KBG

monarch-initiative · Nov 25, 2023 · 54fb41e · 54fb41e
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diff --git a/notebooks/ANKRD11/Martinez-Cayuelas-KBG-2022.ipynb b/notebooks/ANKRD11/Martinez-Cayuelas-KBG-2022.ipynb
diff --git a/notebooks/ANKRD11/input/Martinez-KBG-SupplTable-340-v2.xlsx b/notebooks/ANKRD11/input/Martinez-KBG-SupplTable-340-v2.xlsx
diff --git a/notebooks/ANKRD11/phenopackets/PMID_36446582_Alves2019.json b/notebooks/ANKRD11/phenopackets/PMID_36446582_Alves2019.json
@@ -0,0 +1,141 @@
+{
+  "id": "PMID_36446582_Alves,_2019",
+  "subject": {
+    "id": "Alves, 2019",
+    "timeAtLastEncounter": {
+      "age": {
+        "iso8601duration": "P2Y"
+      }
+    },
+    "sex": "FEMALE"
+  },
+  "phenotypicFeatures": [
+    {
+      "type": {
+        "id": "HP:0001572",
+        "label": "Macrodontia"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001155",
+        "label": "Abnormality of the hand"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0004322",
+        "label": "Short stature"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000365",
+        "label": "Hearing impairment"
+      }
+    }
+  ],
+  "interpretations": [
+    {
+      "id": "Alves, 2019",
+      "progressStatus": "SOLVED",
+      "diagnosis": {
+        "disease": {
+          "id": "OMIM:148050",
+          "label": "KBG syndrome"
+        },
+        "genomicInterpretations": [
+          {
+            "subjectOrBiosampleId": "Alves, 2019",
+            "interpretationStatus": "CAUSATIVE",
+            "variantInterpretation": {
+              "variationDescriptor": {
+                "id": "var_rINdzLNehXDQccIlUhmVIRVBW",
+                "geneContext": {
+                  "valueId": "HGNC:21316",
+                  "symbol": "ANKRD11"
+                },
+                "expressions": [
+                  {
+                    "syntax": "hgvs.c",
+                    "value": "NM_013275.6:c.5145C>G"
+                  },
+                  {
+                    "syntax": "hgvs.g",
+                    "value": "NC_000016.10:g.89281397G>C"
+                  }
+                ],
+                "vcfRecord": {
+                  "genomeAssembly": "hg38",
+                  "chrom": "chr16",
+                  "pos": "89281397",
+                  "ref": "G",
+                  "alt": "C"
+                },
+                "moleculeContext": "genomic",
+                "allelicState": {
+                  "id": "GENO:0000135",
+                  "label": "heterozygous"
+                }
+              }
+            }
+          }
+        ]
+      }
+    }
+  ],
+  "metaData": {
+    "created": "2023-11-25T12:07:35.880573034Z",
+    "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": "2023-10-09",
+        "namespacePrefix": "HP",
+        "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+      }
+    ],
+    "phenopacketSchemaVersion": "2.0",
+    "externalReferences": [
+      {
+        "id": "PMID:36446582",
+        "reference": "https://pubmed.ncbi.nlm.nih.gov/36446582",
+        "description": "Clinical description, molecular delineation and genotype-phenotype correlation in 340 patients with KBG syndrome: addition of 67 new patients"
+      }
+    ]
+  }
+}
diff --git a/notebooks/ANKRD11/phenopackets/PMID_36446582_Behnert2018.json b/notebooks/ANKRD11/phenopackets/PMID_36446582_Behnert2018.json
@@ -0,0 +1,173 @@
+{
+  "id": "PMID_36446582_Behnert,_2018",
+  "subject": {
+    "id": "Behnert, 2018",
+    "timeAtLastEncounter": {
+      "age": {
+        "iso8601duration": "P2Y"
+      }
+    },
+    "sex": "MALE"
+  },
+  "phenotypicFeatures": [
+    {
+      "type": {
+        "id": "HP:0001249",
+        "label": "Intellectual disability"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001572",
+        "label": "Macrodontia"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0010938",
+        "label": "Abnormal external nose morphology"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000325",
+        "label": "Triangular face"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000574",
+        "label": "Thick eyebrow"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000356",
+        "label": "Abnormality of the outer ear"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001155",
+        "label": "Abnormality of the hand"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0004322",
+        "label": "Short stature"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000365",
+        "label": "Hearing impairment"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000729",
+        "label": "Autistic behavior"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0007018",
+        "label": "Attention deficit hyperactivity disorder"
+      },
+      "excluded": true
+    }
+  ],
+  "interpretations": [
+    {
+      "id": "Behnert, 2018",
+      "progressStatus": "SOLVED",
+      "diagnosis": {
+        "disease": {
+          "id": "OMIM:148050",
+          "label": "KBG syndrome"
+        },
+        "genomicInterpretations": [
+          {
+            "subjectOrBiosampleId": "Behnert, 2018",
+            "interpretationStatus": "CAUSATIVE",
+            "variantInterpretation": {
+              "variationDescriptor": {
+                "id": "var_GntpvqcrHznGBFoutpNQVGWmu",
+                "label": "16q24.3(88854757_89577705)x1 (hg19)",
+                "geneContext": {
+                  "valueId": "HGNC:21316",
+                  "symbol": "ANKRD11"
+                },
+                "moleculeContext": "genomic",
+                "structuralType": {
+                  "id": "SO:1000029",
+                  "label": "chromosomal_deletion"
+                },
+                "allelicState": {
+                  "id": "GENO:0000135",
+                  "label": "heterozygous"
+                }
+              }
+            }
+          }
+        ]
+      }
+    }
+  ],
+  "metaData": {
+    "created": "2023-11-25T12:07:35.892725944Z",
+    "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": "2023-10-09",
+        "namespacePrefix": "HP",
+        "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+      }
+    ],
+    "phenopacketSchemaVersion": "2.0",
+    "externalReferences": [
+      {
+        "id": "PMID:36446582",
+        "reference": "https://pubmed.ncbi.nlm.nih.gov/36446582",
+        "description": "Clinical description, molecular delineation and genotype-phenotype correlation in 340 patients with KBG syndrome: addition of 67 new patients"
+      }
+    ]
+  }
+}