Jim Balhoff
Jim Balhoff
Having a mix of xsd:string and language tags makes SPARQL queries more challenging (and sometimes produces duplicates).
cc @cbizon
 Method: exhaustive search Score: -2.7488721956224653 Estimated probability: 0.18348623853211002 Confidence: 0.5 Subsequent scores (max 10): -2.7488721956224653, -2.7488721956224653, -2.7488721956224653, -3.4420193761824103, -3.4420193761824103, -5.051457288616511, -5.051457288616511, -5.051457288616511, -5.051457288616511, -5.744604469176457 - [hydrolase activity, acting on...
 - [x] - [tocotrienol omega-hydroxylase activity](http://purl.obolibrary.org/obo/GO_0052872) ProperSubClassOf [EC:1.14.13.-](http://purl.uniprot.org/enzyme/1.14.13.-) 0.08 - [ ] - [4-chlorobenzaldehyde oxidase activity](http://purl.obolibrary.org/obo/GO_0018471) ProperSubClassOf [EC:1.14.13.-](http://purl.uniprot.org/enzyme/1.14.13.-) 0.08 - [ ] - [carbon disulfide oxygenase activity](http://purl.obolibrary.org/obo/GO_0018643) ProperSubClassOf [EC:1.14.13.-](http://purl.uniprot.org/enzyme/1.14.13.-)...
 - [aclacinomycin T methylesterase activity](http://purl.obolibrary.org/obo/GO_0102530) EquivalentTo [EC:3.1.1.95](http://purl.uniprot.org/enzyme/3.1.1.95) (most probable) 0.8 - [aclacinomycin T + H2O = 15-demethylaclacinomycin T + methanol](http://rdf.rhea-db.org/37891) EquivalentTo [EC:3.1.1.95](http://purl.uniprot.org/enzyme/3.1.1.95) (most probable) 0.75 - [aclacinomycin T methylesterase...
 - [H2O + L-cysteine = H(+) + hydrogen sulfide + NH4(+) + pyruvate](http://rdf.rhea-db.org/24931) EquivalentTo [EC:4.4.1.28](http://purl.uniprot.org/enzyme/4.4.1.28) (most probable) 0.75 - [L-cystine L-cysteine-lyase (deaminating)](http://purl.obolibrary.org/obo/GO_0044540) EquivalentTo [H2O + L-cystine = NH4(+) +...
 - [acetylgalactosaminyl-O-glycosyl-threonyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity](http://purl.obolibrary.org/obo/GO_0106327) EquivalentTo [3-O-[N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + H(+) + UDP](http://rdf.rhea-db.org/46880) (most probable) 0.8 - [acetylgalactosaminyl-O-glycosyl-seryl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity](http://purl.obolibrary.org/obo/GO_0106328) EquivalentTo [3-O-[N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + H(+)...
Currently `robot repair` is run during the ontology build: https://github.com/geneontology/go-ontology/blob/d142d035479bfe17ad796f2c93eca6d335688ce6/src/ontology/Makefile#L197 This moves xrefs from obsolete terms to their replacements. This is occasionally the source of confusion. It would be nice...
Currently we use `robot verify` with SPARQL queries in the ontology checks, but we could get a number of other built-in checks by running `robot report`.
The OWL API parser complains when trying to read `ccdhmodel.owl.ttl`: ``` jim (main)$ robot convert -i owl/ccdhmodel.owl.ttl -o ccdhmodel.ofn 2021-07-09 22:17:39,644 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples...