Remove deprecated relations from GOREL: regulates_expression_of, regulates_translation_of, has_regulation_target, regulates_transport_of, stabilizes

[pgaudet]

• [x] stabilizes: obsolete but still has domain and range, and is still in the subset 'valid for extensions' > 0 annotations
• [x] regulates_translation_of : obsolete but still has domain and range, and is still in the subset 'valid for extensions' > 6 annotations
• [x] has_regulation_target >> 40 annotations
• [x] regulates_expression_of >> obsolete but still has domain and range ' > 7 annotations
• [x] regulates_transport_of >> 72 annotations

The above can be automatically replaced by 'has input' . Please let me know if you disagree - spreadsheet is here: Annotations are here: https://docs.google.com/spreadsheets/d/1Lep6Ov26B5KEc8TgX_2psgiTZ8rNqlcWLKuhNgcYRgE/edit#gid=0

Groups with annotations:

AgBase ARUK-UCL BHF-UCL dictyBase DONE mostly yesterday FlyBase GO_Central ParkinsonsUK-UCL SGD SynGO SynGO-UCL UniProt

[pgaudet]

Hi everyone,

The proposal is to replace the following relations with 'has input' (to be changed to 'has primary input' when everything is in place):

• regulates_translation_of
• has_regulation_target
• regulates_expression_of
• regulates_transport_of

You have annotations using these relations, see https://docs.google.com/spreadsheets/d/1Lep6Ov26B5KEc8TgX_2psgiTZ8rNqlcWLKuhNgcYRgE/edit#gid=0

• BHF (all projects): 61 annotations @RLovering
• dictyBase : 24 annotations @pfey03
• FlyBase : 3 annotations @hattrill
• SGD: 7 annotations @srengel
• UniProt : 23 annotations @Antonialock @sylvainpoux (I fixed a couple, the rest seems OK to me, but please have a look if you have time)

Let me know if you dont agree with the automatic replacement.

Thanks, Pascale

[RLovering]

Hi Pascale

are all has_input relations going to change to 'has primary input' or just the ones listed in this spreadsheet?

Thanks

Ruth

[pgaudet]

Hi @RLovering All has input will become has primary input. We're assuming that the curators always captured the biologically relevant input. Hopefully this is a correct assumption?

[RLovering]

Hi Pascale

Ok, I am not sure that the has_input is always bound by the gp curated ie it could be that the AE includes the ID of a hormone that stimulates the signaling pathway but the gp does not actually bind to the hormone. But I am sure that the biologically relevant input is included

Thanks

Ruth

[pgaudet]

Are you referring to miRNA annotations?

Or do you also have proteins indirectly regulating activities of other proteins?

[RLovering]

For examples see: https://www.ebi.ac.uk/QuickGO/annotations?extension=has_input(UniProtKB:&goId=GO:1990869&goUsageRelationships=is_a&goUsage=descendants

The chemokine is included in the AE to provide information about what chemokine the cell is responding to - the gp plays a role in responding to that chemokine

any thoughts on this?

[pfey03]

@pgaudet I changed them all yesterday, but of course there was just a GOA release so it takes until the next release. But they are all fixed. There was one gene that wasn't there yesterday but all others are fixed. Petra

[pfey03]

@pgaudet There were only 3 genes that I needed to fix something all others I did yesterday and on that table it's evident. I saw which genes were not there yesterday.

[hattrill]

FB done

[srengel]

SGD is fine with automatic replacement

[RLovering]

Hi Pascale, I haven't started these as I am waiting to find out what the relation will be for hormones etc that are listed as the stimulus to a process Thanks Ruth