Merge pull request #601 from monarch-initiative/issue-807-limit-pheni…

…o-db-associations

Updates phenio.db association population to gene & disease phenotype associations

scripts/load_sqlite.sh

@@ -33,7 +33,7 @@ pigz --force output/monarch-kg-denormalized-edges.tsv
 echo "Populate phenio db term_association..."
 cp data/monarch/phenio.db.gz output/phenio.db.gz
 gunzip output/phenio.db.gz
-sqlite3 -cmd "attach 'output/monarch-kg.db' as monarch" output/phenio.db "insert into term_association (id, subject, predicate, object, evidence_type, publication, source) select id, subject, predicate, object, has_evidence as evidence_type, publications as publication, primary_knowledge_source as source from monarch.edges where predicate = 'biolink:has_phenotype' and negated <> 'True'"
+sqlite3 -cmd "attach 'output/monarch-kg.db' as monarch" output/phenio.db "insert into term_association (id, subject, predicate, object, evidence_type, publication, source) select id, subject, predicate, object, has_evidence as evidence_type, publications as publication, primary_knowledge_source as source from monarch.edges where category in ('biolink:GeneToPhenotypicFeatureAssociation','biolink:DiseaseToPhenotypicFeatureAssociation') and predicate = 'biolink:has_phenotype' and negated <> 'True' and has_count <> 0 and has_percentage <> 0"
 
 echo "Compressing databases"
 pigz --force output/phenio.db