add primekg

EBISPOT · Jan 8, 2025 · 7c19443 · 7c19443
1 parent 4d087db
commit 7c19443
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Showing 6 changed files with 47 additions and 5 deletions.
diff --git a/dataload/00_fetch_data/primekg/fetch.sh b/dataload/00_fetch_data/primekg/fetch.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+curl -L https://dataverse.harvard.edu/api/access/datafile/6180620 > kg.csv
+
+
diff --git a/dataload/01_ingest/primekg.py b/dataload/01_ingest/primekg.py
@@ -0,0 +1,26 @@
+
+import pandas
+import sys
+import json
+
+df = pandas.read_csv(sys.stdin, dtype=str)
+
+for row in df.to_dict(orient="records"):
+
+    x_id = row['x_source'] + ':' + row['x_id']
+    y_id = row['y_source'] + ':' + row['y_id']
+
+    res = {
+        'id': x_id,
+        'grebi:name': row['x_name']
+    }
+
+    res["primekg:" + row['relation']] = {
+        'grebi:value': y_id,
+        'grebi:properties': {f"primekg:{key}": value for key, value in row.items()}
+    }
+
+    print(json.dumps(res))
+
+
+
diff --git a/dataload/configs/datasource_configs/primekg.yaml b/dataload/configs/datasource_configs/primekg.yaml
@@ -0,0 +1,6 @@
+name: PrimeKG
+enabled: true
+ingests:
+  - globs: ["./00_fetch_data/primekg/kg.csv"]
+    command: $GREBI_DATALOAD_HOME/01_ingest/primekg.py
+
diff --git a/dataload/configs/subgraph_configs/ebi_monarch.json b/dataload/configs/subgraph_configs/ebi_monarch.json
@@ -30,7 +30,8 @@
     "mondo:0000001",
     "efo:0000408",
     "chebi:36080",
-    "chebi:24431"
+    "chebi:24431",
+    "biolink:ChemicalEntity"
   ],
   "additional_equivalence_groups": [
     [
@@ -167,6 +168,7 @@
     "./configs/datasource_configs/robokop_string.yaml",
     "./configs/datasource_configs/robokop_textmining.yaml",
     "./configs/datasource_configs/robokop_viralproteome.yaml",
-    "./configs/datasource_configs/mesh.yaml"
+    "./configs/datasource_configs/mesh.yaml",
+    "./configs/datasource_configs/primekg.yaml"
   ]
 }
diff --git a/dataload/configs/subgraph_configs/ebi_monarch_xspecies.json b/dataload/configs/subgraph_configs/ebi_monarch_xspecies.json
@@ -31,7 +31,8 @@
     "mondo:0000001",
     "efo:0000408",
     "chebi:36080",
-    "chebi:24431"
+    "chebi:24431",
+    "biolink:ChemicalEntity"
   ],
   "additional_equivalence_groups": [
     [
@@ -168,6 +169,7 @@
     "./configs/datasource_configs/robokop_string.yaml",
     "./configs/datasource_configs/robokop_textmining.yaml",
     "./configs/datasource_configs/robokop_viralproteome.yaml",
-    "./configs/datasource_configs/mesh.yaml"
+    "./configs/datasource_configs/mesh.yaml",
+    "./configs/datasource_configs/primekg.yaml"
   ]
 }
diff --git a/dataload/configs/subgraph_configs/src/ebi_monarch.py b/dataload/configs/subgraph_configs/src/ebi_monarch.py
@@ -37,7 +37,8 @@
     "./configs/datasource_configs/robokop_string.yaml",
     "./configs/datasource_configs/robokop_textmining.yaml",
     "./configs/datasource_configs/robokop_viralproteome.yaml",
-    "./configs/datasource_configs/mesh.yaml"
+    "./configs/datasource_configs/mesh.yaml",
+    "./configs/datasource_configs/primekg.yaml"
 ]
 
 if __name__ == '__main__':
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,5 @@
		#!/bin/bash

		curl -L https://dataverse.harvard.edu/api/access/datafile/6180620 > kg.csv