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geneontology / neo

noctua entity ontology
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Xenbase entities do not seem to propagate to the NEO build from the Xenbase GPI #93

Closed kltm closed 2 years ago

kltm commented 2 years ago

While Xenbase is providing a GPI (https://ftp.xenbase.org/pub/GenePageReports/xenbase.gpi.gz), the entities contained in the file do not appear in the endpoint with the NEO load.

kltm commented 2 years ago

Tagging @malcolmfisher103

kltm commented 2 years ago

Looking at output of make clean && PATH=$PATH:/home/sjcarbon/local/src/git/owltools/OWLTools-Runner/bin/ TEST_SRCS=xenbase make test_obo Appears to be working to that point.

kltm commented 2 years ago

Noting that it seems to be in neo.owl (at least from the load last week, which is not currently in production). sjcarbon@moiraine:/tmp$:) grep 478074 neo.owl

    <owl:Class rdf:about="http://identifiers.org/xenbase/XB-GENE-478074">
        <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XB-GENE-478074</oboInOwl:hasRelatedSynonym>
        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Xenbase:XB-GENE-478074</oboInOwl:id>
kltm commented 2 years ago

Okay, I think this might be a knock on issue related to upstream files and out metadata (https://github.com/geneontology/pipeline/issues/277). Basically, in the last NEO load to reach production, Xenbase was not loaded (from two weeks ago). The test load from last week does indeed seem to have it.

$ zgrep -a "XB-GENE-478054" golr_new.tgz | wc -l
0

vs

$ zgrep -a "XB-GENE-478054" golr-index-contents.tgz | wc -l
8

This should clear Thursday when we update (or sooner on demand).

kltm commented 2 years ago

Apparently now back in NEO and in production (from @vanaukenk )

kltm commented 2 years ago

Also tagging @malcolmfisher103