Add checks for empty literals and URIs as comments. Fix some violatio…

…ns. (#29376)

src/ontology/go-edit.obo

@@ -438876,9 +438876,9 @@ id: GO:0103040
 name: aldose sugar dehydrogenase activity
 namespace: molecular_function
 def: "Catalysis of the reaction: H2O + an aldose + an oxidized electron acceptor = H+ + an aldonate + a reduced electron acceptor." [GOC:pz, MetaCyc:RXN0-6371, PMID:16864586]
-comment: https://github.com/geneontology/go-ontology/issues/28942
 xref: MetaCyc:RXN0-6371
 is_a: GO:0016901 ! oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28942" xsd:anyURI
 
 [Term]
 id: GO:0103041
@@ -468061,9 +468061,9 @@ id: GO:0180044
 name: borate channel activity
 namespace: molecular_function
 def: "Enables the facilitated diffusion of borate (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." [PMID:21710975]
-comment: https://github.com/geneontology/go-ontology/issues/27487
 is_a: GO:0015103 ! inorganic anion transmembrane transporter activity
 is_a: GO:0015267 ! channel activity
+property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27487" xsd:anyURI
 created_by: vw
 creation_date: 2024-07-05T11:36:39Z
 
@@ -497307,9 +497307,9 @@ id: GO:1901638
 name: obsolete copper ion import into ascospore-type prospore
 namespace: biological_process
 def: "OBSOLETE. Any copper ion import that takes place in ascospore-type prospore." [GOC:TermGenie]
-comment: https://sourceforge.net/tracker/index.php?func=detail&aid=3510080&group_id=36855&atid=440764
 synonym: "copper ion import into ascospore-type prospore" EXACT []
 synonym: "copper ion uptake in ascospore-type prospore" EXACT [GOC:TermGenie]
+property_value: term_tracker_item "https://sourceforge.net/tracker/index.php?func=detail&aid=3510080&group_id=36855&atid=440764" xsd:anyURI
 is_obsolete: true
 created_by: al
 creation_date: 2012-11-15T15:44:04Z

src/util/ontology-qc.dl

@@ -1,6 +1,7 @@
 #define RDF_TYPE "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type>"
 #define RDFS_SUBCLASS_OF "<http://www.w3.org/2000/01/rdf-schema#subClassOf>"
 #define RDFS_SUBPROPERTY_OF "<http://www.w3.org/2000/01/rdf-schema#subPropertyOf>"
+#define RDFS_COMMENT "<http://www.w3.org/2000/01/rdf-schema#comment>"
 #define OWL_CLASS "<http://www.w3.org/2002/07/owl#Class>"
 #define OWL_DEPRECATED "<http://www.w3.org/2002/07/owl#deprecated>"
 #define OWL_ANNOTATION_PROPERTY "<http://www.w3.org/2002/07/owl#AnnotationProperty>"
@@ -25,6 +26,7 @@
 .decl synonym_property(iri: symbol)
 .decl declared_subset(iri: symbol)
 .decl subset_assertion(term: symbol, subset: symbol)
+.decl triple_with_literal(s: symbol, p: symbol, o: symbol)
 .decl xref(term: symbol, ref: symbol)
 .decl defxref(term: symbol, ref: symbol)
 .decl synonym_xref(term: symbol, property: symbol, ref: symbol)
@@ -40,6 +42,8 @@ synonym_property(OIO_HAS_BROAD_SYNONYM).
 
 term(iri) :- ontrdf(iri, RDF_TYPE, OWL_CLASS), match("<.+>", iri).
 
+triple_with_literal(s, p, o) :- ontrdf(s, p, o), match("\".*", o).
+
 obsolete_term(iri) :- term(iri), ontrdf(iri, OWL_DEPRECATED, "\"true\"^^<http://www.w3.org/2001/XMLSchema#boolean>").
 
 valid_term(iri) :- term(iri), !obsolete_term(iri).
@@ -66,5 +70,7 @@ error(cat("ERROR: ", term, " has an xref to an obsolete EC: ", ec)) :- xref(term
 error(cat("ERROR: ", term, " has a definition xref to an obsolete EC: ", ec)) :- defxref(term, ec), valid_term(term), obsolete_ec(ec).
 error(cat("ERROR: ", term, " has a synonym xref to an obsolete EC: ", ec)) :- synonym_xref(term, _, ec), valid_term(term), obsolete_ec(ec).
 error(cat("ERROR: ", term, " references an undeclared subset: ", subset)) :- subset_assertion(term, subset), !declared_subset(subset).
+error(cat("ERROR: empty literal value for ", s, " ", p)) :- triple_with_literal(s, p, o), match("\"\".*", o).
+error(cat("ERROR: ", term, " has a comment that seems to be a URI")) :- triple_with_literal(term, RDFS_COMMENT, o), match("\"http.*", o).
 
 .output error(filename="datalog-violations.tsv")