'cell-substrate adherens junctions' annotation review

[BarbaraCzub]

There is no such structure in biology as ‘cell-substrate adherens junctions’, because ‘adherens junctions’ are always ‘cell-cell junctions’. Consequently, we propose to obsolete the term: ‘cell-substrate adherens junctions’. (geneontology/go-ontology#18119)

There are currently 3 experimental manual annotations for the exact term ‘cell-substrate adherens junctions’ and 4 ISS/ISO annotations and the affected groups include:

UniProt – 4 annotations
RGD – 2 annotations @slaulederkind
MGI – 1 annotation @ukemi
https://www.ebi.ac.uk/QuickGO/annotations?goUsage=exact&goUsageRelationships=is_a,part_of,occurs_in&goId=GO:0005924

Could you please track your changes in this spreadsheet: https://docs.google.com/spreadsheets/d/17G-3RrrUNB83uwyQ6LHHEvxayNfslqns71DriqqE1eo/edit

Could you please review your annotations and:

1. Re-annotate to ‘cell-substrate junction’ if there is the evidence for this in the annotated paper (or the paper that the annotation was transferred from by ISS/ISO).
2. Re-annotate to ‘adherens junction’ if there is the evidence in the annotated paper (or the paper that the annotation was transferred from by ISS/ISO) that this is a ‘cell-cell adherens junction’.
3. Re-annotate to another more specific appropriate term – perhaps ‘focal adhesion’ will be correct for some of these.

We propose the deadline of 15 Nov for completing this review.

Thank you,
Barbara, Mila and Ruth

cc @milarolo @RLovering

[ukemi]

Hi @BarbaraCzub. The mouse annotation is through an orthology load from rat. Once @slaulederkind fixes his annotation ours should update automatically.

[pgaudet]

@BarbaraCzub I created an 'Annotation Review' spreadsheet:

https://docs.google.com/spreadsheets/d/17G-3RrrUNB83uwyQ6LHHEvxayNfslqns71DriqqE1eo/edit

Please remove electronic and ISO annotations and paste the annotations to be reviewed there.

This allows us to track changes that are made.

Thanks, Pascale

[slaulederkind]

The single manual RGD rat annotation has been corrected.

[BarbaraCzub]

Thanks @pgaudet, I'll add the annotations and a record of the RGD correction - thanks @slaulederkind

[milarolo]

UniProt/SWIE done

[BarbaraCzub]

UniProt/SWIE done

Thanks, Mila! However, I see there is one annotation here that no one has claimed: UniProt is the contributor, but the gene product has the MGI gene ID...

[ukemi]

What's the paper? I'll have a look. If it doesn't need to be changed we are all set.

[BarbaraCzub]

Oh, I see now. The MGI gene ID is the same as Q62417, which you have added to the table. And the PMID is the same.

[BarbaraCzub]

So, Mila changed it, but in the row below.

[BarbaraCzub]

All experimental annotations have been reviewed and changed. Thank you!