update SPTAN1

monarch-initiative · Jan 19, 2025 · c0956be · c0956be
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diff --git a/notebooks/ITPR1/input/ITPR1_GLSP_individuals.xlsx b/notebooks/ITPR1/input/ITPR1_GLSP_individuals.xlsx
diff --git a/notebooks/NF1/NF1_NF1_individuals.ipynb b/notebooks/NF1/NF1_NF1_individuals.ipynb
@@ -22,7 +22,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Using pyphetools version 0.9.100\n"
+      "Using pyphetools version 0.9.116\n"
      ]
     }
    ],
@@ -46,14 +46,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "HPO version 2024-08-13\n",
+      "HPO version 2024-12-12\n",
       "Created encoders for 55 fields\n",
       "Importing OMIM:162200, Neurofibromatosis, type 1, HGNC:7765, NF1,  NM_001042492.3\n",
       "We output 419 GA4GH phenopackets to the directory phenopackets\n"
@@ -68,7 +68,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -99,7 +99,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -494,7 +494,7 @@
        "<tr><td style=\"text-align: left;\">individual NF00908_GSM_GSM492702 (UNKNOWN; P1Y)</td><td style=\"text-align: left;\">Neurofibromatosis, type 1 (OMIM:162200)</td><td style=\"text-align: left;\">Type-1 microdeletion: chromosomal_deletion (SO:1000029)</td><td style=\"text-align: left;\">Plexiform neurofibroma (HP:0009732): onset ; Multiple cafe-au-lait spots (HP:0007565): onset ; excluded: Freckling (HP:0001480): onset ; excluded: Lisch nodules (HP:0009737): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Optic nerve glioma (HP:0009734): onset </td></tr>\n",
        "<tr><td style=\"text-align: left;\">individual GOD_GSM_GSM492703 (UNKNOWN; P13Y)</td><td style=\"text-align: left;\">Neurofibromatosis, type 1 (OMIM:162200)</td><td style=\"text-align: left;\">Type-1 microdeletion: chromosomal_deletion (SO:1000029)</td><td style=\"text-align: left;\">Plexiform neurofibroma (HP:0009732): onset ; Freckling (HP:0001480): onset ; Lisch nodules (HP:0009737): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Optic nerve glioma (HP:0009734): onset </td></tr>\n",
        "<tr><td style=\"text-align: left;\">individual TRI_GSM_GSM492704 (UNKNOWN; P37Y)</td><td style=\"text-align: left;\">Neurofibromatosis, type 1 (OMIM:162200)</td><td style=\"text-align: left;\">Type-2 microdeletion: chromosomal_deletion (SO:1000029)</td><td style=\"text-align: left;\">Neurofibroma (HP:0001067): onset ; Freckling (HP:0001480): onset ; Lisch nodules (HP:0009737): onset ; Optic nerve glioma (HP:0009734): onset ; excluded: Plexiform neurofibroma (HP:0009732): onset ; excluded: Scoliosis (HP:0002650): onset </td></tr>\n",
-       "<tr><td style=\"text-align: left;\">individual YAH_GSM_GSM492705 (UNKNOWN; P0.5Y)</td><td style=\"text-align: left;\">Neurofibromatosis, type 1 (OMIM:162200)</td><td style=\"text-align: left;\">Type-1 microdeletion: chromosomal_deletion (SO:1000029)</td><td style=\"text-align: left;\">excluded: Plexiform neurofibroma (HP:0009732): onset ; excluded: Freckling (HP:0001480): onset ; excluded: Lisch nodules (HP:0009737): onset ; excluded: Optic nerve glioma (HP:0009734): onset </td></tr>\n",
+       "<tr><td style=\"text-align: left;\">individual YAH_GSM_GSM492705 (UNKNOWN; P6M)</td><td style=\"text-align: left;\">Neurofibromatosis, type 1 (OMIM:162200)</td><td style=\"text-align: left;\">Type-1 microdeletion: chromosomal_deletion (SO:1000029)</td><td style=\"text-align: left;\">excluded: Plexiform neurofibroma (HP:0009732): onset ; excluded: Freckling (HP:0001480): onset ; excluded: Lisch nodules (HP:0009737): onset ; excluded: Optic nerve glioma (HP:0009734): onset </td></tr>\n",
        "<tr><td style=\"text-align: left;\">individual LAP_GSM_GSM492706 (UNKNOWN; P13Y)</td><td style=\"text-align: left;\">Neurofibromatosis, type 1 (OMIM:162200)</td><td style=\"text-align: left;\">Type-1 microdeletion: chromosomal_deletion (SO:1000029)</td><td style=\"text-align: left;\">Neurofibroma (HP:0001067): onset ; Freckling (HP:0001480): onset ; Lisch nodules (HP:0009737): onset ; Scoliosis (HP:0002650): onset ; excluded: Plexiform neurofibroma (HP:0009732): onset ; excluded: Optic nerve glioma (HP:0009734): onset </td></tr>\n",
        "<tr><td style=\"text-align: left;\">individual VID_GSM_GSM492707 (UNKNOWN; P26Y)</td><td style=\"text-align: left;\">Neurofibromatosis, type 1 (OMIM:162200)</td><td style=\"text-align: left;\">Type-2 microdeletion: chromosomal_deletion (SO:1000029)</td><td style=\"text-align: left;\">Plexiform neurofibroma (HP:0009732): onset ; Freckling (HP:0001480): onset ; Lisch nodules (HP:0009737): onset ; excluded: Scoliosis (HP:0002650): onset ; excluded: Optic nerve glioma (HP:0009734): onset </td></tr>\n",
        "<tr><td style=\"text-align: left;\">individual DEN_GSM_GSM492708 (UNKNOWN; P5Y)</td><td style=\"text-align: left;\">Neurofibromatosis, type 1 (OMIM:162200)</td><td style=\"text-align: left;\">Type-1 microdeletion: chromosomal_deletion (SO:1000029)</td><td style=\"text-align: left;\">Freckling (HP:0001480): onset ; excluded: Plexiform neurofibroma (HP:0009732): onset ; excluded: Lisch nodules (HP:0009737): onset ; excluded: Scoliosis (HP:0002650): onset </td></tr>\n",
@@ -745,7 +745,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.4"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/NF1/input/NF1_NF1_individuals.xlsx b/notebooks/NF1/input/NF1_NF1_individuals.xlsx
diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyBRA-R38individualRS.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyBRA-R38individualRS.json
@@ -211,7 +211,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.853703022Z",
+    "created": "2025-01-18T10:25:45.073851823Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -250,7 +250,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyCAR-R18010M61individualF.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyCAR-R18010M61individualF.json
@@ -144,7 +144,7 @@
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   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.873873949Z",
+    "created": "2025-01-18T10:25:45.094660043Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -183,7 +183,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyCAR-R655763individualRS.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyCAR-R655763individualRS.json
@@ -237,7 +237,7 @@
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   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.874291896Z",
+    "created": "2025-01-18T10:25:45.095085144Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -276,7 +276,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyCAR-R66800individualRS.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyCAR-R66800individualRS.json
@@ -235,7 +235,7 @@
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   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.873286962Z",
+    "created": "2025-01-18T10:25:45.094034910Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -274,7 +274,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyCAR-R8012M6individualNS.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyCAR-R8012M6individualNS.json
@@ -145,7 +145,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.874888896Z",
+    "created": "2025-01-18T10:25:45.095714092Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -184,7 +184,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyCAR-RNISindividualF.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyCAR-RNISindividualF.json
@@ -235,7 +235,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.875308990Z",
+    "created": "2025-01-18T10:25:45.096132040Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -274,7 +274,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAD-R3084individualRS.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAD-R3084individualRS.json
@@ -248,7 +248,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.877155065Z",
+    "created": "2025-01-18T10:25:45.097944974Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -287,7 +287,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAD-R3409individualRS.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAD-R3409individualRS.json
@@ -242,7 +242,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.877774Z",
+    "created": "2025-01-18T10:25:45.098533153Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -281,7 +281,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAD-R37001individualRS.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAD-R37001individualRS.json
@@ -240,7 +240,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.875894069Z",
+    "created": "2025-01-18T10:25:45.096693038Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -279,7 +279,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAD-R37101individualRS.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAD-R37101individualRS.json
@@ -222,7 +222,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.829215049Z",
+    "created": "2025-01-18T10:25:45.048570156Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -261,7 +261,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAD-R3793individualRS.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAD-R3793individualRS.json
@@ -246,7 +246,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.876536130Z",
+    "created": "2025-01-18T10:25:45.097366094Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -285,7 +285,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAD-R9232individualPrS.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAD-R9232individualPrS.json
@@ -251,7 +251,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.911190986Z",
+    "created": "2025-01-18T10:25:45.132597923Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -290,7 +290,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAN-R48902G-MindividualF.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAN-R48902G-MindividualF.json
@@ -158,7 +158,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.830527067Z",
+    "created": "2025-01-18T10:25:45.049861907Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -197,7 +197,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAN-R48902GindividualF.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAN-R48902GindividualF.json
@@ -247,7 +247,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.829886913Z",
+    "created": "2025-01-18T10:25:45.049227952Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -286,7 +286,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAN-R88088G-MindividualF.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAN-R88088G-MindividualF.json
@@ -213,7 +213,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.843034982Z",
+    "created": "2025-01-18T10:25:45.062798023Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -252,7 +252,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAN-R88088GindividualF.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAN-R88088GindividualF.json
@@ -225,7 +225,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.842298984Z",
+    "created": "2025-01-18T10:25:45.062088012Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -264,7 +264,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAN-R95417G-CindividualF.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAN-R95417G-CindividualF.json
@@ -256,7 +256,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.912932157Z",
+    "created": "2025-01-18T10:25:45.134305Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -295,7 +295,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }

diff --git a/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAN-R95417G-MindividualF.json b/notebooks/NF1/phenopackets/PMID_29290338_FamilyMAN-R95417G-MindividualF.json
@@ -194,7 +194,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-08-17T11:50:52.912433862Z",
+    "created": "2025-01-18T10:25:45.133779048Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {
@@ -233,7 +233,7 @@
         "id": "hp",
         "name": "human phenotype ontology",
         "url": "http://purl.obolibrary.org/obo/hp.owl",
-        "version": "2024-08-13",
+        "version": "2024-12-12",
         "namespacePrefix": "HP",
         "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
       }