Merge pull request #606 from monarch-initiative/remove-non-modular-hpoa

Remove non modular hpoa

src/monarch_ingest/ingests.yaml

@@ -16,14 +16,11 @@ 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'
-hpoa_disease_mode_of_inheritance:
+hpoa:
   url:
     - 'https://github.com/monarch-initiative/monarch-phenotype-profile-ingest/releases/latest/download/hpoa_disease_mode_of_inheritance_edges.tsv'
-hpoa_disease_to_phenotype:
     - 'https://github.com/monarch-initiative/monarch-phenotype-profile-ingest/releases/latest/download/hpoa_disease_to_phenotype_edges.tsv'
-hpoa_gene_to_disease:
     - 'https://github.com/monarch-initiative/monarch-phenotype-profile-ingest/releases/latest/download/hpoa_gene_to_disease_edges.tsv'
-hpoa_gene_to_phenotype:
     - 'https://github.com/monarch-initiative/monarch-phenotype-profile-ingest/releases/latest/download/hpoa_gene_to_phenotype_edges.tsv'
 ncbi_gene:
   url:
@@ -50,8 +47,6 @@ biogrid:
   config: 'ingests/biogrid/biogrid.yaml'
 ctd_chemical_to_disease:
   config: 'ingests/ctd/chemical_to_disease.yaml'
-# flybase_publication_to_gene::
-#   config: 'ingests/flybase/publication_to_gene.yaml'
 dictybase_gene:
   config: 'ingests/dictybase/gene.yaml'
 dictybase_gene_to_phenotype:
@@ -60,16 +55,6 @@ go_annotation:
   config: 'ingests/go/annotation.yaml'
 hgnc_gene:
   config: 'ingests/hgnc/gene.yaml'
-hpoa_disease_to_phenotype:
-  config: 'ingests/hpoa/disease_to_phenotype.yaml'
-hpoa_gene_to_disease:
-  config: 'ingests/hpoa/gene_to_disease.yaml'
-hpoa_disease_mode_of_inheritance:
-  config: 'ingests/hpoa/disease_mode_of_inheritance.yaml'
-hpoa_gene_to_phenotype:
-  config: 'ingests/hpoa/gene_to_phenotype.yaml'
-# mgi_publication_to_gene:
-#   config: 'ingests/mgi/publication_to_gene.yaml'
 panther_genome_orthologs:
   config: 'ingests/panther/genome_orthologs.yaml'
 pombase_gene:
@@ -82,10 +67,6 @@ reactome_gene_to_pathway:
   config: 'ingests/reactome/gene_to_pathway.yaml'
 reactome_pathway:
   config: 'ingests/reactome/pathway.yaml'
-# rgd_publication_to_gene:
-#   config: 'ingests/rgd/publication_to_gene.yaml'
-# sgd_publication_to_gene:
-#   config: 'ingests/sgd/publication_to_gene.yaml'
 string_protein_links:
   config: 'ingests/string/protein_links.yaml'
 xenbase_gene_to_phenotype:
@@ -94,10 +75,6 @@ xenbase_orthologs:
   config: 'ingests/xenbase/orthologs.yaml'
 xenbase_non_entrez_orthologs:
   config: 'ingests/xenbase/non_entrez_orthologs.yaml'
-# xenbase_publication_to_gene:
-#   config: 'ingests/xenbase/publication_to_gene.yaml'
 zfin_gene_to_phenotype:
   config: 'ingests/zfin/gene_to_phenotype.yaml'
-# zfin_publication_to_gene:
-#   config: 'ingests/zfin/publication_to_gene.yaml'
 

src/monarch_ingest/ingests/hgnc/gene.py

@@ -40,21 +40,4 @@
         in_taxon_label=in_taxon_label,
         provided_by=["infores:hgnc"],
     )
-
-    # Excluding pub to gene associations for now
-    # pubmed_id_list = row["pubmed_id"].split('|')
-    # for each_id in pubmed_id_list:
-    #     publication_id = "PMID:" + each_id
-    #     publication = Publication(
-    #         id=publication_id,
-    #         type=koza_app.translation_table.resolve_term("publication"),
-    #     )
-    #     relation = koza_app.translation_table.resolve_term("mentions"),
-    #     association = InformationContentEntityToNamedThingAssociation(
-    #         id="uuid:" + str(uuid.uuid1()),
-    #         subject=gene.id,
-    #         predicate=Predicate.mentions,
-    #         object=publication.id,
-    #     )
-
     koza_app.write(gene)