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Should located_in be considered redundant with is_active_in? #426

Open ukemi opened 2 years ago

ukemi commented 2 years ago

Spotted as part of the MGI imports. From more complicated GO-CAM models we are generating these two annotations:

MGI MGI:1919358 is_active_in GO:0016020 PMID:25267624 ECO:0000315 MGI:MGI:5662251 20160729 MGI part_of(UBERON:0000955) contributor=https://orcid.org/0000-0001-7476-6306\ noctua-model-id=gomodel:56aac7ad00000079\ model-state=production
MGI MGI:1919358 located_in GO:0016020 PMID:25267624 ECO:0000315 MGI:MGI:5662251 20160729 MGI part_of(UBERON:0000955) contributor=https://orcid.org/0000-0001-7476-6306\|noctua-model-id=gomodel:56aac7ad00000079\|model-state=production

I think these would fall into our (the GOC's) definition of redundant. @loricorbani

ukemi commented 2 years ago

Related to #424

vanaukenk commented 2 years ago

From 2021-10-05 MOD Imports call:

It looks like the 'located in' annotations are coming from annotations that originally use 'part of' but for which the gp2term relation is being corrected by GO_RULE:0000061 to 'located in'.

The 'part of' annotations are generated by a property chain 'enable' o 'occurs in' -> 'part of' that is coming from one of the ontologies imported into GOLEGO.

@balhoff will look at GOLEGO in Protege to see where the chain is coming from and then update the GOLEGO Makefile so we can filter things like this.

balhoff commented 2 years ago

I believe I fixed the issue in go-lego. The bad SWRL rule should be eliminated in the next snapshot build.

vanaukenk commented 2 years ago

Thanks @balhoff So was it the case that the errant SWRL rule was in an old version of RO and we needed to update the RO version that GO uses in the ontology to fix go-lego? Just trying to understand the ontology data flow here. Thx.

balhoff commented 2 years ago

There were two issues:

vanaukenk commented 2 years ago

Okay, great; thank you! Should WB then review and update its WBLS file?

balhoff commented 2 years ago

@vanaukenk it won't impact us now, but I assume they would want to update their RO import for the next release. Maybe that will happen normally anyway?

pgaudet commented 2 years ago

Do the SWRL rules exist in a specific location? It would be good to add this a something to check when we change anything about relations.

balhoff commented 2 years ago

They are part of RO, but sometimes also we will get duplicate axioms from ontologies that import RO, like with the WBLS issue. This is mainly addressed by using input files for those ontologies that exclude their external axioms.

vanaukenk commented 2 years ago

@ukemi - do you know if this issue is fixed for the MGI GPAD?

ukemi commented 2 years ago

It wasn't the last time I checked.

vanaukenk commented 2 years ago

Okay, then we can close this ticket? I am double-checking about the WB ontology files, but Jim has addressed that on GO's end.

vanaukenk commented 2 years ago

Note that the issue with the WBls file was likely a timing issue wrt when the updated RO file was generated and the WBls file used in go-lego was generated.

WBls has now been updated with the most recent RO, so should be okay.

ukemi commented 2 years ago

I am still seeing this in the snapshot QC report:

GAF lines are parsed according to GAF 2.1 specifications

total: 1169

Messages

ERROR - Invalid Qualifier: There can be only one relation entry for the Qualifier field (is_active_in|located_in) -- MGI MGI:1098687 Aak1 is_active_in|located_in GO:0098793 MGI:MGI:4417868|GO_REF:0000096 ISO RGD:1305520 C AP2 associated kinase 1 5530400K14Rik|D6Ertd245e protein taxon:10090 20180711 MGI
ERROR - Invalid Qualifier: There can be only one relation entry for the Qualifier field (is_active_in|located_in) -- MGI MGI:106388 Abhd17a is_active_in|located_in GO:0098978 MGI:MGI:4417868|GO_REF:0000096 ISO RGD:1359682 C abhydrolase domain containing 17A 1700013O15Rik|D10Bwg1364e|Fam108a protein taxon:10090 20180711 MGI
ERROR - Invalid Qualifier: There can be only one relation entry for the Qualifier field (is_active_in|located_in) -- MGI MGI:106388 Abhd17a is_active_in|located_in GO:0099031 MGI:MGI:4417868|GO_REF:0000096 ISO RGD:1359682 C abhydrolase domain containing 17A 1700013O15Rik|D10Bwg1364e|Fam108a protein taxon:10090 20180711 MGI
ERROR - Invalid Qualifier: There can be only one relation entry for the Qualifier field (is_active_in|located_in) -- MGI MGI:106388 Abhd17a is_active_in|located_in GO:0099033 MGI:MGI:4417868|GO_REF:0000096 ISO RGD:1359682 C abhydrolase domain containing 17A 1700013O15Rik|D10Bwg1364e|Fam108a protein taxon:10090 20180711 MGI
ERROR - Invalid Qualifier: There can be only one relation entry for the Qualifier field (is_active_in|located_in) -- MGI MGI:1917816 Abhd17b is_active_in|located_in GO:0098978 MGI:MGI:4417868|GO_REF:0000096 ISO RGD:1305246 C abhydrolase domain containing 17B 5730446C15Rik|Fam108b protein taxon:10090 20180711 MGI
ERROR - Invalid Qualifier: There can be only one relation entry for the Qualifier field (is_active_in|located_in) -- MGI MGI:1917816 Abhd17b is_active_in|located_in GO:0099031 MGI:MGI:4417868|GO_REF:0000096 ISO RGD:1305246 C abhydrolase domain containing 17B 5730446C15Rik|Fam108b protein taxon:10090 20180711 MGI
ERROR - Invalid Qualifier: There can be only one relation entry for the Qualifier field (is_active_in|located_in) -- MGI MGI:1917816 Abhd17b is_active_in|located_in GO:0099033 MGI:MGI:4417868|GO_REF:0000096 ISO RGD:1305246 C abhydrolase domain containing 17B 5730446C15Rik|Fam108b protein taxon:10090 20180711 MGI
ERROR - Invalid Qualifier: There can be only one relation entry for the Qualifier field (is_active_in|located_in) -- MGI MGI:1917428 Abhd17c is_active_in|located_in GO:0098978 MGI:MGI:4417868|GO_REF:0000096 ISO RGD:1308210 C abhydrolase domain containing 17C 2210412D01Rik|Fam108c protein taxon:10090 20180711 MGI
ERROR - Invalid Qualifier: There can be only one relation entry for the Qualifier field (is_active_in|located_in) -- MGI MGI:104913 Abi1 is_active_in|located_in GO:0014069 MGI:MGI:4417868|GO_REF:0000096 ISO RGD:621008 C abl interactor 1 E3B1|Ssh3bp1 protein taxon:10090 20180711 MGI
ERROR - Invalid Qualifier: There can be only one relation entry for the Qualifier field (is_active_in|located_in) -- MGI MGI:104913 Abi1 is_active_in|located_in GO:0098978 MGI:MGI:4417868|GO_REF:0000096 ISO RGD:621008 C abl interactor 1 E3B1|Ssh3bp1 protein taxon:10090 20180711 MGI
ERROR - Invalid Qualifier: There can be only one relation entry for the Qualifier field (is_active_in|located_in) -- MGI MGI:107771 Abr is_active_in|located_in GO:0098978 MGI:MGI:4417868|GO_REF:0000096 ISO RGD:1306279 C active BCR-related gene 6330400K15Rik protein taxon:10090 20180711 MGI
ERROR - Invalid Qualifier: There can be only one relation entry for the Qualifier field (is_active_in|located_in) -- MGI MGI:107771 Abr is_active_in|located_in GO:0099092 MGI:MGI:4417868|GO_REF:0000096 ISO RGD:1306279 C active BCR-related gene 6330400K15Rik protein taxon:10090 20180711 MGI