Re-enable CTD, and filter out taxon nodes until we have a better way …

…to collapse thousands of identical edges before handing to plater. (#108)

Makefile

@@ -98,7 +98,7 @@ ctd-models.nq: CTD_chem_gene_ixns_structured.xml
 # Step 10. Concatenate all RDF files using a single RIOT instance (to make sure blank nodes don't collapse)
 # to create quad.facts. Each quad has a graph IRI that tells you were the quad came from.
 # Must concatenate multiple RDF files using riot before loading into Souffle, so that blank nodes don't collide
-quad.facts: noctua-models.nq aop-models.nq #ctd-models.nq
+quad.facts: noctua-models.nq aop-models.nq ctd-models.nq
 	riot -q --output=N-Quads $^ | sed 's/ /\t/' | sed 's/ /\t/' | sed -E 's/\t(.+) (.+) \.$$/\t\1\t\2/' >$@
 
 # Step 11. Reason over the quad.facts, which:

scripts/kg_edges.dl

@@ -8,6 +8,10 @@
 #define MOLECULAR_FUNCTION "<http://purl.obolibrary.org/obo/GO_0003674>"
 #define BIOLOGICAL_PROCESS "<http://purl.obolibrary.org/obo/GO_0008150>"
 #define CELLULAR_COMPONENT "<http://purl.obolibrary.org/obo/GO_0005575>"
+#define HUMAN "<http://purl.obolibrary.org/obo/NCBITaxon_9606>"
+#define MOUSE "<http://purl.obolibrary.org/obo/NCBITaxon_10090>"
+#define RAT "<http://purl.obolibrary.org/obo/NCBITaxon_10116>"
+#define ZEBRAFISH "<http://purl.obolibrary.org/obo/NCBITaxon_7955>"
 #define CANONICAL_RECORD "<http://geneontology.org/lego/canonical_record>"
 #define MOLECULAR_EVENT "<http://purl.obolibrary.org/obo/go/extensions/reacto.owl#molecular_event>"
 
@@ -61,6 +65,10 @@ direct_type(i, t) :-
     t != BIOLOGICAL_PROCESS,
     t != CELLULAR_COMPONENT,
     t != MOLECULAR_EVENT,
+    t != HUMAN,
+    t != MOUSE,
+    t != RAT,
+    t != ZEBRAFISH,
     !contains("http://purl.obolibrary.org/obo/BFO_", t),
     !contains("http://purl.obolibrary.org/obo/CARO_", t).