Investigate Scov2 polyprotein listed as a species in Noctua

Question

Investigate Scov2 polyprotein listed as a species in Noctua

vanaukenk opened this issue 3 years ago · 13 comments

During the QC checks for bringing Noctua up after the 2022-05-26 outage, I noticed a suspicious entry, pp1ab Scov2, in the list of species:

I thought pp1ab was a polyprotein and that's how it looks in noctua-amigo:

@balhoff @tmushayahama - can you take a look to see why this entry is included as a species? Thanks.

Also tagging @kltm

Answer 1 · 2022-05-27T13:00:26.000Z

@tmushayahama how is that list created? (What service does it call to get it?) 'pp1ab Scov2' does not look like a taxon at least in the latest NEO file.

Answer 2 · 2022-05-27T18:22:42.000Z

@balhoff
@tmushayahama uses the taxon API from minerva (/taxa)

Answer 3 · 2022-05-27T20:45:42.000Z

As a hint, noting that the /taxa API is returning:
{ id: "http://identifiers.org/uniprot/P0DTD1", label: "pp1ab Scov2" }

Answer 4 · 2022-05-27T20:51:49.000Z

Noting this found in neo.obo:

[Term]
id: UniProtKB:P0DTD1-PRO_0000449619
name: nsp1 Scov2
synonym: "nsp1" BROAD []
synonym: "P0DTD1-PRO_0000449619" RELATED []
synonym: "protein" RELATED []
is_a: CHEBI:33695
relationship: has_gene_template PR:000050270%7CUniProtKB%3AP0DTD1-PRO_0000449635%7CPRO_0000449635
relationship: in_taxon UniProtKB:P0DTD1 ! pp1ab Scov2
property_value: https://w3id.org/biolink/vocab/category https://w3id.org/biolink/vocab/GeneProduct
property_value: https://w3id.org/biolink/vocab/category https://w3id.org/biolink/vocab/MacromolecularMachine

I don't believe in_taxon is supposed to work like that.

Answer 5 · 2022-05-27T21:00:25.000Z

Origin seems to be here: https://raw.githubusercontent.com/Knowledge-Graph-Hub/kg-covid-19/master/curated/ORFs/uniprot_sars-cov-2.gpi

Answer 6 · 2022-05-27T21:05:12.000Z

It looks like the taxon is off by one for GPI 1.2?

UniProtKB	P0DTD1-PRO_0000449619	nsp1	Host translation inhibitor nsp1|P0DTD1(1-180)|rep/Clv:nsp1 (SARS2)|PRO_0000449619|nsp1 (SARS2)|UniProtKB:P0DTD1, 1-180|leader protein (SARS2)|UniProtKB:P0DTC1, 1-180|non-structural protein 1 (SARS2)|nsp-1|ns1|ns-1|host translation inhibitor nsp1|Severe acute respiratory syndrome (SARS) coronavirus nonstructural protein 1	protein	taxon:2697049	UniProtKB:P0DTD1	PR:000050270|UniProtKB:P0DTD1-PRO_0000449635|PRO_0000449635

http://geneontology.org/docs/gene-product-information-gpi-format/

Answer 7 · 2022-05-27T21:08:08.000Z

Related to geneontology/go-site#1431

Answer 8 · 2022-05-27T21:10:55.000Z

@kltm it seems like you found the problem. But in the neo.owl I downloaded yesterday I saw in_taxon NCBITaxon:2697049. I wonder why the discrepancy?

Answer 9 · 2022-05-27T21:16:41.000Z

@balhoff Yeah, there's some stuff I'm not sure about here, especially as that file has not been touched in years, so I'm not sure why it's a problem now.
I'm tagging upstream contributors @cmungall and @justaddcoffee to confirm format for GPI 1.2.

Answer 10 · 2022-06-08T00:31:40.000Z

From @cmungall , we can go ahead and manually fix this file ourselves upstream.

Answer 11 · 2022-06-08T23:41:14.000Z

Working branch at https://github.com/Knowledge-Graph-Hub/kg-covid-19/tree/issue_geneontology_minerva-486-fix-sars-cov-2-gpi

Answer 12 · 2022-06-10T22:13:55.000Z

If we understand this correctly, this should be fixed on next NEO release.

Answer 13 · 2022-09-24T00:10:33.000Z

Hm. Apparently not. Still appearing on Noctua landing page.