Open balhoff opened 7 years ago
cc @kltm
Almost. Golr doesn't care much what goes in the id field. Currently the OWLTools loader will contract to OBO-style IDs (using a needs-to-die OWLTools-Core method), producing IDs like MGI:MGI:1336172 .
These get passed on Minerva, which expands them using it's CURIE map, giving the jax URL. But the URI in Minerva's TBox comes from Neo.
ugh
OK, I think the correct fix is to adapt the OWLTools-core golr loader to use a prefixmap, but this is a bit of work.
A workaround is to make minerva aggressively defensive, distrust and rewrite its own TBox. Ugh.
Does your comment mean that it is correct for these terms to use the OBO prefix within NEO?
Once @yy20716 implements this: https://github.com/owlcollab/owltools/issues/245
I will have neo export the same URIs that are used by minerva
Hmm, it looks like https://build.berkeleybop.org/job/build-noctua-entity-ontology/
is configured to take from any branch not master, which means my PR has already leaked out
<!-- http://identifiers.org/flybase/FBgn0000003 -->
<owl:Class rdf:about="http://identifiers.org/flybase/FBgn0000003">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_33695"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002162"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7227"/>
</owl:Restriction>
</rdfs:subClassOf>
<oboInOwl:hasBroadSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7SLRNACR32864</oboInOwl:hasBroadSynonym>
<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Signal recognition particle 7SL RNA CR32864 Dmel</oboInOwl:hasExactSynonym>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FB:FBgn0000003</oboInOwl:id>
<rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">7SLRNACR32864 Dmel</rdfs:label>
</owl:Class>
We need to make sure that the latest owltools (one that incorporates https://github.com/owlcollab/owltools/pull/247) is used to load solr
in this job: https://build.berkeleybop.org/job/load-golr-noctua-neo
it seems this job failed for a different reason.
@cmungall I believe I've cleared the "different reason" on that machine.
I'm seeing updated identifiers in NEO now. In particular, I notice identifiers.org
for MGI and ZFIN. But, a couple of questions:
http://identifiers.org/mgi/MGI%3A99582
. Should they instead be http://identifiers.org/mgi/MGI:99582
? As far as I know the colon doesn't need to be encoded. Although it resolves to the same place, it's not the same identifier.http://purl.obolibrary.org/obo/ComplexPortal_CPX-1
. Is that correct?On 22 May 2018, at 11:19, Jim Balhoff wrote:
I'm seeing updated identifiers in NEO now. In particular, I notice
identifiers.org
for MGI and ZFIN. But, a couple of questions:
- MGI IDs look like this:
http://identifiers.org/mgi/MGI%3A99582
. Should they instead behttp://identifiers.org/mgi/MGI:99582
? As far as I know the colon doesn't need to be encoded. Although it resolves to the same place, it's not the same identifier.
yes, should use : directly
- I seem some OBO-style ComplexPortal IDs:
http://purl.obolibrary.org/obo/ComplexPortal_CPX-1
. Is that correct?
we just haven't gotten around to that one yet
-- You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub: https://github.com/geneontology/neo/issues/17#issuecomment-391031050
Noting that above comment on complex portal has not been resolved yet.
Minerva seems to think that
ComplexPortal:CPX-998 means https://www.ebi.ac.uk/complexportal/complex/CPX-9
but NEO seems to think that it means
http://purl.obolibrary.org/obo/ComplexPortal_CPX-998
there is a really horrific perl hack (my fault) in the neo pipeline, we need to add this to the set of regexes, sorry...
On Thu, Jul 23, 2020 at 2:36 PM goodb notifications@github.com wrote:
Noting that above comment on complex portal has not been resolved yet. Minerva seems to think that ComplexPortal:CPX-998 means https://www.ebi.ac.uk/complexportal/complex/CPX-9 but NEO seems to think that it means http://purl.obolibrary.org/obo/ComplexPortal_CPX-998
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/geneontology/neo/issues/17#issuecomment-663244407, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOPF4ADLEYUGOWUOJODR5CUL7ANCNFSM4DDOXZFQ .
In NEO, terms use OBO PURLs like http://purl.obolibrary.org/obo/MGI_MGI%3A1336172, but the autocomplete in Noctua produces terms like http://www.informatics.jax.org/accession/MGI:MGI:1336172 (which I assume comes from Golr). This is a problem for using NEO to get taxon metadata or to query models for instances of
molecular entity
.