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Review annotations to GO:0000422 autophagy of mitochondrion (and descendants) #4752

Open ValWood opened 12 months ago

ValWood commented 12 months ago

Dear all,

The proposal has been made to obsolete

GO:0000422 autophagy of mitochondrion GO:1903146 regulation of autophagy of mitochondrion GO:1903147 negative regulation of autophagy of mitochondrion GO:1903599 positive regulation of autophagy of mitochondrion

see https://github.com/geneontology/go-ontology/issues/26111

Experimental annotations that need to be reviewed are here: https://docs.google.com/spreadsheets/d/1BXQOaXNawXVxH6k-QIoUAfJIvIzgTM3BaiC9tVg-2Oo/edit#gid=0

Annotate to GO:0000423 mitophagy and appropriate regulation children

Impacted groups:

1 AgBase 2 CGD @jlewsmith 2 DisProt @victorianugnes 12 FlyBase 7 MGI 28 ParkinsonsUK-UCL - DONE 8 PomBase 3 RGD 35 SGD 2 TAIR @tberardini 19 UniProt 6 WB 1 ZFIN

All other annotations should be remapped to the direct replacement "mitophagy" terms

Mappings that need to be reviewed: (InterPro2GO, UniProt-Keywords, UniRule)

GO:0000422 interpro2go InterPro:IPR040040 Autophagy-related protein 11 > GO:autophagy of mitochondrion ; GO:0000422
3 GO:0000422 interpro2go InterPro:IPR040110 PINK1, protein kinase domain > GO:autophagy of mitochondrion ; GO:0000422
4 GO:0000422 interpro2go InterPro:IPR045593 Atg11, middle domain > GO:autophagy of mitochondrion ; GO:0000422
5 GO:0000422 interpro2go InterPro:IPR047118 F-box only protein 7 > GO:autophagy of mitochondrion ; GO:0000422
6 GO:0000422 wikipedia2go Wikipedia:Autophagy_(cellular)#Selective_autophagy > GO:autophagy of mitochondrion ; GO:0000422
7 GO:0000422 wikipedia2go Wikipedia:Mitophagy > GO:autophagy of mitochondrion ; GO:0000422
8 GO:0000422 pfam2go Pfam:PF19697 Atg11_middle > GO:autophagy of mitochondrion ; GO:0000422
9 GO:0000422 unirule2go UniRule:UR001378758 > GO:autophagy of mitochondrion ; GO:0000422

@blazaropinto @esperetta

Thanks.

jlewsmith commented 12 months ago

CGD done

From: Val Wood @.> Sent: Wednesday, September 27, 2023 7:18 AM To: geneontology/go-annotation @.> Cc: Jodi Lew-Smith @.>; Mention @.> Subject: [geneontology/go-annotation] Review annotations to GO:0000422 autophagy of mitochondrion (and descendants) (Issue #4752)

Dear all,

The proposal has been made to obsolete

GO:0000422 autophagy of mitochondrion GO:1903146 regulation of autophagy of mitochondrion GO:1903147 negative regulation of autophagy of mitochondrion GO:1903599 positive regulation of autophagy of mitochondrion

see geneontology/go-ontology#26111https://github.com/geneontology/go-ontology/issues/26111

Experimental annotations that need to be reviewed are here: https://docs.google.com/spreadsheets/d/1BXQOaXNawXVxH6k-QIoUAfJIvIzgTM3BaiC9tVg-2Oo/edit#gid=0

Impacted groups:

1 AgBase 2 CGD @jlewsmithhttps://github.com/jlewsmith 2 DisProt @victorianugneshttps://github.com/victorianugnes 12 FlyBase 7 MGI 28 ParkinsonsUK-UCL 8 PomBase 3 RGD 35 SGD 2 TAIR @tberardinihttps://github.com/tberardini 19 UniProt 6 WB 1 ZFIN

All other annotations should be remapped to the direct replacement "mitophagy" terms

Mappings that need to be reviewed: (InterPro2GO, UniProt-Keywords, UniRule) [LIST IDs + ADD ASSIGNEES]

Thanks.

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victorianugnes commented 12 months ago

DisProt done

sarach06 commented 12 months ago

Dear VAl, Thank you very much. I have removed GO:0000422 from IPR040040 and 3 additional entries which had it (IPR047118 IPR040110 IPR045593). These changes will be visible in InterPro 97.0.

Best regards, Sara

RLovering commented 12 months ago

UCL done

ValWood commented 11 months ago

pinging @blazaropinto @tberardini , please remove yourselves when done. tks v

tberardini commented 11 months ago

TAIR done

PedroRaposo commented 11 months ago

Hello, SGD team, when you change the GO term GO:1903599 (positive regulation of autophagy of mitochondrion) to the 21 proteins, please tag me and let me know as I need so made changes on UniProt side, after it. Please note that the GO I mentioned in this comment (GO:1903599 positive regulation of autophagy of mitochondrion) is different from the GO on this issue (GO:0000422 autophagy of mitochondrion). Thank you

ValWood commented 11 months ago

Everyone please note that it was later decided to keep this grouping term to group mitophagy and micromitophagy, but that it should be to always make the more specific mitophagy or microphagy annotations and so this term is now "do not annotate", so this ticket was kept open as the migration still applies.

@marcfeuermann also proposed some further improvements to this branch that I will implement shortly: If you are interested please follow this ticket: https://github.com/geneontology/go-ontology/issues/26202

vanaukenk commented 10 months ago

WB done

suzialeksander commented 2 months ago

GO:0000422 autophagy of mitochondrion
GO:1903146 regulation of autophagy of mitochondrion
GO:1903147 negative regulation of autophagy of mitochondrion
GO:1903599 positive regulation of autophagy of mitochondrion

These are all still active terms. Is this still a valid ticket or is it a wontfix? @ValWood

ValWood commented 2 months ago

still on my list https://github.com/geneontology/go-ontology/issues/26202 Hopefully in the next couple of weeks.