search

geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
BSD 3-Clause "New" or "Revised" License
34 stars 10 forks source link

Review annotations to actin reorganization & related #4409

Closed pgaudet closed 1 year ago

pgaudet commented 1 year ago

Dear all,

The proposal has been made to obsolete (https://github.com/geneontology/go-ontology/issues/14087)

Experimental annotations that need to be reviewed are here: https://docs.google.com/spreadsheets/d/11iY9Rmb3ZbyNSf8ZdI37whYfwz2pmYrCoPVibz2EE4g/edit#gid=0

Impacted groups: There are 84 EXP annotations to these terms:

BHF-UCL and ARUK-UCL 16x28 (12 added) done CACAO 2 ~dictyBase 4~ FlyBase 8 MGI 4 ~PomBase 1~ done RGD 3 SGD 17 ~UniProt 28~ ~WB 1~ done

Thanks.

Pascale

hattrill commented 1 year ago

FB done

LiNiMGI commented 1 year ago

MGI done.

LiNiMGI commented 1 year ago

@pgaudet while reviewing, I noticed MGI has more annotations to the actin reorganization & related terms than showed in the excel sheet.

pgaudet commented 1 year ago

Hi @LiNiMGI Sorry about that - do you have an example of a missing annotation, so I can see what went wrong with my query ?

Thanks, Pascale

LiNiMGI commented 1 year ago

@pgaudet Thanks for looking into it. MGI Ctsl, I already made change in Noctua yesterday. https://www.informatics.jax.org/go/reference/J:178223 MGI Eps8, not change yet. https://www.informatics.jax.org/go/reference/J:116055

srengel commented 1 year ago

SGD done.

gthayman commented 1 year ago

RGD done.

pfey03 commented 1 year ago

dicty done a while ago, forgot to say it here

LiNiMGI commented 1 year ago

@pgaudet More examples for MGI annotations that are not in the excel sheet. They are in current version of Amigo. PMID:17507657 Cdh1 MGI:MGI:88354 GO:0031532 actin cytoskeleton reorganization. IMP. MGI:1857282 PMID:9808630 Plec MGI:1277961 GO:0031532 actin cytoskeleton reorganization. IMP (not in form but in graph) PMID:17008542 Plek2 MGI:1351466 GO:0031532 actin cytoskeleton reorganization. IDA PMID:27917469. Pak1 MGI:1339975 GO:0031532 actin cytoskeleton reorganization. ISO Q13153 PMID:27917469 Syde1 MGI:1918959 GO:0031532 actin cytoskeleton reorganization. ISO Q6ZW31 PMID:10809671 Shc1 MGI:98296 GO:0031532 actin cytoskeleton reorganization IMP MGI:2384189 PMID:10438476 Lpin1 MGI:1891340 GO:0031532 actin cytoskeleton reorganization IMP MGI:1856603 PMID:17018287. Eps8 MGI:104684 GO:0031532 actin cytoskeleton reorganization IMP MGI:3693626 PMID:12529407 S100a9 MGI:1338947 GO:0031532 actin cytoskeleton reorganization IMP MGI:2450165

There are also one MGI annotation that is in Nocua production, but failed reasoner, so it didn't go to MGI. PMID:24747950 Plek2 MGI:1351466 GO:0031532 actin cytoskeleton reorganization. RNAi Maybe we need a Noctua QC for Noctua models that failed reasoner, so curator will be notified to fix it? thanks, Li

LiNiMGI commented 1 year ago

MGI done with those missing from the annotation review ticket.

RLovering commented 1 year ago

ucl done

Antonialock commented 1 year ago

uniprot done

pgaudet commented 1 year ago

Terms are now obsolete. Any remaining annotation will appear in error reports.