Review annotations to GO:0009405 pathogenesis

[pgaudet]

Hello,

The proposal has been made to obsolete GO:0009405 pathogenesis, see geneontology/go-ontology#11057

The reason for obsoletion is that the term is out of scope for GO, since pathogenesis is a disease process. There are many annotations to this term, mostly genes that contribute pathogens grow, but are not specifically relevant for pathogenesis or even interspecies interaction.

We suggest the annotations be either removed, or replaced by 'GO:0044419 biological process involved in interspecies interaction between organisms' or a child.

Annotations to review are here: https://docs.google.com/spreadsheets/d/1v5W2rmYkYriY8U23XC7IdI1wRRfUdlNqIXMDZCfnvCY/edit#gid=0

Contributor	(Assigned by)
AgBase	5
ASAP	50
AspGD	39
CACAO	60
CAFA	8
CGD	400
EcoliWiki	1
GeneDB	11
MGI	1
MTBBASE	92
PAMGO_MGG	4
PAMGO_VMD	3
ParkinsonsUK-UCL	1
PseudoCAP	56
TAIR	1
TIGR	3
UniProt	184
WB	2

[RLovering]

UCL done

[hdrabkin]

MGI done

[genegodbold]

UniProt has nearly a quarter million accessions tagged with "Pathogenesis" and nobody can say what it means for any particular sequence. Good riddance! FWIW, the JHU APL folks have a much better approach to documenting what is happening in pathogenic symbiosis. It should make it's public debut sometime next year. This is just a guess, though.

[tberardini]

TAIR done

[vanaukenk]

WB done.

[pgarmiri]

Hello,

I am just starting looking at this. It seems that the suggested term to be used has a restriction.

GO:0044419 JSON
biological process involved in interspecies interaction between organisms

Restrictions

This term should not be used for direct annotation.

Is this going to change when the GO:0009405 'pathogenesis' will be obsoleted or should it always be one of the child terms?

We have a few annotations to check and it wouldn't be fun to have to go back to them again for a second time.

Thanks,

Penelope

[pgarmiri]

Hi,
CAFA and UniProt-EBI annotations have been reviewed. Actions reported in the spreadsheet.

Annotations by SWIS and SWIP have been tagged in the spreadsheet with a purple and orange label, respectively.

Thanks,
Penelope

[pgaudet]

Hi @pgarmiri

'GO:0044419 biological process involved in interspecies interaction between organisms' should not change.
Thanks for your understanding and for fixing all those annotations !!

Pascale

[Achchuthan]

GeneDB done.

[marekskrzypek]

CGD done