STXBP1

monarch-initiative · Dec 6, 2024 · fb80b4f · fb80b4f
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diff --git a/notebooks/STXBP1/STXBP1_DEE4_Xian_2022.ipynb b/notebooks/STXBP1/STXBP1_DEE4_Xian_2022.ipynb
@@ -19,7 +19,9 @@
     "including prominent EEG findings.\n",
     "\n",
     "\n",
-    "According to the authors, patients with R406H and R406C mutations were more likely to have a burst suppression pattern on EEG and spastic tetraplegia, and less likely to have ataxia, compared to the rest of the cohort. Additionally, patients with premature termination mutations or deletions in the STXBP1 gene were more likely to have infantile spasms, hypsarrhythmia on EEG, ataxia, hypotonia, and neonatal seizure onset compared to patients with missense mutations."
+    "According to the authors, patients with R406H and R406C mutations were more likely to have a burst suppression pattern on EEG and spastic tetraplegia, and less likely to have ataxia, compared to the rest of the cohort. Additionally, patients with premature termination mutations or deletions in the STXBP1 gene were more likely to have infantile spasms, hypsarrhythmia on EEG, ataxia, hypotonia, and neonatal seizure onset compared to patients with missense mutations.\n",
+    "\n",
+    "Note that we have corrected HGVS syntax for several variants. We omit individual STX_23708187_T23289 because the variant is indicated as no cahnge at all: \"c.A1708A:p.T570T\", and thus we deem the diagnosis uncertain."
    ]
   },
   {
@@ -63,9 +65,9 @@
      "output_type": "stream",
      "text": [
       "HPO version 2024-08-13\n",
-      "Created encoders for 539 fields\n",
+      "Created encoders for 537 fields\n",
       "Importing OMIM:612164, Developmental and epileptic encephalopathy 4, HGNC:11444, STXBP1,  NM_001032221.6\n",
-      "We output 463 GA4GH phenopackets to the directory phenopackets\n"
+      "We output 462 GA4GH phenopackets to the directory phenopackets\n"
      ]
     }
    ],
@@ -83,7 +85,7 @@
      "data": {
       "text/html": [
        "<h2>Cohort validation</h2>\n",
-       "<p>Errors found with 200 of 463 phenopackets.</p>\n",
+       "<p>Errors found with 200 of 462 phenopackets.</p>\n",
        "<table style=\"border: 2px solid black; align: \"left\">\n",
        "<caption>Error counts</caption>\n",
        "<tr><th style=\"text-align: left;font-weight: bold;\">Level</th><th style=\"text-align: left;font-weight: bold;\">Error category</th><th style=\"text-align: left;font-weight: bold;\">Count</th></tr>\n",
@@ -113,11 +115,11 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[pyphetools] Ingested 463 GA4GH phenopackets.\n",
-      "[INFO] Extracted 463 from 463 phenopackets with OMIM:612164\n",
+      "[pyphetools] Ingested 462 GA4GH phenopackets.\n",
+      "[INFO] Extracted 462 from 462 phenopackets with OMIM:612164\n",
       "\n",
-      "\tDevelopmental and epileptic encephalopathy 4 (OMIM:612164): n=463\n",
-      "We found a total of 518 unique HPO terms\n",
+      "\tDevelopmental and epileptic encephalopathy 4 (OMIM:612164): n=462\n",
+      "We found a total of 516 unique HPO terms\n",
       "Extracted disease: Developmental and epileptic encephalopathy 4 (OMIM:612164)\n",
       "Wrote HPOA disease file to OMIM-612164.tab\n"
      ]

diff --git a/notebooks/STXBP1/input/STXBP1_DEE4_Xian_2022.xlsx b/notebooks/STXBP1/input/STXBP1_DEE4_Xian_2022.xlsx
diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_102.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_102.json
@@ -83,7 +83,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.341987133Z",
+    "created": "2024-12-04T14:10:42.553358078Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_129.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_129.json
@@ -89,7 +89,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.342273950Z",
+    "created": "2024-12-04T14:10:42.553658962Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_18469812_Subject_11.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_18469812_Subject_11.json
@@ -137,7 +137,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.252255916Z",
+    "created": "2024-12-04T14:10:42.467053174Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_18469812_Subject_3.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_18469812_Subject_3.json
@@ -125,7 +125,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.253368139Z",
+    "created": "2024-12-04T14:10:42.467839002Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
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diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_18469812_Subject_6.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_18469812_Subject_6.json
@@ -125,7 +125,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.253792047Z",
+    "created": "2024-12-04T14:10:42.468230962Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
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diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_18469812_Subject_7.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_18469812_Subject_7.json
@@ -131,7 +131,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.254164934Z",
+    "created": "2024-12-04T14:10:42.468593835Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_19557857_Patient_1.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_19557857_Patient_1.json
@@ -173,7 +173,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.254539012Z",
+    "created": "2024-12-04T14:10:42.468957901Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_19557857_Patient_2.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_19557857_Patient_2.json
@@ -137,7 +137,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.254956007Z",
+    "created": "2024-12-04T14:10:42.469402790Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
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diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20876469_Patient_1.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20876469_Patient_1.json
@@ -113,7 +113,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.255337953Z",
+    "created": "2024-12-04T14:10:42.469774007Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20876469_Patient_2.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20876469_Patient_2.json
@@ -125,7 +125,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.255668878Z",
+    "created": "2024-12-04T14:10:42.470100879Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20876469_Patient_3.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20876469_Patient_3.json
@@ -125,7 +125,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.256017923Z",
+    "created": "2024-12-04T14:10:42.470443964Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20876469_Patient_6.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20876469_Patient_6.json
@@ -155,7 +155,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.256357908Z",
+    "created": "2024-12-04T14:10:42.470798015Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_1655.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_1655.json
@@ -119,7 +119,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.256844997Z",
+    "created": "2024-12-04T14:10:42.471251964Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_1694.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_1694.json
@@ -125,7 +125,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.257221221Z",
+    "created": "2024-12-04T14:10:42.471615076Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
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diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_1751.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_1751.json
@@ -137,7 +137,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.257586002Z",
+    "created": "2024-12-04T14:10:42.471978902Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_1792.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_1792.json
@@ -143,7 +143,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.257997035Z",
+    "created": "2024-12-04T14:10:42.472344160Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_1979.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_1979.json
@@ -143,7 +143,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.258404016Z",
+    "created": "2024-12-04T14:10:42.472706079Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_1989.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_1989.json
@@ -119,7 +119,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.258816003Z",
+    "created": "2024-12-04T14:10:42.473108053Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_2103.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_2103.json
@@ -137,7 +137,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.259170055Z",
+    "created": "2024-12-04T14:10:42.473459959Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_2123.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_20887364_Subject_2123.json
@@ -143,7 +143,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.259541988Z",
+    "created": "2024-12-04T14:10:42.473828077Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
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diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21204804_Patient_1.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21204804_Patient_1.json
@@ -143,7 +143,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.259902954Z",
+    "created": "2024-12-04T14:10:42.474198102Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21204804_Patient_2.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21204804_Patient_2.json
@@ -107,7 +107,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.260282039Z",
+    "created": "2024-12-04T14:10:42.474581003Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21762454_Patient_1.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21762454_Patient_1.json
@@ -95,7 +95,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.260596036Z",
+    "created": "2024-12-04T14:10:42.474893093Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21770924_Patient_1.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21770924_Patient_1.json
@@ -173,7 +173,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.260916948Z",
+    "created": "2024-12-04T14:10:42.475212097Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21770924_Patient_2.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21770924_Patient_2.json
@@ -143,7 +143,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.261367082Z",
+    "created": "2024-12-04T14:10:42.475682973Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21770924_Patient_3.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21770924_Patient_3.json
@@ -161,7 +161,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.261765956Z",
+    "created": "2024-12-04T14:10:42.476083040Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21770924_Patient_5.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_21770924_Patient_5.json
@@ -166,7 +166,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.262186050Z",
+    "created": "2024-12-04T14:10:42.476500034Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_22596016_Case_Report.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_22596016_Case_Report.json
@@ -101,7 +101,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.262611865Z",
+    "created": "2024-12-04T14:10:42.476909160Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
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diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23020937_ES07E0046.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23020937_ES07E0046.json
@@ -137,7 +137,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.262917995Z",
+    "created": "2024-12-04T14:10:42.477218151Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
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diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23020937_MR_NET001.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23020937_MR_NET001.json
@@ -143,7 +143,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.263301849Z",
+    "created": "2024-12-04T14:10:42.477629899Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23020937_P4276.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23020937_P4276.json
@@ -113,7 +113,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.263751029Z",
+    "created": "2024-12-04T14:10:42.478039026Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23409955_Patient_A.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23409955_Patient_A.json
@@ -131,7 +131,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.264117956Z",
+    "created": "2024-12-04T14:10:42.478379011Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23409955_Patient_B.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23409955_Patient_B.json
@@ -269,7 +269,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.264491081Z",
+    "created": "2024-12-04T14:10:42.478732109Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23409955_Patient_D.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23409955_Patient_D.json
@@ -143,7 +143,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.265125036Z",
+    "created": "2024-12-04T14:10:42.479306936Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23409955_Patient_F.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23409955_Patient_F.json
@@ -119,7 +119,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.265536069Z",
+    "created": "2024-12-04T14:10:42.479715108Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23533165_Patient_1.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23533165_Patient_1.json
@@ -149,7 +149,7 @@
     }
   ],
   "metaData": {
-    "created": "2024-12-04T13:35:12.271394968Z",
+    "created": "2024-12-04T14:10:42.485141038Z",
     "createdBy": "ORCID:0000-0002-0736-9199",
     "resources": [
       {

diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23533165_Patient_2.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23533165_Patient_2.json
@@ -119,7 +119,7 @@
     }
   ],
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diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23708187_T1266.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23708187_T1266.json
@@ -77,7 +77,7 @@
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diff --git a/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23708187_T22595.json b/notebooks/STXBP1/phenopackets/PMID_35190816_STX_23708187_T22595.json
@@ -77,7 +77,7 @@
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