monarch-initiative · pnrobinson · Sep 10, 2024 · Sep 8, 2024 · Sep 9, 2024 · Sep 9, 2024
diff --git a/notebooks/IKZF1/IKZF1_CVID13.ipynb b/notebooks/IKZF1/IKZF1_CVID13.ipynb
diff --git a/notebooks/IKZF1/input/IKZF1_CVID13_individuals.ipynb.xlsx b/notebooks/IKZF1/input/IKZF1_CVID13_individuals.ipynb.xlsx
diff --git a/notebooks/IKZF1/phenopackets/PMID_21548011_Casereport.json b/notebooks/IKZF1/phenopackets/PMID_21548011_Casereport.json
@@ -0,0 +1,335 @@
+{
+  "id": "PMID_21548011_Case_report",
+  "subject": {
+    "id": "Case report",
+    "timeAtLastEncounter": {
+      "age": {
+        "iso8601duration": "P3M"
+      }
+    },
+    "vitalStatus": {
+      "status": "DECEASED",
+      "timeOfDeath": {
+        "age": {
+          "iso8601duration": "P3M"
+        }
+      }
+    },
+    "sex": "MALE"
+  },
+  "phenotypicFeatures": [
+    {
+      "type": {
+        "id": "HP:0001876",
+        "label": "Pancytopenia"
+      },
+      "onset": {
+        "ontologyClass": {
+          "id": "HP:0003577",
+          "label": "Congenital onset"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001873",
+        "label": "Thrombocytopenia"
+      },
+      "onset": {
+        "ontologyClass": {
+          "id": "HP:0003577",
+          "label": "Congenital onset"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001875",
+        "label": "Neutropenia"
+      },
+      "onset": {
+        "ontologyClass": {
+          "id": "HP:0003577",
+          "label": "Congenital onset"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0010976",
+        "label": "B lymphocytopenia"
+      },
+      "onset": {
+        "age": {
+          "iso8601duration": "P5D"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0040218",
+        "label": "Reduced natural killer cell count"
+      },
+      "onset": {
+        "age": {
+          "iso8601duration": "P5D"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0031381",
+        "label": "Decreased lymphocyte proliferation in response to mitogen"
+      },
+      "onset": {
+        "age": {
+          "iso8601duration": "P5D"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0005528",
+        "label": "Bone marrow hypocellularity"
+      },
+      "onset": {
+        "age": {
+          "iso8601duration": "P5D"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0002850",
+        "label": "Decreased circulating total IgM"
+      },
+      "onset": {
+        "age": {
+          "iso8601duration": "P5D"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001561",
+        "label": "Polyhydramnios"
+      },
+      "onset": {
+        "ontologyClass": {
+          "id": "HP:0034197",
+          "label": "Third trimester onset"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001790",
+        "label": "Nonimmune hydrops fetalis"
+      },
+      "onset": {
+        "ontologyClass": {
+          "id": "HP:0034197",
+          "label": "Third trimester onset"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0025716",
+        "label": "Fetal anemia"
+      },
+      "onset": {
+        "ontologyClass": {
+          "id": "HP:0034197",
+          "label": "Third trimester onset"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001622",
+        "label": "Premature birth"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0004812",
+        "label": "B Acute Lymphoblastic Leukemia"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0006727",
+        "label": "T-cell acute lymphoblastic leukemias"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0033222",
+        "label": "Decreased CD4:CD8 ratio"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0001973",
+        "label": "Autoimmune thrombocytopenia"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0032218",
+        "label": "Decreased proportion of CD4-positive T cells"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0032219",
+        "label": "Increased proportion of CD4-positive T cells"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0002170",
+        "label": "Intracranial hemorrhage"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0011842",
+        "label": "Abnormal skeletal morphology"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0040012",
+        "label": "Chromosome breakage"
+      },
+      "excluded": true
+    }
+  ],
+  "interpretations": [
+    {
+      "id": "Case report",
+      "progressStatus": "SOLVED",
+      "diagnosis": {
+        "disease": {
+          "id": "OMIM:616873",
+          "label": "Immunodeficiency, common variable, 13"
+        },
+        "genomicInterpretations": [
+          {
+            "subjectOrBiosampleId": "Case report",
+            "interpretationStatus": "CAUSATIVE",
+            "variantInterpretation": {
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+                "id": "var_eKvHaXfsKDwYvSmdRZmszakYx",
+                "geneContext": {
+                  "valueId": "HGNC:13176",
+                  "symbol": "IKZF1"
+                },
+                "expressions": [
+                  {
+                    "syntax": "hgvs.c",
+                    "value": "NM_006060.6:c.629A>G"
+                  },
+                  {
+                    "syntax": "hgvs.g",
+                    "value": "NC_000007.14:g.50387384A>G"
+                  }
+                ],
+                "vcfRecord": {
+                  "genomeAssembly": "hg38",
+                  "chrom": "chr7",
+                  "pos": "50387384",
+                  "ref": "A",
+                  "alt": "G"
+                },
+                "moleculeContext": "genomic",
+                "allelicState": {
+                  "id": "GENO:0000135",
+                  "label": "heterozygous"
+                }
+              }
+            }
+          }
+        ]
+      }
+    }
+  ],
+  "diseases": [
+    {
+      "term": {
+        "id": "OMIM:616873",
+        "label": "Immunodeficiency, common variable, 13"
+      },
+      "onset": {
+        "ontologyClass": {
+          "id": "HP:0003577",
+          "label": "Congenital onset"
+        }
+      }
+    }
+  ],
+  "metaData": {
+    "created": "2024-09-10T10:44:47.705117940Z",
+    "createdBy": "ORCID:0000-0002-0736-9199",
+    "resources": [
+      {
+        "id": "geno",
+        "name": "Genotype Ontology",
+        "url": "http://purl.obolibrary.org/obo/geno.owl",
+        "version": "2022-03-05",
+        "namespacePrefix": "GENO",
+        "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+      },
+      {
+        "id": "hgnc",
+        "name": "HUGO Gene Nomenclature Committee",
+        "url": "https://www.genenames.org",
+        "version": "06/01/23",
+        "namespacePrefix": "HGNC",
+        "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"
+      },
+      {
+        "id": "omim",
+        "name": "An Online Catalog of Human Genes and Genetic Disorders",
+        "url": "https://www.omim.org",
+        "version": "January 4, 2023",
+        "namespacePrefix": "OMIM",
+        "iriPrefix": "https://www.omim.org/entry/"
+      },
+      {
+        "id": "so",
+        "name": "Sequence types and features ontology",
+        "url": "http://purl.obolibrary.org/obo/so.obo",
+        "version": "2021-11-22",
+        "namespacePrefix": "SO",
+        "iriPrefix": "http://purl.obolibrary.org/obo/SO_"
+      },
+      {
+        "id": "hp",
+        "name": "human phenotype ontology",
+        "url": "http://purl.obolibrary.org/obo/hp.owl",
+        "version": "2024-08-13",
+        "namespacePrefix": "HP",
+        "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+      }
+    ],
+    "phenopacketSchemaVersion": "2.0",
+    "externalReferences": [
+      {
+        "id": "PMID:21548011",
+        "reference": "https://pubmed.ncbi.nlm.nih.gov/21548011",
+        "description": "Congenital pancytopenia and absence of B lymphocytes in a neonate with a mutation in the Ikaros gene"
+      }
+    ]
+  }
+}