captured as a resource (entity reference) rather than a string (see curation_rule element), which enables higher levels of transparency and sharing across mapping sets. The textual representation of curation rule is intended to be used in cases where (1) the creation of a resource is not practical from the perspective of the mapping_provider and (2) as an additional piece of metadata to augment the curation_rule element with a human readable text.", + "from_schema": "https://w3id.org/sssom/schema/", + "see_also": [ + "https://github.com/mapping-commons/sssom/issues/166", + "https://github.com/mapping-commons/sssom/pull/258", + "https://github.com/mapping-commons/sssom/blob/master/examples/schema/curation_rule_text.sssom.tsv" + ], + "slot_uri": "https://w3id.org/sssom/curation_rule_text", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, { "name": "semantic_similarity_score", "definition_uri": "https://w3id.org/sssom/semantic_similarity_score", @@ -1486,6 +1699,7 @@ "mapping_set_id", "mapping_set_version", "mapping_set_source", + "mapping_set_title", "mapping_set_description", "creator_id", "creator_label", @@ -1498,6 +1712,7 @@ "object_source_version", "mapping_provider", "mapping_tool", + "mapping_tool_version", "mapping_date", "subject_match_field", "object_match_field", @@ -1544,11 +1759,14 @@ "object_source", "object_source_version", "mapping_provider", + "mapping_source", "mapping_cardinality", "mapping_tool", "mapping_tool_version", "mapping_date", "confidence", + "curation_rule", + "curation_rule_text", "subject_match_field", "object_match_field", "match_string", @@ -1571,6 +1789,8 @@ "from_schema": "https://w3id.org/sssom/schema/", "slots": [ "mapping_registry_id", + "mapping_registry_title", + "mapping_registry_description", "imports", "mapping_set_references", "documentation", @@ -1600,9 +1820,9 @@ ], "metamodel_version": "1.7.0", "source_file": "sssom_schema.yaml", - "source_file_date": "2022-06-07T11:14:57", - "source_file_size": 21401, - "generation_date": "2022-06-07T11:23:13", + "source_file_date": "2023-07-25T10:02:33", + "source_file_size": 25711, + "generation_date": "2023-07-25T10:05:03", "@type": "SchemaDefinition", "@context": [ "project/jsonld/sssom_schema.context.jsonld", diff --git a/project/jsonschema/sssom_schema.schema.json b/project/jsonschema/sssom_schema.schema.json index 27d99efc..8f786466 100644 --- a/project/jsonschema/sssom_schema.schema.json +++ b/project/jsonschema/sssom_schema.schema.json @@ -1,469 +1,530 @@ { - "$defs": { - "EntityTypeEnum": { - "description": "", - "enum": [ - "owl class", - "owl object property", - "owl data property", - "owl annotation property", - "owl named individual", - "skos concept", - "rdfs resource", - "rdfs class", - "rdfs literal", - "rdfs datatype", - "rdf property" - ], - "title": "EntityTypeEnum", - "type": "string" - }, - "Mapping": { - "additionalProperties": false, - "description": "Represents an individual mapping between a pair of entities", - "properties": { - "author_id": { - "description": "Identifies the persons or groups responsible for asserting the mappings. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible.", - "items": { - "type": "string" - }, - "type": "array" - }, - "author_label": { - "description": "A string identifying the author of this mapping. In the spirit of provenance, consider to use author_id instead.", - "items": { - "type": "string" - }, - "type": "array" - }, - "comment": { - "description": "Free text field containing either curator notes or text generated by tool providing additional informative information.", - "type": "string" - }, - "confidence": { - "description": "A score between 0 and 1 to denote the confidence or probability that the match is correct, where 1 denotes total confidence.", - "type": "number" - }, - "creator_id": { - "description": "Identifies the persons or groups responsible for the creation of the mapping. The creator is the agent that put the mapping in its published form, which may be different from the author, which is a person that was actively involved in the assertion of the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible.", - "items": { - "type": "string" - }, - "type": "array" - }, - "creator_label": { - "description": "A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead.", - "items": { - "type": "string" - }, - "type": "array" - }, - "license": { - "description": "A url to the license of the mapping. In absence of a license we assume no license.", - "type": "string" - }, - "mapping_cardinality": { - "$ref": "#/$defs/MappingCardinalityEnum", - "description": "A string indicating whether this mapping is from a 1:1 (the subject_id maps to a single object_id), 1:n (the subject maps to more than one object_id), n:1, 1:0, 0:1 or n:n group. Note that this is a convenience field that should be derivable from the mapping set." - }, - "mapping_date": { - "description": "The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file.", - "format": "date", - "type": "string" - }, - "mapping_justification": { - "description": "A mapping justification is an action (or the written representation of that action) of showing a mapping to be right or reasonable.", - "pattern": "^semapv:(MappingReview|ManualMappingCuration|LogicalReasoning|LexicalMatching|CompositeMatching|UnspecifiedMatching|SemanticSimilarityThresholdMatching|LexicalSimilarityThresholdMatching|MappingChaining)$", - "type": "string" - }, - "mapping_provider": { - "description": "URL pointing to the source that provided the mapping, for example an ontology that already contains the mappings, or a database from which it was derived.", - "type": "string" - }, - "mapping_tool": { - "description": "A reference to the tool or algorithm that was used to generate the mapping. Should be a URL pointing to more info about it, but can be free text.", - "type": "string" - }, - "mapping_tool_version": { - "description": "Version string that denotes the version of the mapping tool used.", - "type": "string" - }, - "match_string": { - "description": "Strings that are shared by subj/obj. It is recommended to indicate the fields for the match using the object and subject_match_field slots.", - "items": { - "type": "string" - }, - "type": "array" - }, - "object_category": { - "description": "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary.", - "type": "string" - }, - "object_id": { - "description": "The ID of the object of the mapping.", - "type": "string" - }, - "object_label": { - "description": "The label of object of the mapping", - "type": "string" - }, - "object_match_field": { - "description": "A tuple of fields (term annotations on the object) that was used for the match.", - "items": { - "type": "string" - }, - "type": "array" - }, - "object_preprocessing": { - "description": "Method of preprocessing applied to the fields of the object. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows.", - "items": { - "type": "string" - }, - "type": "array" - }, - "object_source": { - "description": "IRI of ontology source for the object. Version IRI preferred.", - "type": "string" - }, - "object_source_version": { - "description": "Version IRI or version string of the source of the object term.", - "type": "string" - }, - "object_type": { - "$ref": "#/$defs/EntityTypeEnum", - "description": "The type of entity that is being mapped." - }, - "other": { - "description": "Pipe separated list of key value pairs for properties not part of the SSSOM spec. Can be used to encode additional provenance data.", - "type": "string" - }, - "predicate_id": { - "description": "The ID of the predicate or relation that relates the subject and object of this match.", - "type": "string" - }, - "predicate_label": { - "description": "The label of the predicate/relation of the mapping", - "type": "string" - }, - "predicate_modifier": { - "$ref": "#/$defs/PredicateModifierEnum", - "description": "A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40 for discussion" - }, - "reviewer_id": { - "description": "Identifies the persons or groups that reviewed and confirmed the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible.", - "items": { - "type": "string" - }, - "type": "array" - }, - "reviewer_label": { - "description": "A string identifying the reviewer of this mapping. In the spirit of provenance, consider to use author_id instead.", - "items": { - "type": "string" - }, - "type": "array" - }, - "see_also": { - "description": "A URL specific for the mapping instance. E.g. for kboom we have a per-mapping image that shows surrounding axioms that drive probability. Could also be a github issue URL that discussed a complicated alignment", - "items": { - "type": "string" - }, - "type": "array" - }, - "semantic_similarity_measure": { - "description": "The measure used for computing the the semantic similarity score. To make processing this field as unambiguous as possible, we recommend using wikidata identifiers, but wikipedia pages could also be acceptable.", - "type": "string" - }, - "semantic_similarity_score": { - "description": "A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence.", - "type": "number" - }, - "subject_category": { - "description": "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary.", - "type": "string" - }, - "subject_id": { - "description": "The ID of the subject of the mapping.", - "type": "string" - }, - "subject_label": { - "description": "The label of subject of the mapping", - "type": "string" - }, - "subject_match_field": { - "description": "A tuple of fields (term annotations on the subject) that was used for the match.", - "items": { - "type": "string" - }, - "type": "array" - }, - "subject_preprocessing": { - "description": "Method of preprocessing applied to the fields of the subject. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows.", - "items": { - "type": "string" - }, - "type": "array" - }, - "subject_source": { - "description": "URI of ontology source for the subject.", - "type": "string" - }, - "subject_source_version": { - "description": "Version IRI or version string of the source of the subject term.", - "type": "string" - }, - "subject_type": { - "$ref": "#/$defs/EntityTypeEnum", - "description": "The type of entity that is being mapped." - } - }, - "required": [ - "subject_id", - "predicate_id", - "object_id", - "mapping_justification" - ], - "title": "Mapping", - "type": "object" - }, - "MappingCardinalityEnum": { - "description": "", - "enum": [ - "1:1", - "1:n", - "n:1", - "1:0", - "0:1", - "n:n" - ], - "title": "MappingCardinalityEnum", - "type": "string" - }, - "MappingRegistry": { - "additionalProperties": false, - "description": "A registry for managing mapping sets. It holds a set of mapping set references, and can import other registries.", - "properties": { - "documentation": { - "description": "A URL to the documentation of this mapping commons.", - "type": "string" - }, - "homepage": { - "description": "A URL to a homepage of this mapping commons.", - "type": "string" - }, - "imports": { - "description": "A list of registries that should be imported into this one.", - "items": { - "type": "string" - }, - "type": "array" - }, - "mapping_registry_id": { - "description": "The unique identifier of a mapping registry.", - "type": "string" - }, - "mapping_set_references": { - "description": "A list of mapping set references.", - "items": { - "$ref": "#/$defs/MappingSetReference" - }, - "type": "array" - } - }, - "required": [ - "mapping_registry_id" - ], - "title": "MappingRegistry", - "type": "object" - }, - "MappingSet": { - "additionalProperties": false, - "description": "Represents a set of mappings", - "properties": { - "comment": { - "description": "Free text field containing either curator notes or text generated by tool providing additional informative information.", - "type": "string" - }, - "creator_id": { - "description": "Identifies the persons or groups responsible for the creation of the mapping. The creator is the agent that put the mapping in its published form, which may be different from the author, which is a person that was actively involved in the assertion of the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible.", - "items": { - "type": "string" - }, - "type": "array" - }, - "creator_label": { - "description": "A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead.", - "items": { - "type": "string" - }, - "type": "array" - }, - "license": { - "description": "A url to the license of the mapping. In absence of a license we assume no license.", - "type": "string" - }, - "mapping_date": { - "description": "The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file.", - "format": "date", - "type": "string" - }, - "mapping_provider": { - "description": "URL pointing to the source that provided the mapping, for example an ontology that already contains the mappings, or a database from which it was derived.", - "type": "string" - }, - "mapping_set_description": { - "description": "A description of the mapping set.", - "type": "string" - }, - "mapping_set_id": { - "description": "A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable.", - "type": "string" - }, - "mapping_set_source": { - "description": "A mapping set or set of mapping set that was used to derive the mapping set.", - "items": { - "type": "string" - }, - "type": "array" - }, - "mapping_set_version": { - "description": "A version string for the mapping.", - "type": "string" - }, - "mapping_tool": { - "description": "A reference to the tool or algorithm that was used to generate the mapping. Should be a URL pointing to more info about it, but can be free text.", - "type": "string" - }, - "mappings": { - "description": "Contains a list of mapping objects", - "items": { - "$ref": "#/$defs/Mapping" - }, - "type": "array" - }, - "object_match_field": { - "description": "A tuple of fields (term annotations on the object) that was used for the match.", - "items": { - "type": "string" - }, - "type": "array" - }, - "object_preprocessing": { - "description": "Method of preprocessing applied to the fields of the object. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows.", - "items": { - "type": "string" - }, - "type": "array" - }, - "object_source": { - "description": "IRI of ontology source for the object. Version IRI preferred.", - "type": "string" - }, - "object_source_version": { - "description": "Version IRI or version string of the source of the object term.", - "type": "string" - }, - "object_type": { - "$ref": "#/$defs/EntityTypeEnum", - "description": "The type of entity that is being mapped." - }, - "other": { - "description": "Pipe separated list of key value pairs for properties not part of the SSSOM spec. Can be used to encode additional provenance data.", - "type": "string" - }, - "see_also": { - "description": "A URL specific for the mapping instance. E.g. for kboom we have a per-mapping image that shows surrounding axioms that drive probability. Could also be a github issue URL that discussed a complicated alignment", - "items": { - "type": "string" - }, - "type": "array" - }, - "subject_match_field": { - "description": "A tuple of fields (term annotations on the subject) that was used for the match.", - "items": { - "type": "string" - }, - "type": "array" - }, - "subject_preprocessing": { - "description": "Method of preprocessing applied to the fields of the subject. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows.", - "items": { - "type": "string" - }, - "type": "array" - }, - "subject_source": { - "description": "URI of ontology source for the subject.", - "type": "string" - }, - "subject_source_version": { - "description": "Version IRI or version string of the source of the subject term.", - "type": "string" - }, - "subject_type": { - "$ref": "#/$defs/EntityTypeEnum", - "description": "The type of entity that is being mapped." - } - }, - "required": [ - "mapping_set_id", - "license" - ], - "title": "MappingSet", - "type": "object" - }, - "MappingSetReference": { - "additionalProperties": false, - "description": "A reference to a mapping set. It allows to augment mapping set metadata from the perspective of the registry, for example, providing confidence, or a local filename or a grouping.", - "properties": { - "last_updated": { - "description": "The date this reference was last updated.", - "format": "date", - "type": "string" - }, - "local_name": { - "description": "The local name assigned to file that corresponds to the downloaded mapping set.", - "type": "string" - }, - "mapping_set_group": { - "description": "Set by the owners of the mapping registry. A way to group .", - "type": "string" - }, - "mapping_set_id": { - "description": "A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable.", - "type": "string" - }, - "mirror_from": { - "description": "A URL location from which to obtain a resource, such as a mapping set.", - "type": "string" - }, - "registry_confidence": { - "description": "This value is set by the registry that indexes the mapping set. It reflects the confidence the registry has in the correctness of the mappings in the mapping set.", - "type": "number" - } - }, - "required": [ - "mapping_set_id" - ], - "title": "MappingSetReference", - "type": "object" - }, - "PredicateModifierEnum": { - "description": "", - "enum": [ - "Not" - ], - "title": "PredicateModifierEnum", - "type": "string" - } - }, - "$id": "https://w3id.org/sssom/schema/", - "$schema": "http://json-schema.org/draft-07/schema#", - "additionalProperties": true, - "metamodel_version": "1.7.0", - "properties": {}, - "required": [], - "title": "sssom", - "type": "object", - "version": null -} + "$defs": { + "EntityTypeEnum": { + "description": "", + "enum": [ + "owl class", + "owl object property", + "owl data property", + "owl annotation property", + "owl named individual", + "skos concept", + "rdfs resource", + "rdfs class", + "rdfs literal", + "rdfs datatype", + "rdf property" + ], + "title": "EntityTypeEnum", + "type": "string" + }, + "Mapping": { + "additionalProperties": false, + "description": "Represents an individual mapping between a pair of entities", + "properties": { + "author_id": { + "description": "Identifies the persons or groups responsible for asserting the mappings. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible.", + "items": { + "type": "string" + }, + "type": "array" + }, + "author_label": { + "description": "A string identifying the author of this mapping. In the spirit of provenance, consider to use author_id instead.", + "items": { + "type": "string" + }, + "type": "array" + }, + "comment": { + "description": "Free text field containing either curator notes or text generated by tool providing additional informative information.", + "type": "string" + }, + "confidence": { + "description": "A score between 0 and 1 to denote the confidence or probability that the match is correct, where 1 denotes total confidence.", + "type": "number" + }, + "creator_id": { + "description": "Identifies the persons or groups responsible for the creation of the mapping. The creator is the agent that put the mapping in its published form, which may be different from the author, which is a person that was actively involved in the assertion of the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible.", + "items": { + "type": "string" + }, + "type": "array" + }, + "creator_label": { + "description": "A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead.", + "items": { + "type": "string" + }, + "type": "array" + }, + "curation_rule": { + "description": "A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation rule is captured as a resource rather than a string, which enables higher levels of transparency and sharing across mapping sets. The URI representation of the curation rule is expected to be a resolvable identifier which provides details about the nature of the curation rule.", + "items": { + "type": "string" + }, + "type": "array" + }, + "curation_rule_text": { + "description": "A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation rule should be captured as a resource (entity reference) rather than a string (see curation_rule element), which enables higher levels of transparency and sharing across mapping sets. The textual representation of curation rule is intended to be used in cases where (1) the creation of a resource is not practical from the perspective of the mapping_provider and (2) as an additional piece of metadata to augment the curation_rule element with a human readable text.", + "items": { + "type": "string" + }, + "type": "array" + }, + "license": { + "description": "A url to the license of the mapping. In absence of a license we assume no license.", + "type": "string" + }, + "mapping_cardinality": { + "$ref": "#/$defs/MappingCardinalityEnum", + "description": "A string indicating whether this mapping is from a 1:1 (the subject_id maps to a single object_id), 1:n (the subject maps to more than one object_id), n:1, 1:0, 0:1 or n:n group. Note that this is a convenience field that should be derivable from the mapping set." + }, + "mapping_date": { + "description": "The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file.", + "format": "date", + "type": "string" + }, + "mapping_justification": { + "anyOf": [ + { + "const": "semapv:LexicalMatching" + }, + { + "const": "semapv:LogicalReasoning" + }, + { + "const": "semapv:CompositeMatching" + }, + { + "const": "semapv:UnspecifiedMatching" + }, + { + "const": "semapv:SemanticSimilarityThresholdMatching" + }, + { + "const": "semapv:LexicalSimilarityThresholdMatching" + }, + { + "const": "semapv:MappingChaining" + }, + { + "const": "semapv:MappingReview" + }, + { + "const": "semapv:ManualMappingCuration" + } + ], + "description": "A mapping justification is an action (or the written representation of that action) of showing a mapping to be right or reasonable.", + "pattern": "^semapv:(MappingReview|ManualMappingCuration|LogicalReasoning|LexicalMatching|CompositeMatching|UnspecifiedMatching|SemanticSimilarityThresholdMatching|LexicalSimilarityThresholdMatching|MappingChaining)$", + "type": "string" + }, + "mapping_provider": { + "description": "URL pointing to the source that provided the mapping, for example an ontology that already contains the mappings, or a database from which it was derived.", + "type": "string" + }, + "mapping_source": { + "description": "The mapping set this mapping was originally defined in. mapping_source is used for example when merging multiple mapping sets or deriving one mapping set from another.", + "type": "string" + }, + "mapping_tool": { + "description": "A reference to the tool or algorithm that was used to generate the mapping. Should be a URL pointing to more info about it, but can be free text.", + "type": "string" + }, + "mapping_tool_version": { + "description": "Version string that denotes the version of the mapping tool used.", + "type": "string" + }, + "match_string": { + "description": "Strings that are shared by subj/obj. It is recommended to indicate the fields for the match using the object and subject_match_field slots.", + "items": { + "type": "string" + }, + "type": "array" + }, + "object_category": { + "description": "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases.", + "type": "string" + }, + "object_id": { + "description": "The ID of the object of the mapping.", + "type": "string" + }, + "object_label": { + "description": "The label of object of the mapping", + "type": "string" + }, + "object_match_field": { + "description": "A tuple of fields (term annotations on the object) that was used for the match.", + "items": { + "type": "string" + }, + "type": "array" + }, + "object_preprocessing": { + "description": "Method of preprocessing applied to the fields of the object. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows.", + "items": { + "type": "string" + }, + "type": "array" + }, + "object_source": { + "description": "IRI of ontology source for the object. Version IRI preferred.", + "type": "string" + }, + "object_source_version": { + "description": "Version IRI or version string of the source of the object term.", + "type": "string" + }, + "object_type": { + "$ref": "#/$defs/EntityTypeEnum", + "description": "The type of entity that is being mapped." + }, + "other": { + "description": "Pipe separated list of key value pairs for properties not part of the SSSOM spec. Can be used to encode additional provenance data.", + "type": "string" + }, + "predicate_id": { + "description": "The ID of the predicate or relation that relates the subject and object of this match.", + "type": "string" + }, + "predicate_label": { + "description": "The label of the predicate/relation of the mapping", + "type": "string" + }, + "predicate_modifier": { + "$ref": "#/$defs/PredicateModifierEnum", + "description": "A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40 for discussion" + }, + "reviewer_id": { + "description": "Identifies the persons or groups that reviewed and confirmed the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible.", + "items": { + "type": "string" + }, + "type": "array" + }, + "reviewer_label": { + "description": "A string identifying the reviewer of this mapping. In the spirit of provenance, consider to use reviewer_id instead.", + "items": { + "type": "string" + }, + "type": "array" + }, + "see_also": { + "description": "A URL specific for the mapping instance. E.g. for kboom we have a per-mapping image that shows surrounding axioms that drive probability. Could also be a github issue URL that discussed a complicated alignment", + "items": { + "type": "string" + }, + "type": "array" + }, + "semantic_similarity_measure": { + "description": "The measure used for computing the the semantic similarity score. To make processing this field as unambiguous as possible, we recommend using wikidata identifiers, but wikipedia pages could also be acceptable.", + "type": "string" + }, + "semantic_similarity_score": { + "description": "A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence.", + "type": "number" + }, + "subject_category": { + "description": "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases.", + "type": "string" + }, + "subject_id": { + "description": "The ID of the subject of the mapping.", + "type": "string" + }, + "subject_label": { + "description": "The label of subject of the mapping", + "type": "string" + }, + "subject_match_field": { + "description": "A tuple of fields (term annotations on the subject) that was used for the match.", + "items": { + "type": "string" + }, + "type": "array" + }, + "subject_preprocessing": { + "description": "Method of preprocessing applied to the fields of the subject. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows.", + "items": { + "type": "string" + }, + "type": "array" + }, + "subject_source": { + "description": "URI of ontology source for the subject.", + "type": "string" + }, + "subject_source_version": { + "description": "Version IRI or version string of the source of the subject term.", + "type": "string" + }, + "subject_type": { + "$ref": "#/$defs/EntityTypeEnum", + "description": "The type of entity that is being mapped." + } + }, + "required": [ + "subject_id", + "predicate_id", + "object_id", + "mapping_justification" + ], + "title": "Mapping", + "type": "object" + }, + "MappingCardinalityEnum": { + "description": "", + "enum": [ + "1:1", + "1:n", + "n:1", + "1:0", + "0:1", + "n:n" + ], + "title": "MappingCardinalityEnum", + "type": "string" + }, + "MappingRegistry": { + "additionalProperties": false, + "description": "A registry for managing mapping sets. It holds a set of mapping set references, and can import other registries.", + "properties": { + "documentation": { + "description": "A URL to the documentation of this mapping commons.", + "type": "string" + }, + "homepage": { + "description": "A URL to a homepage of this mapping commons.", + "type": "string" + }, + "imports": { + "description": "A list of registries that should be imported into this one.", + "items": { + "type": "string" + }, + "type": "array" + }, + "mapping_registry_description": { + "description": "The description of a mapping registry.", + "type": "string" + }, + "mapping_registry_id": { + "description": "The unique identifier of a mapping registry.", + "type": "string" + }, + "mapping_registry_title": { + "description": "The title of a mapping registry.", + "type": "string" + }, + "mapping_set_references": { + "description": "A list of mapping set references.", + "items": { + "$ref": "#/$defs/MappingSetReference" + }, + "type": "array" + } + }, + "required": [ + "mapping_registry_id" + ], + "title": "MappingRegistry", + "type": "object" + }, + "MappingSet": { + "additionalProperties": false, + "description": "Represents a set of mappings", + "properties": { + "comment": { + "description": "Free text field containing either curator notes or text generated by tool providing additional informative information.", + "type": "string" + }, + "creator_id": { + "description": "Identifies the persons or groups responsible for the creation of the mapping. The creator is the agent that put the mapping in its published form, which may be different from the author, which is a person that was actively involved in the assertion of the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible.", + "items": { + "type": "string" + }, + "type": "array" + }, + "creator_label": { + "description": "A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead.", + "items": { + "type": "string" + }, + "type": "array" + }, + "license": { + "description": "A url to the license of the mapping. In absence of a license we assume no license.", + "type": "string" + }, + "mapping_date": { + "description": "The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file.", + "format": "date", + "type": "string" + }, + "mapping_provider": { + "description": "URL pointing to the source that provided the mapping, for example an ontology that already contains the mappings, or a database from which it was derived.", + "type": "string" + }, + "mapping_set_description": { + "description": "A description of the mapping set.", + "type": "string" + }, + "mapping_set_id": { + "description": "A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable.", + "type": "string" + }, + "mapping_set_source": { + "description": "A mapping set or set of mapping set that was used to derive the mapping set.", + "items": { + "type": "string" + }, + "type": "array" + }, + "mapping_set_title": { + "description": "The display name of a mapping set.", + "type": "string" + }, + "mapping_set_version": { + "description": "A version string for the mapping.", + "type": "string" + }, + "mapping_tool": { + "description": "A reference to the tool or algorithm that was used to generate the mapping. Should be a URL pointing to more info about it, but can be free text.", + "type": "string" + }, + "mapping_tool_version": { + "description": "Version string that denotes the version of the mapping tool used.", + "type": "string" + }, + "mappings": { + "description": "Contains a list of mapping objects", + "items": { + "$ref": "#/$defs/Mapping" + }, + "type": "array" + }, + "object_match_field": { + "description": "A tuple of fields (term annotations on the object) that was used for the match.", + "items": { + "type": "string" + }, + "type": "array" + }, + "object_preprocessing": { + "description": "Method of preprocessing applied to the fields of the object. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows.", + "items": { + "type": "string" + }, + "type": "array" + }, + "object_source": { + "description": "IRI of ontology source for the object. Version IRI preferred.", + "type": "string" + }, + "object_source_version": { + "description": "Version IRI or version string of the source of the object term.", + "type": "string" + }, + "object_type": { + "$ref": "#/$defs/EntityTypeEnum", + "description": "The type of entity that is being mapped." + }, + "other": { + "description": "Pipe separated list of key value pairs for properties not part of the SSSOM spec. Can be used to encode additional provenance data.", + "type": "string" + }, + "see_also": { + "description": "A URL specific for the mapping instance. E.g. for kboom we have a per-mapping image that shows surrounding axioms that drive probability. Could also be a github issue URL that discussed a complicated alignment", + "items": { + "type": "string" + }, + "type": "array" + }, + "subject_match_field": { + "description": "A tuple of fields (term annotations on the subject) that was used for the match.", + "items": { + "type": "string" + }, + "type": "array" + }, + "subject_preprocessing": { + "description": "Method of preprocessing applied to the fields of the subject. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows.", + "items": { + "type": "string" + }, + "type": "array" + }, + "subject_source": { + "description": "URI of ontology source for the subject.", + "type": "string" + }, + "subject_source_version": { + "description": "Version IRI or version string of the source of the subject term.", + "type": "string" + }, + "subject_type": { + "$ref": "#/$defs/EntityTypeEnum", + "description": "The type of entity that is being mapped." + } + }, + "required": [ + "mapping_set_id", + "license" + ], + "title": "MappingSet", + "type": "object" + }, + "MappingSetReference": { + "additionalProperties": false, + "description": "A reference to a mapping set. It allows to augment mapping set metadata from the perspective of the registry, for example, providing confidence, or a local filename or a grouping.", + "properties": { + "last_updated": { + "description": "The date this reference was last updated.", + "format": "date", + "type": "string" + }, + "local_name": { + "description": "The local name assigned to file that corresponds to the downloaded mapping set.", + "type": "string" + }, + "mapping_set_group": { + "description": "Set by the owners of the mapping registry. A way to group .", + "type": "string" + }, + "mapping_set_id": { + "description": "A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable.", + "type": "string" + }, + "mirror_from": { + "description": "A URL location from which to obtain a resource, such as a mapping set.", + "type": "string" + }, + "registry_confidence": { + "description": "This value is set by the registry that indexes the mapping set. It reflects the confidence the registry has in the correctness of the mappings in the mapping set.", + "type": "number" + } + }, + "required": [ + "mapping_set_id" + ], + "title": "MappingSetReference", + "type": "object" + }, + "PredicateModifierEnum": { + "description": "", + "enum": [ + "Not" + ], + "title": "PredicateModifierEnum", + "type": "string" + } + }, + "$id": "https://w3id.org/sssom/schema/", + "$schema": "http://json-schema.org/draft-07/schema#", + "additionalProperties": true, + "metamodel_version": "1.7.0", + "title": "sssom", + "type": "object", + "version": null +} \ No newline at end of file diff --git a/project/owl/sssom_schema.owl.ttl b/project/owl/sssom_schema.owl.ttl index c4108908..795e15bb 100644 --- a/project/owl/sssom_schema.owl.ttl +++ b/project/owl/sssom_schema.owl.ttl @@ -11,25 +11,18 @@ @prefix xsd: . linkml:SubsetDefinition a owl:Class ; - rdfs:label "subset_definition" . + rdfs:label "subset_definition" ; + linkml:attributes "{}" ; + linkml:is_a "element" . linkml:topValue a owl:DatatypeProperty ; rdfs:label "value" . -sssom:mapping_source a owl:ObjectProperty, - linkml:SlotDefinition ; - rdfs:label "mapping_source" ; - rdfs:range sssom:EntityReference ; - skos:definition "The mapping set this mapping was originally defined in. mapping_source is used for example when merging multiple mapping sets or deriving one mapping set from another." ; - linkml:examples "Example(value='MONDO_MAPPINGS:mondo_exactmatch_ncit.sssom.tsv', description=None)" . - sssom:predicate_type a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "predicate_type" ; rdfs:range sssom:EntityTypeEnum ; - skos:definition "The type of entity that is being mapped." ; - linkml:examples "Example(value='owl:AnnotationProperty', description=None)", - "Example(value='owl:ObjectProperty', description=None)" . + skos:definition "The type of entity that is being mapped." . a owl:Ontology ; rdfs:label "sssom" ; @@ -37,14 +30,11 @@ sssom:predicate_type a owl:ObjectProperty, sssom:MappingRegistry, sssom:MappingSet, sssom:MappingSetReference ; - dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - rdfs:seeAlso "https://github.com/mapping-commons/sssom", - "https://mapping-commons.github.io/sssom/home/" ; - linkml:generation_date "2022-06-07T11:23:18" ; - linkml:metamodel_version "1.7.0" ; - linkml:source_file "sssom_schema.yaml" ; - linkml:source_file_date "2022-06-07T11:14:57" ; - linkml:source_file_size 21401 . + linkml:classes "{'mapping set': ClassDefinition(name='mapping set', id_prefixes=[], definition_uri='https://w3id.org/sssom/MappingSet', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Represents a set of mappings', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/sssom/schema/', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['mappings', 'mapping_set_id', 'mapping_set_version', 'mapping_set_source', 'mapping_set_title', 'mapping_set_description', 'creator_id', 'creator_label', 'mapping set_license', 'subject_type', 'subject_source', 'subject_source_version', 'object_type', 'object_source', 'object_source_version', 'mapping_provider', 'mapping_tool', 'mapping_tool_version', 'mapping_date', 'subject_match_field', 'object_match_field', 'subject_preprocessing', 'object_preprocessing', 'see_also', 'other', 'comment'], slot_usage={'license': SlotDefinition(name='license', id_prefixes=[], definition_uri=None, local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, singular_name=None, domain=None, slot_uri=None, multivalued=None, inherited=None, readonly=None, ifabsent=None, list_elements_unique=None, list_elements_ordered=None, shared=None, key=None, identifier=None, designates_type=None, alias=None, owner=None, domain_of=[], subproperty_of=None, symmetric=None, reflexive=None, locally_reflexive=None, irreflexive=None, asymmetric=None, transitive=None, inverse=None, is_class_field=None, transitive_form_of=None, reflexive_transitive_form_of=None, role=None, is_usage_slot=None, usage_slot_name=None, relational_role=None, slot_group=None, is_grouping_slot=None, path_rule=None, disjoint_with=[], children_are_mutually_disjoint=None, union_of=[], range=None, range_expression=None, enum_range=None, required=True, recommended=None, inlined=None, inlined_as_list=None, minimum_value=None, maximum_value=None, pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, value_presence=None, equals_string=None, equals_string_in=[], equals_number=None, equals_expression=None, minimum_cardinality=None, maximum_cardinality=None, has_member=None, all_members=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}, attributes={}, class_uri='sssom:MappingSet', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'mapping': ClassDefinition(name='mapping', id_prefixes=[], definition_uri='https://w3id.org/sssom/Mapping', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Represents an individual mapping between a pair of entities', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/sssom/schema/', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=['owl:Axiom'], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['subject_id', 'subject_label', 'subject_category', 'predicate_id', 'predicate_label', 'predicate_modifier', 'object_id', 'object_label', 'object_category', 'mapping_justification', 'author_id', 'author_label', 'reviewer_id', 'reviewer_label', 'creator_id', 'creator_label', 'license', 'subject_type', 'subject_source', 'subject_source_version', 'object_type', 'object_source', 'object_source_version', 'mapping_provider', 'mapping_source', 'mapping_cardinality', 'mapping_tool', 'mapping_tool_version', 'mapping_date', 'confidence', 'curation_rule', 'curation_rule_text', 'subject_match_field', 'object_match_field', 'match_string', 'subject_preprocessing', 'object_preprocessing', 'semantic_similarity_score', 'semantic_similarity_measure', 'see_also', 'other', 'comment'], slot_usage={}, attributes={}, class_uri='owl:Axiom', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'mapping registry': ClassDefinition(name='mapping registry', id_prefixes=[], definition_uri='https://w3id.org/sssom/MappingRegistry', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A registry for managing mapping sets. It holds a set of mapping set references, and can import other registries.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/sssom/schema/', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['mapping_registry_id', 'mapping_registry_title', 'mapping_registry_description', 'imports', 'mapping_set_references', 'documentation', 'homepage'], slot_usage={}, attributes={}, class_uri='sssom:MappingRegistry', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={}), 'mapping set reference': ClassDefinition(name='mapping set reference', id_prefixes=[], definition_uri='https://w3id.org/sssom/MappingSetReference', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A reference to a mapping set. It allows to augment mapping set metadata from the perspective of the registry, for example, providing confidence, or a local filename or a grouping.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/sssom/schema/', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, slots=['mapping_set_id', 'mirror_from', 'registry_confidence', 'mapping_set_group', 'last_updated', 'local_name'], slot_usage={}, attributes={}, class_uri='sssom:MappingSetReference', subclass_of=None, union_of=[], defining_slots=[], tree_root=None, unique_keys={}, rules=[], classification_rules=[], slot_names_unique=None, represents_relationship=None, disjoint_with=[], children_are_mutually_disjoint=None, any_of=[], exactly_one_of=[], none_of=[], all_of=[], slot_conditions={})}" ; + linkml:enums "{'entity_type_enum': EnumDefinition(name='entity_type_enum', id_prefixes=[], definition_uri='https://w3id.org/sssom/EntityTypeEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/sssom/schema/', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'owl class': PermissibleValue(text='owl class', description=None, meaning='owl:Class', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'owl object property': PermissibleValue(text='owl object property', description=None, meaning='owl:ObjectProperty', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'owl data property': PermissibleValue(text='owl data property', description=None, meaning='owl:DataProperty', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'owl annotation property': PermissibleValue(text='owl annotation property', description=None, meaning='owl:AnnotationProperty', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'owl named individual': PermissibleValue(text='owl named individual', description=None, meaning='owl:NamedIndividual', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'skos concept': PermissibleValue(text='skos concept', description=None, meaning='skos:Concept', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'rdfs resource': PermissibleValue(text='rdfs resource', description=None, meaning='rdfs:Resource', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'rdfs class': PermissibleValue(text='rdfs class', description=None, meaning='rdfs:Class', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'rdfs literal': PermissibleValue(text='rdfs literal', description=None, meaning='rdfs:Literal', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'rdfs datatype': PermissibleValue(text='rdfs datatype', description=None, meaning='rdfs:Datatype', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'rdf property': PermissibleValue(text='rdf property', description=None, meaning='rdf:Property', unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'predicate_modifier_enum': EnumDefinition(name='predicate_modifier_enum', id_prefixes=[], definition_uri='https://w3id.org/sssom/PredicateModifierEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/sssom/schema/', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'Not': PermissibleValue(text='Not', description='Negating the mapping predicate. The meaning of the triple becomes subject_id is not a predicate_id match to object_id.', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[]), 'mapping_cardinality_enum': EnumDefinition(name='mapping_cardinality_enum', id_prefixes=[], definition_uri='https://w3id.org/sssom/MappingCardinalityEnum', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description=None, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/sssom/schema/', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, is_a=None, abstract=None, mixin=None, mixins=[], apply_to=[], values_from=[], string_serialization=None, enum_uri=None, code_set=None, code_set_tag=None, code_set_version=None, pv_formula=None, permissible_values={'1:1': PermissibleValue(text='1:1', description='One-to-one mapping', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), '1:n': PermissibleValue(text='1:n', description='One-to-many mapping', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'n:1': PermissibleValue(text='n:1', description='Many-to-one mapping', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), '1:0': PermissibleValue(text='1:0', description='One-to-none mapping', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), '0:1': PermissibleValue(text='0:1', description='None-to-one mapping', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None), 'n:n': PermissibleValue(text='n:n', description='Many-to-many mapping', meaning=None, unit=None, is_a=None, mixins=[], extensions={}, annotations={}, alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema=None, imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None)}, include=[], minus=[], inherits=[], reachable_from=None, matches=None, concepts=[])}" ; + linkml:id "https://w3id.org/sssom/schema/" ; + linkml:imports "linkml:types" ; + linkml:types "{'EntityReference': TypeDefinition(name='EntityReference', id_prefixes=[], definition_uri='https://w3id.org/sssom/EntityReference', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A reference to a mapped entity. This is represented internally as a string, and as a resource in RDF', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/sssom/schema/', imported_from=None, source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof='uriorcurie', base='str', uri='rdfs:Resource', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'string': TypeDefinition(name='string', id_prefixes=[], definition_uri='https://w3id.org/linkml/String', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A character string', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Text'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'integer': TypeDefinition(name='integer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Integer', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='An integer', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Integer'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='int', uri='xsd:integer', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'boolean': TypeDefinition(name='boolean', id_prefixes=[], definition_uri='https://w3id.org/linkml/Boolean', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A binary (true or false) value', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Boolean'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Bool', uri='xsd:boolean', repr='bool', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'float': TypeDefinition(name='float', id_prefixes=[], definition_uri='https://w3id.org/linkml/Float', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:float specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Float'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:float', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'double': TypeDefinition(name='double', id_prefixes=[], definition_uri='https://w3id.org/linkml/Double', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number that conforms to the xsd:double specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:Float'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='float', uri='xsd:double', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'decimal': TypeDefinition(name='decimal', id_prefixes=[], definition_uri='https://w3id.org/linkml/Decimal', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A real number with arbitrary precision that conforms to the xsd:decimal specification', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=['schema:Number'], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Decimal', uri='xsd:decimal', repr=None, union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'time': TypeDefinition(name='time', id_prefixes=[], definition_uri='https://w3id.org/linkml/Time', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A time object represents a (local) time of day, independent of any particular day', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=['URI is dateTime because OWL reasoners do not work with straight date or time'], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Time'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDTime', uri='xsd:time', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date': TypeDefinition(name='date', id_prefixes=[], definition_uri='https://w3id.org/linkml/Date', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a date (year, month and day) in an idealized calendar', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[\"URI is dateTime because OWL reasoners don't work with straight date or time\"], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:Date'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDate', uri='xsd:date', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'datetime': TypeDefinition(name='datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/Datetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='The combination of a date and time', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=['schema:DateTime'], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='XSDDateTime', uri='xsd:dateTime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'date_or_datetime': TypeDefinition(name='date_or_datetime', id_prefixes=[], definition_uri='https://w3id.org/linkml/DateOrDatetime', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Either a date or a datetime', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='linkml:DateOrDatetime', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uriorcurie': TypeDefinition(name='uriorcurie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uriorcurie', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='a URI or a CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URIorCURIE', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'curie': TypeDefinition(name='curie', id_prefixes=[], definition_uri='https://w3id.org/linkml/Curie', local_names={}, conforms_to='https://www.w3.org/TR/curie/', implements=[], extensions={}, annotations={}, description='a compact URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations this MUST be expanded to a URI', 'in non-RDF serializations MAY be serialized as the compact representation'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='Curie', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'uri': TypeDefinition(name='uri', id_prefixes=[], definition_uri='https://w3id.org/linkml/Uri', local_names={}, conforms_to='https://www.ietf.org/rfc/rfc3987.txt', implements=[], extensions={}, annotations={}, description='a complete URI', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=['schema:URL'], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='URI', uri='xsd:anyURI', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'ncname': TypeDefinition(name='ncname', id_prefixes=[], definition_uri='https://w3id.org/linkml/Ncname', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='Prefix part of CURIE', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NCName', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'objectidentifier': TypeDefinition(name='objectidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Objectidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI or CURIE that represents an object in the model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=['Used for inheritance and type checking'], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='ElementIdentifier', uri='shex:iri', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'nodeidentifier': TypeDefinition(name='nodeidentifier', id_prefixes=[], definition_uri='https://w3id.org/linkml/Nodeidentifier', local_names={}, conforms_to=None, implements=[], extensions={}, annotations={}, description='A URI, CURIE or BNODE that represents a node in a model.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='NodeIdentifier', uri='shex:nonLiteral', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpointer': TypeDefinition(name='jsonpointer', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpointer', local_names={}, conforms_to='https://datatracker.ietf.org/doc/html/rfc6901', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'jsonpath': TypeDefinition(name='jsonpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Jsonpath', local_names={}, conforms_to='https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html', implements=[], extensions={}, annotations={}, description='A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[]), 'sparqlpath': TypeDefinition(name='sparqlpath', id_prefixes=[], definition_uri='https://w3id.org/linkml/Sparqlpath', local_names={}, conforms_to='https://www.w3.org/TR/sparql11-query/#propertypaths', implements=[], extensions={}, annotations={}, description='A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.', alt_descriptions={}, title=None, deprecated=None, todos=[], notes=[], comments=[], examples=[], in_subset=[], from_schema='https://w3id.org/linkml/types', imported_from='linkml:types', source=None, in_language=None, see_also=[], deprecated_element_has_exact_replacement=None, deprecated_element_has_possible_replacement=None, aliases=[], structured_aliases={}, mappings=[], exact_mappings=[], close_mappings=[], related_mappings=[], narrow_mappings=[], broad_mappings=[], created_by=None, created_on=None, last_updated_on=None, modified_by=None, status=None, rank=None, typeof=None, base='str', uri='xsd:string', repr='str', union_of=[], pattern=None, structured_pattern=None, unit=None, implicit_prefix=None, equals_string=None, equals_string_in=[], equals_number=None, minimum_value=None, maximum_value=None, none_of=[], exactly_one_of=[], any_of=[], all_of=[])}" . dcterms:created a owl:ObjectProperty, linkml:SlotDefinition ; @@ -54,122 +44,143 @@ dcterms:created a owl:ObjectProperty, skos:exactMatch dcterms:created . linkml:TypeDefinition a owl:Class ; - rdfs:label "type_definition" . + rdfs:label "type_definition" ; + linkml:attributes "{}" ; + linkml:is_a "element" ; + linkml:mixins "type_expression" . sssom:MappingRegistry a owl:Class, linkml:ClassDefinition ; rdfs:label "mapping registry" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass sssom:EntityReference ; - owl:onProperty sssom:mapping_registry_id ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom linkml:Uri ; + owl:onProperty sssom:imports ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Uri ; - owl:onProperty sssom:documentation ], + owl:onClass linkml:String ; + owl:onProperty sssom:mapping_registry_description ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uri ; - owl:onProperty sssom:imports ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty sssom:mapping_registry_title ], [ a owl:Restriction ; owl:allValuesFrom sssom:MappingSetReference ; owl:onProperty sssom:mapping_set_references ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Uri ; + owl:onProperty sssom:documentation ], + [ a owl:Restriction ; + owl:onClass sssom:EntityReference ; + owl:onProperty sssom:mapping_registry_id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Uri ; owl:onProperty sssom:homepage ] ; - skos:definition "A registry for managing mapping sets. It holds a set of mapping set references, and can import other registries." . + skos:definition "A registry for managing mapping sets. It holds a set of mapping set references, and can import other registries." ; + linkml:attributes "{}" . sssom:MappingSet a owl:Class, linkml:ClassDefinition ; rdfs:label "mapping set" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:Uri ; - owl:onProperty dcterms:license ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass sssom:EntityReference ; - owl:onProperty sssom:object_source ], + owl:onClass linkml:String ; + owl:onProperty sssom:mapping_tool ], [ a owl:Restriction ; - owl:onClass linkml:Uri ; - owl:onProperty sssom:mapping_set_id ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom sssom:EntityReference ; + owl:onProperty sssom:subject_preprocessing ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uri ; - owl:onProperty prov:wasDerivedFrom ], + owl:allValuesFrom linkml:String ; + owl:onProperty sssom:creator_label ], [ a owl:Restriction ; - owl:allValuesFrom sssom:EntityReference ; - owl:onProperty sssom:object_match_field ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty dcterms:title ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass sssom:EntityTypeEnum ; - owl:onProperty sssom:object_type ], + owl:onClass linkml:String ; + owl:onProperty sssom:object_source_version ], [ a owl:Restriction ; owl:allValuesFrom sssom:EntityReference ; owl:onProperty sssom:subject_match_field ], [ a owl:Restriction ; - owl:allValuesFrom sssom:EntityReference ; - owl:onProperty dcterms:creator ], + owl:allValuesFrom sssom:Mapping ; + owl:onProperty sssom:mappings ], + [ a owl:Restriction ; + owl:onClass linkml:Uri ; + owl:onProperty sssom:mapping_set_id ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass sssom:EntityReference ; - owl:onProperty sssom:subject_source ], + owl:onClass linkml:String ; + owl:onProperty owl:versionInfo ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty dcterms:description ], + owl:onProperty sssom:subject_source_version ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Date ; - owl:onProperty pav:authoredOn ], + owl:onClass sssom:EntityTypeEnum ; + owl:onProperty sssom:object_type ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass sssom:EntityReference ; + owl:onProperty sssom:subject_source ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty sssom:subject_source_version ], + owl:onProperty sssom:other ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty rdfs:seeAlso ], + [ a owl:Restriction ; + owl:onClass linkml:Uri ; + owl:onProperty dcterms:license ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom sssom:EntityReference ; - owl:onProperty sssom:subject_preprocessing ], + owl:onProperty dcterms:creator ], + [ a owl:Restriction ; + owl:allValuesFrom sssom:EntityReference ; + owl:onProperty sssom:object_match_field ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty rdfs:comment ], + owl:onClass sssom:EntityReference ; + owl:onProperty sssom:object_source ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty sssom:object_source_version ], + owl:onClass linkml:Date ; + owl:onProperty pav:authoredOn ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty sssom:other ], + owl:onClass linkml:Uri ; + owl:onProperty sssom:mapping_provider ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass sssom:EntityTypeEnum ; - owl:onProperty sssom:subject_type ], + owl:onClass linkml:String ; + owl:onProperty rdfs:comment ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty sssom:creator_label ], + owl:allValuesFrom linkml:Uri ; + owl:onProperty prov:wasDerivedFrom ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty owl:versionInfo ], + owl:onProperty sssom:mapping_tool_version ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Uri ; - owl:onProperty sssom:mapping_provider ], + owl:allValuesFrom sssom:EntityReference ; + owl:onProperty sssom:object_preprocessing ], [ a owl:Restriction ; - owl:allValuesFrom sssom:Mapping ; - owl:onProperty sssom:mappings ], + owl:maxQualifiedCardinality 1 ; + owl:onClass sssom:EntityTypeEnum ; + owl:onProperty sssom:subject_type ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty sssom:mapping_tool ], - [ a owl:Restriction ; - owl:allValuesFrom sssom:EntityReference ; - owl:onProperty sssom:object_preprocessing ] ; - skos:definition "Represents a set of mappings" . + owl:onProperty dcterms:description ] ; + skos:definition "Represents a set of mappings" ; + linkml:attributes "{}" . sssom:author_label a owl:ObjectProperty, linkml:SlotDefinition ; @@ -183,6 +194,18 @@ sssom:confidence a owl:ObjectProperty, rdfs:range linkml:Double ; skos:definition "A score between 0 and 1 to denote the confidence or probability that the match is correct, where 1 denotes total confidence." . +sssom:curation_rule a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "curation_rule" ; + rdfs:range sssom:EntityReference ; + skos:definition "A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation rule is captured as a resource rather than a string, which enables higher levels of transparency and sharing across mapping sets. The URI representation of the curation rule is expected to be a resolvable identifier which provides details about the nature of the curation rule." . + +sssom:curation_rule_text a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "curation_rule_text" ; + rdfs:range linkml:String ; + skos:definition "A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation rule should be captured as a resource (entity reference) rather than a string (see curation_rule element), which enables higher levels of transparency and sharing across mapping sets. The textual representation of curation rule is intended to be used in cases where (1) the creation of a resource is not practical from the perspective of the mapping_provider and (2) as an additional piece of metadata to augment the curation_rule element with a human readable text." . + sssom:documentation a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "documentation" ; @@ -223,9 +246,13 @@ sssom:mapping_justification a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "mapping_justification" ; rdfs:range sssom:EntityReference ; - skos:definition "A mapping justification is an action (or the written representation of that action) of showing a mapping to be right or reasonable." ; - linkml:examples "Example(value='semapv:LexicalMatching', description=None)", - "Example(value='semapv:ManualMappingCuration', description=None)" . + skos:definition "A mapping justification is an action (or the written representation of that action) of showing a mapping to be right or reasonable." . + +sssom:mapping_registry_description a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "mapping_registry_description" ; + rdfs:range linkml:String ; + skos:definition "The description of a mapping registry." . sssom:mapping_registry_id a owl:ObjectProperty, linkml:SlotDefinition ; @@ -233,6 +260,12 @@ sssom:mapping_registry_id a owl:ObjectProperty, rdfs:range sssom:EntityReference ; skos:definition "The unique identifier of a mapping registry." . +sssom:mapping_registry_title a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "mapping_registry_title" ; + rdfs:range linkml:String ; + skos:definition "The title of a mapping registry." . + sssom:mapping_set_group a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "mapping_set_group" ; @@ -245,12 +278,11 @@ sssom:mapping_set_references a owl:ObjectProperty, rdfs:range sssom:MappingSetReference ; skos:definition "A list of mapping set references." . -sssom:mapping_tool_version a owl:ObjectProperty, +sssom:mapping_source a owl:ObjectProperty, linkml:SlotDefinition ; - rdfs:label "mapping_tool_version" ; - rdfs:range linkml:String ; - skos:definition "Version string that denotes the version of the mapping tool used." ; - linkml:examples "Example(value='v3.2', description=None)" . + rdfs:label "mapping_source" ; + rdfs:range sssom:EntityReference ; + skos:definition "The mapping set this mapping was originally defined in. mapping_source is used for example when merging multiple mapping sets or deriving one mapping set from another." . sssom:mappings a owl:ObjectProperty, linkml:SlotDefinition ; @@ -274,41 +306,25 @@ sssom:object_category a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "object_category" ; rdfs:range linkml:String ; - skos:definition "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary." ; - linkml:examples "Example(value='UBERON:0001062', description='(The CURIE of the Uberon term for \"anatomical entity\".)')", - "Example(value='biolink:Gene', description='(The CURIE of the biolink class for genes.)')" . + skos:definition "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases." . sssom:object_label a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "object_label" ; rdfs:range linkml:String ; - skos:definition "The label of object of the mapping" ; - linkml:examples "Example(value='Thickened ears', description=None)" . + skos:definition "The label of object of the mapping" . sssom:predicate_label a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "predicate_label" ; rdfs:range linkml:String ; - skos:definition "The label of the predicate/relation of the mapping" ; - linkml:examples "Example(value='oboInOwl:database_cross_reference', description='Two terms are related in some way. The meaning is frequently consistent across a single set of mappings. Note this property is often overloaded even where the terms are of a different nature (e.g. interpro2go)')", - "Example(value='owl:equivalentClass', description='The subject and the object are classes (owl class), and the two classes are the same.')", - "Example(value='owl:equivalentProperty', description='The subject and the object are properties (owl object, data, annotation properties), and the two properties are the same.')", - "Example(value='owl:sameAs', description='The subject and the object are instances (owl individuals), and the two instances are the same.')", - "Example(value='rdfs:seeAlso', description='The subject and the object are associated in some unspecified way. The object IRI often resolves to a resource on the web that provides additional information.')", - "Example(value='rdfs:subClassOf', description='The subject and the object are classes (owl class), and the subject is a subclass of the object.')", - "Example(value='rdfs:subPropertyOf', description='The subject and the object are properties (owl object, data, annotation properties), and the subject is a subproperty of the object.')", - "Example(value='skos:broadMatch', description='From the SKOS primer: A triple skos:broader (and skos:broadMatch) asserts that , the object of the triple, is a broader concept than , the subject of the triple.')", - "Example(value='skos:closeMatch', description='The subject and the object are sufficiently similar that they can be used interchangeably in some information retrieval applications.')", - "Example(value='skos:exactMatch', description='The subject and the object can, with a high degree of confidence, be used interchangeably across a wide range of information retrieval applications.')", - "Example(value='skos:narrowMatch', description='From the SKOS primer: A triple skos:narrower (and skos:narrowMatch) asserts that , the object of the triple, is a narrower concept than , the subject of the triple.')", - "Example(value='skos:relatedMatch', description='The subject and the object are associated in some unspecified way.')" . + skos:definition "The label of the predicate/relation of the mapping" . sssom:predicate_modifier a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "predicate_modifier" ; rdfs:range sssom:PredicateModifierEnum ; - skos:definition "A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40 for discussion" ; - linkml:examples "Example(value='Not', description='Negates the predicate, see documentation of predicate_modifier_enum')" . + skos:definition "A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40 for discussion" . sssom:registry_confidence a owl:ObjectProperty, linkml:SlotDefinition ; @@ -326,14 +342,13 @@ sssom:reviewer_label a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "reviewer_label" ; rdfs:range linkml:String ; - skos:definition "A string identifying the reviewer of this mapping. In the spirit of provenance, consider to use author_id instead." . + skos:definition "A string identifying the reviewer of this mapping. In the spirit of provenance, consider to use reviewer_id instead." . sssom:semantic_similarity_measure a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "semantic_similarity_measure" ; rdfs:range linkml:String ; - skos:definition "The measure used for computing the the semantic similarity score. To make processing this field as unambiguous as possible, we recommend using wikidata identifiers, but wikipedia pages could also be acceptable." ; - linkml:examples "Example(value='https://www.wikidata.org/wiki/Q865360', description='(the Wikidata identifier for the Jaccard index measure).')" . + skos:definition "The measure used for computing the the semantic similarity score. To make processing this field as unambiguous as possible, we recommend using wikidata identifiers, but wikipedia pages could also be acceptable." . sssom:semantic_similarity_score a owl:ObjectProperty, linkml:SlotDefinition ; @@ -345,24 +360,27 @@ sssom:subject_category a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "subject_category" ; rdfs:range linkml:String ; - skos:definition "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary." ; - linkml:examples "Example(value='UBERON:0001062', description='(The CURIE of the Uberon term for \"anatomical entity\".)')", - "Example(value='biolink:Gene', description='(The CURIE of the biolink class for genes.)')" . + skos:definition "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases." . sssom:subject_label a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "subject_label" ; rdfs:range linkml:String ; - skos:definition "The label of subject of the mapping" ; - linkml:examples "Example(value='Thickened ears', description=None)" . + skos:definition "The label of subject of the mapping" . dcterms:description a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "mapping_set_description" ; rdfs:range linkml:String ; skos:definition "A description of the mapping set." ; - skos:exactMatch dcterms:description ; - linkml:examples "Example(value='This mapping set was produced to integrate human and mouse phenotype data at the IMPC. It is primarily used for making mouse phenotypes searchable by human synonyms at https://mousephenotype.org/.', description=None)" . + skos:exactMatch dcterms:description . + +dcterms:title a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "mapping_set_title" ; + rdfs:range linkml:String ; + skos:definition "The display name of a mapping set." ; + skos:exactMatch dcterms:title . pav:authoredBy a owl:ObjectProperty, linkml:SlotDefinition ; @@ -408,33 +426,28 @@ owl:annotatedProperty a owl:ObjectProperty, rdfs:label "predicate_id" ; rdfs:range sssom:EntityReference ; skos:definition "The ID of the predicate or relation that relates the subject and object of this match." ; - skos:exactMatch owl:annotatedProperty ; - linkml:examples "Example(value='skos:exactMatch', description=None)" . + skos:exactMatch owl:annotatedProperty . owl:annotatedSource a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "subject_id" ; rdfs:range sssom:EntityReference ; skos:definition "The ID of the subject of the mapping." ; - skos:exactMatch owl:annotatedSource ; - linkml:examples "Example(value='HP:0009894', description=\"The CURIE denoting the Human Phenotype Ontology concept of 'Thickened ears'\")" . + skos:exactMatch owl:annotatedSource . owl:annotatedTarget a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "object_id" ; rdfs:range sssom:EntityReference ; skos:definition "The ID of the object of the mapping." ; - skos:exactMatch owl:annotatedTarget ; - linkml:examples "Example(value='HP:0009894', description=\"The CURIE denoting the Human Phenotype Ontology concept of 'Thickened ears'\")" . + skos:exactMatch owl:annotatedTarget . owl:versionInfo a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "mapping_set_version" ; rdfs:range linkml:String ; skos:definition "A version string for the mapping." ; - skos:exactMatch owl:versionInfo ; - linkml:examples "Example(value='1.2.1', description='(A semantic version tag that indicates that this is the 1st major, 2nd minor version, patch 1 (https://semver.org/).)')", - "Example(value='2020-01-01', description='(A date-based version that indicates that the mapping was published on the 1st January in 2021.)')" . + skos:exactMatch owl:versionInfo . skos:Concept a owl:Class, sssom:EntityTypeEnum ; @@ -445,8 +458,7 @@ prov:wasDerivedFrom a owl:ObjectProperty, rdfs:label "mapping_set_source" ; rdfs:range linkml:Uri ; skos:definition "A mapping set or set of mapping set that was used to derive the mapping set." ; - skos:exactMatch prov:wasDerivedFrom ; - linkml:examples "Example(value='http://purl.obolibrary.org/obo/mondo/mappings/2022-05-20/mondo_exactmatch_ncit.sssom.tsv', description='A persistent, ideally versioned, link to the mapping set from which the current mapping set is derived.')" . + skos:exactMatch prov:wasDerivedFrom . a owl:Class, sssom:MappingCardinalityEnum ; @@ -492,15 +504,19 @@ sssom:mapping_set_id a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "mapping_set_id" ; rdfs:range linkml:Uri ; - skos:definition "A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable." ; - linkml:examples "Example(value='http://purl.obolibrary.org/obo/mondo/mappings/mondo_exactmatch_ncit.sssom.tsv', description='(A persistent URI pointing to the latest version of the Mondo - NCIT mapping in the Mondo namespace.)')" . + skos:definition "A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable." . sssom:mapping_tool a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "mapping_tool" ; rdfs:range linkml:String ; - skos:definition "A reference to the tool or algorithm that was used to generate the mapping. Should be a URL pointing to more info about it, but can be free text." ; - linkml:examples "Example(value='https://github.com/AgreementMakerLight/AML-Project', description=None)" . + skos:definition "A reference to the tool or algorithm that was used to generate the mapping. Should be a URL pointing to more info about it, but can be free text." . + +sssom:mapping_tool_version a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "mapping_tool_version" ; + rdfs:range linkml:String ; + skos:definition "Version string that denotes the version of the mapping tool used." . sssom:object_match_field a owl:ObjectProperty, linkml:SlotDefinition ; @@ -512,31 +528,25 @@ sssom:object_preprocessing a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "object_preprocessing" ; rdfs:range sssom:EntityReference ; - skos:definition "Method of preprocessing applied to the fields of the object. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows." ; - linkml:examples "Example(value='semapv:Stemming', description=None)", - "Example(value='semapv:StopWordRemoval', description=None)" . + skos:definition "Method of preprocessing applied to the fields of the object. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows." . sssom:object_source a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "object_source" ; rdfs:range sssom:EntityReference ; - skos:definition "IRI of ontology source for the object. Version IRI preferred." ; - linkml:examples "Example(value='obo:mondo.owl', description='A persistent OBO CURIE pointing to the latest version of the Mondo ontology.')", - "Example(value='wikidata:Q7876491', description='A Wikidata identifier for the Uberon ontology resource.')" . + skos:definition "IRI of ontology source for the object. Version IRI preferred." . sssom:object_source_version a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "object_source_version" ; rdfs:range linkml:String ; - skos:definition "Version IRI or version string of the source of the object term." ; - linkml:examples "Example(value='http://purl.obolibrary.org/obo/mondo/releases/2021-01-30/mondo.owl', description=\"(A persistent Version IRI pointing to the Mondo version '2021-01-30')\")" . + skos:definition "Version IRI or version string of the source of the object term." . sssom:object_type a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "object_type" ; rdfs:range sssom:EntityTypeEnum ; - skos:definition "The type of entity that is being mapped." ; - linkml:examples "Example(value='owl:Class', description=None)" . + skos:definition "The type of entity that is being mapped." . sssom:other a owl:ObjectProperty, linkml:SlotDefinition ; @@ -554,31 +564,25 @@ sssom:subject_preprocessing a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "subject_preprocessing" ; rdfs:range sssom:EntityReference ; - skos:definition "Method of preprocessing applied to the fields of the subject. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows." ; - linkml:examples "Example(value='semapv:Stemming', description=None)", - "Example(value='semapv:StopWordRemoval', description=None)" . + skos:definition "Method of preprocessing applied to the fields of the subject. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows." . sssom:subject_source a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "subject_source" ; rdfs:range sssom:EntityReference ; - skos:definition "URI of ontology source for the subject." ; - linkml:examples "Example(value='obo:mondo.owl', description='A persistent OBO CURIE pointing to the latest version of the Mondo ontology.')", - "Example(value='wikidata:Q7876491', description='A Wikidata identifier for the Uberon ontology resource.')" . + skos:definition "URI of ontology source for the subject." . sssom:subject_source_version a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "subject_source_version" ; rdfs:range linkml:String ; - skos:definition "Version IRI or version string of the source of the subject term." ; - linkml:examples "Example(value='http://purl.obolibrary.org/obo/mondo/releases/2021-01-30/mondo.owl', description=\"(A persistent Version IRI pointing to the Mondo version '2021-01-30')\")" . + skos:definition "Version IRI or version string of the source of the subject term." . sssom:subject_type a owl:ObjectProperty, linkml:SlotDefinition ; rdfs:label "subject_type" ; rdfs:range sssom:EntityTypeEnum ; - skos:definition "The type of entity that is being mapped." ; - linkml:examples "Example(value='owl:Class', description=None)" . + skos:definition "The type of entity that is being mapped." . dcterms:creator a owl:ObjectProperty, linkml:SlotDefinition ; @@ -619,160 +623,167 @@ sssom:Mapping a owl:Class, linkml:ClassDefinition ; rdfs:label "mapping" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom sssom:EntityReference ; - owl:onProperty sssom:subject_match_field ], + owl:maxQualifiedCardinality 1 ; + owl:onClass sssom:EntityReference ; + owl:onProperty sssom:mapping_source ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass sssom:EntityReference ; owl:onProperty sssom:object_source ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass sssom:MappingCardinalityEnum ; - owl:onProperty sssom:mapping_cardinality ], + owl:allValuesFrom linkml:String ; + owl:onProperty sssom:reviewer_label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty sssom:semantic_similarity_measure ], + owl:onClass linkml:Double ; + owl:onProperty sssom:confidence ], + [ a owl:Restriction ; + owl:allValuesFrom sssom:EntityReference ; + owl:onProperty sssom:subject_preprocessing ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Uri ; - owl:onProperty dcterms:license ], + owl:onClass linkml:String ; + owl:onProperty sssom:subject_category ], [ a owl:Restriction ; owl:allValuesFrom sssom:EntityReference ; - owl:onProperty sssom:object_match_field ], + owl:onProperty sssom:subject_match_field ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty sssom:match_string ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty sssom:mapping_tool_version ], + [ a owl:Restriction ; + owl:allValuesFrom sssom:EntityReference ; + owl:onProperty sssom:reviewer_id ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty sssom:author_label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty sssom:other ], + owl:onProperty sssom:subject_label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty sssom:mapping_tool ], - [ a owl:Restriction ; - owl:allValuesFrom sssom:EntityReference ; - owl:onProperty sssom:reviewer_id ], + owl:onProperty sssom:object_source_version ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty sssom:predicate_label ], [ a owl:Restriction ; owl:onClass sssom:EntityReference ; - owl:onProperty owl:annotatedTarget ; + owl:onProperty owl:annotatedSource ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:allValuesFrom sssom:EntityReference ; - owl:onProperty sssom:object_preprocessing ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty sssom:subject_category ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty sssom:object_label ], - [ a owl:Restriction ; - owl:allValuesFrom sssom:EntityReference ; - owl:onProperty sssom:subject_preprocessing ], + owl:onClass sssom:EntityTypeEnum ; + owl:onProperty sssom:subject_type ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty sssom:author_label ], + owl:onClass sssom:EntityReference ; + owl:onProperty owl:annotatedProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty rdfs:seeAlso ], + owl:onClass sssom:EntityReference ; + owl:onProperty owl:annotatedTarget ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty sssom:confidence ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty sssom:match_string ], + owl:onClass sssom:PredicateModifierEnum ; + owl:onProperty sssom:predicate_modifier ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty sssom:object_category ], - [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty sssom:creator_label ], + owl:onProperty sssom:object_label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty sssom:subject_label ], + owl:onProperty sssom:semantic_similarity_measure ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass sssom:EntityReference ; - owl:onProperty sssom:subject_source ], + owl:onClass sssom:EntityTypeEnum ; + owl:onProperty sssom:object_type ], [ a owl:Restriction ; owl:onClass sssom:EntityReference ; - owl:onProperty owl:annotatedProperty ; + owl:onProperty sssom:mapping_justification ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom sssom:EntityReference ; + owl:onProperty sssom:curation_rule ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass sssom:EntityTypeEnum ; - owl:onProperty sssom:object_type ], + owl:onClass linkml:Double ; + owl:onProperty sssom:semantic_similarity_score ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Date ; - owl:onProperty pav:authoredOn ], + owl:onClass linkml:String ; + owl:onProperty rdfs:comment ], [ a owl:Restriction ; owl:allValuesFrom sssom:EntityReference ; - owl:onProperty dcterms:creator ], + owl:onProperty sssom:object_match_field ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty rdfs:comment ], + owl:onProperty sssom:object_category ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty sssom:reviewer_label ], + owl:onProperty rdfs:seeAlso ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Uri ; + owl:onProperty dcterms:license ], [ a owl:Restriction ; owl:allValuesFrom sssom:EntityReference ; - owl:onProperty pav:authoredBy ], + owl:onProperty sssom:object_preprocessing ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass sssom:EntityTypeEnum ; - owl:onProperty sssom:subject_type ], + owl:onClass linkml:String ; + owl:onProperty sssom:mapping_tool ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Uri ; - owl:onProperty sssom:mapping_provider ], + owl:onClass linkml:String ; + owl:onProperty sssom:subject_source_version ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty sssom:object_source_version ], + owl:onProperty sssom:other ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty sssom:semantic_similarity_score ], + owl:allValuesFrom sssom:EntityReference ; + owl:onProperty dcterms:creator ], [ a owl:Restriction ; - owl:onClass sssom:EntityReference ; - owl:onProperty owl:annotatedSource ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Date ; + owl:onProperty pav:authoredOn ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty sssom:subject_source_version ], + owl:onClass sssom:MappingCardinalityEnum ; + owl:onProperty sssom:mapping_cardinality ], [ a owl:Restriction ; + owl:allValuesFrom sssom:EntityReference ; + owl:onProperty pav:authoredBy ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass sssom:EntityReference ; - owl:onProperty sssom:mapping_justification ; - owl:qualifiedCardinality 1 ], + owl:onProperty sssom:subject_source ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty sssom:curation_rule_text ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty sssom:creator_label ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass sssom:PredicateModifierEnum ; - owl:onProperty sssom:predicate_modifier ] ; + owl:onClass linkml:Uri ; + owl:onProperty sssom:mapping_provider ] ; skos:definition "Represents an individual mapping between a pair of entities" ; - skos:exactMatch owl:Axiom . + skos:exactMatch owl:Axiom ; + linkml:attributes "{}" . sssom:MappingSetReference a owl:Class, linkml:ClassDefinition ; rdfs:label "mapping set reference" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty sssom:mapping_set_group ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Date ; owl:onProperty sssom:last_updated ], @@ -780,10 +791,6 @@ sssom:MappingSetReference a owl:Class, owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty sssom:local_name ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty sssom:registry_confidence ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Uri ; @@ -791,8 +798,17 @@ sssom:MappingSetReference a owl:Class, [ a owl:Restriction ; owl:onClass linkml:Uri ; owl:onProperty sssom:mapping_set_id ; - owl:qualifiedCardinality 1 ] ; - skos:definition "A reference to a mapping set. It allows to augment mapping set metadata from the perspective of the registry, for example, providing confidence, or a local filename or a grouping." . + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty sssom:mapping_set_group ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty sssom:registry_confidence ] ; + skos:definition "A reference to a mapping set. It allows to augment mapping set metadata from the perspective of the registry, for example, providing confidence, or a local filename or a grouping." ; + linkml:attributes "{}" . sssom:PredicateModifierEnum a owl:Class, linkml:EnumDefinition ; @@ -801,7 +817,10 @@ sssom:PredicateModifierEnum a owl:Class, linkml:permissible_values . linkml:ClassDefinition a owl:Class ; - rdfs:label "class_definition" . + rdfs:label "class_definition" ; + linkml:attributes "{}" ; + linkml:is_a "definition" ; + linkml:mixins "class_expression" . sssom:MappingCardinalityEnum a owl:Class, linkml:EnumDefinition ; @@ -840,7 +859,10 @@ sssom:EntityReference a owl:Class, rdfs:subClassOf linkml:Uriorcurie . linkml:SlotDefinition a owl:Class ; - rdfs:label "slot_definition" . + rdfs:label "slot_definition" ; + linkml:attributes "{}" ; + linkml:is_a "definition" ; + linkml:mixins "slot_expression" . owl:ObjectProperty a owl:Class, sssom:EntityTypeEnum ; diff --git a/project/prefixmap/sssom_schema.yaml b/project/prefixmap/sssom_schema.yaml index a2d4f83d..f886e67d 100644 --- a/project/prefixmap/sssom_schema.yaml +++ b/project/prefixmap/sssom_schema.yaml @@ -1,5 +1,4 @@ { - "dc": "http://purl.org/dc/terms/", "dcterms": "http://purl.org/dc/terms/", "linkml": "https://w3id.org/linkml/", "oboInOwl": "http://www.geneontology.org/formats/oboInOwl#", @@ -8,7 +7,7 @@ "prov": "http://www.w3.org/ns/prov#", "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", - "semapv": "https://w3id.org/semapv/", + "semapv": "https://w3id.org/semapv/vocab/", "skos": "http://www.w3.org/2004/02/skos/core#", "sssom": "https://w3id.org/sssom/", "Mapping": { diff --git a/project/protobuf/sssom_schema.proto b/project/protobuf/sssom_schema.proto index 969b125f..18d5cf46 100644 --- a/project/protobuf/sssom_schema.proto +++ b/project/protobuf/sssom_schema.proto @@ -25,11 +25,14 @@ message Mapping entityReference objectSource = 0 string objectSourceVersion = 0 uri mappingProvider = 0 + entityReference mappingSource = 0 mappingCardinalityEnum mappingCardinality = 0 string mappingTool = 0 string mappingToolVersion = 0 date mappingDate = 0 double confidence = 0 + repeated entityReference curationRule = 0 + repeated string curationRuleText = 0 repeated entityReference subjectMatchField = 0 repeated entityReference objectMatchField = 0 repeated string matchString = 0 @@ -45,6 +48,8 @@ message Mapping message MappingRegistry { entityReference mappingRegistryId = 0 + string mappingRegistryTitle = 0 + string mappingRegistryDescription = 0 repeated uri imports = 0 repeated mappingSetReference mappingSetReferences = 0 uri documentation = 0 @@ -57,6 +62,7 @@ message MappingSet uri mappingSetId = 0 string mappingSetVersion = 0 repeated uri mappingSetSource = 0 + string mappingSetTitle = 0 string mappingSetDescription = 0 repeated entityReference creatorId = 0 repeated string creatorLabel = 0 @@ -69,6 +75,7 @@ message MappingSet string objectSourceVersion = 0 uri mappingProvider = 0 string mappingTool = 0 + string mappingToolVersion = 0 date mappingDate = 0 repeated entityReference subjectMatchField = 0 repeated entityReference objectMatchField = 0 diff --git a/project/shacl/sssom_schema.shacl.ttl b/project/shacl/sssom_schema.shacl.ttl index af071b58..3a9bfcce 100644 --- a/project/shacl/sssom_schema.shacl.ttl +++ b/project/shacl/sssom_schema.shacl.ttl @@ -13,292 +13,322 @@ sssom:MappingRegistry a sh:NodeShape ; sh:closed true ; sh:description "A registry for managing mapping sets. It holds a set of mapping set references, and can import other registries." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "The unique identifier of a mapping registry." ; + sh:property [ sh:class sssom:MappingSetReference ; + sh:description "A list of mapping set references." ; + sh:nodeKind sh:BlankNode ; + sh:order 4 ; + sh:path sssom:mapping_set_references ], + [ sh:description "The description of a mapping registry." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path sssom:mapping_registry_id ], + sh:order 2 ; + sh:path sssom:mapping_registry_description ], + [ sh:description "The title of a mapping registry." ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path sssom:mapping_registry_title ], [ sh:description "A URL to the documentation of this mapping commons." ; sh:maxCount 1 ; - sh:order 3 ; + sh:order 5 ; sh:path sssom:documentation ], [ sh:description "A URL to a homepage of this mapping commons." ; sh:maxCount 1 ; - sh:order 4 ; + sh:order 6 ; sh:path sssom:homepage ], [ sh:description "A list of registries that should be imported into this one." ; - sh:order 1 ; + sh:order 3 ; sh:path sssom:imports ], - [ sh:class sssom:MappingSetReference ; - sh:description "A list of mapping set references." ; - sh:nodeKind sh:BlankNode ; - sh:order 2 ; - sh:path sssom:mapping_set_references ] ; + [ sh:description "The unique identifier of a mapping registry." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path sssom:mapping_registry_id ] ; sh:targetClass sssom:MappingRegistry . sssom:MappingSet a sh:NodeShape ; sh:closed true ; sh:description "Represents a set of mappings" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A description of the mapping set." ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path dcterms:description ], - [ sh:description "Method of preprocessing applied to the fields of the subject. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows." ; - sh:order 19 ; - sh:path sssom:subject_preprocessing ], - [ sh:description "The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file." ; - sh:maxCount 1 ; - sh:order 16 ; - sh:path pav:authoredOn ], - [ sh:description "URL pointing to the source that provided the mapping, for example an ontology that already contains the mappings, or a database from which it was derived." ; + sh:property [ sh:description "Version IRI or version string of the source of the object term." ; sh:maxCount 1 ; sh:order 14 ; - sh:path sssom:mapping_provider ], - [ sh:description "The type of entity that is being mapped." ; - sh:in ( owl:Class owl:ObjectProperty owl:DataProperty owl:AnnotationProperty owl:NamedIndividual skos:Concept rdfs:Resource rdfs:Class rdfs:Literal rdfs:Datatype rdf:Property ) ; + sh:path sssom:object_source_version ], + [ sh:description "A url to the license of the mapping. In absence of a license we assume no license." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path sssom:object_type ], - [ sh:description "Identifies the persons or groups responsible for the creation of the mapping. The creator is the agent that put the mapping in its published form, which may be different from the author, which is a person that was actively involved in the assertion of the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible." ; - sh:order 5 ; - sh:path dcterms:creator ], - [ sh:description "A URL specific for the mapping instance. E.g. for kboom we have a per-mapping image that shows surrounding axioms that drive probability. Could also be a github issue URL that discussed a complicated alignment" ; - sh:order 21 ; - sh:path rdfs:seeAlso ], + sh:minCount 1 ; + sh:order 8 ; + sh:path dcterms:license ], [ sh:description "A tuple of fields (term annotations on the subject) that was used for the match." ; - sh:order 17 ; + sh:order 19 ; sh:path sssom:subject_match_field ], - [ sh:description "Version IRI or version string of the source of the subject term." ; + [ sh:description "A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead." ; + sh:order 7 ; + sh:path sssom:creator_label ], + [ sh:description "A URL specific for the mapping instance. E.g. for kboom we have a per-mapping image that shows surrounding axioms that drive probability. Could also be a github issue URL that discussed a complicated alignment" ; + sh:order 23 ; + sh:path rdfs:seeAlso ], + [ sh:description "Identifies the persons or groups responsible for the creation of the mapping. The creator is the agent that put the mapping in its published form, which may be different from the author, which is a person that was actively involved in the assertion of the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible." ; + sh:order 6 ; + sh:path dcterms:creator ], + [ sh:description "URI of ontology source for the subject." ; sh:maxCount 1 ; sh:order 10 ; + sh:path sssom:subject_source ], + [ sh:description "A mapping set or set of mapping set that was used to derive the mapping set." ; + sh:order 3 ; + sh:path prov:wasDerivedFrom ], + [ sh:description "A tuple of fields (term annotations on the object) that was used for the match." ; + sh:order 20 ; + sh:path sssom:object_match_field ], + [ sh:description "A version string for the mapping." ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path owl:versionInfo ], + [ sh:description "Version IRI or version string of the source of the subject term." ; + sh:maxCount 1 ; + sh:order 11 ; sh:path sssom:subject_source_version ], - [ sh:description "The type of entity that is being mapped." ; - sh:in ( owl:Class owl:ObjectProperty owl:DataProperty owl:AnnotationProperty owl:NamedIndividual skos:Concept rdfs:Resource rdfs:Class rdfs:Literal rdfs:Datatype rdf:Property ) ; + [ sh:description "A description of the mapping set." ; sh:maxCount 1 ; - sh:order 8 ; - sh:path sssom:subject_type ], - [ sh:description "URI of ontology source for the subject." ; + sh:order 5 ; + sh:path dcterms:description ], + [ sh:description "URL pointing to the source that provided the mapping, for example an ontology that already contains the mappings, or a database from which it was derived." ; + sh:maxCount 1 ; + sh:order 15 ; + sh:path sssom:mapping_provider ], + [ sh:description "Method of preprocessing applied to the fields of the subject. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows." ; + sh:order 21 ; + sh:path sssom:subject_preprocessing ], + [ sh:description "The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path sssom:subject_source ], - [ sh:description "A tuple of fields (term annotations on the object) that was used for the match." ; sh:order 18 ; - sh:path sssom:object_match_field ], - [ sh:description "A url to the license of the mapping. In absence of a license we assume no license." ; + sh:path pav:authoredOn ], + [ sh:description "Pipe separated list of key value pairs for properties not part of the SSSOM spec. Can be used to encode additional provenance data." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 7 ; - sh:path dcterms:license ], - [ sh:description "IRI of ontology source for the object. Version IRI preferred." ; + sh:order 24 ; + sh:path sssom:other ], + [ sh:description "The display name of a mapping set." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path sssom:object_source ], + sh:order 4 ; + sh:path dcterms:title ], + [ sh:class owl:Axiom ; + sh:description "Contains a list of mapping objects" ; + sh:nodeKind sh:BlankNode ; + sh:order 0 ; + sh:path sssom:mappings ], + [ sh:description "Free text field containing either curator notes or text generated by tool providing additional informative information." ; + sh:maxCount 1 ; + sh:order 25 ; + sh:path rdfs:comment ], [ sh:description "A reference to the tool or algorithm that was used to generate the mapping. Should be a URL pointing to more info about it, but can be free text." ; sh:maxCount 1 ; - sh:order 15 ; + sh:order 16 ; sh:path sssom:mapping_tool ], - [ sh:description "A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead." ; - sh:order 6 ; - sh:path sssom:creator_label ], - [ sh:description "Version IRI or version string of the source of the object term." ; + [ sh:description "Version string that denotes the version of the mapping tool used." ; sh:maxCount 1 ; - sh:order 13 ; - sh:path sssom:object_source_version ], - [ sh:description "A mapping set or set of mapping set that was used to derive the mapping set." ; - sh:order 3 ; - sh:path prov:wasDerivedFrom ], + sh:order 17 ; + sh:path sssom:mapping_tool_version ], [ sh:description "Method of preprocessing applied to the fields of the object. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows." ; - sh:order 20 ; + sh:order 22 ; sh:path sssom:object_preprocessing ], - [ sh:description "Free text field containing either curator notes or text generated by tool providing additional informative information." ; + [ sh:description "The type of entity that is being mapped." ; + sh:in ( owl:Class owl:ObjectProperty owl:DataProperty owl:AnnotationProperty owl:NamedIndividual skos:Concept rdfs:Resource rdfs:Class rdfs:Literal rdfs:Datatype rdf:Property ) ; sh:maxCount 1 ; - sh:order 23 ; - sh:path rdfs:comment ], + sh:order 12 ; + sh:path sssom:object_type ], + [ sh:description "IRI of ontology source for the object. Version IRI preferred." ; + sh:maxCount 1 ; + sh:order 13 ; + sh:path sssom:object_source ], [ sh:description "A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path sssom:mapping_set_id ], - [ sh:description "A version string for the mapping." ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path owl:versionInfo ], - [ sh:class owl:Axiom ; - sh:description "Contains a list of mapping objects" ; - sh:nodeKind sh:BlankNode ; - sh:order 0 ; - sh:path sssom:mappings ], - [ sh:description "Pipe separated list of key value pairs for properties not part of the SSSOM spec. Can be used to encode additional provenance data." ; + [ sh:description "The type of entity that is being mapped." ; + sh:in ( owl:Class owl:ObjectProperty owl:DataProperty owl:AnnotationProperty owl:NamedIndividual skos:Concept rdfs:Resource rdfs:Class rdfs:Literal rdfs:Datatype rdf:Property ) ; sh:maxCount 1 ; - sh:order 22 ; - sh:path sssom:other ] ; + sh:order 9 ; + sh:path sssom:subject_type ] ; sh:targetClass sssom:MappingSet . owl:Axiom a sh:NodeShape ; sh:closed true ; sh:description "Represents an individual mapping between a pair of entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Version IRI or version string of the source of the subject term." ; - sh:maxCount 1 ; - sh:order 19 ; - sh:path sssom:subject_source_version ], + sh:property [ sh:description "A string identifying the author of this mapping. In the spirit of provenance, consider to use author_id instead." ; + sh:order 11 ; + sh:path sssom:author_label ], + [ sh:description "Method of preprocessing applied to the fields of the object. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows." ; + sh:order 36 ; + sh:path sssom:object_preprocessing ], [ sh:description "A string indicating whether this mapping is from a 1:1 (the subject_id maps to a single object_id), 1:n (the subject maps to more than one object_id), n:1, 1:0, 0:1 or n:n group. Note that this is a convenience field that should be derivable from the mapping set." ; sh:in ( "1:1" "1:n" "n:1" "1:0" "0:1" "n:n" ) ; - sh:maxCount 1 ; - sh:order 24 ; - sh:path sssom:mapping_cardinality ], - [ sh:description "A URL specific for the mapping instance. E.g. for kboom we have a per-mapping image that shows surrounding axioms that drive probability. Could also be a github issue URL that discussed a complicated alignment" ; - sh:order 36 ; - sh:path rdfs:seeAlso ], - [ sh:description "The label of the predicate/relation of the mapping" ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path sssom:predicate_label ], - [ sh:description "Version string that denotes the version of the mapping tool used." ; - sh:maxCount 1 ; - sh:order 26 ; - sh:path sssom:mapping_tool_version ], - [ sh:description "A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead." ; - sh:order 15 ; - sh:path sssom:creator_label ], - [ sh:description "A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence." ; - sh:maxCount 1 ; - sh:order 34 ; - sh:path sssom:semantic_similarity_score ], - [ sh:description "The ID of the predicate or relation that relates the subject and object of this match." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 3 ; - sh:path owl:annotatedProperty ], - [ sh:description "The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file." ; - sh:maxCount 1 ; - sh:order 27 ; - sh:path pav:authoredOn ], - [ sh:description "A reference to the tool or algorithm that was used to generate the mapping. Should be a URL pointing to more info about it, but can be free text." ; sh:maxCount 1 ; sh:order 25 ; - sh:path sssom:mapping_tool ], - [ sh:description "A tuple of fields (term annotations on the object) that was used for the match." ; - sh:order 30 ; - sh:path sssom:object_match_field ], - [ sh:description "A mapping justification is an action (or the written representation of that action) of showing a mapping to be right or reasonable." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 9 ; - sh:path sssom:mapping_justification ; - sh:pattern "^semapv:(MappingReview|ManualMappingCuration|LogicalReasoning|LexicalMatching|CompositeMatching|UnspecifiedMatching|SemanticSimilarityThresholdMatching|LexicalSimilarityThresholdMatching|MappingChaining)$" ], - [ sh:description "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary." ; - sh:maxCount 1 ; - sh:order 8 ; - sh:path sssom:object_category ], - [ sh:description "Method of preprocessing applied to the fields of the object. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows." ; - sh:order 33 ; - sh:path sssom:object_preprocessing ], - [ sh:description "Version IRI or version string of the source of the object term." ; + sh:path sssom:mapping_cardinality ], + [ sh:description "The label of object of the mapping" ; sh:maxCount 1 ; - sh:order 22 ; - sh:path sssom:object_source_version ], - [ sh:description "Method of preprocessing applied to the fields of the subject. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows." ; - sh:order 32 ; - sh:path sssom:subject_preprocessing ], + sh:order 7 ; + sh:path sssom:object_label ], [ sh:description "The measure used for computing the the semantic similarity score. To make processing this field as unambiguous as possible, we recommend using wikidata identifiers, but wikipedia pages could also be acceptable." ; sh:maxCount 1 ; - sh:order 35 ; + sh:order 38 ; sh:path sssom:semantic_similarity_measure ], - [ sh:description "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary." ; + [ sh:description "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases." ; sh:maxCount 1 ; sh:order 2 ; sh:path sssom:subject_category ], + [ sh:description "A reference to the tool or algorithm that was used to generate the mapping. Should be a URL pointing to more info about it, but can be free text." ; + sh:maxCount 1 ; + sh:order 26 ; + sh:path sssom:mapping_tool ], + [ sh:description "The type of entity that is being mapped." ; + sh:in ( owl:Class owl:ObjectProperty owl:DataProperty owl:AnnotationProperty owl:NamedIndividual skos:Concept rdfs:Resource rdfs:Class rdfs:Literal rdfs:Datatype rdf:Property ) ; + sh:maxCount 1 ; + sh:order 20 ; + sh:path sssom:object_type ], [ sh:description "A score between 0 and 1 to denote the confidence or probability that the match is correct, where 1 denotes total confidence." ; sh:maxCount 1 ; - sh:order 28 ; + sh:order 29 ; sh:path sssom:confidence ], + [ sh:description "Version IRI or version string of the source of the subject term." ; + sh:maxCount 1 ; + sh:order 19 ; + sh:path sssom:subject_source_version ], + [ sh:description "A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation rule should be captured as a resource (entity reference) rather than a string (see curation_rule element), which enables higher levels of transparency and sharing across mapping sets. The textual representation of curation rule is intended to be used in cases where (1) the creation of a resource is not practical from the perspective of the mapping_provider and (2) as an additional piece of metadata to augment the curation_rule element with a human readable text." ; + sh:order 31 ; + sh:path sssom:curation_rule_text ], [ sh:description "Identifies the persons or groups that reviewed and confirmed the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible." ; sh:order 12 ; sh:path sssom:reviewer_id ], - [ sh:description "The label of object of the mapping" ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path sssom:object_label ], - [ sh:description "A string identifying the author of this mapping. In the spirit of provenance, consider to use author_id instead." ; - sh:order 11 ; - sh:path sssom:author_label ], - [ sh:description "A string identifying the reviewer of this mapping. In the spirit of provenance, consider to use author_id instead." ; - sh:order 13 ; - sh:path sssom:reviewer_label ], - [ sh:description "The label of subject of the mapping" ; + [ sh:description "A tuple of fields (term annotations on the subject) that was used for the match." ; + sh:order 32 ; + sh:path sssom:subject_match_field ], + [ sh:description "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path sssom:subject_label ], + sh:order 8 ; + sh:path sssom:object_category ], [ sh:description "Identifies the persons or groups responsible for asserting the mappings. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible." ; sh:order 10 ; sh:path pav:authoredBy ], - [ sh:description "A tuple of fields (term annotations on the subject) that was used for the match." ; - sh:order 29 ; - sh:path sssom:subject_match_field ], [ sh:description "Pipe separated list of key value pairs for properties not part of the SSSOM spec. Can be used to encode additional provenance data." ; sh:maxCount 1 ; - sh:order 37 ; + sh:order 40 ; sh:path sssom:other ], - [ sh:description "The ID of the subject of the mapping." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path owl:annotatedSource ], - [ sh:description "URI of ontology source for the subject." ; - sh:maxCount 1 ; - sh:order 18 ; - sh:path sssom:subject_source ], [ sh:description "A url to the license of the mapping. In absence of a license we assume no license." ; sh:maxCount 1 ; sh:order 16 ; sh:path dcterms:license ], - [ sh:description "Strings that are shared by subj/obj. It is recommended to indicate the fields for the match using the object and subject_match_field slots." ; - sh:order 31 ; - sh:path sssom:match_string ], + [ sh:description "The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file." ; + sh:maxCount 1 ; + sh:order 28 ; + sh:path pav:authoredOn ], + [ sh:description "The mapping set this mapping was originally defined in. mapping_source is used for example when merging multiple mapping sets or deriving one mapping set from another." ; + sh:maxCount 1 ; + sh:order 24 ; + sh:path sssom:mapping_source ], + [ sh:description "A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead." ; + sh:order 15 ; + sh:path sssom:creator_label ], + [ sh:description "A tuple of fields (term annotations on the object) that was used for the match." ; + sh:order 33 ; + sh:path sssom:object_match_field ], + [ sh:description "Free text field containing either curator notes or text generated by tool providing additional informative information." ; + sh:maxCount 1 ; + sh:order 41 ; + sh:path rdfs:comment ], + [ sh:description "IRI of ontology source for the object. Version IRI preferred." ; + sh:maxCount 1 ; + sh:order 21 ; + sh:path sssom:object_source ], + [ sh:description "Version IRI or version string of the source of the object term." ; + sh:maxCount 1 ; + sh:order 22 ; + sh:path sssom:object_source_version ], + [ sh:description "A mapping justification is an action (or the written representation of that action) of showing a mapping to be right or reasonable." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 9 ; + sh:path sssom:mapping_justification ; + sh:pattern "^semapv:(MappingReview|ManualMappingCuration|LogicalReasoning|LexicalMatching|CompositeMatching|UnspecifiedMatching|SemanticSimilarityThresholdMatching|LexicalSimilarityThresholdMatching|MappingChaining)$" ], [ sh:description "URL pointing to the source that provided the mapping, for example an ontology that already contains the mappings, or a database from which it was derived." ; sh:maxCount 1 ; sh:order 23 ; sh:path sssom:mapping_provider ], - [ sh:description "Identifies the persons or groups responsible for the creation of the mapping. The creator is the agent that put the mapping in its published form, which may be different from the author, which is a person that was actively involved in the assertion of the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible." ; - sh:order 14 ; - sh:path dcterms:creator ], - [ sh:description "Free text field containing either curator notes or text generated by tool providing additional informative information." ; + [ sh:description "A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence." ; sh:maxCount 1 ; - sh:order 38 ; - sh:path rdfs:comment ], + sh:order 37 ; + sh:path sssom:semantic_similarity_score ], [ sh:description "A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40 for discussion" ; sh:in ( "Not" ) ; sh:maxCount 1 ; sh:order 5 ; sh:path sssom:predicate_modifier ], + [ sh:description "The ID of the object of the mapping." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 6 ; + sh:path owl:annotatedTarget ], + [ sh:description "Identifies the persons or groups responsible for the creation of the mapping. The creator is the agent that put the mapping in its published form, which may be different from the author, which is a person that was actively involved in the assertion of the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible." ; + sh:order 14 ; + sh:path dcterms:creator ], + [ sh:description "A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation rule is captured as a resource rather than a string, which enables higher levels of transparency and sharing across mapping sets. The URI representation of the curation rule is expected to be a resolvable identifier which provides details about the nature of the curation rule." ; + sh:order 30 ; + sh:path sssom:curation_rule ], + [ sh:description "The label of subject of the mapping" ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path sssom:subject_label ], + [ sh:description "Strings that are shared by subj/obj. It is recommended to indicate the fields for the match using the object and subject_match_field slots." ; + sh:order 34 ; + sh:path sssom:match_string ], [ sh:description "The type of entity that is being mapped." ; sh:in ( owl:Class owl:ObjectProperty owl:DataProperty owl:AnnotationProperty owl:NamedIndividual skos:Concept rdfs:Resource rdfs:Class rdfs:Literal rdfs:Datatype rdf:Property ) ; sh:maxCount 1 ; sh:order 17 ; sh:path sssom:subject_type ], - [ sh:description "The type of entity that is being mapped." ; - sh:in ( owl:Class owl:ObjectProperty owl:DataProperty owl:AnnotationProperty owl:NamedIndividual skos:Concept rdfs:Resource rdfs:Class rdfs:Literal rdfs:Datatype rdf:Property ) ; + [ sh:description "A string identifying the reviewer of this mapping. In the spirit of provenance, consider to use reviewer_id instead." ; + sh:order 13 ; + sh:path sssom:reviewer_label ], + [ sh:description "Version string that denotes the version of the mapping tool used." ; sh:maxCount 1 ; - sh:order 20 ; - sh:path sssom:object_type ], - [ sh:description "IRI of ontology source for the object. Version IRI preferred." ; + sh:order 27 ; + sh:path sssom:mapping_tool_version ], + [ sh:description "Method of preprocessing applied to the fields of the subject. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows." ; + sh:order 35 ; + sh:path sssom:subject_preprocessing ], + [ sh:description "A URL specific for the mapping instance. E.g. for kboom we have a per-mapping image that shows surrounding axioms that drive probability. Could also be a github issue URL that discussed a complicated alignment" ; + sh:order 39 ; + sh:path rdfs:seeAlso ], + [ sh:description "The ID of the predicate or relation that relates the subject and object of this match." ; sh:maxCount 1 ; - sh:order 21 ; - sh:path sssom:object_source ], - [ sh:description "The ID of the object of the mapping." ; + sh:minCount 1 ; + sh:order 3 ; + sh:path owl:annotatedProperty ], + [ sh:description "URI of ontology source for the subject." ; + sh:maxCount 1 ; + sh:order 18 ; + sh:path sssom:subject_source ], + [ sh:description "The ID of the subject of the mapping." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 6 ; - sh:path owl:annotatedTarget ] ; + sh:order 0 ; + sh:path owl:annotatedSource ], + [ sh:description "The label of the predicate/relation of the mapping" ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path sssom:predicate_label ] ; sh:targetClass owl:Axiom . sssom:MappingSetReference a sh:NodeShape ; sh:closed true ; sh:description "A reference to a mapping set. It allows to augment mapping set metadata from the perspective of the registry, for example, providing confidence, or a local filename or a grouping." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable." ; + sh:property [ sh:description "The date this reference was last updated." ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path sssom:last_updated ], + [ sh:description "A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable." ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 0 ; @@ -311,17 +341,13 @@ sssom:MappingSetReference a sh:NodeShape ; sh:maxCount 1 ; sh:order 2 ; sh:path sssom:registry_confidence ], - [ sh:description "The date this reference was last updated." ; + [ sh:description "The local name assigned to file that corresponds to the downloaded mapping set." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path sssom:last_updated ], + sh:order 5 ; + sh:path sssom:local_name ], [ sh:description "Set by the owners of the mapping registry. A way to group ." ; sh:maxCount 1 ; sh:order 3 ; - sh:path sssom:mapping_set_group ], - [ sh:description "The local name assigned to file that corresponds to the downloaded mapping set." ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path sssom:local_name ] ; + sh:path sssom:mapping_set_group ] ; sh:targetClass sssom:MappingSetReference . diff --git a/project/shex/sssom_schema.shex b/project/shex/sssom_schema.shex index 25b1f8cd..de629e87 100644 --- a/project/shex/sssom_schema.shex +++ b/project/shex/sssom_schema.shex @@ -1,12 +1,12 @@ BASE -PREFIX dcterms: -PREFIX owl: PREFIX prov: +PREFIX owl: PREFIX rdf: PREFIX rdfs: PREFIX xsd: PREFIX linkml: PREFIX pav: +PREFIX dcterms: rdfs:Resource @@ -23,14 +23,18 @@ linkml:Double xsd:double linkml:Decimal xsd:decimal -linkml:Time xsd:dateTime +linkml:Time xsd:time linkml:Date xsd:date linkml:Datetime xsd:dateTime +linkml:DateOrDatetime linkml:DateOrDatetime + linkml:Uriorcurie IRI +linkml:Curie xsd:string + linkml:Uri IRI linkml:Ncname xsd:string @@ -39,6 +43,12 @@ linkml:Objectidentifier IRI linkml:Nodeidentifier NONLITERAL +linkml:Jsonpointer xsd:string + +linkml:Jsonpath xsd:string + +linkml:Sparqlpath xsd:string + CLOSED { ( $ ( owl:annotatedSource @ ; @linkml:String ? ; @@ -64,11 +74,14 @@ linkml:Nodeidentifier NONLITERAL @ ? ; @linkml:String ? ; @linkml:Uri ? ; + @ ? ; @ ? ; @linkml:String ? ; @linkml:String ? ; pav:authoredOn @linkml:Date ? ; @linkml:Double ? ; + @ * ; + @linkml:String * ; @ * ; @ * ; @linkml:String * ; @@ -86,6 +99,8 @@ linkml:Nodeidentifier NONLITERAL CLOSED { ( $ ( @ ; + @linkml:String ? ; + @linkml:String ? ; @linkml:Uri * ; @ * ; @linkml:Uri ? ; @@ -100,6 +115,7 @@ linkml:Nodeidentifier NONLITERAL @linkml:Uri ; owl:versionInfo @linkml:String ? ; prov:wasDerivedFrom @linkml:Uri * ; + dcterms:title @linkml:String ? ; dcterms:description @linkml:String ? ; dcterms:creator @ * ; @linkml:String * ; @@ -112,6 +128,7 @@ linkml:Nodeidentifier NONLITERAL @linkml:String ? ; @linkml:Uri ? ; @linkml:String ? ; + @linkml:String ? ; pav:authoredOn @linkml:Date ? ; @ * ; @ * ; diff --git a/project/sqlschema/sssom_schema.sql b/project/sqlschema/sssom_schema.sql index 648d1ff4..1b14eb7b 100644 --- a/project/sqlschema/sssom_schema.sql +++ b/project/sqlschema/sssom_schema.sql @@ -25,11 +25,14 @@ CREATE TABLE mapping ( object_source TEXT, object_source_version TEXT, mapping_provider TEXT, + mapping_source TEXT, mapping_cardinality VARCHAR(3), mapping_tool TEXT, mapping_tool_version TEXT, mapping_date DATE, confidence FLOAT, + curation_rule TEXT, + curation_rule_text TEXT, subject_match_field TEXT, object_match_field TEXT, match_string TEXT, @@ -40,16 +43,18 @@ CREATE TABLE mapping ( see_also TEXT, other TEXT, comment TEXT, - PRIMARY KEY (subject_id, subject_label, subject_category, predicate_id, predicate_label, predicate_modifier, object_id, object_label, object_category, mapping_justification, author_id, author_label, reviewer_id, reviewer_label, creator_id, creator_label, license, subject_type, subject_source, subject_source_version, object_type, object_source, object_source_version, mapping_provider, mapping_cardinality, mapping_tool, mapping_tool_version, mapping_date, confidence, subject_match_field, object_match_field, match_string, subject_preprocessing, object_preprocessing, semantic_similarity_score, semantic_similarity_measure, see_also, other, comment) + PRIMARY KEY (subject_id, subject_label, subject_category, predicate_id, predicate_label, predicate_modifier, object_id, object_label, object_category, mapping_justification, author_id, author_label, reviewer_id, reviewer_label, creator_id, creator_label, license, subject_type, subject_source, subject_source_version, object_type, object_source, object_source_version, mapping_provider, mapping_source, mapping_cardinality, mapping_tool, mapping_tool_version, mapping_date, confidence, curation_rule, curation_rule_text, subject_match_field, object_match_field, match_string, subject_preprocessing, object_preprocessing, semantic_similarity_score, semantic_similarity_measure, see_also, other, comment) ); CREATE TABLE mapping_registry ( mapping_registry_id TEXT NOT NULL, + mapping_registry_title TEXT, + mapping_registry_description TEXT, imports TEXT, mapping_set_references TEXT, documentation TEXT, homepage TEXT, - PRIMARY KEY (mapping_registry_id, imports, mapping_set_references, documentation, homepage) + PRIMARY KEY (mapping_registry_id, mapping_registry_title, mapping_registry_description, imports, mapping_set_references, documentation, homepage) ); CREATE TABLE mapping_set ( @@ -57,6 +62,7 @@ CREATE TABLE mapping_set ( mapping_set_id TEXT NOT NULL, mapping_set_version TEXT, mapping_set_source TEXT, + mapping_set_title TEXT, mapping_set_description TEXT, creator_id TEXT, creator_label TEXT, @@ -69,6 +75,7 @@ CREATE TABLE mapping_set ( object_source_version TEXT, mapping_provider TEXT, mapping_tool TEXT, + mapping_tool_version TEXT, mapping_date DATE, subject_match_field TEXT, object_match_field TEXT, @@ -77,7 +84,7 @@ CREATE TABLE mapping_set ( see_also TEXT, other TEXT, comment TEXT, - PRIMARY KEY (mappings, mapping_set_id, mapping_set_version, mapping_set_source, mapping_set_description, creator_id, creator_label, license, subject_type, subject_source, subject_source_version, object_type, object_source, object_source_version, mapping_provider, mapping_tool, mapping_date, subject_match_field, object_match_field, subject_preprocessing, object_preprocessing, see_also, other, comment) + PRIMARY KEY (mappings, mapping_set_id, mapping_set_version, mapping_set_source, mapping_set_title, mapping_set_description, creator_id, creator_label, license, subject_type, subject_source, subject_source_version, object_type, object_source, object_source_version, mapping_provider, mapping_tool, mapping_tool_version, mapping_date, subject_match_field, object_match_field, subject_preprocessing, object_preprocessing, see_also, other, comment) ); CREATE TABLE mapping_set_reference ( diff --git a/src/docs/chaining_rules.md b/src/docs/chaining_rules.md index c18e9d60..9a0489f8 100644 --- a/src/docs/chaining_rules.md +++ b/src/docs/chaining_rules.md @@ -92,6 +92,12 @@ This excludes the exact predicates for which inverse rules are redundant. - RI1: `(:A)-[skos:narrowMatch]->(:B)` -> `(:B)-[skos:broadMatch]->(:A)` - RI2: `(:A)-[skos:broadMatch]->(:B)` -> `(:B)-[skos:narrowMatch]->(:A)` +### Rules for SEMAPV + +- RI3: `(:A)-[semapv:crossSpeciesExactMatch]->(:B)` -> `(:B)-[semapv:crossSpeciesExactMatch]->(:A)` +- RI4: `(:A)-[semapv:crossSpeciesNarrowMatch]->(:B)` -> `(:B)-[semapv:crossSpeciesBroadMatch]->(:A)` +- RI5: `(:A)-[semapv:crossSpeciesBroadMatch]->(:B)` -> `(:B)-[semapv:crossSpeciesNarrowMatch]->(:A)` + ## Generalisation Rules diff --git a/src/docs/create-mapping-commons.md b/src/docs/create-mapping-commons.md new file mode 100644 index 00000000..bd88f3ff --- /dev/null +++ b/src/docs/create-mapping-commons.md @@ -0,0 +1,66 @@ +# Getting started + +- First, create a virtual environment of your choice (anaconda, venv, pyenv, poetry etc.). If you need assistance with virtual environments, [here's a guide](https://berkeleybop.github.io/best_practice/python_environments) to help you setup pyenv and use poetry with it. +- Install the [cruft](https://github.com/cruft/cruft) package. Cruft enables keeping projects up-to-date with future updates made to this original template. + + ``` + pip install cruft + ``` +- Create a project using the [mapping-commons-cookiecutter](https://github.com/mapping-commons/mapping-commons-cookiecutter) template. + ``` + cruft create https://github.com/mapping-commons/mapping-commons-cookiecutter + ``` + +This kickstarts an interactive session where you declare the following: +- `project_name`: Name of the project. [defaults to: my-commons-name] +- `github_org`: Name of the github org the project belongs to. [defaults to: my-org] +- `project_description`: Description of the project [defaults to: 'This is the project description.'] +- `full_name`: Name of the author [defaults to: 'My Name'] +- `email`: Author's email [defaults to: 'my-name@my-org.org'] +- `yo`: Choose from [1]: Yes, [2]: No [**TEST OPTION FOR NOW**] +- `license`: Choose from [1]: Yes, [2]: No [**TEST OPTION FOR NOW**] + +# What does this do? + +The following files and directories are autogenerated in the project: +# TODO + +# Version control +## GitHub + +1. Go to [https://github.com/new] and follow the instructions, being sure to + NOT add a README or .gitignore file (this cookiecutter template will take + care of this for you) + +2. Add the remote to your local git repository + + ```bash + git remote add origin https://github.com/my-user-or-organization/my-commons-name.git + git branch -M main + git push -u origin main + ``` + +## GitLab + +### TODO + +# Future updates to the project's boilerplate code + +In order to be up-to-date with the template, first check if there is a mismatch between the project's boilerplate code and the template by running: +``` +cruft check +``` + +This indicates if there is a difference between the current project's boilerplate code and the latest version of the project template. If the project is up-to-date with the template: +``` +SUCCESS: Good work! Project's cruft is up to date and as clean as possible :). +``` + +Otherwise, it will indicate that the project's boilerplate code is not up-to-date by the following: +``` +FAILURE: Project's cruft is out of date! Run `cruft update` to clean this mess up. +``` + +For viewing the difference, run `cruft diff`. This shows the difference between the project's boilerplate code and the template's latest version. + +After running `cruft update`, the project's boilerplate code will be updated to the latest version of the template. \ No newline at end of file diff --git a/src/docs/editors.md b/src/docs/editors.md index 6f67c275..b6a1a62b 100644 --- a/src/docs/editors.md +++ b/src/docs/editors.md @@ -1,66 +1,20 @@ -# Still under development -- not yet ready for prime time - - - -# Template for LinkML based schemas - -## Requirements -* __Python >= 3.7.1__ -* __GNU make__ - A command line gnu make process (Windows users can use [cygwin](https://www.cygwin.com/) - make comes built in on a Mac) -* __pip__ - comes with most python distros - you should be ok -* __virtualenv__ - can be added via `pip install virtualenv` -* __pipenv__ - can be added via `pip install pipenv` -* - -## What is this? - -This is a GitHub template for a [LinkML](https://github.com/linkml/) based projects. - -It allows you to create a project for your schema as quickly as -possible. It takes care of generating a beautiful readthedocs themed -site, as well as downstream artefacts, including: - - * JSON-Schema - * ShEx - * OWL - * RDF (direct mapping) - * JSON-LD Contexts - * SQL DDL (TODO) - * Python classes to represent model elements - * TSV/CSV reports (TODO) - -## Quickstart - - 1. Click the big green "Use this template" button on this page - 2. Name your repo according to your schema, e.g. my-awsome-project-model, and clone it - 3. Edit `model/CONFIG.yaml` to set your specific parameters. The details on the parameters can be found in -the [LinkML Template Configuration Model](https://linkml.github.io/template-config-model/) directory. - (_Note that the Template Configuration Model was built using this very template._) - 4. Configure the repository: - * `make -f MakeConfig reset` - - This will generate a number of files that can be used to make, test, and distribute your final model. Note - that the template-configurator only needs to be run once as a rule. You can, however, re-generate allof - the target artifacts with `make -f MakeConfig reset`. You can also selectively remove artifacts and get them - regenerated with `make -f MakeConfig update` - 5. Rename the schema file in [model/schema](model/schema) to match the `root_schema` named in the CONFIG.yaml file. - Note: `root_schema` does not have the `.yaml` suffix, the file does. As an example, if you specified `root_schema: my-schema`, - the schema would be named model/schema/my-schema.yaml - 6. Edit the root_schema to add your own types, classes and slots. - 7. Type `make` to build your downstream artefacts (jsonschema, owl, etc) - 8. Once satisfied, commit your new project to github, which will rerun the make process. - 9. The package can also be installed in `pypi` - this is an advanced topic, see [PYPI_SETUP]() for details -10. This file (ABOUT.md) and the `images` directory can be removed once you are satisfied - - -## How it works - -This repo is a GitHub "template" repo. When you "Use this template" it will make a copy for your project. - -Everything is orchestrated by a generic single [Makefile](Makefile). For this to work you should follow certain conventions: - - * Keep your schema in src/schema - * Use the `.yaml` suffix for all schema files - * Use the suggested directory layout here. - -To run the Makefile you will need Python (>=3.7): +# Simple Standard for Sharing Ontological Mappings (SSSOM) + +## How to make a new release +* Automated: + * On the main code page, click on Releases (right hand column) + * Click on the `Draft a new release` button + * Click the `Choose a tag` button, create a new tag: `X.X.X` + * Click on the `Generate a new release` button + * Make sure only the `Select as the latest release` checkbox is checked. + * Click `Publish release` button +* Manual: + * `make build` + * `make pypi` + +This triggers a GitHub Action workflow that releases the new version of SSSOM to PyPi. + +## Documentation deployment +This can be done in two ways: +* Automated: Every time a pull request is merged into the `main` branch, a github action is triggered to deploy documentation automatically. +* Manually: The make command to deploy documentation is `make deploy`. \ No newline at end of file diff --git a/src/docs/events/mc2023.md b/src/docs/events/mc2023.md index c1a96a58..4c4a85aa 100644 --- a/src/docs/events/mc2023.md +++ b/src/docs/events/mc2023.md @@ -1,4 +1,53 @@ -# 2nd Mapping Commons Workshop on Simple Standard for Sharing Ontology Mappings +# 2nd Mapping Commons Workshop on Simple Standard for Sharing Ontology Mappings (SSSOM) -When: TBD, co-located with [Biocuration 2023](https://biocuration2023.github.io/). +**When**: Sunday, 23rd April, 2:30 pm Italy (CET), 1:30 pm BST, 8:30 am EDT, 5:30 am PDT (3 hours total) + +**Where**: co-located with [Biocuration 2023](https://biocuration2023.github.io/). For information about the venue see https://biocuration2023.github.io/workshops. + +During the workshop, we will work a lot with Slido for interactive sharing of ideas, rather than relying on open discussions. +We recommend having your laptop / phone with you to be able to participate. + +## Recordings + +https://www.youtube.com/watch?v=juMQQ01Q540&list=PLqu_J7ADQtKyX55F7RqZtaSS7TwGd3MoR&ab_channel=BiocurationConference2023 + +## Recommended preparation + +- Scroll through [the documentation](https://mapping-commons.github.io/sssom/home/), in particular [the paper](https://doi.org/10.1093/database/baac035) and the [basic tutorial](https://mapping-commons.github.io/sssom/tutorial/) to get a basic sense of SSSOM +- Skim through, or even watch, the [SSSOM CCB Seminar recording](https://www.youtube.com/watch?v=4vqeRECuAKE) +- Scroll through the slide decks describing the problems we will be adressing (note, they are all works in progress): + - [Complex Mappings: Examples from OMOP2OBO (Tiffany Callahan)](https://docs.google.com/presentation/d/1Jn0W9gjRn19ISDB8N-sEwKwXsJySLPlNIsOL6ng_nEA/edit?usp=sharing) + - [Complex mappings - the journey towards a proposal (Nico Matentzoglu)](https://docs.google.com/presentation/d/1kFD33S_WMgEGmCnT7IjVCeEyKI7OpcUw1ZzRXGqt1hs/edit?usp=sharing) + - [Literal mappings with SSSOM (James McLaughlin)](https://docs.google.com/presentation/d/1mBZK6KS7JgmXlEtszQiOa_Cl7SXg_Z8wRp0tZHaL57Y/edit?usp=sharing) + - FAIR Impact and schema mappings (Yann Le Franc) - slides TBD + - [Mapping Data Structures: Challenges and Approaches](https://docs.google.com/presentation/d/191jQYOe8KAGoktVOA408NW_WWk_Gon0q9idyylbEQck/edit?usp=sharing) (Chris Mungall) + - [Concept Set Mappings](https://docs.google.com/presentation/d/1055Etr0kgHHkguwgizecb_SEhj2nNd7my3q0u8fCDvk/edit?usp=sharing) (Chris Roeder) - slides TBD + +## Preliminary agenda + +| Time | Topic | Led by | +| ------ | ----- | ------ | +| 2:30pm | [Welcome, introduction, SSSOM overview and introduction of the problem of "non-simple mappings"](https://docs.google.com/presentation/d/1bHcZsYU9GpZDyeDxO4uopnuw0-ETfldn1EFYQwBbNro/edit?usp=sharing) | Nico Matentzoglu | +| 2:55pm | [FAIR Impact and schema mappings](https://drive.google.com/file/d/1cDSfvBehegy3edJU4LxZK3S-xI0LNbmn/view?usp=sharing) | Yann Le Franc | +| 3:10pm | [Literal mappings with SSSOM](https://docs.google.com/presentation/d/1mBZK6KS7JgmXlEtszQiOa_Cl7SXg_Z8wRp0tZHaL57Y/edit?usp=sharing) | James McLaughlin | +| 3:20pm | Literal Mappings - Discussion | | +| 3:30pm | [Concept Set Mappings](https://docs.google.com/presentation/d/1055Etr0kgHHkguwgizecb_SEhj2nNd7my3q0u8fCDvk/edit?usp=sharing) | Chris Roeder | +| 3:45pm | Concept Set Mappings - discussion | | +| 3:55pm | Break | | +| 4:05pm | [Complex Mappings: Examples from OMOP2OBO](https://docs.google.com/presentation/d/1Jn0W9gjRn19ISDB8N-sEwKwXsJySLPlNIsOL6ng_nEA/edit?usp=sharing) | Tiffany Callahan | +| 4:20pm | [Complex mappings - the journey towards a proposal](https://docs.google.com/presentation/d/1kFD33S_WMgEGmCnT7IjVCeEyKI7OpcUw1ZzRXGqt1hs/edit?usp=sharing) | Nico Matentzoglu | +| 4:35pm | Complex Mappings - discussion | | +| 4:50pm | [Mapping Data Structures: Challenges and Approaches](https://docs.google.com/presentation/d/191jQYOe8KAGoktVOA408NW_WWk_Gon0q9idyylbEQck/edit?usp=sharing) | Chris Mungall | +| 5:05pm | Schema Mappings - discussion | | +| 5:20pm | Summary and closing remarks | Nico Matentzoglu | + +## Organisers + +- Nicolas Matentzoglu +- Yann Le Franc +- Tiffany Callahan +- Chris Mungall +- Chris Roeder +- James McLaughlin +- Nomi Harris diff --git a/src/docs/events/ohdsi2023.md b/src/docs/events/ohdsi2023.md new file mode 100644 index 00000000..e15d0e4e --- /dev/null +++ b/src/docs/events/ohdsi2023.md @@ -0,0 +1,17 @@ +## Poster presentation at OHDSI 2023 Symposium, Rotterdam + +*Title*: "Synergizing Simple Standard for Sharing Ontology Mappings (SSSOM) and the Observational Health Data Sciences and Informatics (OHDSI)" + +*Where*: https://www.ohdsi-europe.org/index.php/symposium-2023 + +*When*: 3rd July 2023 + +*Presenters*: + +- Polina Talapova +- Nicolas Matentzoglu + +*Links*: + +- [Link to poster](https://www.dropbox.com/s/qru8lel4ahrluwo/ohdsi2023_matentzoglu_talapova_poster.pdf?dl=0) +- [Link to short report](https://www.dropbox.com/s/gvnjq16cfwvnna4/ohdsi2023_matentzoglu_talapova_extended_abstract.pdf?dl=0) diff --git a/src/docs/glossary.md b/src/docs/glossary.md new file mode 100644 index 00000000..7af26eeb --- /dev/null +++ b/src/docs/glossary.md @@ -0,0 +1,3 @@ +# Glossary + +The glossary is currently being developed [here](https://docs.google.com/document/d/1QqR8j7szjaq6wzE9YLBnZ2kOD9eN14d3SYd312X8JjQ/edit?usp=sharing). \ No newline at end of file diff --git a/src/docs/home.md b/src/docs/home.md index 2783a21f..1da0f8b9 100644 --- a/src/docs/home.md +++ b/src/docs/home.md @@ -11,7 +11,8 @@ SSSOM is a Simple Standard for Sharing Ontological Mappings: - [GitHub page](https://github.com/mapping-commons/sssom) - [Detailed description](spec.md) -- [A Simple Standard for Sharing Ontological Mappings (SSSOM)](https://arxiv.org/abs/2112.07051) (publication) +- [A Simple Standard for Sharing Ontological Mappings (SSSOM)](https://doi.org/10.1093/database/baac035) (publication in the Database Journal) +- [A Simple Standard for Ontological Mappings 2022: Updates of data model and outlook](https://ceur-ws.org/Vol-3324/om2022_LTpaper6.pdf) (Paper and presentation at the Ontology Matching Workshop 2022). - [Specification](index.md) - [Presentations](presentations.md) - [SSSOM Toolkit](https://mapping-commons.github.io/sssom-py/) diff --git a/src/docs/mapping-commons.md b/src/docs/mapping-commons.md new file mode 100644 index 00000000..97b37f05 --- /dev/null +++ b/src/docs/mapping-commons.md @@ -0,0 +1,21 @@ +# How to set up a Mapping Commons + +A mapping commons is an open, collaborative space for managing and reconciling mappings. The goal is to collect mappings from a variety of sources into a _mapping set registry_, standardise them into a common representation, curate some basic metrics such as "confidence" (how much does the community managing the commons trust a specific mapping source?) and provenance (where exactly did this mapping come from before it was integrated). + +There is no agreed upon standard for mapping registries yet. SSSOM itself provides a [lighweight metadata model for mapping registries](https://mapping-commons.github.io/sssom/) which is, as of August 2023, under active development. + +## Typical setup of a mapping commons + +We recommend to base your mapping commons on a combination of GitHub (or GitLab) collaborative workflows (issues and discussions for the community, access management etc) and a git repository based on the [Mapping Commons Cookiecutter Template](https://github.com/mapping-commons/mapping-commons-cookiecutter) for version control of the mappings. + +Using the template system above allows you to: + +1. make use of basic CI and quality control for your mappings, +2. provides a standard way to document metadata about your mapping sets +3. provides a basic ETL system based on `gnu make` (which you dont have to use, its just convenient) +4. Provides a standardised registry format that can be re-used/imported by others. + +Examples of Mapping Commons are: + +1. https://github.com/mapping-commons/mh_mapping_initiative +1. https://gitlab.c-path.org/c-pathontology/mapping-commons diff --git a/src/docs/mapping-justifications.md b/src/docs/mapping-justifications.md new file mode 100644 index 00000000..d18a6430 --- /dev/null +++ b/src/docs/mapping-justifications.md @@ -0,0 +1,118 @@ +# Guide to using Mapping Justifications + +The goal of this document is to provide the user with a few pointers into the art of mapping justification construction. As of Summer 2023, the SSSOM justification system is still evolving, and will likely benefit from yoru input. Where informative metadata properties or values are missing from the [SSSOM datamodel](https://mapping-commons.github.io/sssom/) or [SEMAPV](https://mapping-commons.github.io/semantic-mapping-vocabulary/), request them on the [SSSOM](https://github.com/mapping-commons/sssom/issues) or [SEMAPV issue tracker](https://github.com/mapping-commons/semantic-mapping-vocabulary/issues) respectively. + +## Table of contents + +1. [lexical matching](#lexical-matching) +1. [semantic similarity threshold-based matching](#semantic-matching) +1. [manual mapping curation](#manual-mapping-curation) +1. [mapping review](#mapping-review) +1. Other justifications + 1. background knowledge-based matching + 1. composite matching + 1. instance-based matching + 1. lexical similarity threshold-based matching + 1. logical reasoning + 1. mapping chaining-based matching + 1. mapping inversion-based matching + 1. semantic similarity threshold-based matching + 1. structural matching + 1. unspecified matching + + + + +## Lexical matching + +There are two kinds of lexical matching justifications we try to distinguish: + +- [semapv:LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching): The match is exact (potentially after pre-processing) +- [semapv:LexicalSimilarityThresholdMatching](https://w3id.org/semapv/vocab/LexicalSimilarityThresholdMatching): The match is fuzzy (for example, Levenshtein distance). Note: embedding similarity, even if constructed purely of a word embedding, is considered a form of _semantic_ similarity. + +#### Level 1: Track the fact that the match was based on a lexical process + +Whenever a mapping was established by a lexical matching process, track at least that fact: + +- [mapping_justification](https://mapping-commons.github.io/sssom/mapping_justification/)`: `[semapv:LexicalMatching](https://w3id.org/semapv/vocab/CompositeMatching). This indicates that the mapping was determined through some form of exact lexical matching. + +#### Level 2: Track the specific datamodel fields involved in the matching process + +Regardless of which specific lexical matching justification you are working on, it is often useful to document the source field of the values used to aquire the match. For example: + +- [subject_match_field](https://mapping-commons.github.io/sssom/subject_match_field/)`: rdfs:label` indicates that the value of the `rdfs:label` property on the subject entity was used to establish the match. +- [object_match_field](https://mapping-commons.github.io/sssom/object_match_field/)`: skos:prefLabel` indicates that the value of the `skos:prefLabel` property on the object entity was used to establish the match. +- [match_string](https://mapping-commons.github.io/sssom/match_string/)`: somestring` the exact string that was used to establish the match. This is especially useful if preprocessing methods are applied, see below (Level 3). + +#### Level 3: Pre-processing + +There are many pre-processing techniques for text in the NLP literature, such as lower-casing or lemmatisation. To judge the fidelity of a match, it is often useful to document the exact techniques used. + +- [subject_preprocessing](https://mapping-commons.github.io/sssom/match_string/)`: semapv:BlankNormalisation` indicates that before determining the match, blank characters (spaces etc) where standardised in some way. There are plenty of preprocessing techniques already recorded in [SEMAPV](https://mapping-commons.github.io/semantic-mapping-vocabulary/), including semapv:BlankNormalisation, semapv:CaseNormalization, semapv:DiacriticsSuppression, semapv:DigitSuppression, semapv:Lemmatization, semapv:LinkStripping, semapv:PunctuationElemination, semapv:RegexRemoval, semapv:RegexReplacement, semapv:Stemming, semapv:StopWordRemoval, semapv:TermExtraction, semapv:Tokenization, but feel free to add more. + +However, there is one aspect that makes this process quite difficult to implement: Most matchers will blindly apply a set of normalisation techniques prior to processing, but not document which exact technique **had an effect**. It is obviously less useful to say: we applied all these 20 techniques, if only one of them was actually effectual (i.e. caused the string to change). + +If there is no (easy) way to keep track of which technique was effectual for any given match, we believe that it is still better to document all techniques, but doing so on `mapping set` level rather than for each individual mappings (to keep the mapping sets smaller). + + + +## Semantic similarity threshold-based matching + +The basic idea behind "Semantic similarity threshold-based matching" is that a process that is "semantics aware" (in the loose sense, either by being cognisant about the graph structure, the logical structure, or a contextual textual knowledge such as an embedded Wikipedia article) enabled computing a score between the subject and object entity that to some degree reflects the "similarity" between the two entities. There are many examples of this: + +1. The (graph-)structure around the subject and object entities are projected into a common embedding space, and the similarity between the subject and object entities are expressed as cosine similarity between the two embeddings. +1. The jaccard similarity between a set of properties of the subject and object entities is calculated. +1. The Resnik score is calculated between the subject and object entities. + +**Important note on applicability of SSSOM for semantic similarity profiles**: SSSOM is not used for documenting semantic similarity profiles, i.e. cross-tables where some set of terms are compared with another set of terms and the semantic similarity is recorded as a score. SSSOM is used to document mappings, and only if a mapping decision is influenced by a semantic similarity based approach, especially in conjunction with as specific thresshold, SSSOM is applicable. For pure semantic similarity tables use [OAK Semantic Similarity](https://incatools.github.io/ontology-access-kit/datamodels/similarity/index.html). + +**Semantic vs lexical similarity?**: Semantic similarity is different from lexical similarity intuitively because the context (the graph structure, the background information) is taken into account and provides an (often crude) model of the actual entity, rather than of the word describing it. However, the distinctions can become a bit hazy. Imagine learning a graph embedding on a graph without edges, or a word embedding purely on a single label - there is definitely a grey zone where lexical similarity finishes and semantic similarity begins. In practice though, it should be mostly clear. + +#### Level 1: Documenting semantic similarity matches + +The suggested metadata for semantic similarity threshold-based matching approach is: + +- [semantic_similarity_measure](https://mapping-commons.github.io/sssom/semantic_similarity_measure/) +- [semantic_similarity_score](https://mapping-commons.github.io/sssom/semantic_similarity_score/) +- ((authors note: Maybe we need a [value for similarity threshold](https://github.com/mapping-commons/sssom/issues/296)?)) + + + +## Manual mapping curation + +[semapv:ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) is a process conducted by a (usually human) agent to determine a mapping by virtue of domain expertise. The task usually involves the agent determining, for a given `subject_id`, a suitable `obect_id` in the `object_source`. + +#### Level 1: Documenting manual mapping curation + +The suggested minimal metadata for manual mapping curation is: + +- [author_id](https://mapping-commons.github.io/sssom/author_id/): Documenting, using a unique identifier such as an ORCID, the identity of the author performing the expert curation. +- [comment](https://mapping-commons.github.io/sssom/comment/): When no formal [curation_rule](https://mapping-commons.github.io/sssom/curation_rule/) is provided (see below), it is recommended to provide a short comment with the mapping justification, especially if there is some uncertainty or ambiguity about the mapping decision. + +#### Level 2: Documenting the confidence of expert curation + +[confidence](https://mapping-commons.github.io/sssom/confidence/) is an incredibly useful metric for downstream users, including ETL engineers and data analysts. In an ideal world, all mappings have some kind of confidence associated with them. `confidence` scores should be read as "the strength of evidence provided in this record/table row (i.e mapping justification) leads us to believe the mapping (e.g. OMOP:44499396 --[skos:broadMatch]--> OMOP:4028717) is correct with 90% confidence. + +In manual curation, confidence expresses the domain expertise degree of conviction that the asserted mapping holds true. While manual mapping curation is still considered a gold standard, in practice human agents have (a) varying levels of expertise on the subject domain, (b) varying levels of understanding of the intuitions behind "semantic spaces" and associated concepts and (c) varying levels of metadata associated with a concept to be able to determine a match (definitions, labels, papers, synonyms, etc). Documenting confidence can be very useful both to increase the transparency of data science pipelines that involve entity mappings, and as a means to increase curation speed: rather than trying to achieve 100% confidence for a mapping, which can be extremely time-consuming, it is often better to first "wave through" a mapping with lower confidence to reach coverage, and later revisit low confidence mappings iteratively. + +#### Level 3: Documenting curation rules + +For manual matches, it is often unclear by what criteria a match was established. Documenting the `curation rule`s can help increase consistency for manual curation, and transparency for downstream users. + +For example `OHDSI_CURATION_RULE:19` could correspond to the following rule: + +OHDSI_CURATION_RULE:19 = If the subject concept does not have an exact match in the object source vocabulary, we select the nearest broad ("up-hill") concept applicable. Conceptually, if both terms would exist in the same terminology, the subject concept can be defined as a subconcept of the object concept. The determination for both criteria (nearest broad, conceptally subconcept) is performed through medical expert judgement. + +Curation rules are often very use case-specific and difficult to standardise. As of August 2023, SSSOM does not provide any standardised curation rules, but encourages the community to define them locally. + + + +## Mapping review + +[semapv:MappingReview](https://w3id.org/semapv/vocab/MappingReview) is a process conducted by a (usually human) agent to determine the validity of a specific given mapping. It differs from [semapv:ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) in that it does not involve looking for alternative mappings or indeed, necessarily determining if a mapping is the best possible mapping. It should be considered cheaper, less trustworthy evidence compared to [semapv:ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration). + +There are two kinds of mapping reviews in SSSOM: + +- Review as an independent justification: [semapv:MappingReview](https://w3id.org/semapv/vocab/MappingReview) is an independent process that determines the validity of a mapping. +- Review _of_ an existing justification: Instead of evaluating an entire mapping, you can record the fact that someone has looked at a specific justification and deemed it acceptable. In this case, simply record the reviewers identify using the [reviewer_id](https://mapping-commons.github.io/sssom/reviewer_id/) or [reviewer_label](https://mapping-commons.github.io/sssom/reviewer_label/) fields. + diff --git a/src/docs/mapping-predicates.md b/src/docs/mapping-predicates.md index 365c989c..7cbf66b8 100644 --- a/src/docs/mapping-predicates.md +++ b/src/docs/mapping-predicates.md @@ -36,8 +36,8 @@ The **precision** is simply: is the mapping `exact`, `close`, `broad`, `narrow` - `exact`: The two terms are intended to refer to the same thing. For example, both the subject and the object identifiers refer to the concept of [Gala cultivar](https://en.wikipedia.org/wiki/Gala_(apple)). - `close`: The two terms are intended to refer to roughly the same thing, but not quite. This is a hazy category and should be avoided in practice, because when taken too literally, most mappings could be interpreted as close mappings. This is not the point of creating mappings, if their intention is to be useful (see "use case" considerations later in this document). An example of a `close` mapping is one between the "heart" concept in a database of anatomical entities for biological research on chimpanzees and the "human heart" in an electronic health record for humans. -- `broad`: The object refers to a broader term. For example, "human heart" in an electronic health record refers to "heart" in a general anatomy ontology that covers all species, such as Uberon. Another example is "Gala (cultivar)" in one ontology or database to "Apple (cultivar)" in another: the Apple (cultivar) has a broader meaning then "Gala (cultivar)". For a good mapping, it is advisable that "broad" and "narrow" are applied a bit more strictly than is technically permitted by the SKOS specification: both the subject and the object should belong to the same **category**. For example, you should use broad (or narrow) only if both the subject and the object are "cultivars" (in the above example). -- `narrow`: The object refers to a narrower term. For example "Apple (cultivar)" is a narrow match to "Gala (cultivar)". Think of it as the opposite of "broad". `broad` and `narrow` are so-called inverse categories: If "Gala (cultivar)" is a `broad` match to "Apple (cultivar)", then "Apple (cultivar)" is a `narrow` match to "Gala (cultivar)"! One **note of caution**: `narrow` matches generally have less useful applications then `broad` ones. For example, if we want to _group_ subject entities in a database under an ontology to make them queryable in a knowledge graph, only `broad` matches to the ontology can be retrieved. For example, if we map "Gala (cultivar)" in a database to "Apple (cultivar)" in an ontology, and we wish to write a semantic query to obtain all records that are about "Apple (cultivar)" according to the ontology, we obtain "Gala (cultivar)". This is not true the other way around: if the ontology term is _more_ specific then the database term, it can't be used to group the database data. +- `broad`: The object is conceptually broader than the subject. For example, "human heart" in an electronic health record refers to "heart" in a general anatomy ontology that covers all species, such as Uberon. Another example is "Gala (cultivar)" in one ontology or database to "Apple (cultivar)" in another: the Apple (cultivar) has a broader meaning then "Gala (cultivar)". For a good mapping, it is advisable that "broad" and "narrow" are applied a bit more strictly than is technically permitted by the SKOS specification: both the subject and the object should belong to the same **category**. For example, you should use broad (or narrow) only if both the subject and the object are "cultivars" (in the above example). +- `narrow`: The object is conceptually narrower than the subject. For example "Apple (cultivar)" is a narrow match to "Gala (cultivar)". Think of it as the opposite of "broad". `broad` and `narrow` are so-called inverse categories: If "Gala (cultivar)" is a `broad` match to "Apple (cultivar)", then "Apple (cultivar)" is a `narrow` match to "Gala (cultivar)"! One **note of caution**: `narrow` matches generally have less useful applications then `broad` ones. For example, if we want to _group_ subject entities in a database under an ontology to make them queryable in a knowledge graph, only `broad` matches to the ontology can be retrieved. For example, if we map "Gala (cultivar)" in a database to "Apple (cultivar)" in an ontology, and we wish to write a semantic query to obtain all records that are about "Apple (cultivar)" according to the ontology, we obtain "Gala (cultivar)". This is not true the other way around: if the ontology term is _more_ specific then the database term, it can't be used to group the database data. - `related`: The subject refers to an analogous concept of a different category. For example "Apple" and "Apple tree" are considered `related` matches, but not `exact` matches, as "Apple" is of the "fruit" category, and "Apple tree" of the "tree" category. Other examples include: "disease" and "phenotype", "chemical" and "chemical exposure", "car" and "car manufacturing process". In general, `related` mappings should be reserved for "direct analogues". For example, we should not try to map to `related` and `broad` categories at the same time, like, for example, "Gala (cultivar)" to "Apple tree". This causes a huge amount of proliferation of very "low value" mappings (see use case section later). diff --git a/src/docs/matching-tool-implementation-guide.md b/src/docs/matching-tool-implementation-guide.md new file mode 100644 index 00000000..d1a4c8f1 --- /dev/null +++ b/src/docs/matching-tool-implementation-guide.md @@ -0,0 +1,75 @@ +# Matching Tools: Implementation Guide for SSSOM + +*Summary**: The goal of this document is to advice matching tool developers how to implement SSSOM-style matching justifications as part of their output. For example, if a mapping was determined (or is supported by) a lexical matching process, we can document that, alongside metadata that further describes the details about that process. + +As of 17.07.2023, this guide is a _work in progress_. If you are a tool developer interested to implement these recommendations, feel free to reach out on https://github.com/mapping-commons/sssom/issues for support and feel empowered to help us improve this guide! + +## Basics + +1. A (semantic) mapping in the sense of this guide is a tuple `` that describes the correspondence of a subject `s` to an object `o` via a mapping predicate `p`. `|j|` is a non-empty set of mapping justifications that provide evidence towards the validity of the correspondence. +1. As stated above, but re-stated for clarity: **every mapping can be associated with 1 or more justifications**. +1. Carefully consider if a piece of metadata should be applied on [mapping](https://mapping-commons.github.io/sssom/Mapping/) or [mapping set](https://mapping-commons.github.io/sssom/MappingSet/) level. As a rule of thumb, if a piece of metadata applies to absolutely all mappings in the target set, then consider adding it as metadata to the mapping set, to safe space. +1. Justifications in the sense of this guide comprise a *category* (documented in the [mapping_justification](https://mapping-commons.github.io/sssom/mapping_justification/) field), which is represented as a specific matching activity such as "lexical matching", "logical matching", "manual mapping curation", etc, a confidence value that represents the amount of confidence the justification contributes to the perceived truthfulness of a mapping, and additional metadata that provide additional provenance. +1. The basic vocabulary for the justification category is the [Semantic Mapping Vocabulary](https://github.com/mapping-commons/semantic-mapping-vocabulary). Feel free to use the [issue tracker](https://github.com/mapping-commons/semantic-mapping-vocabulary/issues) to request new categories to be added. There is a fast turnaround. +1. The goal of providing mapping justifications is to enable cross-purpose re-use of mappings, sharing of mappings and [mapping reconciliation](glossary.md). Mapping justifications make individual mapping decisions transparent. +1. Adding justifications is always valueable, even if **not all detailed metadata is provided**. +1. Many justifications are combinations of other justifications. For example, we may decide that a match is justified if (a) there is a lexical match and (b) the surrounding graph-structure is isomorphic or (c) the entities involved share the same properties. In this case, we should add individual justifications for each individual justification. The [confidence](https://mapping-commons.github.io/sssom/confidence/) value expresses how **confident the specific justification makes you feel about the truthfulness of the mapping**. If a joint probability is calculated from multiple justifications, add a separate justification for that, e.g. [semapv:CompositeMatching](https://w3id.org/semapv/vocab/CompositeMatching). +1. In the SSSOM TSV formats, every row corresponds to a justification, not a mapping. So the same mapping with three justifications will result in three rows in the SSSOM TSV file. + +## Background + +Before reading on, please skim through the [technical documentation of SSSOM](index.md) to get a sense of what kind of properties exist, and read our primer on [mapping justifications](mapping-justifications.md) first, which explains how to design a number of frequently used mapping justifications. + +As the collection of justifications can impact the performance of he matching process (at least for huge matching tasks), it is adviseable that the process can be switched off by the CLI. + +For most matching processes, we first construct a candidate mapping set from a combination of sources, for example: + +1. Mappings provided by user as input to the matching process +1. Lexical exact matching +1. Lexical fuzzy matching (traditional and word embeddings) + +As a second step, we use often complex combinations of techniques to refine and expand the candidate mapping set: + +1. Structural matching (graph-based approaches etc) +1. Semantic matching + 1. Logical matching (for example by deconstructing complex terms into composites and then using logical reasoning). + 1. Similarity based matching, including graph-embedding similarity (machine learning), old-school semantic similarity measures like Resnik or even Jaccard (over some part of the ontology/schema structure) + +As a rule of thumb, the more complex the rules by which a match is determined, the harder it is to provide a useful justification. To put it slighly differently: the more complex a justification, the less useful it is if the goal is to make matching decisions **transparent for human users**. A good example of this are decisions based on embedding (e.g. graph, node) similarity: while it is often useful to understand that a match has been determined by a threshold (e.g. >=0.9) of cosine similarity of a node embedding, it is less important to communicate exactly how the embedding space was constructed. + +This insight guides our implementation in two ways: + +1. We start by focusing on the "easy" cases with clear mapping justifications (like the lexical ones used to construct the _candidate mapping set_), and incrementally work our way up towards harder ones. +1. We have a default justification for "complex" cases which we have not covered yet. This is necessary not only because it may be hard to construct complex justifications from within a matching tool, but also because SSSOM simply does not have a way to express the justification yet (in this case, request clarification on the [SSSOM issue tracker](https://github.com/mapping-commons/sssom/issues)). + +## Step-by-step guide for implementation + +This step by step guide is roughly according to our own thinking of what should be done first, second, and so on. + +1. Add an option to your matching tool to output legal SSSOM TSV (recommended format now), for example `--export-sssom` or similar. +1. OPTIONAL: Add an option to your matching tool to accept legal SSSOM TSV as user input as an alternative to Alignment API (recommended format now). +1. Always provide basic provenance in the SSSOM output: + - [mapping_tool](https://mapping-commons.github.io/sssom/mapping_tool/): The canonical reference to your tool, ideally a persistent identifier. + - [mapping_tool_version](https://mapping-commons.github.io/sssom/mapping_tool_version/): The version of the tool used to compute the mapping set. + - [mapping_set_id](https://mapping-commons.github.io/sssom/mapping_set_id/): A (often randomly generated) mapping set identifier. + - [mapping_date](https://mapping-commons.github.io/sssom/mapping_date/): The date the mapping was generated. + - OPTIONAL: if available, add [subject_source](https://mapping-commons.github.io/sssom/subject_source/), [object_source](https://mapping-commons.github.io/sssom/object_source/) and [subject_source_version](https://mapping-commons.github.io/sssom/subject_source_version/), [object_source_version](https://mapping-commons.github.io/sssom/object_source_version/). +1. Document some basic entity metadata, this can help reading the mapping set: + - [subject_label](https://mapping-commons.github.io/sssom/subject_label/), [object_label](https://mapping-commons.github.io/sssom/object_label/): If available, add the label of the subject, and object id. +1. Add basic justification support + 1. Track lexical matching-based mapping decisions. A good chunk of candidate mappings will be computed by some form of lexical matching. See [here](mapping-justifications.md#lexical-matching) for details. + 1. If something more complex than a simple lexical matching has happened, try to find an appropriate one in [SEMAPV](https://mapping-commons.github.io/semantic-mapping-vocabulary/). If none exists, or its too much work to create one, use as a fall-through: + - [semapv:CompositeMatching](https://w3id.org/semapv/vocab/CompositeMatching) in the case that the match was established through a combination of approaches, but you don't want to provide justifications for each individual one. + - [semapv:UnspecifiedMatching](https://w3id.org/semapv/vocab/UnspecifiedMatching) in the case you dont know why the match happened. + 1. All justifications should come with a [confidence](https://mapping-commons.github.io/sssom/confidence/) value that expresses how **confident the specific justification makes you feel about the truthfulness of the mapping**. +1. Track if a mapping was provided (as input) by a user. Ideally, if the input to the matching process is SSSOM, simply adopt all of the mapping justifications provided by the user. If the provided mapping has no metadata, add a suitable [mapping_provider](https://mapping-commons.github.io/sssom/mapping_provider/) value (e.g. `MYTOOL:USER`, to indicate that the mapping was provided by the user). +1. Add advanced justification support. Add all metadata explained in [mapping justifications](mapping-justifications.md). Where suitable fields or values are missing from the [SSSOM datamodel](https://mapping-commons.github.io/sssom/) or [SEMAPV](https://mapping-commons.github.io/semantic-mapping-vocabulary/), request them on the [SSSOM](https://github.com/mapping-commons/sssom/issues) or [SEMAPV issue tracker](https://github.com/mapping-commons/semantic-mapping-vocabulary/issues) respectively. There is likely a lot of interesting details to be added, so dont be shy to request/suggest! +1. If you reject a user provided mapping, it makes sense to include that in a negative mapping set in SSSOM. You could provide [predicate_modifier](https://mapping-commons.github.io/sssom/predicate_modifier/)`= NOT` to ensure the file is not interpreted wrongly. +1. HIGHLY OPTIONAL: In some few cases, it may be interesting to inform the user that not all mappings are 1:1. In this case, it could be advisable to use the `mapping_cardinality` field. +1. OPTIONAL: If relevant you can add the [subject_type](https://mapping-commons.github.io/sssom/subject_type/) and [object_type](https://mapping-commons.github.io/sssom/object_type/) fields to your output, if known. This can be interesting in some cases with mixed content (being able to separate `owl:Class` related mappings from those about `owl:ObjectProperty`). +1. You can always use the [comment](https://mapping-commons.github.io/sssom/comment/) or [other](https://mapping-commons.github.io/sssom/other/)* fields to deposit additional useful metadata that can later be turned into structured content. + +## Examples + +- [MGI Mouse-Human mappings](https://github.com/mapping-commons/mh_mapping_initiative/blob/master/mappings/mp_hp_mgi_all.sssom.tsv) +- [SSSOM examples](https://github.com/mapping-commons/sssom/tree/master/examples/embedded) diff --git a/src/docs/presentations.md b/src/docs/presentations.md index 73cc1111..ce43cb82 100644 --- a/src/docs/presentations.md +++ b/src/docs/presentations.md @@ -1,5 +1,24 @@ # Presentations +## OHDSI 2023 Symposium: Synergizing Simple Standard for Sharing Ontology Mappings (SSSOM) and the Observational Health Data Sciences and Informatics (OHDSI) + +- 3rd July 2023, https://www.ohdsi-europe.org/index.php/symposium-2023 +- [Seminar info](events/ohdsi2023.md) + +## Elixir Data Interoperability Meeting: Introduction to SSSOM + +- 6th March 2023 +- This talk is a variant of the CCB Seminar Series talk below +- [Slides](https://docs.google.com/presentation/d/1w-rNLTprIbW8IUBu6YokDsPe98AKg4VwfR1gSsJrae8/edit#slide=id.g167f28e52df_0_22) + +## Ontology Summit 2023: Open, FAIR and standardised mappings for ontologies, controlled vocabularies and database entities + +- 22 February 2023, virtual +- This talk is a variant of the CCB Seminar Series talk below +- [Seminar info](https://ontologforum.org/index.php/ConferenceCall_2023_02_22) +- [Video recording (scroll to minute 46)](https://ontologforum.s3.amazonaws.com/OntologySummit2023/Part1/Ubergraph--JimBalhoff_20230222.mp4) +- [Slides](https://docs.google.com/presentation/d/1_TuimFiJ_7VP0ZFkQrHYky_ktFZc981Vse0-_hZjKtc/edit#slide=id.g167f28e52df_0_22) + ## CCB Seminar Series: Open SSSOM - Unlocking the wealth of biomedical data using shared standardized entity mappings - December 2022 talk, virtual diff --git a/src/docs/spec.md b/src/docs/spec.md index 955e1ec7..c65d8289 100644 --- a/src/docs/spec.md +++ b/src/docs/spec.md @@ -151,8 +151,6 @@ Note this is a public copy of the editors’ draft. It is provided for discussio ## SSSOM Metadata Elements -The SSSOM specification defines a set of SSSOM metadata elements that are used to describe mappings. Apart from the elements themselves, some example usage and a description, **_[the SSSOM spec](https://mapping-commons.github.io/sssom/Mapping/) defines the canonical order for the metadata_** in which the elements should appear when serialised. This precludes spurious diffs in a git setting, which is an important concern for the continuous reviewing of mappings by curators and users. - A "term" is defined in a controlled vocabulary / ontology, and usually corresponds to a class, an individual or a property (entity in OWL, concept in SKOS, resource in RDF). The "subject" is the term on the left side of the mapping, and the "object" is the term on the right side of the mapping. A "predicate" relates the subject with the object and is typically an annotation or object property. A "mapping set" is a set of mappings that can be shared using the SSSOM standard. The conceptual model of SSSOM has two main elements: @@ -229,7 +227,7 @@ The use of predicates is not restricted by SSSOM, but for maximum re-use, the fo From the SKOS primer: A triple skos:broader (and skos:broadMatch) asserts that , the object of the triple, is a broader concept than , the subject of the triple. - oio:database_cross_reference + oboInOwl:database_cross_reference Two terms are related in some way. The meaning is frequently consistent across a single set of mappings. Note this property is often overloaded even where the terms are of a different nature (e.g. interpro2go) @@ -351,16 +349,21 @@ SubClassOf(Annotation(sssom:creator_id ) ### TSV: -All SSSOM metadata elements labelled with L in the metadata table are permissible as column names in the TSV. List elements (such as creator) are "|"-separated. The columns MUST be sorted according to the order as they appear in the [SSSOM metadata](https://mapping-commons.github.io/sssom/Mapping/). For example, the first columns of a mapping set TSV should always be, in that order: subject_id, predicate_id, object_id, mapping_justification, if labels are not included; if they are included, the order should be: subject_id, subject_label, predicate_id, predicate_label, object_id, object_label, mapping_justification. For easier review of diffs, for example git diff or unix diff, we recommend to serialise the TSV by a fixed row order, sorted column by column from left to right. +All SSSOM metadata elements labelled with L in the metadata table are permissible as column names in the TSV. List elements (such as creator) are "|"-separated. The columns SHOULD be sorted according to the order as they appear in the [SSSOM metadata](https://mapping-commons.github.io/sssom/Mapping/). For example, the first columns of a mapping set TSV should always be, in that order: subject_id, predicate_id, object_id, mapping_justification, if labels are not included; if they are included, the order should be: subject_id, subject_label, predicate_id, predicate_label, object_id, object_label, mapping_justification. For easier review of diffs, for example git diff or unix diff, we recommend to serialise the TSV by a fixed row order, sorted column by column from left to right. -Metadata about a set of mappings can be supplied as part of the mappings (embedded mode) and as a simple yaml file alongside the primary mapping file. Note that for the TSV, it will be required to supply a valid curie map that allows the unambiguous interpretation of CURIEs. A curie map is supplied after a `curie_map:` parameter in the yaml file. The value can be either a dictionary of CURIE->URLPREFIX pairs or a link to a valid curie map of the same shape. +Metadata about a set of mappings can be supplied as part of the mappings (embedded mode) and as a simple yaml file alongside the primary mapping file. The YAML metadata block MUST contain a curie map that allows the unambiguous interpretation of CURIES. A curie map is supplied after a `curie_map:` parameter in the yaml file. The value is a dictionary of CURIE->URLPREFIX pairs. +Note that the following prefixes are built-in and (1) MUST NOT be changed from their [SSSOM default interpretation](https://github.com/mapping-commons/sssom/blob/master/project/jsonld/sssom_schema.context.jsonld) and (2) MAY be omitted from the curie map: "`sssom`", "`owl`", "`rdf`", "`rdfs`", "`skos`", "`semapv`". + +**Canonical ordering of columns**. Apart from the elements themselves, some example usage and a description, **_[the SSSOM spec](https://mapping-commons.github.io/sssom/Mapping/) defines the canonical order for the metadata_** in which the elements SHOULD appear when serialised. +(The "canonical order" corresponds to the exact order of elements as seen in the specification.) +This precludes spurious diffs in a git setting, which is an important concern for the continuous reviewing of mappings by curators and users. Note that only metadata elements permissible in a global context (G, or L/G) can be used in the metadata-file. We recommend to use the following *filename conventions* for SSSOM metadatafiles: - TSV files should have the extension `.sssom.tsv`, for example: `mp-hp-exact-0.0.1.sssom.tsv`. -- External yaml metadata files should have the extension `.sssom.yml`, for example `mp-hp-exact-0.0.1.sssom.tsv` +- External yaml metadata files should have the extension `.sssom.yml`, for example `mp-hp-exact-0.0.1.sssom.yml` Example ([download](https://raw.githubusercontent.com/mapping-commons/sssom/master/examples/external/mp-hp-exact-0.0.1.sssom.yml)): @@ -376,7 +379,7 @@ mapping_provider: "http://purl.obolibrary.org/obo/upheno.owl" #### External mode -In external mode, the mapping set metadata is supplied by a separate YAML file having the same base-name of the mapping file, with the extension `-meta.yml`. By default, tools will look for the file of that name in the same directory as the the mapping set table. +In external mode, the mapping set metadata MUST be supplied in a separate YAML file; that file SHOULD have the same base name as the mapping file, with the extension `.sssom.yml`. Example ([download](https://raw.githubusercontent.com/mapping-commons/sssom/master/examples/external/mp-hp-exact-0.0.1.sssom.tsv)): @@ -469,7 +472,7 @@ JSON translation is fully managed by [LinkML dumper classes](https://linkml.io/l * Is the format optimized for google refine? * Maintain mappings in github/tsvs * Rendering - * Drive-by PRs + * [Drive-by Curation](https://doi.org/10.32388/KBX9VO) PRs * Providers * Autogenerate pages like diff --git a/src/docs/tutorial.md b/src/docs/tutorial.md index dcf2de0d..58855b43 100644 --- a/src/docs/tutorial.md +++ b/src/docs/tutorial.md @@ -50,10 +50,6 @@ A 10 minute deep-dive into Jerome Euzenat classification of ontology matching te -A 10 minute overview of Clinical Terminology Mappings by Michael Kahn at CU Anschutz can be seen in the following. This video is highly optional and reveals a very non-semantic webby perspective on the subject. It is focussed on OMOP mappings, one of the many terminology standards in the medical domain. - - - ### What are we mapping? @@ -361,7 +357,7 @@ curie_map: KF_FOOD: https://kewl-foodie.inc/food/ wikidata: http://www.wikidata.org/entity/ FOODON: http://purl.obolibrary.org/obo/FOODON_ - sempav: https://w3id.org/semapv/ + sempav: https://w3id.org/semapv/vocab/ skos: "http://www.w3.org/2004/02/skos/core#" sssom: https://w3id.org/sssom/ ``` diff --git a/src/docs/tutorials/omop-mappings.md b/src/docs/tutorials/omop-mappings.md new file mode 100644 index 00000000..7dfff49b --- /dev/null +++ b/src/docs/tutorials/omop-mappings.md @@ -0,0 +1,73 @@ +# How to gradually enrich OMOP mappings with SSSOM + +This document is a guide for OMOP ETL developers to think about gradually improving the (documentation of the) strength of evidence for their vocabulary mappings. + +## Example table from OMOP + +Generated manually with Athena on the 20th July 2023. The start and end dates are invented. + +| concept_id_1 | concept_id_2 | relationship_id | valid_start_date | valid_end_date | invalid_reason | +|--------------|--------------|-----------------|------------------|----------------|----------------| +| 44499396 | 4028717 | Maps to | 19700101 | 20991231 | | +| 45586281 | 4028717 | Maps to | 73754 | 20991231 | | + +## Level 1, basic mapping table, basic provenance + +The SSSOM metadata provided is conceptually correct, but fictious. + +The reader should imagine this being provided as a separate CONCEPT_MAPPINGS.CSV table that can be joined on `subject_id`->`concept_id_1`, `object_id`->`concept_id_2` for all rows with a `Maps to` `relationship_id` (this is assuming that the `concept_id_1`,`concept_id_2` tuple is unique for `Maps to`). + +| subject_id | object_id | predicate_id | mapping_provider | mapping_tool | mapping_tool_version | mapping_justification | reviewer_id | author_id | +|---|---|---|---|---|---|---|---|---| +| OMOP:44499396 | OMOP:4028717 | omoprel:mapsTo | OHDSI:Odysseus | | | semapv:ManualMappingCuration | | ORCID:0000-0003-4147-1485 | +| OMOP:45586281 | OMOP:4028717 | omoprel:mapsTo | OHDSI:Odysseus | OHDSI_TOOLS:Usagi | 1.4.3 | semapv:LexicalMatching | ORCID:0000-0003-4147-1485 | +| OMOP:45610575 | OMOP:441554 | omoprel:mapsTo | OHDSI:UMLS | | | semapv:UnspecifiedMatching | | | + +What we see here: + +1. all identifiers are prefixed to make sure they are interpreted correctly when they are reused. This includes OMOP ids (e.g. `OMOP:44499396`) as well as ORCIDs (OPTIONAL) +1. "Maps to" is encoded using a proper identifier rather than a string (OPTIONAL) +1. All three mappings have a `mapping_justification` to distinguish for example if the mapping was determined by human manual curation (`semapv:ManualMappingCuration`) or lexical matching (`semapv:LexicalMatching`). Many other justifications exist and/or can be created. If the justification for the mapping is unknown, we can make our lack of knowledge transparent by using `semapv:UnspecifiedMatching`. +1. `author_id`, in the case of `semapv:ManualMappingCuration`, tells us who the person is that determined the mapping. This is basic provenance. If the identity of the author can be connected with an public record such as ORCID, this can help mapping users to increase trust in a mapping. `reviewer_id` tells us that some human looked at the mapping after it was proposed by a tool, and "signed off" on it. This can be valueable, again, to increase trust. +1. If the match was generated by the tool, some basic provenance is added (`mapping_tool`, `mapping_tool_version`). + +## Level 2: Curate semantic mapping predicate + +| subject_id | object_id | predicate_id | mapping_provider | mapping_tool | mapping_tool_version | mapping_justification | reviewer_id | author_id | +|---|---|---|---|---|---|---|---|---| +| OMOP:44499396 | OMOP:4028717 | skos:broadMatch | OHDSI:Odysseus | | | semapv:ManualMappingCuration | | ORCID:0000-0003-4147-1485 | +| OMOP:45586281 | OMOP:4028717 | skos:exactMatch | OHDSI:Odysseus | OHDSI_TOOLS:Usagi | 1.4.3 | semapv:LexicalMatching | ORCID:0000-0003-4147-1485 | +| OMOP:45610575 | OMOP:441554 | skos:exactMatch | OHDSI:UMLS | | | semapv:UnspecifiedMatching | | | + +What do we see here? + +1. Rather than `Maps to`, the mapping predicate (e.g. `skos:exactMatch`) is a semantic mapping predicate from a standardised vocabulary ([SKOS](https://www.w3.org/TR/skos-reference)). Here, we distinguish between `skos:exactMatch` and `skos:broadMatch`, but there are other predicates, see for example in the [Semantic Mapping Vocabulary](https://github.com/mapping-commons/semantic-mapping-vocabulary/blob/main/semapv-properties.tsv). + +## Level 3: Document confidence widely + +`confidence` is an incredibly useful metric for downstream users, including ETL engineers and data analysts. In an ideal world, all mappings have some kind of `confidence` associated with them. `confidence` scores should be read as "the strength of evidence provided in this record/table row (i.e mapping justification) leads us to believe the mapping (e.g. `OMOP:44499396 --[skos:broadMatch]--> OMOP:4028717`) is correct with 90% confidence. + +| subject_id | object_id | predicate_id | mapping_provider | mapping_tool | mapping_tool_version | mapping_justification | reviewer_id | author_id | confidence | +|---|---|---|---|---|---|---|---|---|---| +| OMOP:44499396 | OMOP:4028717 | skos:broadMatch | OHDSI:Odysseus | | | semapv:ManualMappingCuration | | ORCID:0000-0003-4147-1485 | 0.9 | +| OMOP:45586281 | OMOP:4028717 | skos:exactMatch | OHDSI:Odysseus | OHDSI_TOOLS:Usagi | 1.4.3 | semapv:LexicalMatching | ORCID:0000-0003-4147-1485 | 0.8 | +| OMOP:45610575 | OMOP:441554 | skos:exactMatch | OHDSI:UMLS | | | semapv:UnspecifiedMatching | | | 0.6 | + +What do we see here? + +- For matching tools, confidence can be calculated by proxies such as "lexical similarity", "edit distance", "cosine similarity of node embedding" and other metrics. IN the example above, Usagi has determined that the subject and objects match, but it was only 80% sure (we dont know why - this is [more advance SSSOM](mapping-justifications.md)) +- For case where an external mapping is re-used using ETL, `confidence` describes the level of trust you as an ETL expert have in the fidelty of the mapping provided by the source. + +## Level 4: Document curation rules + +| subject_id | object_id | predicate_id | mapping_provider | mapping_tool | mapping_tool_version | mapping_justification | reviewer_id | author_id | confidence | curation_rule | +|---|---|---|---|---|---|---|---|---|---|---| +| OMOP:44499396 | OMOP:4028717 | skos:broadMatch | OHDSI:Odysseus | | | semapv:ManualMappingCuration | | ORCID:0000-0003-4147-1485 | 0.9 | OHDSI_CURATION_RULE:19 | + +What do we see here? + +- For manual matches, it is often unclear by what criteria a match was established. Documenting the curation rules can help increasing consistency for manual curation, and transparency for downstream users. +- `OHDSI_CURATION_RULE:19` is a rule defined by your own curation rulebook. This can be _anything_. For example `OHDSI_CURATION_RULE:19` could correspond to the following rule: +``` +OHDSI_CURATION_RULE:19 = If the subject concept does not have an exact match in the object source vocabulary, we select the nearest broad ("up-hill") concept applicable. Conceptually, if both terms would exist in the same terminology, the subject concept can be defined as a subconcept of the object concept. The determination for both criteria (nearest broad, conceptally subconcept) is performed through medical expert judgement. +``` diff --git a/src/docs/update.md b/src/docs/update.md new file mode 100644 index 00000000..36402bab --- /dev/null +++ b/src/docs/update.md @@ -0,0 +1,10 @@ +## Final process + +1. Finish your edits and merge them into master +2. Rebuild the LinkML model using the [“build” action](https://github.com/mapping-commons/sssom/blob/master/.github/workflows/build.yml) +3. Create a [GitHub release](https://github.com/mapping-commons/sssom/releases) + - This will automatically trigger a PyPI release using [this action](https://github.com/mapping-commons/sssom/blob/master/.github/workflows/pypi-publish.yaml), of the sssom_schema module + - The context file is packaged and delivered to projects that depend on `sssom-schema`. +4. Updating sssom-py + 1. After the pypi release is completed, update sssom-schema dependency using `poetry update sssom-schema`. The new context is available and accessible via `pkg_resources`. + 1. Release `sssom-py` using the same method as `sssom-schema` above. \ No newline at end of file diff --git a/src/sssom_schema/context/sssom_schema.context.jsonld b/src/sssom_schema/context/sssom_schema.context.jsonld new file mode 100644 index 00000000..50efb3c2 --- /dev/null +++ b/src/sssom_schema/context/sssom_schema.context.jsonld @@ -0,0 +1,184 @@ +{ + "comments": { + "description": "Auto generated by LinkML jsonld context generator", + "generation_date": "2023-07-25T10:05:02", + "source": "sssom_schema.yaml" + }, + "@context": { + "dcterms": "http://purl.org/dc/terms/", + "linkml": "https://w3id.org/linkml/", + "oboInOwl": "http://www.geneontology.org/formats/oboInOwl#", + "owl": "http://www.w3.org/2002/07/owl#", + "pav": "http://purl.org/pav/", + "prov": "http://www.w3.org/ns/prov#", + "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", + "rdfs": "http://www.w3.org/2000/01/rdf-schema#", + "semapv": "https://w3id.org/semapv/vocab/", + "skos": "http://www.w3.org/2004/02/skos/core#", + "sssom": "https://w3id.org/sssom/", + "@vocab": "https://w3id.org/sssom/", + "author_id": { + "@type": "rdfs:Resource", + "@id": "pav:authoredBy" + }, + "comment": { + "@id": "rdfs:comment" + }, + "confidence": { + "@type": "xsd:double" + }, + "creator_id": { + "@type": "rdfs:Resource", + "@id": "dcterms:creator" + }, + "curation_rule": { + "@type": "rdfs:Resource" + }, + "documentation": { + "@type": "@id" + }, + "homepage": { + "@type": "@id" + }, + "imports": { + "@type": "@id" + }, + "last_updated": { + "@type": "xsd:date" + }, + "license": { + "@type": "@id", + "@id": "dcterms:license" + }, + "mapping_cardinality": { + "@context": { + "@vocab": "@null", + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + } + }, + "mapping_date": { + "@type": "xsd:date", + "@id": "pav:authoredOn" + }, + "mapping_justification": { + "@type": "rdfs:Resource" + }, + "mapping_provider": { + "@type": "@id" + }, + "mapping_registry_id": { + "@type": "rdfs:Resource" + }, + "mapping_set_description": { + "@id": "dcterms:description" + }, + "mapping_set_id": { + "@type": "@id" + }, + "mapping_set_references": { + "@type": "@id" + }, + "mapping_set_source": { + "@type": "@id", + "@id": "prov:wasDerivedFrom" + }, + "mapping_set_title": { + "@id": "dcterms:title" + }, + "mapping_set_version": { + "@id": "owl:versionInfo" + }, + "mapping_source": { + "@type": "rdfs:Resource" + }, + "mappings": { + "@type": "@id" + }, + "mirror_from": { + "@type": "@id" + }, + "object_id": { + "@type": "rdfs:Resource", + "@id": "owl:annotatedTarget" + }, + "object_match_field": { + "@type": "rdfs:Resource" + }, + "object_preprocessing": { + "@type": "rdfs:Resource" + }, + "object_source": { + "@type": "rdfs:Resource" + }, + "object_type": { + "@context": { + "@vocab": "@null", + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + } + }, + "predicate_id": { + "@type": "rdfs:Resource", + "@id": "owl:annotatedProperty" + }, + "predicate_modifier": { + "@context": { + "@vocab": "@null", + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + } + }, + "predicate_type": { + "@context": { + "@vocab": "@null", + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + } + }, + "publication_date": { + "@type": "xsd:date", + "@id": "dcterms:created" + }, + "registry_confidence": { + "@type": "xsd:double" + }, + "reviewer_id": { + "@type": "rdfs:Resource" + }, + "see_also": { + "@id": "rdfs:seeAlso" + }, + "semantic_similarity_score": { + "@type": "xsd:double" + }, + "subject_id": { + "@type": "rdfs:Resource", + "@id": "owl:annotatedSource" + }, + "subject_match_field": { + "@type": "rdfs:Resource" + }, + "subject_preprocessing": { + "@type": "rdfs:Resource" + }, + "subject_source": { + "@type": "rdfs:Resource" + }, + "subject_type": { + "@context": { + "@vocab": "@null", + "text": "skos:notation", + "description": "skos:prefLabel", + "meaning": "@id" + } + }, + "Mapping": { + "@id": "owl:Axiom" + } + } +} diff --git a/src/sssom_schema/context/sssom_schema.jsonld b/src/sssom_schema/context/sssom_schema.jsonld new file mode 100644 index 00000000..27148822 --- /dev/null +++ b/src/sssom_schema/context/sssom_schema.jsonld @@ -0,0 +1,1834 @@ +{ + "name": "sssom", + "description": "Datamodel for Simple Standard for Sharing Ontological Mappings (SSSOM)", + "see_also": [ + "https://github.com/mapping-commons/sssom", + "https://mapping-commons.github.io/sssom/home/" + ], + "id": "https://w3id.org/sssom/schema/", + "imports": [ + "linkml:types" + ], + "license": "https://creativecommons.org/publicdomain/zero/1.0/", + "prefixes": [ + { + "prefix_prefix": "dcterms", + "prefix_reference": "http://purl.org/dc/terms/" + }, + { + "prefix_prefix": "linkml", + "prefix_reference": "https://w3id.org/linkml/" + }, + { + "prefix_prefix": "sssom", + "prefix_reference": "https://w3id.org/sssom/" + }, + { + "prefix_prefix": "rdfs", + "prefix_reference": "http://www.w3.org/2000/01/rdf-schema#" + }, + { + "prefix_prefix": "rdf", + "prefix_reference": "http://www.w3.org/1999/02/22-rdf-syntax-ns#" + }, + { + "prefix_prefix": "oboInOwl", + "prefix_reference": "http://www.geneontology.org/formats/oboInOwl#" + }, + { + "prefix_prefix": "pav", + "prefix_reference": "http://purl.org/pav/" + }, + { + "prefix_prefix": "prov", + "prefix_reference": "http://www.w3.org/ns/prov#" + }, + { + "prefix_prefix": "skos", + "prefix_reference": "http://www.w3.org/2004/02/skos/core#" + }, + { + "prefix_prefix": "semapv", + "prefix_reference": "https://w3id.org/semapv/vocab/" + } + ], + "default_curi_maps": [ + "semweb_context", + "obo_context" + ], + "default_prefix": "sssom", + "default_range": "string", + "types": [ + { + "name": "EntityReference", + "definition_uri": "https://w3id.org/sssom/EntityReference", + "description": "A reference to a mapped entity. This is represented internally as a string, and as a resource in RDF", + "from_schema": "https://w3id.org/sssom/schema/", + "typeof": "uriorcurie", + "base": "str", + "uri": "http://www.w3.org/2000/01/rdf-schema#Resource", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "string", + "definition_uri": "https://w3id.org/linkml/String", + "description": "A character string", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "exact_mappings": [ + "schema:Text" + ], + "base": "str", + "uri": "http://www.w3.org/2001/XMLSchema#string", + "@type": "TypeDefinition" + }, + { + "name": "integer", + "definition_uri": "https://w3id.org/linkml/Integer", + "description": "An integer", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "exact_mappings": [ + "schema:Integer" + ], + "base": "int", + "uri": "http://www.w3.org/2001/XMLSchema#integer", + "@type": "TypeDefinition" + }, + { + "name": "boolean", + "definition_uri": "https://w3id.org/linkml/Boolean", + "description": "A binary (true or false) value", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "exact_mappings": [ + "schema:Boolean" + ], + "base": "Bool", + "uri": "http://www.w3.org/2001/XMLSchema#boolean", + "repr": "bool", + "@type": "TypeDefinition" + }, + { + "name": "float", + "definition_uri": "https://w3id.org/linkml/Float", + "description": "A real number that conforms to the xsd:float specification", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "exact_mappings": [ + "schema:Float" + ], + "base": "float", + "uri": "http://www.w3.org/2001/XMLSchema#float", + "@type": "TypeDefinition" + }, + { + "name": "double", + "definition_uri": "https://w3id.org/linkml/Double", + "description": "A real number that conforms to the xsd:double specification", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "close_mappings": [ + "schema:Float" + ], + "base": "float", + "uri": "http://www.w3.org/2001/XMLSchema#double", + "@type": "TypeDefinition" + }, + { + "name": "decimal", + "definition_uri": "https://w3id.org/linkml/Decimal", + "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "broad_mappings": [ + "schema:Number" + ], + "base": "Decimal", + "uri": "http://www.w3.org/2001/XMLSchema#decimal", + "@type": "TypeDefinition" + }, + { + "name": "time", + "definition_uri": "https://w3id.org/linkml/Time", + "description": "A time object represents a (local) time of day, independent of any particular day", + "notes": [ + "URI is dateTime because OWL reasoners do not work with straight date or time" + ], + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "exact_mappings": [ + "schema:Time" + ], + "base": "XSDTime", + "uri": "http://www.w3.org/2001/XMLSchema#time", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "date", + "definition_uri": "https://w3id.org/linkml/Date", + "description": "a date (year, month and day) in an idealized calendar", + "notes": [ + "URI is dateTime because OWL reasoners don't work with straight date or time" + ], + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "exact_mappings": [ + "schema:Date" + ], + "base": "XSDDate", + "uri": "http://www.w3.org/2001/XMLSchema#date", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "datetime", + "definition_uri": "https://w3id.org/linkml/Datetime", + "description": "The combination of a date and time", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "exact_mappings": [ + "schema:DateTime" + ], + "base": "XSDDateTime", + "uri": "http://www.w3.org/2001/XMLSchema#dateTime", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "date_or_datetime", + "definition_uri": "https://w3id.org/linkml/DateOrDatetime", + "description": "Either a date or a datetime", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "str", + "uri": "https://w3id.org/linkml/DateOrDatetime", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "uriorcurie", + "definition_uri": "https://w3id.org/linkml/Uriorcurie", + "description": "a URI or a CURIE", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "URIorCURIE", + "uri": "http://www.w3.org/2001/XMLSchema#anyURI", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "curie", + "definition_uri": "https://w3id.org/linkml/Curie", + "conforms_to": "https://www.w3.org/TR/curie/", + "description": "a compact URI", + "comments": [ + "in RDF serializations this MUST be expanded to a URI", + "in non-RDF serializations MAY be serialized as the compact representation" + ], + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "Curie", + "uri": "http://www.w3.org/2001/XMLSchema#string", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "uri", + "definition_uri": "https://w3id.org/linkml/Uri", + "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", + "description": "a complete URI", + "comments": [ + "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" + ], + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "close_mappings": [ + "schema:URL" + ], + "base": "URI", + "uri": "http://www.w3.org/2001/XMLSchema#anyURI", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "ncname", + "definition_uri": "https://w3id.org/linkml/Ncname", + "description": "Prefix part of CURIE", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "NCName", + "uri": "http://www.w3.org/2001/XMLSchema#string", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "objectidentifier", + "definition_uri": "https://w3id.org/linkml/Objectidentifier", + "description": "A URI or CURIE that represents an object in the model.", + "comments": [ + "Used for inheritance and type checking" + ], + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "ElementIdentifier", + "uri": "http://www.w3.org/ns/shex#iri", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "nodeidentifier", + "definition_uri": "https://w3id.org/linkml/Nodeidentifier", + "description": "A URI, CURIE or BNODE that represents a node in a model.", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "NodeIdentifier", + "uri": "http://www.w3.org/ns/shex#nonLiteral", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "jsonpointer", + "definition_uri": "https://w3id.org/linkml/Jsonpointer", + "conforms_to": "https://datatracker.ietf.org/doc/html/rfc6901", + "description": "A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "str", + "uri": "http://www.w3.org/2001/XMLSchema#string", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "jsonpath", + "definition_uri": "https://w3id.org/linkml/Jsonpath", + "conforms_to": "https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html", + "description": "A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "str", + "uri": "http://www.w3.org/2001/XMLSchema#string", + "repr": "str", + "@type": "TypeDefinition" + }, + { + "name": "sparqlpath", + "definition_uri": "https://w3id.org/linkml/Sparqlpath", + "conforms_to": "https://www.w3.org/TR/sparql11-query/#propertypaths", + "description": "A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.", + "from_schema": "https://w3id.org/linkml/types", + "imported_from": "linkml:types", + "base": "str", + "uri": "http://www.w3.org/2001/XMLSchema#string", + "repr": "str", + "@type": "TypeDefinition" + } + ], + "enums": [ + { + "name": "entity_type_enum", + "definition_uri": "https://w3id.org/sssom/EntityTypeEnum", + "from_schema": "https://w3id.org/sssom/schema/", + "permissible_values": [ + { + "text": "owl class", + "meaning": "owl:Class" + }, + { + "text": "owl object property", + "meaning": "owl:ObjectProperty" + }, + { + "text": "owl data property", + "meaning": "owl:DataProperty" + }, + { + "text": "owl annotation property", + "meaning": "owl:AnnotationProperty" + }, + { + "text": "owl named individual", + "meaning": "owl:NamedIndividual" + }, + { + "text": "skos concept", + "meaning": "skos:Concept" + }, + { + "text": "rdfs resource", + "meaning": "rdfs:Resource" + }, + { + "text": "rdfs class", + "meaning": "rdfs:Class" + }, + { + "text": "rdfs literal", + "meaning": "rdfs:Literal" + }, + { + "text": "rdfs datatype", + "meaning": "rdfs:Datatype" + }, + { + "text": "rdf property", + "meaning": "rdf:Property" + } + ] + }, + { + "name": "predicate_modifier_enum", + "definition_uri": "https://w3id.org/sssom/PredicateModifierEnum", + "from_schema": "https://w3id.org/sssom/schema/", + "permissible_values": [ + { + "text": "Not", + "description": "Negating the mapping predicate. The meaning of the triple becomes subject_id is not a predicate_id match to object_id." + } + ] + }, + { + "name": "mapping_cardinality_enum", + "definition_uri": "https://w3id.org/sssom/MappingCardinalityEnum", + "from_schema": "https://w3id.org/sssom/schema/", + "permissible_values": [ + { + "text": "1:1", + "description": "One-to-one mapping" + }, + { + "text": "1:n", + "description": "One-to-many mapping" + }, + { + "text": "n:1", + "description": "Many-to-one mapping" + }, + { + "text": "1:0", + "description": "One-to-none mapping" + }, + { + "text": "0:1", + "description": "None-to-one mapping" + }, + { + "text": "n:n", + "description": "Many-to-many mapping" + } + ] + } + ], + "slots": [ + { + "name": "mirror_from", + "definition_uri": "https://w3id.org/sssom/mirror_from", + "description": "A URL location from which to obtain a resource, such as a mapping set.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mirror_from", + "owner": "MappingSetReference", + "domain_of": [ + "MappingSetReference" + ], + "range": "uri", + "@type": "SlotDefinition" + }, + { + "name": "registry_confidence", + "definition_uri": "https://w3id.org/sssom/registry_confidence", + "description": "This value is set by the registry that indexes the mapping set. It reflects the confidence the registry has in the correctness of the mappings in the mapping set.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/registry_confidence", + "owner": "MappingSetReference", + "domain_of": [ + "MappingSetReference" + ], + "range": "double", + "@type": "SlotDefinition" + }, + { + "name": "last_updated", + "definition_uri": "https://w3id.org/sssom/last_updated", + "description": "The date this reference was last updated.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/last_updated", + "owner": "MappingSetReference", + "domain_of": [ + "MappingSetReference" + ], + "range": "date", + "@type": "SlotDefinition" + }, + { + "name": "local_name", + "definition_uri": "https://w3id.org/sssom/local_name", + "description": "The local name assigned to file that corresponds to the downloaded mapping set.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/local_name", + "owner": "MappingSetReference", + "domain_of": [ + "MappingSetReference" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "mapping_set_references", + "definition_uri": "https://w3id.org/sssom/mapping_set_references", + "description": "A list of mapping set references.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_set_references", + "multivalued": true, + "owner": "MappingRegistry", + "domain_of": [ + "MappingRegistry" + ], + "range": "MappingSetReference", + "recommended": true, + "inlined": true, + "@type": "SlotDefinition" + }, + { + "name": "mapping_registry_id", + "definition_uri": "https://w3id.org/sssom/mapping_registry_id", + "description": "The unique identifier of a mapping registry.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_registry_id", + "owner": "MappingRegistry", + "domain_of": [ + "MappingRegistry" + ], + "range": "EntityReference", + "required": true, + "@type": "SlotDefinition" + }, + { + "name": "mapping_registry_title", + "definition_uri": "https://w3id.org/sssom/mapping_registry_title", + "description": "The title of a mapping registry.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_registry_title", + "owner": "MappingRegistry", + "domain_of": [ + "MappingRegistry" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "mapping_registry_description", + "definition_uri": "https://w3id.org/sssom/mapping_registry_description", + "description": "The description of a mapping registry.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_registry_description", + "owner": "MappingRegistry", + "domain_of": [ + "MappingRegistry" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "imports", + "definition_uri": "https://w3id.org/sssom/imports", + "description": "A list of registries that should be imported into this one.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/imports", + "multivalued": true, + "owner": "MappingRegistry", + "domain_of": [ + "MappingRegistry" + ], + "range": "uri", + "@type": "SlotDefinition" + }, + { + "name": "documentation", + "definition_uri": "https://w3id.org/sssom/documentation", + "description": "A URL to the documentation of this mapping commons.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/documentation", + "owner": "MappingRegistry", + "domain_of": [ + "MappingRegistry" + ], + "range": "uri", + "@type": "SlotDefinition" + }, + { + "name": "homepage", + "definition_uri": "https://w3id.org/sssom/homepage", + "description": "A URL to a homepage of this mapping commons.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/homepage", + "owner": "MappingRegistry", + "domain_of": [ + "MappingRegistry" + ], + "range": "uri", + "@type": "SlotDefinition" + }, + { + "name": "mappings", + "definition_uri": "https://w3id.org/sssom/mappings", + "description": "Contains a list of mapping objects", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mappings", + "multivalued": true, + "owner": "MappingSet", + "domain_of": [ + "MappingSet" + ], + "range": "Mapping", + "recommended": true, + "inlined": true, + "inlined_as_list": true, + "@type": "SlotDefinition" + }, + { + "name": "subject_id", + "definition_uri": "https://w3id.org/sssom/subject_id", + "description": "The ID of the subject of the mapping.", + "examples": [ + { + "value": "HP:0009894", + "description": "The CURIE denoting the Human Phenotype Ontology concept of 'Thickened ears'", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://www.w3.org/2002/07/owl#annotatedSource", + "http://www.w3.org/2002/07/owl#annotatedSource" + ], + "slot_uri": "http://www.w3.org/2002/07/owl#annotatedSource", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "EntityReference", + "required": true, + "@type": "SlotDefinition" + }, + { + "name": "subject_label", + "definition_uri": "https://w3id.org/sssom/subject_label", + "description": "The label of subject of the mapping", + "examples": [ + { + "value": "Thickened ears", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/subject_label", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "string", + "recommended": true, + "@type": "SlotDefinition" + }, + { + "name": "subject_category", + "definition_uri": "https://w3id.org/sssom/subject_category", + "description": "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases.", + "examples": [ + { + "value": "UBERON:0001062", + "description": "(The CURIE of the Uberon term for \"anatomical entity\".)", + "@type": "Example" + }, + { + "value": "anatomical entity", + "description": "(A string, rather than ID, describing the \"anatomical entity\" category. This is possible, but less preferred than using an ID.)", + "@type": "Example" + }, + { + "value": "biolink:Gene", + "description": "(The CURIE of the biolink class for genes.)", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "see_also": [ + "https://github.com/mapping-commons/sssom/issues/13", + "https://github.com/mapping-commons/sssom/issues/256" + ], + "slot_uri": "https://w3id.org/sssom/subject_category", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "subject_type", + "definition_uri": "https://w3id.org/sssom/subject_type", + "description": "The type of entity that is being mapped.", + "examples": [ + { + "value": "owl:Class", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/subject_type", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "entity_type_enum", + "@type": "SlotDefinition" + }, + { + "name": "predicate_id", + "definition_uri": "https://w3id.org/sssom/predicate_id", + "description": "The ID of the predicate or relation that relates the subject and object of this match.", + "examples": [ + { + "value": "skos:exactMatch", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://www.w3.org/2002/07/owl#annotatedProperty", + "http://www.w3.org/2002/07/owl#annotatedProperty" + ], + "slot_uri": "http://www.w3.org/2002/07/owl#annotatedProperty", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "EntityReference", + "required": true, + "@type": "SlotDefinition" + }, + { + "name": "predicate_modifier", + "definition_uri": "https://w3id.org/sssom/predicate_modifier", + "description": "A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40 for discussion", + "examples": [ + { + "value": "Not", + "description": "Negates the predicate, see documentation of predicate_modifier_enum", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "see_also": [ + "https://github.com/mapping-commons/sssom/issues/107" + ], + "slot_uri": "https://w3id.org/sssom/predicate_modifier", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "predicate_modifier_enum", + "@type": "SlotDefinition" + }, + { + "name": "predicate_label", + "definition_uri": "https://w3id.org/sssom/predicate_label", + "description": "The label of the predicate/relation of the mapping", + "examples": [ + { + "value": "owl:sameAs", + "description": "The subject and the object are instances (owl individuals), and the two instances are the same.", + "@type": "Example" + }, + { + "value": "owl:equivalentClass", + "description": "The subject and the object are classes (owl class), and the two classes are the same.", + "@type": "Example" + }, + { + "value": "owl:equivalentProperty", + "description": "The subject and the object are properties (owl object, data, annotation properties), and the two properties are the same.", + "@type": "Example" + }, + { + "value": "rdfs:subClassOf", + "description": "The subject and the object are classes (owl class), and the subject is a subclass of the object.", + "@type": "Example" + }, + { + "value": "rdfs:subPropertyOf", + "description": "The subject and the object are properties (owl object, data, annotation properties), and the subject is a subproperty of the object.", + "@type": "Example" + }, + { + "value": "skos:relatedMatch", + "description": "The subject and the object are associated in some unspecified way.", + "@type": "Example" + }, + { + "value": "skos:closeMatch", + "description": "The subject and the object are sufficiently similar that they can be used interchangeably in some information retrieval applications.", + "@type": "Example" + }, + { + "value": "skos:exactMatch", + "description": "The subject and the object can, with a high degree of confidence, be used interchangeably across a wide range of information retrieval applications.", + "@type": "Example" + }, + { + "value": "skos:narrowMatch", + "description": "From the SKOS primer: A triple skos:narrower (and skos:narrowMatch) asserts that , the object of the triple, is a narrower concept than , the subject of the triple.", + "@type": "Example" + }, + { + "value": "skos:broadMatch", + "description": "From the SKOS primer: A triple skos:broader (and skos:broadMatch) asserts that , the object of the triple, is a broader concept than , the subject of the triple.", + "@type": "Example" + }, + { + "value": "oboInOwl:hasDbXref", + "description": "Two terms are related in some way. The meaning is frequently consistent across a single set of mappings. Note this property is often overloaded even where the terms are of a different nature (e.g. interpro2go)", + "@type": "Example" + }, + { + "value": "rdfs:seeAlso", + "description": "The subject and the object are associated in some unspecified way. The object IRI often resolves to a resource on the web that provides additional information.", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/predicate_label", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "predicate_type", + "definition_uri": "https://w3id.org/sssom/predicate_type", + "description": "The type of entity that is being mapped.", + "examples": [ + { + "value": "owl:AnnotationProperty", + "@type": "Example" + }, + { + "value": "owl:ObjectProperty", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/predicate_type", + "range": "entity_type_enum", + "@type": "SlotDefinition" + }, + { + "name": "object_id", + "definition_uri": "https://w3id.org/sssom/object_id", + "description": "The ID of the object of the mapping.", + "examples": [ + { + "value": "HP:0009894", + "description": "The CURIE denoting the Human Phenotype Ontology concept of 'Thickened ears'", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://www.w3.org/2002/07/owl#annotatedTarget", + "http://www.w3.org/2002/07/owl#annotatedTarget" + ], + "slot_uri": "http://www.w3.org/2002/07/owl#annotatedTarget", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "EntityReference", + "required": true, + "@type": "SlotDefinition" + }, + { + "name": "object_label", + "definition_uri": "https://w3id.org/sssom/object_label", + "description": "The label of object of the mapping", + "examples": [ + { + "value": "Thickened ears", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/object_label", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "string", + "recommended": true, + "@type": "SlotDefinition" + }, + { + "name": "object_category", + "definition_uri": "https://w3id.org/sssom/object_category", + "description": "The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. This slot is deliberately underspecified. Conceptual categories can range from those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this optional field is documentation for human reviewers - when a category is known and documented clearly, the cost of interpreting and evaluating the mapping decreases.", + "examples": [ + { + "value": "UBERON:0001062", + "description": "(The CURIE of the Uberon term for \"anatomical entity\".)", + "@type": "Example" + }, + { + "value": "anatomical entity", + "description": "(A string, rather than ID, describing the \"anatomical entity\" category. This is possible, but less preferred than using an ID.)", + "@type": "Example" + }, + { + "value": "biolink:Gene", + "description": "(The CURIE of the biolink class for genes.)", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "see_also": [ + "https://github.com/mapping-commons/sssom/issues/13", + "https://github.com/mapping-commons/sssom/issues/256" + ], + "slot_uri": "https://w3id.org/sssom/object_category", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "mapping_justification", + "definition_uri": "https://w3id.org/sssom/mapping_justification", + "description": "A mapping justification is an action (or the written representation of that action) of showing a mapping to be right or reasonable.", + "examples": [ + { + "value": "semapv:LexicalMatching", + "@type": "Example" + }, + { + "value": "semapv:ManualMappingCuration", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_justification", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "EntityReference", + "required": true, + "pattern": "^semapv:(MappingReview|ManualMappingCuration|LogicalReasoning|LexicalMatching|CompositeMatching|UnspecifiedMatching|SemanticSimilarityThresholdMatching|LexicalSimilarityThresholdMatching|MappingChaining)$", + "any_of": [ + { + "equals_string": "semapv:LexicalMatching", + "@type": "AnonymousSlotExpression" + }, + { + "equals_string": "semapv:LogicalReasoning", + "@type": "AnonymousSlotExpression" + }, + { + "equals_string": "semapv:CompositeMatching", + "@type": "AnonymousSlotExpression" + }, + { + "equals_string": "semapv:UnspecifiedMatching", + "@type": "AnonymousSlotExpression" + }, + { + "equals_string": "semapv:SemanticSimilarityThresholdMatching", + "@type": "AnonymousSlotExpression" + }, + { + "equals_string": "semapv:LexicalSimilarityThresholdMatching", + "@type": "AnonymousSlotExpression" + }, + { + "equals_string": "semapv:MappingChaining", + "@type": "AnonymousSlotExpression" + }, + { + "equals_string": "semapv:MappingReview", + "@type": "AnonymousSlotExpression" + }, + { + "equals_string": "semapv:ManualMappingCuration", + "@type": "AnonymousSlotExpression" + } + ], + "@type": "SlotDefinition" + }, + { + "name": "object_type", + "definition_uri": "https://w3id.org/sssom/object_type", + "description": "The type of entity that is being mapped.", + "examples": [ + { + "value": "owl:Class", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/object_type", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "entity_type_enum", + "@type": "SlotDefinition" + }, + { + "name": "mapping_set_id", + "definition_uri": "https://w3id.org/sssom/mapping_set_id", + "description": "A globally unique identifier for the mapping set (not each individual mapping). Should be IRI, ideally resolvable.", + "examples": [ + { + "value": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_exactmatch_ncit.sssom.tsv", + "description": "(A persistent URI pointing to the latest version of the Mondo - NCIT mapping in the Mondo namespace.)", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_set_id", + "owner": "MappingSetReference", + "domain_of": [ + "MappingSet", + "MappingSetReference" + ], + "range": "uri", + "required": true, + "@type": "SlotDefinition" + }, + { + "name": "mapping_set_version", + "definition_uri": "https://w3id.org/sssom/mapping_set_version", + "description": "A version string for the mapping.", + "examples": [ + { + "value": "2020-01-01", + "description": "(A date-based version that indicates that the mapping was published on the 1st January in 2021.)", + "@type": "Example" + }, + { + "value": "1.2.1", + "description": "(A semantic version tag that indicates that this is the 1st major, 2nd minor version, patch 1 (https://semver.org/).)", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://www.w3.org/2002/07/owl#versionInfo" + ], + "slot_uri": "http://www.w3.org/2002/07/owl#versionInfo", + "owner": "MappingSet", + "domain_of": [ + "MappingSet" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "mapping_set_group", + "definition_uri": "https://w3id.org/sssom/mapping_set_group", + "description": "Set by the owners of the mapping registry. A way to group .", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_set_group", + "owner": "MappingSetReference", + "domain_of": [ + "MappingSetReference" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "mapping_set_title", + "definition_uri": "https://w3id.org/sssom/mapping_set_title", + "description": "The display name of a mapping set.", + "examples": [ + { + "value": "The Mondo-OMIM mappings by Monarch Initiative.", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://purl.org/dc/terms/title" + ], + "slot_uri": "http://purl.org/dc/terms/title", + "owner": "MappingSet", + "domain_of": [ + "MappingSet" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "mapping_set_description", + "definition_uri": "https://w3id.org/sssom/mapping_set_description", + "description": "A description of the mapping set.", + "examples": [ + { + "value": "This mapping set was produced to integrate human and mouse phenotype data at the IMPC. It is primarily used for making mouse phenotypes searchable by human synonyms at https://mousephenotype.org/.", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://purl.org/dc/terms/description" + ], + "slot_uri": "http://purl.org/dc/terms/description", + "owner": "MappingSet", + "domain_of": [ + "MappingSet" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "creator_id", + "definition_uri": "https://w3id.org/sssom/creator_id", + "description": "Identifies the persons or groups responsible for the creation of the mapping. The creator is the agent that put the mapping in its published form, which may be different from the author, which is a person that was actively involved in the assertion of the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible.", + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://purl.org/dc/terms/creator" + ], + "slot_uri": "http://purl.org/dc/terms/creator", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "EntityReference", + "@type": "SlotDefinition" + }, + { + "name": "creator_label", + "definition_uri": "https://w3id.org/sssom/creator_label", + "description": "A string identifying the creator of this mapping. In the spirit of provenance, consider to use creator_id instead.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/creator_label", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "author_id", + "definition_uri": "https://w3id.org/sssom/author_id", + "description": "Identifies the persons or groups responsible for asserting the mappings. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible.", + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://purl.org/pav/authoredBy" + ], + "slot_uri": "http://purl.org/pav/authoredBy", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "EntityReference", + "@type": "SlotDefinition" + }, + { + "name": "author_label", + "definition_uri": "https://w3id.org/sssom/author_label", + "description": "A string identifying the author of this mapping. In the spirit of provenance, consider to use author_id instead.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/author_label", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "reviewer_id", + "definition_uri": "https://w3id.org/sssom/reviewer_id", + "description": "Identifies the persons or groups that reviewed and confirmed the mapping. Recommended to be a (pipe-separated) list of ORCIDs or otherwise identifying URLs, but any identifying string (such as name and affiliation) is permissible.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/reviewer_id", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "EntityReference", + "@type": "SlotDefinition" + }, + { + "name": "reviewer_label", + "definition_uri": "https://w3id.org/sssom/reviewer_label", + "description": "A string identifying the reviewer of this mapping. In the spirit of provenance, consider to use reviewer_id instead.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/reviewer_label", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "license", + "definition_uri": "https://w3id.org/sssom/license", + "description": "A url to the license of the mapping. In absence of a license we assume no license.", + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://purl.org/dc/terms/license" + ], + "slot_uri": "http://purl.org/dc/terms/license", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "uri", + "@type": "SlotDefinition" + }, + { + "name": "subject_source", + "definition_uri": "https://w3id.org/sssom/subject_source", + "description": "URI of ontology source for the subject.", + "examples": [ + { + "value": "obo:mondo.owl", + "description": "A persistent OBO CURIE pointing to the latest version of the Mondo ontology.", + "@type": "Example" + }, + { + "value": "wikidata:Q7876491", + "description": "A Wikidata identifier for the Uberon ontology resource.", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/subject_source", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "EntityReference", + "@type": "SlotDefinition" + }, + { + "name": "subject_source_version", + "definition_uri": "https://w3id.org/sssom/subject_source_version", + "description": "Version IRI or version string of the source of the subject term.", + "examples": [ + { + "value": "http://purl.obolibrary.org/obo/mondo/releases/2021-01-30/mondo.owl", + "description": "(A persistent Version IRI pointing to the Mondo version '2021-01-30')", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/subject_source_version", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "object_source", + "definition_uri": "https://w3id.org/sssom/object_source", + "description": "IRI of ontology source for the object. Version IRI preferred.", + "examples": [ + { + "value": "obo:mondo.owl", + "description": "A persistent OBO CURIE pointing to the latest version of the Mondo ontology.", + "@type": "Example" + }, + { + "value": "wikidata:Q7876491", + "description": "A Wikidata identifier for the Uberon ontology resource.", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/object_source", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "EntityReference", + "@type": "SlotDefinition" + }, + { + "name": "object_source_version", + "definition_uri": "https://w3id.org/sssom/object_source_version", + "description": "Version IRI or version string of the source of the object term.", + "examples": [ + { + "value": "http://purl.obolibrary.org/obo/mondo/releases/2021-01-30/mondo.owl", + "description": "(A persistent Version IRI pointing to the Mondo version '2021-01-30')", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/object_source_version", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "mapping_provider", + "definition_uri": "https://w3id.org/sssom/mapping_provider", + "description": "URL pointing to the source that provided the mapping, for example an ontology that already contains the mappings, or a database from which it was derived.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_provider", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "uri", + "@type": "SlotDefinition" + }, + { + "name": "mapping_set_source", + "definition_uri": "https://w3id.org/sssom/mapping_set_source", + "description": "A mapping set or set of mapping set that was used to derive the mapping set.", + "examples": [ + { + "value": "http://purl.obolibrary.org/obo/mondo/mappings/2022-05-20/mondo_exactmatch_ncit.sssom.tsv", + "description": "A persistent, ideally versioned, link to the mapping set from which the current mapping set is derived.", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://www.w3.org/ns/prov#wasDerivedFrom" + ], + "slot_uri": "http://www.w3.org/ns/prov#wasDerivedFrom", + "multivalued": true, + "owner": "MappingSet", + "domain_of": [ + "MappingSet" + ], + "range": "uri", + "@type": "SlotDefinition" + }, + { + "name": "mapping_source", + "definition_uri": "https://w3id.org/sssom/mapping_source", + "description": "The mapping set this mapping was originally defined in. mapping_source is used for example when merging multiple mapping sets or deriving one mapping set from another.", + "examples": [ + { + "value": "MONDO_MAPPINGS:mondo_exactmatch_ncit.sssom.tsv", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_source", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "EntityReference", + "@type": "SlotDefinition" + }, + { + "name": "mapping_cardinality", + "definition_uri": "https://w3id.org/sssom/mapping_cardinality", + "description": "A string indicating whether this mapping is from a 1:1 (the subject_id maps to a single object_id), 1:n (the subject maps to more than one object_id), n:1, 1:0, 0:1 or n:n group. Note that this is a convenience field that should be derivable from the mapping set.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_cardinality", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "mapping_cardinality_enum", + "@type": "SlotDefinition" + }, + { + "name": "mapping_tool", + "definition_uri": "https://w3id.org/sssom/mapping_tool", + "description": "A reference to the tool or algorithm that was used to generate the mapping. Should be a URL pointing to more info about it, but can be free text.", + "examples": [ + { + "value": "https://github.com/AgreementMakerLight/AML-Project", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_tool", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "mapping_tool_version", + "definition_uri": "https://w3id.org/sssom/mapping_tool_version", + "description": "Version string that denotes the version of the mapping tool used.", + "examples": [ + { + "value": "v3.2", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/mapping_tool_version", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "mapping_date", + "definition_uri": "https://w3id.org/sssom/mapping_date", + "description": "The date the mapping was asserted. This is different from the date the mapping was published or compiled in a SSSOM file.", + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://purl.org/pav/authoredOn" + ], + "slot_uri": "http://purl.org/pav/authoredOn", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "date", + "@type": "SlotDefinition" + }, + { + "name": "publication_date", + "definition_uri": "https://w3id.org/sssom/publication_date", + "description": "The date the mapping was published. This is different from the date the mapping was asserted.", + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://purl.org/dc/terms/created" + ], + "slot_uri": "http://purl.org/dc/terms/created", + "range": "date", + "@type": "SlotDefinition" + }, + { + "name": "confidence", + "definition_uri": "https://w3id.org/sssom/confidence", + "description": "A score between 0 and 1 to denote the confidence or probability that the match is correct, where 1 denotes total confidence.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/confidence", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "double", + "@type": "SlotDefinition" + }, + { + "name": "subject_match_field", + "definition_uri": "https://w3id.org/sssom/subject_match_field", + "description": "A tuple of fields (term annotations on the subject) that was used for the match.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/subject_match_field", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "EntityReference", + "@type": "SlotDefinition" + }, + { + "name": "object_match_field", + "definition_uri": "https://w3id.org/sssom/object_match_field", + "description": "A tuple of fields (term annotations on the object) that was used for the match.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/object_match_field", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "EntityReference", + "@type": "SlotDefinition" + }, + { + "name": "match_string", + "definition_uri": "https://w3id.org/sssom/match_string", + "description": "Strings that are shared by subj/obj. It is recommended to indicate the fields for the match using the object and subject_match_field slots.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/match_string", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "subject_preprocessing", + "definition_uri": "https://w3id.org/sssom/subject_preprocessing", + "description": "Method of preprocessing applied to the fields of the subject. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows.", + "examples": [ + { + "value": "semapv:Stemming", + "@type": "Example" + }, + { + "value": "semapv:StopWordRemoval", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/subject_preprocessing", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "EntityReference", + "@type": "SlotDefinition" + }, + { + "name": "object_preprocessing", + "definition_uri": "https://w3id.org/sssom/object_preprocessing", + "description": "Method of preprocessing applied to the fields of the object. If different preprocessing steps were performed on different fields, it is recommended to store the match in separate rows.", + "examples": [ + { + "value": "semapv:Stemming", + "@type": "Example" + }, + { + "value": "semapv:StopWordRemoval", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/object_preprocessing", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "EntityReference", + "@type": "SlotDefinition" + }, + { + "name": "curation_rule", + "definition_uri": "https://w3id.org/sssom/curation_rule", + "description": "A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation rule is captured as a resource rather than a string, which enables higher levels of transparency and sharing across mapping sets. The URI representation of the curation rule is expected to be a resolvable identifier which provides details about the nature of the curation rule.", + "from_schema": "https://w3id.org/sssom/schema/", + "see_also": [ + "https://github.com/mapping-commons/sssom/issues/166", + "https://github.com/mapping-commons/sssom/pull/258", + "https://github.com/mapping-commons/sssom/blob/master/examples/schema/curation_rule.sssom.tsv" + ], + "slot_uri": "https://w3id.org/sssom/curation_rule", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "EntityReference", + "@type": "SlotDefinition" + }, + { + "name": "curation_rule_text", + "definition_uri": "https://w3id.org/sssom/curation_rule_text", + "description": "A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation rule should be captured as a resource (entity reference) rather than a string (see curation_rule element), which enables higher levels of transparency and sharing across mapping sets. The textual representation of curation rule is intended to be used in cases where (1) the creation of a resource is not practical from the perspective of the mapping_provider and (2) as an additional piece of metadata to augment the curation_rule element with a human readable text.", + "from_schema": "https://w3id.org/sssom/schema/", + "see_also": [ + "https://github.com/mapping-commons/sssom/issues/166", + "https://github.com/mapping-commons/sssom/pull/258", + "https://github.com/mapping-commons/sssom/blob/master/examples/schema/curation_rule_text.sssom.tsv" + ], + "slot_uri": "https://w3id.org/sssom/curation_rule_text", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "semantic_similarity_score", + "definition_uri": "https://w3id.org/sssom/semantic_similarity_score", + "description": "A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/semantic_similarity_score", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "double", + "@type": "SlotDefinition" + }, + { + "name": "semantic_similarity_measure", + "definition_uri": "https://w3id.org/sssom/semantic_similarity_measure", + "description": "The measure used for computing the the semantic similarity score. To make processing this field as unambiguous as possible, we recommend using wikidata identifiers, but wikipedia pages could also be acceptable.", + "examples": [ + { + "value": "https://www.wikidata.org/wiki/Q865360", + "description": "(the Wikidata identifier for the Jaccard index measure).", + "@type": "Example" + } + ], + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/semantic_similarity_measure", + "owner": "Mapping", + "domain_of": [ + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "see_also", + "definition_uri": "https://w3id.org/sssom/see_also", + "description": "A URL specific for the mapping instance. E.g. for kboom we have a per-mapping image that shows surrounding axioms that drive probability. Could also be a github issue URL that discussed a complicated alignment", + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://www.w3.org/2000/01/rdf-schema#seeAlso" + ], + "slot_uri": "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "multivalued": true, + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "other", + "definition_uri": "https://w3id.org/sssom/other", + "description": "Pipe separated list of key value pairs for properties not part of the SSSOM spec. Can be used to encode additional provenance data.", + "from_schema": "https://w3id.org/sssom/schema/", + "slot_uri": "https://w3id.org/sssom/other", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "comment", + "definition_uri": "https://w3id.org/sssom/comment", + "description": "Free text field containing either curator notes or text generated by tool providing additional informative information.", + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://www.w3.org/2000/01/rdf-schema#comment" + ], + "slot_uri": "http://www.w3.org/2000/01/rdf-schema#comment", + "owner": "Mapping", + "domain_of": [ + "MappingSet", + "Mapping" + ], + "range": "string", + "@type": "SlotDefinition" + }, + { + "name": "mapping_set_license", + "definition_uri": "https://w3id.org/sssom/license", + "description": "A url to the license of the mapping. In absence of a license we assume no license.", + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "http://purl.org/dc/terms/license" + ], + "is_a": "license", + "domain": "MappingSet", + "slot_uri": "http://purl.org/dc/terms/license", + "alias": "license", + "owner": "MappingSet", + "domain_of": [ + "MappingSet" + ], + "is_usage_slot": true, + "usage_slot_name": "license", + "range": "uri", + "required": true, + "@type": "SlotDefinition" + } + ], + "classes": [ + { + "name": "MappingSet", + "definition_uri": "https://w3id.org/sssom/MappingSet", + "description": "Represents a set of mappings", + "from_schema": "https://w3id.org/sssom/schema/", + "slots": [ + "mappings", + "mapping_set_id", + "mapping_set_version", + "mapping_set_source", + "mapping_set_title", + "mapping_set_description", + "creator_id", + "creator_label", + "mapping_set_license", + "subject_type", + "subject_source", + "subject_source_version", + "object_type", + "object_source", + "object_source_version", + "mapping_provider", + "mapping_tool", + "mapping_tool_version", + "mapping_date", + "subject_match_field", + "object_match_field", + "subject_preprocessing", + "object_preprocessing", + "see_also", + "other", + "comment" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/sssom/MappingSet", + "@type": "ClassDefinition" + }, + { + "name": "Mapping", + "definition_uri": "https://w3id.org/sssom/Mapping", + "description": "Represents an individual mapping between a pair of entities", + "from_schema": "https://w3id.org/sssom/schema/", + "mappings": [ + "owl:Axiom" + ], + "slots": [ + "subject_id", + "subject_label", + "subject_category", + "predicate_id", + "predicate_label", + "predicate_modifier", + "object_id", + "object_label", + "object_category", + "mapping_justification", + "author_id", + "author_label", + "reviewer_id", + "reviewer_label", + "creator_id", + "creator_label", + "license", + "subject_type", + "subject_source", + "subject_source_version", + "object_type", + "object_source", + "object_source_version", + "mapping_provider", + "mapping_source", + "mapping_cardinality", + "mapping_tool", + "mapping_tool_version", + "mapping_date", + "confidence", + "curation_rule", + "curation_rule_text", + "subject_match_field", + "object_match_field", + "match_string", + "subject_preprocessing", + "object_preprocessing", + "semantic_similarity_score", + "semantic_similarity_measure", + "see_also", + "other", + "comment" + ], + "slot_usage": {}, + "class_uri": "http://www.w3.org/2002/07/owl#Axiom", + "@type": "ClassDefinition" + }, + { + "name": "MappingRegistry", + "definition_uri": "https://w3id.org/sssom/MappingRegistry", + "description": "A registry for managing mapping sets. It holds a set of mapping set references, and can import other registries.", + "from_schema": "https://w3id.org/sssom/schema/", + "slots": [ + "mapping_registry_id", + "mapping_registry_title", + "mapping_registry_description", + "imports", + "mapping_set_references", + "documentation", + "homepage" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/sssom/MappingRegistry", + "@type": "ClassDefinition" + }, + { + "name": "MappingSetReference", + "definition_uri": "https://w3id.org/sssom/MappingSetReference", + "description": "A reference to a mapping set. It allows to augment mapping set metadata from the perspective of the registry, for example, providing confidence, or a local filename or a grouping.", + "from_schema": "https://w3id.org/sssom/schema/", + "slots": [ + "mapping_set_id", + "mirror_from", + "registry_confidence", + "mapping_set_group", + "last_updated", + "local_name" + ], + "slot_usage": {}, + "class_uri": "https://w3id.org/sssom/MappingSetReference", + "@type": "ClassDefinition" + } + ], + "metamodel_version": "1.7.0", + "source_file": "sssom_schema.yaml", + "source_file_date": "2023-07-25T10:02:33", + "source_file_size": 25711, + "generation_date": "2023-07-25T10:05:03", + "@type": "SchemaDefinition", + "@context": [ + "project/jsonld/sssom_schema.context.jsonld", + "https://w3id.org/linkml/types.context.jsonld", + { + "@base": "https://w3id.org/sssom/" + } + ] +} diff --git a/src/sssom_schema/datamodel/sssom_schema.py b/src/sssom_schema/datamodel/sssom_schema.py index b5a3245d..4519e3dd 100644 --- a/src/sssom_schema/datamodel/sssom_schema.py +++ b/src/sssom_schema/datamodel/sssom_schema.py @@ -1,5 +1,5 @@ # Auto generated from sssom_schema.yaml by pythongen.py version: 0.9.0 -# Generation date: 2022-06-07T11:23:26 +# Generation date: 2023-07-25T10:05:11 # Schema: sssom # # id: https://w3id.org/sssom/schema/ @@ -32,7 +32,6 @@ dataclasses._init_fn = dataclasses_init_fn_with_kwargs # Namespaces -DC = CurieNamespace('dc', 'http://purl.org/dc/terms/') DCTERMS = CurieNamespace('dcterms', 'http://purl.org/dc/terms/') LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') OBOINOWL = CurieNamespace('oboInOwl', 'http://www.geneontology.org/formats/oboInOwl#') @@ -41,7 +40,7 @@ PROV = CurieNamespace('prov', 'http://www.w3.org/ns/prov#') RDF = CurieNamespace('rdf', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#') RDFS = CurieNamespace('rdfs', 'http://www.w3.org/2000/01/rdf-schema#') -SEMAPV = CurieNamespace('semapv', 'https://w3id.org/semapv/') +SEMAPV = CurieNamespace('semapv', 'https://w3id.org/semapv/vocab/') SKOS = CurieNamespace('skos', 'http://www.w3.org/2004/02/skos/core#') SSSOM = CurieNamespace('sssom', 'https://w3id.org/sssom/') DEFAULT_ = SSSOM @@ -77,6 +76,7 @@ class MappingSet(YAMLRoot): mappings: Optional[Union[Union[dict, "Mapping"], List[Union[dict, "Mapping"]]]] = empty_list() mapping_set_version: Optional[str] = None mapping_set_source: Optional[Union[Union[str, URI], List[Union[str, URI]]]] = empty_list() + mapping_set_title: Optional[str] = None mapping_set_description: Optional[str] = None creator_id: Optional[Union[Union[str, EntityReference], List[Union[str, EntityReference]]]] = empty_list() creator_label: Optional[Union[str, List[str]]] = empty_list() @@ -88,6 +88,7 @@ class MappingSet(YAMLRoot): object_source_version: Optional[str] = None mapping_provider: Optional[Union[str, URI]] = None mapping_tool: Optional[str] = None + mapping_tool_version: Optional[str] = None mapping_date: Optional[Union[str, XSDDate]] = None subject_match_field: Optional[Union[Union[str, EntityReference], List[Union[str, EntityReference]]]] = empty_list() object_match_field: Optional[Union[Union[str, EntityReference], List[Union[str, EntityReference]]]] = empty_list() @@ -119,6 +120,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): self.mapping_set_source = [self.mapping_set_source] if self.mapping_set_source is not None else [] self.mapping_set_source = [v if isinstance(v, URI) else URI(v) for v in self.mapping_set_source] + if self.mapping_set_title is not None and not isinstance(self.mapping_set_title, str): + self.mapping_set_title = str(self.mapping_set_title) + if self.mapping_set_description is not None and not isinstance(self.mapping_set_description, str): self.mapping_set_description = str(self.mapping_set_description) @@ -154,6 +158,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.mapping_tool is not None and not isinstance(self.mapping_tool, str): self.mapping_tool = str(self.mapping_tool) + if self.mapping_tool_version is not None and not isinstance(self.mapping_tool_version, str): + self.mapping_tool_version = str(self.mapping_tool_version) + if self.mapping_date is not None and not isinstance(self.mapping_date, XSDDate): self.mapping_date = XSDDate(self.mapping_date) @@ -222,11 +229,14 @@ class Mapping(YAMLRoot): object_source: Optional[Union[str, EntityReference]] = None object_source_version: Optional[str] = None mapping_provider: Optional[Union[str, URI]] = None + mapping_source: Optional[Union[str, EntityReference]] = None mapping_cardinality: Optional[Union[str, "MappingCardinalityEnum"]] = None mapping_tool: Optional[str] = None mapping_tool_version: Optional[str] = None mapping_date: Optional[Union[str, XSDDate]] = None confidence: Optional[float] = None + curation_rule: Optional[Union[Union[str, EntityReference], List[Union[str, EntityReference]]]] = empty_list() + curation_rule_text: Optional[Union[str, List[str]]] = empty_list() subject_match_field: Optional[Union[Union[str, EntityReference], List[Union[str, EntityReference]]]] = empty_list() object_match_field: Optional[Union[Union[str, EntityReference], List[Union[str, EntityReference]]]] = empty_list() match_string: Optional[Union[str, List[str]]] = empty_list() @@ -325,6 +335,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.mapping_provider is not None and not isinstance(self.mapping_provider, URI): self.mapping_provider = URI(self.mapping_provider) + if self.mapping_source is not None and not isinstance(self.mapping_source, EntityReference): + self.mapping_source = EntityReference(self.mapping_source) + if self.mapping_cardinality is not None and not isinstance(self.mapping_cardinality, MappingCardinalityEnum): self.mapping_cardinality = MappingCardinalityEnum(self.mapping_cardinality) @@ -340,6 +353,14 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if self.confidence is not None and not isinstance(self.confidence, float): self.confidence = float(self.confidence) + if not isinstance(self.curation_rule, list): + self.curation_rule = [self.curation_rule] if self.curation_rule is not None else [] + self.curation_rule = [v if isinstance(v, EntityReference) else EntityReference(v) for v in self.curation_rule] + + if not isinstance(self.curation_rule_text, list): + self.curation_rule_text = [self.curation_rule_text] if self.curation_rule_text is not None else [] + self.curation_rule_text = [v if isinstance(v, str) else str(v) for v in self.curation_rule_text] + if not isinstance(self.subject_match_field, list): self.subject_match_field = [self.subject_match_field] if self.subject_match_field is not None else [] self.subject_match_field = [v if isinstance(v, EntityReference) else EntityReference(v) for v in self.subject_match_field] @@ -392,6 +413,8 @@ class MappingRegistry(YAMLRoot): class_model_uri: ClassVar[URIRef] = SSSOM.MappingRegistry mapping_registry_id: Union[str, EntityReference] = None + mapping_registry_title: Optional[str] = None + mapping_registry_description: Optional[str] = None imports: Optional[Union[Union[str, URI], List[Union[str, URI]]]] = empty_list() mapping_set_references: Optional[Union[Union[dict, "MappingSetReference"], List[Union[dict, "MappingSetReference"]]]] = empty_list() documentation: Optional[Union[str, URI]] = None @@ -403,6 +426,12 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]): if not isinstance(self.mapping_registry_id, EntityReference): self.mapping_registry_id = EntityReference(self.mapping_registry_id) + if self.mapping_registry_title is not None and not isinstance(self.mapping_registry_title, str): + self.mapping_registry_title = str(self.mapping_registry_title) + + if self.mapping_registry_description is not None and not isinstance(self.mapping_registry_description, str): + self.mapping_registry_description = str(self.mapping_registry_description) + if not isinstance(self.imports, list): self.imports = [self.imports] if self.imports is not None else [] self.imports = [v if isinstance(v, URI) else URI(v) for v in self.imports] @@ -563,6 +592,12 @@ class slots: slots.mapping_registry_id = Slot(uri=SSSOM.mapping_registry_id, name="mapping_registry_id", curie=SSSOM.curie('mapping_registry_id'), model_uri=SSSOM.mapping_registry_id, domain=None, range=Union[str, EntityReference]) +slots.mapping_registry_title = Slot(uri=SSSOM.mapping_registry_title, name="mapping_registry_title", curie=SSSOM.curie('mapping_registry_title'), + model_uri=SSSOM.mapping_registry_title, domain=None, range=Optional[str]) + +slots.mapping_registry_description = Slot(uri=SSSOM.mapping_registry_description, name="mapping_registry_description", curie=SSSOM.curie('mapping_registry_description'), + model_uri=SSSOM.mapping_registry_description, domain=None, range=Optional[str]) + slots.imports = Slot(uri=SSSOM.imports, name="imports", curie=SSSOM.curie('imports'), model_uri=SSSOM.imports, domain=None, range=Optional[Union[Union[str, URI], List[Union[str, URI]]]]) @@ -624,10 +659,13 @@ class slots: slots.mapping_set_group = Slot(uri=SSSOM.mapping_set_group, name="mapping_set_group", curie=SSSOM.curie('mapping_set_group'), model_uri=SSSOM.mapping_set_group, domain=None, range=Optional[str]) -slots.mapping_set_description = Slot(uri=DC.description, name="mapping_set_description", curie=DC.curie('description'), +slots.mapping_set_title = Slot(uri=DCTERMS.title, name="mapping_set_title", curie=DCTERMS.curie('title'), + model_uri=SSSOM.mapping_set_title, domain=None, range=Optional[str]) + +slots.mapping_set_description = Slot(uri=DCTERMS.description, name="mapping_set_description", curie=DCTERMS.curie('description'), model_uri=SSSOM.mapping_set_description, domain=None, range=Optional[str]) -slots.creator_id = Slot(uri=DC.creator, name="creator_id", curie=DC.curie('creator'), +slots.creator_id = Slot(uri=DCTERMS.creator, name="creator_id", curie=DCTERMS.curie('creator'), model_uri=SSSOM.creator_id, domain=None, range=Optional[Union[Union[str, EntityReference], List[Union[str, EntityReference]]]]) slots.creator_label = Slot(uri=SSSOM.creator_label, name="creator_label", curie=SSSOM.curie('creator_label'), @@ -681,7 +719,7 @@ class slots: slots.mapping_date = Slot(uri=PAV.authoredOn, name="mapping_date", curie=PAV.curie('authoredOn'), model_uri=SSSOM.mapping_date, domain=None, range=Optional[Union[str, XSDDate]]) -slots.publication_date = Slot(uri=DC.created, name="publication_date", curie=DC.curie('created'), +slots.publication_date = Slot(uri=DCTERMS.created, name="publication_date", curie=DCTERMS.curie('created'), model_uri=SSSOM.publication_date, domain=None, range=Optional[Union[str, XSDDate]]) slots.confidence = Slot(uri=SSSOM.confidence, name="confidence", curie=SSSOM.curie('confidence'), @@ -702,6 +740,12 @@ class slots: slots.object_preprocessing = Slot(uri=SSSOM.object_preprocessing, name="object_preprocessing", curie=SSSOM.curie('object_preprocessing'), model_uri=SSSOM.object_preprocessing, domain=None, range=Optional[Union[Union[str, EntityReference], List[Union[str, EntityReference]]]]) +slots.curation_rule = Slot(uri=SSSOM.curation_rule, name="curation_rule", curie=SSSOM.curie('curation_rule'), + model_uri=SSSOM.curation_rule, domain=None, range=Optional[Union[Union[str, EntityReference], List[Union[str, EntityReference]]]]) + +slots.curation_rule_text = Slot(uri=SSSOM.curation_rule_text, name="curation_rule_text", curie=SSSOM.curie('curation_rule_text'), + model_uri=SSSOM.curation_rule_text, domain=None, range=Optional[Union[str, List[str]]]) + slots.semantic_similarity_score = Slot(uri=SSSOM.semantic_similarity_score, name="semantic_similarity_score", curie=SSSOM.curie('semantic_similarity_score'), model_uri=SSSOM.semantic_similarity_score, domain=None, range=Optional[float]) diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml index 6886e327..66c855cd 100644 --- a/src/sssom_schema/schema/sssom_schema.yaml +++ b/src/sssom_schema/schema/sssom_schema.yaml @@ -4,6 +4,7 @@ description: Datamodel for Simple Standard for Sharing Ontological Mappings (SSS imports: - linkml:types prefixes: + dcterms: http://purl.org/dc/terms/ linkml: https://w3id.org/linkml/ sssom: https://w3id.org/sssom/ rdfs: http://www.w3.org/2000/01/rdf-schema# @@ -12,7 +13,7 @@ prefixes: pav: http://purl.org/pav/ prov: http://www.w3.org/ns/prov# skos: http://www.w3.org/2004/02/skos/core# - semapv: https://w3id.org/semapv/ + semapv: https://w3id.org/semapv/vocab/ see_also: - https://github.com/mapping-commons/sssom - https://mapping-commons.github.io/sssom/home/ @@ -20,6 +21,7 @@ default_curi_maps: - semweb_context - obo_context default_prefix: sssom +default_range: string enums: entity_type_enum: @@ -128,10 +130,20 @@ slots: subject_category: description: The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. + This slot is deliberately underspecified. Conceptual categories can range from + those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve + as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this + optional field is documentation for human reviewers - when a category is known + and documented clearly, the cost of interpreting and evaluating the mapping decreases. range: string + see_also: + - https://github.com/mapping-commons/sssom/issues/13 + - https://github.com/mapping-commons/sssom/issues/256 examples: - value: UBERON:0001062 description: (The CURIE of the Uberon term for "anatomical entity".) + - value: anatomical entity + description: (A string, rather than ID, describing the "anatomical entity" category. This is possible, but less preferred than using an ID.) - value: biolink:Gene description: (The CURIE of the biolink class for genes.) subject_type: @@ -152,6 +164,8 @@ slots: predicate_modifier: description: A modifier for negating the prediate. See https://github.com/mapping-commons/sssom/issues/40 for discussion range: predicate_modifier_enum + see_also: + - https://github.com/mapping-commons/sssom/issues/107 examples: - value: Not description: Negates the predicate, see documentation of predicate_modifier_enum @@ -208,10 +222,20 @@ slots: object_category: description: The conceptual category to which the subject belongs to. This can be a string denoting the category or a term from a controlled vocabulary. + This slot is deliberately underspecified. Conceptual categories can range from + those that are found in general upper ontologies such as BFO (e.g. process, temporal region, etc) to those that serve + as upper ontologies in specific domains, such as COB or BioLink (e.g. gene, disease, chemical entity). The purpose of this + optional field is documentation for human reviewers - when a category is known + and documented clearly, the cost of interpreting and evaluating the mapping decreases. range: string + see_also: + - https://github.com/mapping-commons/sssom/issues/13 + - https://github.com/mapping-commons/sssom/issues/256 examples: - value: UBERON:0001062 description: (The CURIE of the Uberon term for "anatomical entity".) + - value: anatomical entity + description: (A string, rather than ID, describing the "anatomical entity" category. This is possible, but less preferred than using an ID.) - value: biolink:Gene description: (The CURIE of the biolink class for genes.) mapping_justification: @@ -260,13 +284,13 @@ slots: mapping_set_title: description: The display name of a mapping set. range: string - slot_uri: dc:title + slot_uri: dcterms:title examples: - value: "The Mondo-OMIM mappings by Monarch Initiative." mapping_set_description: description: A description of the mapping set. range: string - slot_uri: dc:description + slot_uri: dcterms:description examples: - value: "This mapping set was produced to integrate human and mouse phenotype data at the IMPC. It is primarily used for making mouse phenotypes searchable by human synonyms at https://mousephenotype.org/." creator_id: @@ -274,40 +298,37 @@ slots: the mapping. The creator is the agent that put the mapping in its published form, which may be different from the author, which is a person that was actively involved in the assertion of the mapping. - Recommended to be a (pipe-separated) list of ORCIDs or otherwise - identifying URLs, but any identifying string (such as name and affiliation) - is permissible. - slot_uri: dc:creator + Recommended to be a list of ORCIDs or otherwise + identifying URIs. + slot_uri: dcterms:creator range: EntityReference multivalued: true creator_label: description: A string identifying the creator of this mapping. In the spirit of - provenance, consider to use creator_id instead. + provenance, consider using creator_id instead. range: string multivalued: true author_id: description: Identifies the persons or groups responsible for asserting the mappings. - Recommended to be a (pipe-separated) list of ORCIDs or otherwise - identifying URLs, but any identifying string (such as name and affiliation) - is permissible. + Recommended to be a list of ORCIDs or otherwise + identifying URIs. slot_uri: pav:authoredBy range: EntityReference multivalued: true author_label: description: A string identifying the author of this mapping. In the spirit of - provenance, consider to use author_id instead. + provenance, consider using author_id instead. range: string multivalued: true reviewer_id: description: Identifies the persons or groups that reviewed and confirmed the mapping. - Recommended to be a (pipe-separated) list of ORCIDs or otherwise - identifying URLs, but any identifying string (such as name and affiliation) - is permissible. + Recommended to be a list of ORCIDs or otherwise + identifying URIs. range: EntityReference multivalued: true reviewer_label: description: A string identifying the reviewer of this mapping. In the spirit of - provenance, consider to use author_id instead. + provenance, consider using reviewer_id instead. range: string multivalued: true license: @@ -316,7 +337,7 @@ slots: range: uri slot_uri: dcterms:license subject_source: - description: URI of ontology source for the subject. + description: URI of vocabulary or identifier source for the subject. range: EntityReference examples: - value: obo:mondo.owl @@ -330,7 +351,7 @@ slots: - value: http://purl.obolibrary.org/obo/mondo/releases/2021-01-30/mondo.owl description: (A persistent Version IRI pointing to the Mondo version '2021-01-30') object_source: - description: IRI of ontology source for the object. Version IRI preferred. + description: URI of vocabulary or identifier source for the object. range: EntityReference examples: - value: obo:mondo.owl @@ -384,19 +405,19 @@ slots: range: date publication_date: description: The date the mapping was published. This is different from the date the mapping was asserted. - slot_uri: dc:created + slot_uri: dcterms:created range: date confidence: description: A score between 0 and 1 to denote the confidence or probability that the match is correct, where 1 denotes total confidence. range: double subject_match_field: - description: A tuple of fields (term annotations on the subject) that was used + description: A list of properties (term annotations on the subject) that was used for the match. range: EntityReference multivalued: true object_match_field: - description: A tuple of fields (term annotations on the object) that was used + description: A list of properties (term annotations on the object) that was used for the match. range: EntityReference multivalued: true @@ -423,6 +444,29 @@ slots: examples: - value: semapv:Stemming - value: semapv:StopWordRemoval + curation_rule: + description: A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. + Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation + rule is captured as a resource rather than a string, which enables higher levels of transparency and sharing across mapping sets. + The URI representation of the curation rule is expected to be a resolvable identifier which provides details about the nature of the curation rule. + range: EntityReference + multivalued: true + see_also: + - https://github.com/mapping-commons/sssom/issues/166 + - https://github.com/mapping-commons/sssom/pull/258 + - https://github.com/mapping-commons/sssom/blob/master/examples/schema/curation_rule.sssom.tsv + curation_rule_text: + description: A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. + Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation + rule should be captured as a resource (entity reference) rather than a string (see curation_rule element), which enables higher levels of transparency and sharing across mapping sets. + The textual representation of curation rule is intended to be used in cases where (1) the creation of a resource is not practical from the + perspective of the mapping_provider and (2) as an additional piece of metadata to augment the curation_rule element with a human readable text. + range: string + multivalued: true + see_also: + - https://github.com/mapping-commons/sssom/issues/166 + - https://github.com/mapping-commons/sssom/pull/258 + - https://github.com/mapping-commons/sssom/blob/master/examples/schema/curation_rule_text.sssom.tsv semantic_similarity_score: description: A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence. @@ -487,7 +531,9 @@ classes: - object_source_version - mapping_provider - mapping_tool + - mapping_tool_version - mapping_date + - publication_date - subject_match_field - object_match_field - subject_preprocessing @@ -528,7 +574,10 @@ classes: - mapping_tool - mapping_tool_version - mapping_date + - publication_date - confidence + - curation_rule + - curation_rule_text - subject_match_field - object_match_field - match_string