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monarch-initiative / monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza
https://monarchinitiative.org
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Populate primary_knowledge_source for all edges #422

Closed kevinschaper closed 1 year ago

kevinschaper commented 1 year ago

We're missing primary_knowledge_source on BGee (my fault, I wanted to treat it as just an aggregator, but I think it's reasonable to call it primary for the species that we're getting data from, since the data isn't coming from a MOD expression database), and also on all Phenio edges. I checked with @sierra-moxon and she thought it sounded good to add infores:phenio to infores_catalog_nodes.tsv in biolink-model and use it on all of the edges coming in from phenio.

primary_knowledge_source aggregator_knowledge_source knowledge_source provided_by count(*)
infores:goa infores:monarchinitiative goa_go_annotation_edges 2378026
infores:panther infores:monarchinitiative panther_genome_orthologs_edges 874014
infores:mgi infores:monarchinitiative infores:alliancegenome alliance_gene_to_expression_edges 740697
infores:zfin infores:monarchinitiative infores:alliancegenome alliance_gene_to_expression_edges 512352
infores:string infores:monarchinitiative string_protein_links_edges 492844
Graph phenio_edges 488755
infores:flybase infores:monarchinitiative infores:alliancegenome alliance_gene_to_expression_edges 406873
infores:mgi infores:monarchinitiative infores:alliancegenome alliance_gene_to_phenotype_edges 268816
infores:hpoa infores:monarchinitiative hpoa_gene_to_phenotype_edges 268685
infores:monarchinitiative infores:bgee bgee_gene_to_expression_edges 236565
infores:zfin infores:monarchinitiative zfin_gene_to_phenotype_edges 139344
infores:hpoa infores:monarchinitiative hpoa_disease_phenotype_edges 120048
infores:wormbase infores:monarchinitiative infores:alliancegenome alliance_gene_to_expression_edges 102947
infores:reactome infores:monarchinitiative reactome_chemical_to_pathway_edges 53976
infores:reactome infores:monarchinitiative reactome_gene_to_pathway_edges 49019
infores:wormbase infores:monarchinitiative infores:alliancegenome alliance_gene_to_phenotype_edges 26089
infores:sgd infores:monarchinitiative infores:alliancegenome alliance_gene_to_expression_edges 16561
infores:rgd infores:monarchinitiative infores:alliancegenome alliance_gene_to_expression_edges 11414
infores:hpoa infores:monarchinitiative hpoa_disease_mode_of_inheritance_edges 8431
infores:omim infores:monarchinitiative omim_gene_to_disease_edges 6387
infores:rgd infores:monarchinitiative infores:alliancegenome alliance_gene_to_phenotype_edges 3179
infores:xenbase infores:monarchinitiative xenbase_gene_to_phenotype_edges 2317
kevinschaper commented 1 year ago

Closed by #423