Open kimrutherford opened 6 years ago
Hi was this fixed? Val
@kimrutherford - does this work
@balhoff - what's the best way of preventing these typos in the ontology in future? A custom sparql query?
We should probably just have a SPARQL check that never_in_taxon
only has IRI values. This has happened repeatedly.
@kimrutherford - does this work
It works for me now.
When I run the above command I get an error catalog-v001.xml (No such file or directory)
and I was wondering where to get the catalog file specific for gene ontology?
@wkpalan you don't need the catalog file; just delete that part from the command. You can just provide the ontology file directly. The catalog provides a customized map from ontology IRIs to ontology files.
Thank you. I could get the command working, but wasn't sure whether not having a catalog file would change the results.
Hi.
We're having trouble with processing the latest go-plus.owl with owltools.
With this command line:
(cd /tmp/; wget http://purl.obolibrary.org/obo/go/extensions/go-plus.owl) && (cd go-svn/ontology/extensions; owltools /tmp/go-plus.owl --use-catalog --reasoner elk --make-species-subset -t NCBITaxon:4896 -o -f obo /tmp/go-plus-pombe-only.obo)
we get this exception:
It last worked successfully on August 2nd.
Thanks in advance.
CC: @ValWood