In some cases bad identifiers are getting into the load

[kltm]

In the most recent successful load, the following error was noticed going by:

    20:35:45  2023-01-12 04:35:45,757 WARN  (OWLGraphWrapperExtended:936) Unable to retrieve the value of oboInOw#id as the identifier for http://identifiers.org/wormbase/T10C6.13%7CWB%3AF45F2.13%7CWB%3AZK131.3%7CWB%3AZK131.7%7CWB%3AK06C4.5%7CWB%3AZK131.2%7CWB%3AK06C4.13%7CWB%3AF17E9.10%7CWB%3AK03A1.1%7CWB%3AF08G2.3%7CWB%3AB0035.10%7CWB%3AF07B7.5%7CWB%3AF54E12.1%7CWB%3AF55G1.2%7CWB%3AF22B3.2; we will use an original iri as the identifier.

Nothing like this seems to be in the WB GPI. In fact, no GPI seems to have this, so it may be coming from a parsed GAF? Weird.
Before digging in more, does this ring any bells @vanaukenk ?

[kltm]

Okay, I take that back: I've found the source in the wb.gpi:

bbop@wok:/home/skyhook/release/products/annotations$ zcat wb-src.gpi.gz | grep "F07B7.5"
WB	WBGene00001923	his-49	HIStone	CELE_F07B7.5	gene	taxon:6239	UniProtKB:P08898	
WB	F07B7.5	his-49	HIStone	CELE_F07B7.5	transcript	taxon:6239	WB:WBGene00001923		
WB	CE03253	HIS-2	HIStone	CELE_T10C6.13	protein	taxon:6239	WB:T10C6.13|WB:F45F2.13|WB:ZK131.3|WB:ZK131.7|WB:K06C4.5|WB:ZK131.2|WB:K06C4.13|WB:F17E9.10|WB:K03A1.1|WB:F08G2.3|WB:B0035.10|WB:F07B7.5|WB:F54E12.1|WB:F55G1.2|WB:F22B3.2	UniProtKB:P08898|UniProtKB:K7ZUH9	

This is ringing a bell; I'm going to dig around to see if I can find a previous instance of this.

[vanaukenk]

Interesting.
This didn't ring any bells, but there are WB sequence identifiers buried in that string and when I check a few of them, I see that they correspond to genes that produce the exact same protein.

[kltm]

Hm, it looks like we've asked similar questions in the past, and felt that it didn't matter much in the grand scheme of things #88 (comment) (note the WB identifier).

[vanaukenk]

Okay.
The way the C. elegans protein identifiers are assigned in WB right now, we don't have unique protein ids for each gene if they ultimately produce a protein with the same amino acid sequence.
If you think we need a better way of handling this, we can discuss some more.

[kltm]

@vanaukenk @pgaudet As we come up on a few months on this issue (and about a year since closing the variant #111), I was wondering if we're just documenting this (as we did previously with #88 (comment)) or if we're going to take the time to try and fix this this time around? I'm not sure how much of a problem this is in this case or if it's causing a problem that's valued as worth fixing right now?