load curated gpi file for sars-cov-2
cmungall opened this issue · 7 comments
We recurated the uniprot goa GPI for sars-cov-2 for another project, we should use this one in Neo
https://github.com/Knowledge-Graph-Hub/kg-covid-19/blob/master/curated/ORFs/uniprot_sars-cov-2.gpi
Background:
geneontology/go-site#1431
URL: https://raw.githubusercontent.com/Knowledge-Graph-Hub/kg-covid-19/master/curated/ORFs/uniprot_sars-cov-2.gpi
Is this still to replace the currently use URL, or has this moved on?
@kltm looking at the line for the protein we've been discussing it looks different from that file. The label on noctua is showing 'nsp12 Scov2' but here its just 'nsp12'
UniProtKB P0DTD1-PRO_0000449629 nsp12 RNA-directed RNA polymerase Pol|RdRp|P0DTD1(4393-5324)|Pol (SARS2)|RdRp (SARS2)|nsp12 (SARS2)|UniProtKB:P0DTD1, 4393-5324|ORF1ab/Clv:nsp12 (SARS2)|Non-structural protein 12|nsp-12|ns12|ns-12|RNA-dependent RNA polymerase|RdRp|Pol|Severe acute respiratory syndrome (SARS) coronavirus nonstructural protein 12|holo-RdRp protein taxon:2697049 UniProtKB:P0DTD1 PR:000050284|PRO_0000449629
IIRC, the NEO build process adds the species.
Sorry, I let this one slip. The gpi file is good. We should replace the uniprot one with https://raw.githubusercontent.com/Knowledge-Graph-Hub/kg-covid-19/master/curated/ORFs/uniprot_sars-cov-2.gpi
@kltm is correct, the species label is not include in the gpi, it is appended as part of neo generation
@cmungall I believe this should now be loaded (http://noctua-amigo.berkeleybop.org/amigo/search/ontology)