Adding EDAM, Phenio, EFO

Author: cmungall

Makefile

@@ -133,7 +133,7 @@ db/monarch.owl:
 	robot merge -I http://purl.obolibrary.org/obo/upheno/monarch.owl -o $@
 
 db/phenio.owl:
-	curl -L -s https://kg-hub.berkeleybop.io/frozen_incoming_data/phenio-base.owl.tar.gz > $@.tmp && mv $@.tmp $@
+	curl -L -s https://github.com/monarch-initiative/phenio/releases/download/latest/phenio.owl > $@.tmp && mv $@.tmp $@
 
 db/bero.owl:
 	curl -L -s https://github.com/berkeleybop/bero/releases/download/2022-05-26/bero.owl > $@.tmp && mv $@.tmp $@
@@ -158,6 +158,9 @@ db/enanomapper.owl:
 db/efo.owl: STAMP
 	robot merge -I http://www.ebi.ac.uk/efo/efo.owl -o $@
 
+db/edam.owl:
+	curl -L -s http://edamontology.org/EDAM.owl > $@
+
 db/sweetAll.owl:
 	robot merge -I http://sweetontology.net/sweetAll -o $@
 

src/semsql/builder/prefixes/prefixes.csv

@@ -9,9 +9,13 @@ dct,http://purl.org/dc/terms/
 foaf,http://xmlns.com/foaf/0.1/
 protege,http://protege.stanford.edu/plugins/owl/protege#
 skos,http://www.w3.org/2004/02/skos/core#
+dbpedia,http://dbpedia.org/resource/
 ex,http://example.com/
 obo,http://purl.obolibrary.org/obo/
 gocam,http://model.geneontology.org/
+EDAM,http://edamontology.org/
+EFO,http://www.ebi.ac.uk/efo/EFO_
+ORDO,http://www.orpha.net/ORDO/Orphanet_
 UP,http://purl.uniprot.org/uniprot/
 UC,http://purl.uniprot.org/core/
 PRO,http://www.uniprot.org/annotation/PRO_
@@ -25,6 +29,7 @@ ENM,http://purl.enanomapper.org/onto/ENM_
 BAO,http://www.bioassayontology.org/bao#BAO_
 biopax,http://www.biopax.org/release/biopax-level3.owl#
 reactome.biopax,http://www.reactome.org/biopax/81/48887#
+sweet,http://sweetontology.net/
 PSO,http://purl.obolibrary.org/obo/PSO_
 CHIRO,http://purl.obolibrary.org/obo/CHIRO_
 PW,http://purl.obolibrary.org/obo/PW_

src/semsql/builder/prefixes/prefixes_curated.csv

@@ -9,9 +9,13 @@ dct,http://purl.org/dc/terms/
 foaf,http://xmlns.com/foaf/0.1/
 protege,http://protege.stanford.edu/plugins/owl/protege#
 skos,http://www.w3.org/2004/02/skos/core#
+dbpedia,http://dbpedia.org/resource/
 ex,http://example.com/
 obo,http://purl.obolibrary.org/obo/
 gocam,http://model.geneontology.org/
+EDAM,http://edamontology.org/
+EFO,http://www.ebi.ac.uk/efo/EFO_
+ORDO,http://www.orpha.net/ORDO/Orphanet_
 UP,http://purl.uniprot.org/uniprot/
 UC,http://purl.uniprot.org/core/
 PRO,http://www.uniprot.org/annotation/PRO_
@@ -25,3 +29,4 @@ ENM,http://purl.enanomapper.org/onto/ENM_
 BAO,http://www.bioassayontology.org/bao#BAO_
 biopax,http://www.biopax.org/release/biopax-level3.owl#
 reactome.biopax,http://www.reactome.org/biopax/81/48887#
+sweet,http://sweetontology.net/

src/semsql/linkml/relation_graph.yaml

@@ -45,8 +45,16 @@ classes:
     notes:
     - this should hold direct edges. See also entailed_edge
     comments:
-    - "sqlview>>\n  SELECT subject, predicate, object FROM owl_subclass_of_some_values_from\
-      \ UNION\n    SELECT subject, predicate, object FROM rdfs_subclass_of_named_statement"
+    - |-
+      sqlview>>
+        SELECT subject, predicate, object
+        FROM owl_subclass_of_some_values_from
+         UNION
+        SELECT subject, predicate, object
+        FROM rdfs_subclass_of_named_statement
+         UNION
+        SELECT subject, predicate, object
+        FROM rdf_type_statement WHERE object IN (SELECT id FROM class_node)
     in_subset:
     - base table
     is_a: relation_graph_construct