TBCK

monarch-initiative · Oct 4, 2024 · 248a36d · 248a36d
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diff --git a/notebooks/TBCK/TBCK_IHPRF3_individuals.ipynb b/notebooks/TBCK/TBCK_IHPRF3_individuals.ipynb
diff --git a/notebooks/TBCK/input/TBCK_IHPRF3_individuals.xlsx b/notebooks/TBCK/input/TBCK_IHPRF3_individuals.xlsx
diff --git a/notebooks/TBCK/phenopackets/PMID_27040691_Individual1-1a.json b/notebooks/TBCK/phenopackets/PMID_27040691_Individual1-1a.json
@@ -1,12 +1,20 @@
 {
-  "id": "PMID_27040691_Individual_1-1a",
+  "id": "PMID_27040691_Individual_1_1a",
   "subject": {
     "id": "Individual 1-1a",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P5Y"
       }
     },
+    "vitalStatus": {
+      "status": "DECEASED",
+      "timeOfDeath": {
+        "age": {
+          "iso8601duration": "P5Y"
+        }
+      }
+    },
     "sex": "MALE"
   },
   "phenotypicFeatures": [
@@ -315,7 +323,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-04-28T17:04:44.479068994Z",
+    "created": "2024-10-04T18:13:39.631210088Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -354,7 +362,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-26",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/TBCK/phenopackets/PMID_27040691_Individual1-2a.json b/notebooks/TBCK/phenopackets/PMID_27040691_Individual1-2a.json
@@ -1,12 +1,15 @@
 {
-  "id": "PMID_27040691_Individual_1-2a",
+  "id": "PMID_27040691_Individual_1_2a",
   "subject": {
     "id": "Individual 1-2a",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P11Y"
       }
     },
+    "vitalStatus": {
+      "status": "ALIVE"
+    },
     "sex": "FEMALE"
   },
   "phenotypicFeatures": [
@@ -311,7 +314,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-04-28T17:04:44.480370998Z",
+    "created": "2024-10-04T18:13:39.632406949Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -350,7 +353,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-26",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/TBCK/phenopackets/PMID_27040691_Individual2-1.json b/notebooks/TBCK/phenopackets/PMID_27040691_Individual2-1.json
@@ -1,12 +1,15 @@
 {
-  "id": "PMID_27040691_Individual_2-1",
+  "id": "PMID_27040691_Individual_2_1",
   "subject": {
     "id": "Individual 2-1",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P5Y"
       }
     },
+    "vitalStatus": {
+      "status": "ALIVE"
+    },
     "sex": "MALE"
   },
   "phenotypicFeatures": [
@@ -314,7 +317,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-04-28T17:04:44.481378078Z",
+    "created": "2024-10-04T18:13:39.633231163Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -353,7 +356,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-26",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/TBCK/phenopackets/PMID_27040691_Individual3-1.json b/notebooks/TBCK/phenopackets/PMID_27040691_Individual3-1.json
@@ -1,12 +1,15 @@
 {
-  "id": "PMID_27040691_Individual_3-1",
+  "id": "PMID_27040691_Individual_3_1",
   "subject": {
     "id": "Individual 3-1",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P11Y"
       }
     },
+    "vitalStatus": {
+      "status": "ALIVE"
+    },
     "sex": "MALE"
   },
   "phenotypicFeatures": [
@@ -320,7 +323,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-04-28T17:04:44.482364892Z",
+    "created": "2024-10-04T18:13:39.633987188Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -359,7 +362,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-26",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/TBCK/phenopackets/PMID_27040691_Individual4-1.json b/notebooks/TBCK/phenopackets/PMID_27040691_Individual4-1.json
@@ -1,12 +1,15 @@
 {
-  "id": "PMID_27040691_Individual_4-1",
+  "id": "PMID_27040691_Individual_4_1",
   "subject": {
     "id": "Individual 4-1",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P4Y"
       }
     },
+    "vitalStatus": {
+      "status": "ALIVE"
+    },
     "sex": "FEMALE"
   },
   "phenotypicFeatures": [
@@ -344,7 +347,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-04-28T17:04:44.483371019Z",
+    "created": "2024-10-04T18:13:39.635034799Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -383,7 +386,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-26",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/TBCK/phenopackets/PMID_27040691_Individual4-2.json b/notebooks/TBCK/phenopackets/PMID_27040691_Individual4-2.json
@@ -1,12 +1,15 @@
 {
-  "id": "PMID_27040691_Individual_4-2",
+  "id": "PMID_27040691_Individual_4_2",
   "subject": {
     "id": "Individual 4-2",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P2Y"
       }
     },
+    "vitalStatus": {
+      "status": "ALIVE"
+    },
     "sex": "FEMALE"
   },
   "phenotypicFeatures": [
@@ -357,7 +360,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-04-28T17:04:44.484419107Z",
+    "created": "2024-10-04T18:13:39.636062860Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -396,7 +399,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-26",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/TBCK/phenopackets/PMID_27040691_Individual5-1.json b/notebooks/TBCK/phenopackets/PMID_27040691_Individual5-1.json
@@ -1,12 +1,15 @@
 {
-  "id": "PMID_27040691_Individual_5-1",
+  "id": "PMID_27040691_Individual_5_1",
   "subject": {
     "id": "Individual 5-1",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P10Y"
       }
     },
+    "vitalStatus": {
+      "status": "ALIVE"
+    },
     "sex": "FEMALE"
   },
   "phenotypicFeatures": [
@@ -307,7 +310,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-04-28T17:04:44.485736846Z",
+    "created": "2024-10-04T18:13:39.636994123Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -346,7 +349,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-26",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/TBCK/phenopackets/PMID_27040691_Individual6-1.json b/notebooks/TBCK/phenopackets/PMID_27040691_Individual6-1.json
@@ -1,12 +1,15 @@
 {
-  "id": "PMID_27040691_Individual_6-1",
+  "id": "PMID_27040691_Individual_6_1",
   "subject": {
     "id": "Individual 6-1",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P12Y"
       }
     },
+    "vitalStatus": {
+      "status": "ALIVE"
+    },
     "sex": "MALE"
   },
   "phenotypicFeatures": [
@@ -317,7 +320,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-04-28T17:04:44.486725807Z",
+    "created": "2024-10-04T18:13:39.637748003Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -356,7 +359,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-26",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/TBCK/phenopackets/PMID_27040691_Individual6-2.json b/notebooks/TBCK/phenopackets/PMID_27040691_Individual6-2.json
@@ -1,12 +1,15 @@
 {
-  "id": "PMID_27040691_Individual_6-2",
+  "id": "PMID_27040691_Individual_6_2",
   "subject": {
     "id": "Individual 6-2",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P3Y"
       }
     },
+    "vitalStatus": {
+      "status": "ALIVE"
+    },
     "sex": "FEMALE"
   },
   "phenotypicFeatures": [
@@ -327,7 +330,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-04-28T17:04:44.487763881Z",
+    "created": "2024-10-04T18:13:39.638494014Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -366,7 +369,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-26",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/TBCK/phenopackets/PMID_27040691_Individual7-1.json b/notebooks/TBCK/phenopackets/PMID_27040691_Individual7-1.json
@@ -1,12 +1,15 @@
 {
-  "id": "PMID_27040691_Individual_7-1",
+  "id": "PMID_27040691_Individual_7_1",
   "subject": {
     "id": "Individual 7-1",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P6Y"
       }
     },
+    "vitalStatus": {
+      "status": "ALIVE"
+    },
     "sex": "MALE"
   },
   "phenotypicFeatures": [
@@ -323,7 +326,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-04-28T17:04:44.488849878Z",
+    "created": "2024-10-04T18:13:39.639515876Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -362,7 +365,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-26",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/TBCK/phenopackets/PMID_27040691_Individual8-1.json b/notebooks/TBCK/phenopackets/PMID_27040691_Individual8-1.json
@@ -1,12 +1,15 @@
 {
-  "id": "PMID_27040691_Individual_8-1",
+  "id": "PMID_27040691_Individual_8_1",
   "subject": {
     "id": "Individual 8-1",
     "timeAtLastEncounter": {
       "age": {
         "iso8601duration": "P12Y"
       }
     },
+    "vitalStatus": {
+      "status": "ALIVE"
+    },
     "sex": "FEMALE"
   },
   "phenotypicFeatures": [
@@ -311,7 +314,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-04-28T17:04:44.489935874Z",
+    "created": "2024-10-04T18:13:39.640480995Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -350,7 +353,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-04-26",
+        "version": "2024-08-13",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }