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monarch-initiative · Nov 12, 2024 · cfb0ced · cfb0ced
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diff --git a/notebooks/WWOX/WWOX_DEE28_individuals.ipynb b/notebooks/WWOX/WWOX_DEE28_individuals.ipynb
diff --git a/notebooks/WWOX/WWOX_SCAR12_individuals.ipynb b/notebooks/WWOX/WWOX_SCAR12_individuals.ipynb
diff --git a/notebooks/WWOX/input/WWOX_DEE28_individuals.xlsx b/notebooks/WWOX/input/WWOX_DEE28_individuals.xlsx
diff --git a/notebooks/WWOX/phenopackets/PMID_24369382_Family1II1.json b/notebooks/WWOX/phenopackets/PMID_24369382_Family1II1.json
@@ -1,12 +1,13 @@
 {
-  "id": "PMID_24369382_Family_1_II.1",
+  "id": "PMID_24369382_Family_1_II_1",
   "subject": {
     "id": "Family 1 II.1",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P19Y"
       }
     },
+    "vitalStatus": {},
     "sex": "FEMALE"
   },
   "phenotypicFeatures": [
@@ -81,7 +82,7 @@
             "interpretationStatus": "CAUSATIVE",
             "variantInterpretation": {
               "variationDescriptor": {
-                "id": "var_eYNRBxNvYmgUbHigxXoHMRlIw",
+                "id": "var_OBJyleYGKBiPNGljtrHHBvbJZ",
                 "geneContext": {
                   "valueId": "HGNC:12799",
                   "symbol": "WWOX"
@@ -129,7 +130,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-03-27T21:44:02.633293151Z",
+    "created": "2024-11-12T08:04:44.274138927Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -168,7 +169,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-03-06",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/WWOX/phenopackets/PMID_24369382_Family1II2.json b/notebooks/WWOX/phenopackets/PMID_24369382_Family1II2.json
@@ -1,12 +1,13 @@
 {
-  "id": "PMID_24369382_Family_1_II.2",
+  "id": "PMID_24369382_Family_1_II_2",
   "subject": {
     "id": "Family 1 II.2",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P18Y"
       }
     },
+    "vitalStatus": {},
     "sex": "FEMALE"
   },
   "phenotypicFeatures": [
@@ -87,7 +88,7 @@
             "interpretationStatus": "CAUSATIVE",
             "variantInterpretation": {
               "variationDescriptor": {
-                "id": "var_eYNRBxNvYmgUbHigxXoHMRlIw",
+                "id": "var_OBJyleYGKBiPNGljtrHHBvbJZ",
                 "geneContext": {
                   "valueId": "HGNC:12799",
                   "symbol": "WWOX"
@@ -135,7 +136,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-03-27T21:44:02.636599063Z",
+    "created": "2024-11-12T08:04:44.274778127Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -174,7 +175,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-03-06",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/WWOX/phenopackets/PMID_24369382_Family1II3.json b/notebooks/WWOX/phenopackets/PMID_24369382_Family1II3.json
@@ -1,12 +1,13 @@
 {
-  "id": "PMID_24369382_Family_1_II.3",
+  "id": "PMID_24369382_Family_1_II_3",
   "subject": {
     "id": "Family 1 II.3",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P16Y"
       }
     },
+    "vitalStatus": {},
     "sex": "MALE"
   },
   "phenotypicFeatures": [
@@ -87,7 +88,7 @@
             "interpretationStatus": "CAUSATIVE",
             "variantInterpretation": {
               "variationDescriptor": {
-                "id": "var_eYNRBxNvYmgUbHigxXoHMRlIw",
+                "id": "var_OBJyleYGKBiPNGljtrHHBvbJZ",
                 "geneContext": {
                   "valueId": "HGNC:12799",
                   "symbol": "WWOX"
@@ -135,7 +136,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-03-27T21:44:02.638509988Z",
+    "created": "2024-11-12T08:04:44.275202035Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -174,7 +175,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-03-06",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/WWOX/phenopackets/PMID_24369382_Family1II4.json b/notebooks/WWOX/phenopackets/PMID_24369382_Family1II4.json
@@ -1,12 +1,13 @@
 {
-  "id": "PMID_24369382_Family_1_II.4",
+  "id": "PMID_24369382_Family_1_II_4",
   "subject": {
     "id": "Family 1 II.4",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P10Y"
       }
     },
+    "vitalStatus": {},
     "sex": "FEMALE"
   },
   "phenotypicFeatures": [
@@ -74,7 +75,7 @@
             "interpretationStatus": "CAUSATIVE",
             "variantInterpretation": {
               "variationDescriptor": {
-                "id": "var_eYNRBxNvYmgUbHigxXoHMRlIw",
+                "id": "var_OBJyleYGKBiPNGljtrHHBvbJZ",
                 "geneContext": {
                   "valueId": "HGNC:12799",
                   "symbol": "WWOX"
@@ -122,7 +123,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-03-27T21:44:02.640470981Z",
+    "created": "2024-11-12T08:04:44.275619983Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -161,7 +162,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-03-06",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/WWOX/phenopackets/PMID_24369382_Family2II1.json b/notebooks/WWOX/phenopackets/PMID_24369382_Family2II1.json
@@ -1,12 +1,13 @@
 {
-  "id": "PMID_24369382_Family_2_II.1",
+  "id": "PMID_24369382_Family_2_II_1",
   "subject": {
     "id": "Family 2 II.1",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P10Y"
       }
     },
+    "vitalStatus": {},
     "sex": "MALE"
   },
   "phenotypicFeatures": [
@@ -68,7 +69,7 @@
             "interpretationStatus": "CAUSATIVE",
             "variantInterpretation": {
               "variationDescriptor": {
-                "id": "var_WCrGJzoAmeRdstxtunYQcSMNu",
+                "id": "var_DZiNCKadKPUJpFaRcpPsyQUEV",
                 "geneContext": {
                   "valueId": "HGNC:12799",
                   "symbol": "WWOX"
@@ -117,7 +118,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-03-27T21:44:02.642099857Z",
+    "created": "2024-11-12T08:04:44.276021003Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -156,7 +157,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-03-06",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/WWOX/phenopackets/PMID_24369382_Family2II2.json b/notebooks/WWOX/phenopackets/PMID_24369382_Family2II2.json
@@ -1,12 +1,13 @@
 {
-  "id": "PMID_24369382_Family_2_II.2",
+  "id": "PMID_24369382_Family_2_II_2",
   "subject": {
     "id": "Family 2 II.2",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P5Y"
       }
     },
+    "vitalStatus": {},
     "sex": "FEMALE"
   },
   "phenotypicFeatures": [
@@ -68,7 +69,7 @@
             "interpretationStatus": "CAUSATIVE",
             "variantInterpretation": {
               "variationDescriptor": {
-                "id": "var_WCrGJzoAmeRdstxtunYQcSMNu",
+                "id": "var_DZiNCKadKPUJpFaRcpPsyQUEV",
                 "geneContext": {
                   "valueId": "HGNC:12799",
                   "symbol": "WWOX"
@@ -117,7 +118,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-03-27T21:44:02.644987821Z",
+    "created": "2024-11-12T08:04:44.276421070Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -156,7 +157,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-03-06",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/WWOX/phenopackets/PMID_25411445_Abdel-SalametalII4.json b/notebooks/WWOX/phenopackets/PMID_25411445_Abdel-SalametalII4.json
@@ -2,6 +2,7 @@
   "id": "PMID_25411445_Abdel_Salam_et_al_II_4",
   "subject": {
     "id": "Abdel-Salam et al II:4",
+    "vitalStatus": {},
     "sex": "FEMALE"
   },
   "phenotypicFeatures": [
@@ -163,15 +164,15 @@
             "interpretationStatus": "CAUSATIVE",
             "variantInterpretation": {
               "variationDescriptor": {
-                "id": "var_clLFLCUTUkTuCQvsKSrSitQmg",
+                "id": "var_AvnJyJMPmxXFRxiMExdQAdeLC",
                 "geneContext": {
                   "valueId": "HGNC:12799",
                   "symbol": "WWOX"
                 },
                 "expressions": [
                   {
                     "syntax": "hgvs.c",
-                    "value": "NM_016373.2:c.160C>T"
+                    "value": "NM_016373.4:c.160C>T"
                   },
                   {
                     "syntax": "hgvs.g",
@@ -206,7 +207,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-05-11T07:23:35.095093011Z",
+    "created": "2024-11-12T08:05:52.209033966Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -245,7 +246,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-04",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/WWOX/phenopackets/PMID_25411445_Patient1.json b/notebooks/WWOX/phenopackets/PMID_25411445_Patient1.json
@@ -7,6 +7,9 @@
         "iso8601duration": "P3Y"
       }
     },
+    "vitalStatus": {
+      "status": "ALIVE"
+    },
     "sex": "FEMALE"
   },
   "phenotypicFeatures": [
@@ -192,8 +195,8 @@
             "interpretationStatus": "CAUSATIVE",
             "variantInterpretation": {
               "variationDescriptor": {
-                "id": "var_nobCAXndhfLvtXtXdjSfevcUJ",
-                "label": "DEL:c.-366-?_516+?del",
+                "id": "var_mJMAkuNOpJsrfeYwUNIaezNqD",
+                "label": "DEL exon 1-5",
                 "geneContext": {
                   "valueId": "HGNC:12799",
                   "symbol": "WWOX"
@@ -215,8 +218,8 @@
             "interpretationStatus": "CAUSATIVE",
             "variantInterpretation": {
               "variationDescriptor": {
-                "id": "var_DUnShCaxABOmvgypSGBVHXazw",
-                "label": "DEL:c.517-?_1056+?del",
+                "id": "var_bfElexTqfwlLnSsYlZvfDrurc",
+                "label": "DEL exon 6-8",
                 "geneContext": {
                   "valueId": "HGNC:12799",
                   "symbol": "WWOX"
@@ -252,7 +255,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-05-11T07:23:35.087779998Z",
+    "created": "2024-11-12T08:05:52.205399036Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -291,7 +294,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-04",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }