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geneontology / neo

noctua entity ontology
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Some PR identifiers are not making it into the final (GOlr pipeline) product #51

Closed kltm closed 3 years ago

kltm commented 4 years ago

From @hdrabkin

Newer PRO ids are still not getting into Noctua although they are in the GPI file.

Examples:

===

kltm commented 4 years ago

...weird, we just did an update

in the GPI:

PR      000050230       mAKT2/iso:1/Phos:1      RAC-beta serine/threonine-protein kinase isoform 1 phosphorylated 1 (mouse)             protein taxon:10090     MGI:MGI:104874

Change TEST_SRCS = mgi

~/local/src/git/neo[master]$:) PATH=/home/sjcarbon/local/src/git/owltools/OWLTools-Runner/bin:$PATH make test_obo
hdrabkin commented 4 years ago

Sorry; do you mean the two I list are not in the GPI used?

kltm commented 4 years ago

@hdrabkin Could you check to see if these are available now?

hdrabkin commented 4 years ago

I just checked these two and they are both available in FORM and GRAPH. Did this use the most recent MGI GPI? I can ask Li and Karen to try anything they have recently requested also.

krchristie commented 4 years ago

I confirmed that this ID, PR:Q3V365, which was created on 3/10/20, was available in both the Form and the Graph.

hdrabkin commented 4 years ago

I have confirmed PR:000050230 is now available (Jan 2020 request)

hdrabkin commented 4 years ago

Li just confirmed that a new request PR:000050231 is now also available in Noctua

kltm commented 4 years ago

@hdrabkin Okay, great--we seem to have a building method that is more sensible now.

kltm commented 3 years ago

Current problem list from @hdrabkin 

PR:000050486
name: alanine--tRNA ligase, cytoplasmic isoform 1 methylated 1 (mouse)

PR:000050487
name: alanine--tRNA ligase, cytoplasmic isoform 1 unmethylated 1 (mouse)
kltm commented 3 years ago

@hdrabkin These seem to be in the system, albeit under different names:

http://noctua-amigo.berkeleybop.org/amigo/term/PR:000050486 http://noctua-amigo.berkeleybop.org/amigo/term/PR:000050487

They both appear in the dropdown for me.

hdrabkin commented 3 years ago

I tried Monday but now they ARE there; Sorry. You can close this. Thanks Seth!

kltm commented 3 years ago

@hdrabkin No worries. It is a little odd though. We rolled out (two separate) new release for NEO on Thursday and Friday last week, after a long hiatus due to a conflict upstream. If you were still having issues on Monday, I wonder if something might be getting cached somewhere along the way...