fix CTD chemical edges, remove some redundant OLS props

EBISPOT · Nov 2, 2024 · 3d205df · 3d205df
1 parent 71a195d
commit 3d205df
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diff --git a/configs/datasource_configs/ctd.yaml b/configs/datasource_configs/ctd.yaml
@@ -43,6 +43,7 @@ ingests:
           --json-inject-key-prefix ctd:
           --json-inject-value-prefix PubMedIDs:pmid:
           --json-inject-value-prefix OmimIDs:omim:
+          --json-inject-value-prefix ChemicalID:mesh:
       | grebi_nodes2edges
           --from-field ctd:ChemicalID
           --to-field ctd:DiseaseID
@@ -61,6 +62,7 @@ ingests:
          --tsv-columns ChemicalName,ChemicalID,CasRN,PathwayName,PathwayID,PValue,CorrectedPValue,TargetMatchQty,TargetTotalQty,BackgroundMatchQty,BackgroundTotalQty
       | grebi_transform_jsonl 
           --json-inject-key-prefix ctd:
+          --json-inject-value-prefix ChemicalID:mesh:
       | grebi_nodes2edges
           --from-field ctd:ChemicalID
           --to-field ctd:PathwayID
@@ -74,6 +76,7 @@ ingests:
       | grebi_transform_jsonl 
           --json-inject-type ctd:Chemical
           --json-inject-value-prefix CasRN:cas:
+          --json-inject-value-prefix ChemicalID:mesh:
       | grebi_transform_jsonl 
           --json-rename-field ChemicalID:id
           --json-rename-field CasRN:grebi:equivalentTo'

diff --git a/configs/subgraph_configs/ebi_full_monarch.json b/configs/subgraph_configs/ebi_full_monarch.json
@@ -50,6 +50,12 @@
         "ols:iri",
         "ols:uri",
         "ols:imported",
+        "ols:hasHierarchicalParents",
+        "ols:hasHierarchicalChildren",
+        "ols:hasDirectParents",
+        "ols:hasDirectChildren",
+        "ols:numDescendants",
+        "ols:numHierarchicalDescendants",
         "oboinowl:id",
         "oboinowl:url",
         "monarch:iri",