new MAPK8IP3 phenopackets

monarch-initiative · Sep 20, 2023 · 1435c3f · 1435c3f
1 parent 8459bef
commit 1435c3f
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diff --git a/...APK8IP3/phenopackets/PMID_30612693_1.json → ...books/MAPK8IP3/input/PMID_30612693_1.json b/...APK8IP3/phenopackets/PMID_30612693_1.json → ...books/MAPK8IP3/input/PMID_30612693_1.json
@@ -1,5 +1,5 @@
 {
-  "id": "1",
+  "id": "PMID_30612693_1",
   "subject": {
     "id": "1",
     "timeAtLastEncounter": {
@@ -14,92 +14,82 @@
       "type": {
         "id": "HP:0001251",
         "label": "Ataxia"
-      },
-      "onset": {
-        "age": {
-          "iso8601duration": "P14Y8M"
-        }
       }
     },
     {
       "type": {
-        "id": "HP:0001263",
-        "label": "Global developmental delay"
-      },
-      "onset": {
-        "age": {
-          "iso8601duration": "P14Y8M"
-        }
+        "id": "HP:0002342",
+        "label": "Intellectual disability, moderate"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0002342",
+        "label": "Intellectual disability, moderate"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001272",
+        "label": "Cerebellar atrophy"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000712",
+        "label": "Emotional lability"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0002650",
+        "label": "Scoliosis"
       }
     },
     {
       "type": {
         "id": "HP:0002376",
         "label": "Developmental regression"
       },
-      "excluded": true,
-      "onset": {
-        "age": {
-          "iso8601duration": "P14Y8M"
-        }
-      }
+      "excluded": true
     },
     {
       "type": {
         "id": "HP:0000717",
         "label": "Autism"
-      },
-      "onset": {
-        "age": {
-          "iso8601duration": "P14Y8M"
-        }
       }
     },
     {
       "type": {
         "id": "HP:0001252",
         "label": "Hypotonia"
-      },
-      "onset": {
-        "age": {
-          "iso8601duration": "P14Y8M"
-        }
       }
     },
     {
       "type": {
         "id": "HP:0100022",
         "label": "Abnormality of movement"
       },
-      "excluded": true,
-      "onset": {
-        "age": {
-          "iso8601duration": "P14Y8M"
-        }
-      }
+      "excluded": true
     },
     {
       "type": {
         "id": "HP:0100704",
         "label": "Cerebral visual impairment"
       },
-      "excluded": true,
-      "onset": {
-        "age": {
-          "iso8601duration": "P14Y8M"
-        }
-      }
+      "excluded": true
     },
     {
       "type": {
         "id": "HP:0001250",
         "label": "Seizure"
       },
-      "excluded": true,
-      "onset": {
-        "age": {
-          "iso8601duration": "P14Y8M"
-        }
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0001263",
+        "label": "Global developmental delay"
       }
     }
   ],
@@ -109,7 +99,7 @@
       "progressStatus": "SOLVED",
       "diagnosis": {
         "disease": {
-          "id": "618443",
+          "id": "OMIM:618443",
           "label": "Neurodevelopmental disorder with or without variable brain abnormalities"
         },
         "genomicInterpretations": [
@@ -118,14 +108,15 @@
             "interpretationStatus": "CAUSATIVE",
             "variantInterpretation": {
               "variationDescriptor": {
+                "id": "var_FLnzUDQSxWwunMdLEGBiUcwmZ",
                 "geneContext": {
                   "valueId": "HGNC:6884",
                   "symbol": "MAPK8IP3"
                 },
                 "expressions": [
                   {
                     "syntax": "hgvs.c",
-                    "value": "NM_015133.4:c.65del"
+                    "value": "NM_001318852.2:c.65del"
                   },
                   {
                     "syntax": "hgvs.g",
@@ -152,7 +143,7 @@
     }
   ],
   "metaData": {
-    "created": "2023-01-10T17:24:09.598505973Z",
+    "created": "2023-09-19T16:34:36.554000377Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -179,15 +170,30 @@
         "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": "2022-12-15",
+        "version": "2023-09-01",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }
     ],
-    "phenopacketSchemaVersion": "2.0"
+    "phenopacketSchemaVersion": "2.0",
+    "externalReferences": [
+      {
+        "id": "PMID:30612693",
+        "reference": "https://pubmed.ncbi.nlm.nih.gov/30612693",
+        "description": "De Novo Variants in MAPK8IP3 Cause Intellectual Disability with Variable Brain Anomalies"
+      }
+    ]
   }
 }
diff --git a/...PK8IP3/phenopackets/PMID_30612693_10.json → ...ooks/MAPK8IP3/input/PMID_30612693_10.json b/...PK8IP3/phenopackets/PMID_30612693_10.json → ...ooks/MAPK8IP3/input/PMID_30612693_10.json
@@ -1,5 +1,5 @@
 {
-  "id": "10",
+  "id": "PMID_30612693_10",
   "subject": {
     "id": "10",
     "timeAtLastEncounter": {
@@ -10,72 +10,42 @@
     "sex": "MALE"
   },
   "phenotypicFeatures": [
-    {
-      "type": {
-        "id": "HP:0001263",
-        "label": "Global developmental delay"
-      },
-      "onset": {
-        "age": {
-          "iso8601duration": "P4Y"
-        }
-      }
-    },
     {
       "type": {
         "id": "HP:0002342",
         "label": "Intellectual disability, moderate"
-      },
-      "onset": {
-        "age": {
-          "iso8601duration": "P4Y"
-        }
       }
     },
     {
       "type": {
         "id": "HP:0002376",
         "label": "Developmental regression"
       },
-      "excluded": true,
-      "onset": {
-        "age": {
-          "iso8601duration": "P4Y"
-        }
-      }
+      "excluded": true
     },
     {
       "type": {
         "id": "HP:0000717",
         "label": "Autism"
       },
-      "excluded": true,
-      "onset": {
-        "age": {
-          "iso8601duration": "P4Y"
-        }
-      }
+      "excluded": true
     },
     {
       "type": {
         "id": "HP:0001252",
         "label": "Hypotonia"
-      },
-      "onset": {
-        "age": {
-          "iso8601duration": "P4Y"
-        }
       }
     },
     {
       "type": {
         "id": "HP:0001250",
         "label": "Seizure"
-      },
-      "onset": {
-        "age": {
-          "iso8601duration": "P4Y"
-        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001263",
+        "label": "Global developmental delay"
       }
     }
   ],
@@ -85,7 +55,7 @@
       "progressStatus": "SOLVED",
       "diagnosis": {
         "disease": {
-          "id": "618443",
+          "id": "OMIM:618443",
           "label": "Neurodevelopmental disorder with or without variable brain abnormalities"
         },
         "genomicInterpretations": [
@@ -94,14 +64,15 @@
             "interpretationStatus": "CAUSATIVE",
             "variantInterpretation": {
               "variationDescriptor": {
+                "id": "var_JYitIepHRmwbwGTVXnHnlIRjt",
                 "geneContext": {
                   "valueId": "HGNC:6884",
                   "symbol": "MAPK8IP3"
                 },
                 "expressions": [
                   {
                     "syntax": "hgvs.c",
-                    "value": "NM_015133.4:c.2982C>G"
+                    "value": "NM_001318852.2:c.2985C>G"
                   },
                   {
                     "syntax": "hgvs.g",
@@ -128,7 +99,7 @@
     }
   ],
   "metaData": {
-    "created": "2023-01-10T17:24:09.598505973Z",
+    "created": "2023-09-19T16:34:36.554000377Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -155,15 +126,30 @@
         "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": "2022-12-15",
+        "version": "2023-09-01",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }
     ],
-    "phenopacketSchemaVersion": "2.0"
+    "phenopacketSchemaVersion": "2.0",
+    "externalReferences": [
+      {
+        "id": "PMID:30612693",
+        "reference": "https://pubmed.ncbi.nlm.nih.gov/30612693",
+        "description": "De Novo Variants in MAPK8IP3 Cause Intellectual Disability with Variable Brain Anomalies"
+      }
+    ]
   }
 }