WBP4

monarch-initiative · Dec 14, 2024 · d98a0b2 · d98a0b2
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diff --git a/notebooks/WBP4/WBP4_NEDHFDB_individuals.ipynb b/notebooks/WBP4/WBP4_NEDHFDB_individuals.ipynb
diff --git a/notebooks/WBP4/input/WBP4_NEDHFDB_individuals.xlsx b/notebooks/WBP4/input/WBP4_NEDHFDB_individuals.xlsx
diff --git a/notebooks/WBP4/phenopackets/PMID_37963460_Family1individualIII1.json b/notebooks/WBP4/phenopackets/PMID_37963460_Family1individualIII1.json
diff --git a/notebooks/WBP4/phenopackets/PMID_37963460_Family1individualIII4.json b/notebooks/WBP4/phenopackets/PMID_37963460_Family1individualIII4.json
@@ -0,0 +1,189 @@
+{
+  "id": "PMID_37963460_Family_1_individual_III_4",
+  "subject": {
+    "id": "Family 1 individual III:4",
+    "vitalStatus": {},
+    "sex": "FEMALE"
+  },
+  "phenotypicFeatures": [
+    {
+      "type": {
+        "id": "HP:0001263",
+        "label": "Global developmental delay"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0006695",
+        "label": "Atrioventricular canal defect"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000126",
+        "label": "Hydronephrosis"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0002023",
+        "label": "Anal atresia"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0001562",
+        "label": "Oligohydramnios"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0001561",
+        "label": "Polyhydramnios"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0001629",
+        "label": "Ventricular septal defect"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0001631",
+        "label": "Atrial septal defect"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0001653",
+        "label": "Mitral regurgitation"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0001643",
+        "label": "Patent ductus arteriosus"
+      },
+      "excluded": true
+    }
+  ],
+  "interpretations": [
+    {
+      "id": "Family 1 individual III:4",
+      "progressStatus": "SOLVED",
+      "diagnosis": {
+        "disease": {
+          "id": "OMIM:620852",
+          "label": "Neurodevelopemental disorder with hypotonia, feeding difficulties, facial dysmorphism, and brain abnormalities"
+        },
+        "genomicInterpretations": [
+          {
+            "subjectOrBiosampleId": "Family 1 individual III:4",
+            "interpretationStatus": "CAUSATIVE",
+            "variantInterpretation": {
+              "variationDescriptor": {
+                "id": "var_hjZUbMjgDyuaczHMjaYoDNDTH",
+                "geneContext": {
+                  "valueId": "HGNC:12739",
+                  "symbol": "WBP4"
+                },
+                "expressions": [
+                  {
+                    "syntax": "hgvs.c",
+                    "value": "NM_007187.5:c.499del"
+                  },
+                  {
+                    "syntax": "hgvs.g",
+                    "value": "NC_000013.11:g.41072794del"
+                  }
+                ],
+                "vcfRecord": {
+                  "genomeAssembly": "hg38",
+                  "chrom": "chr13",
+                  "pos": "41072793",
+                  "ref": "GA",
+                  "alt": "G"
+                },
+                "moleculeContext": "genomic",
+                "allelicState": {
+                  "id": "GENO:0000136",
+                  "label": "homozygous"
+                }
+              }
+            }
+          }
+        ]
+      }
+    }
+  ],
+  "diseases": [
+    {
+      "term": {
+        "id": "OMIM:620852",
+        "label": "Neurodevelopemental disorder with hypotonia, feeding difficulties, facial dysmorphism, and brain abnormalities"
+      }
+    }
+  ],
+  "metaData": {
+    "created": "2024-12-14T20:12:20.733358144Z",
+    "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": "2024-12-12",
+        "namespacePrefix": "HP",
+        "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+      }
+    ],
+    "phenopacketSchemaVersion": "2.0",
+    "externalReferences": [
+      {
+        "id": "PMID:37963460",
+        "reference": "https://pubmed.ncbi.nlm.nih.gov/37963460",
+        "description": "Bi-allelic loss-of-function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental syndrome"
+      }
+    ]
+  }
+}