Merge pull request #604 from monarch-initiative/issue-712-use-modular…

…-ncbi-gene Bring ncbi gene nodes in from modular ingest
monarch-initiative · Oct 14, 2024 · 78d651b · 78d651b
2 parents 363b0c1 + a2c272a
commit 78d651b
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Showing 6 changed files with 20 additions and 191 deletions.
diff --git a/src/monarch_ingest/ingests.yaml b/src/monarch_ingest/ingests.yaml
@@ -19,6 +19,14 @@ clinvar_variant:
   url:
     - 'https://github.com/monarch-initiative/clinvar-ingest/releases/latest/download/clinvar_variant_nodes.tsv'
     - 'https://github.com/monarch-initiative/clinvar-ingest/releases/latest/download/clinvar_variant_edges.tsv'
+ncbi_gene:
+  url:
+      - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_9615_nodes.tsv'
+      - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_9913_nodes.tsv'
+      - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_9823_nodes.tsv'
+      - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_9031_nodes.tsv'
+      - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_227321_nodes.tsv'
+
 
 ## Ingests within this repository
 
@@ -54,8 +62,6 @@ hpoa_gene_to_phenotype:
   config: 'ingests/hpoa/gene_to_phenotype.yaml'
 # mgi_publication_to_gene:
 #   config: 'ingests/mgi/publication_to_gene.yaml'
-ncbi_gene:
-  config: 'ingests/ncbi/gene.yaml'
 panther_genome_orthologs:
   config: 'ingests/panther/genome_orthologs.yaml'
 pombase_gene:

diff --git a/src/monarch_ingest/ingests/ncbi/gene.py b/src/monarch_ingest/ingests/ncbi/gene.py
diff --git a/src/monarch_ingest/ingests/ncbi/gene.yaml b/src/monarch_ingest/ingests/ncbi/gene.yaml
diff --git a/src/monarch_ingest/ingests/ncbi/metadata.yaml b/src/monarch_ingest/ingests/ncbi/metadata.yaml
diff --git a/src/monarch_ingest/qc_expect.yaml b/src/monarch_ingest/qc_expect.yaml
@@ -8,8 +8,17 @@ nodes:
       min: 14000
     hgnc_gene_nodes:
       min: 43000
-    ncbi_gene_nodes:
-      min: 196000
+    ncbi_gene_9823_nodes:
+      min: 45000
+    ncbi_gene_9031_nodes:
+      min: 32000
+    ncbi_gene_227321_nodes:
+      min: 10000
+    ncbi_gene_9615_nodes:
+      min: 50000
+    ncbi_gene_9913_nodes:
+      min: 57000
+
     phenio_nodes:
       min: 288000
     pombase_gene_nodes:
@@ -19,7 +28,7 @@ nodes:
     clinvar_variant_nodes:
       min: 7000
     clingen_variant_nodes:
-      min: 7000
+      min: 5600
 edges:
   provided_by:
     alliance_gene_to_expression_edges:

diff --git a/tests/unit/ncbi/test_ncbi_gene.py b/tests/unit/ncbi/test_ncbi_gene.py