Generate RO-Biolink predicate mappings based on a particular Biolink model

Makefile

@@ -126,24 +126,27 @@ biolink.facts: biolink-model.owl.ttl
 biolink-model-prefix-map.json:
 	curl -L -O 'https://raw.githubusercontent.com/biolink/biolink-model/$(BIOLINK)/prefix-map/biolink-model-prefix-map.json'
 
-# Step 15. Load all the data and ontologies.
+# Step 15. Download the Biolink Model predicate mappings.
+ro-to-biolink-predicate-mappings.tsv:
+	$(SCALA_RUN) scripts/generate_ro_biolink_mapping.sc -- $@
+
+# Step 16. Load all the data and ontologies.
 # - ./scripts/kg_edges: compiled from ./scripts/kg_edges.dl with Souffle (see above).
 # - inferred.csv: All inferred quads.
 # - quad.facts: All asserted quads.
 # - biolink.facts: Biolink model.
 # - ontology.facts: only used to convert REACTOME identifiers into UniProtKB identifiers.
 # - Also uses: ro-to-biolink-local-mappings.tsv to map from RO to Biolink.
-#	- TODO: add as a prereq
 # Creates a TSV file named kg_edge.csv with five columns:
 # - subj: direct type of subject
 # - pred: Biolink predicate
 # - obj: direct type of object
 # - ps: primary_source
 # - prov: graph that this is coming from (without brackets -- if it had brackets, it would
 #   be ignored by scripts/compact_iris.sc)
-kg_edge.csv: scripts/kg_edges inferred.csv quad.facts biolink.facts ontology.facts
+kg_edge.csv: scripts/kg_edges inferred.csv quad.facts biolink.facts ontology.facts ro-to-biolink-local-mappings.tsv ro-to-biolink-predicate-mappings.tsv
 	./scripts/kg_edges
 
-# Step 16. Compact IRIs in the kg_edge.csv file using the specified prefixes.
+# Step 17. Compact IRIs in the kg_edge.csv file using the specified prefixes.
 kg.tsv: kg_edge.csv scripts/compact_iris.sc biolink-model-prefix-map.json supplemental-namespaces.json
 	$(SCALA_RUN) scripts/compact_iris.sc --  biolink-model-prefix-map.json supplemental-namespaces.json kg_edge.csv $@

kubernetes/build-cam-database-storage.yaml

@@ -10,5 +10,5 @@ spec:
   - ReadWriteMany
   resources:
     requests:
-      storage: 500Gi
+      storage: 100Gi
   storageClassName: basic

ro-to-biolink-local-mappings.tsv

@@ -35,7 +35,6 @@
 <http://purl.obolibrary.org/obo/RO_0002297>	<https://w3id.org/biolink/vocab/has_output>	narrow
 <http://purl.obolibrary.org/obo/RO_0002298>	<https://w3id.org/biolink/vocab/has_output>	narrow
 <http://purl.obolibrary.org/obo/RO_0002299>	<https://w3id.org/biolink/vocab/has_output>	narrow
-<http://purl.obolibrary.org/obo/RO_0002313>	<https://w3id.org/biolink/vocab/affects>	narrow
 <http://purl.obolibrary.org/obo/RO_0002315>	<https://w3id.org/biolink/vocab/causes>	narrow
 <http://purl.obolibrary.org/obo/RO_0002325>	<https://w3id.org/biolink/vocab/colocalizes_with>	exact
 <http://purl.obolibrary.org/obo/RO_0002326>	<https://w3id.org/biolink/vocab/contributes_to>	exact

ro-to-biolink-predicate-mappings.tsv

@@ -0,0 +1,15 @@
+mapping_type	predicate	biolink_predicate	qualifier_set
+exact	<http://purl.obolibrary.org/obo/RO_0003003>	<https://w3id.org/biolink/vocab/affects>	{"biolink:qualified_predicate":"biolink:causes"}||{"biolink:object_aspect_qualifier":"expression"}||{"biolink:object_direction_qualifier":"increased"}
+exact	<http://purl.obolibrary.org/obo/RO_0003002>	<https://w3id.org/biolink/vocab/affects>	{"biolink:qualified_predicate":"biolink:causes"}||{"biolink:object_aspect_qualifier":"expression"}||{"biolink:object_direction_qualifier":"decreased"}
+exact	<http://purl.obolibrary.org/obo/GOREL_0002003>	<https://w3id.org/biolink/vocab/affects>	{"biolink:object_aspect_qualifier":"localization"}
+narrow	<http://purl.obolibrary.org/obo/RO_0002313>	<https://w3id.org/biolink/vocab/affects>	{"biolink:qualified_predicate":"biolink:causes"}||{"biolink:object_aspect_qualifier":"transport"}||{"biolink:object_direction_qualifier":"increased"}
+narrow	<http://purl.obolibrary.org/obo/RO_0002340>	<https://w3id.org/biolink/vocab/affects>	{"biolink:qualified_predicate":"biolink:causes"}||{"biolink:object_aspect_qualifier":"transport"}||{"biolink:object_direction_qualifier":"increased"}
+narrow	<http://purl.obolibrary.org/obo/RO_0002345>	<https://w3id.org/biolink/vocab/affects>	{"biolink:qualified_predicate":"biolink:causes"}||{"biolink:object_aspect_qualifier":"transport"}||{"biolink:object_direction_qualifier":"increased"}
+exact	<http://purl.obolibrary.org/obo/GOREL_0002004>	<https://w3id.org/biolink/vocab/affects>	{"biolink:qualified_predicate":"biolink:causes"}||{"biolink:object_aspect_qualifier":"degradation"}||{"biolink:object_direction_qualifier":"increased"}
+exact	<http://purl.obolibrary.org/obo/RO_0002212>	<https://w3id.org/biolink/vocab/regulates>	{"biolink:object_direction_qualifier":"downregulated"}
+exact	<http://purl.obolibrary.org/obo/RO_0002449>	<https://w3id.org/biolink/vocab/regulates>	{"biolink:object_direction_qualifier":"downregulated"}
+exact	<http://purl.obolibrary.org/obo/RO_0002450>	<https://w3id.org/biolink/vocab/regulates>	{"biolink:object_direction_qualifier":"upregulated"}
+exact	<http://purl.obolibrary.org/obo/RO_0002213>	<https://w3id.org/biolink/vocab/regulates>	{"biolink:object_direction_qualifier":"upregulated"}
+exact	<http://purl.obolibrary.org/obo/RO_0002212>	<https://w3id.org/biolink/vocab/regulates>	{"biolink:object_direction_qualifier":"downregulated"}
+exact	<http://purl.obolibrary.org/obo/RO_0002305>	<https://w3id.org/biolink/vocab/regulates>	{"biolink:object_direction_qualifier":"downregulated"}
+exact	<http://purl.obolibrary.org/obo/RO_0002304>	<https://w3id.org/biolink/vocab/regulates>	{"biolink:object_direction_qualifier":"upregulated"}