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Published 20 hours ago • verified publisher icon geneontology

Review annotations to unnecessary grouping terms

Open raymond91125 opened this issue 10 months ago • 12 comments

Dear all,

The proposal has been made to obsolete 'organic substance biosynthetic process' GO:1901576 'organic substance catabolic process' GO:1901575 'organic substance metabolic process' GO:0071704 'organic substance transport' GO:0071702 'response to organic substance' GO:0010033 'detection of organic substance' GO0071703 'response to inorganic substance' GO0010035 'cellular response to organic substance' GO:0071310 'cellular response to inorganic substance' GO:0071241 organic cyclic compound catabolic process GO:1901362 organic cyclic compound biosynthetic process GO:1901362 organic cyclic compound metabolic process GO:1901360

see https://github.com/geneontology/go-ontology/issues/27386

Experimental annotations that need to be reviewed are here: https://docs.google.com/spreadsheets/d/1HzTyTZM3vq1182I2yAphuRbZpboEI58oouhHwZaBZ5Y/edit#gid=0

Impacted groups:

  • [x] CGD 1
  • [x] Complex Portal 1
  • [x] EcoCyc 2
  • [x] FlyBase 9
  • [ ] MGI 157
  • [x] MTBBASE 8
  • [ ] PseudoCAP 1
  • [x] RGD 157
  • [x] TAIR 2
  • [x] UniProt 20

Mappings that need to be reviewed: InterPro:IPR007543 LptD, C-terminal > GO:response to organic substance ; GO:0010033 InterPro:IPR020889 LPS-assembly protein LptD > GO:response to organic substance ; GO:0010033 Rfam:RF00760 mir-342 > GO:cellular response to inorganic substance ; GO:0071241 Rfam:RF04052 mir-466 > GO:cellular response to inorganic substance ; GO:0071241 UniProtKB-KW:KW-0762 Sugar transport > GO:organic substance transport ; GO:0071702 InterPro:IPR001547 Glycoside hydrolase, family 5 > GO:organic substance metabolic process ; GO:0071704 InterPro:IPR005843 Alpha-D-phosphohexomutase, C-terminal > GO:organic substance metabolic process ; GO:0071704 InterPro:IPR036900 Alpha-D-phosphohexomutase, C-terminal domain superfamily > GO:organic substance metabolic process ; GO:0071704

Thanks.

raymond91125 avatar Mar 29 '24 17:03 raymond91125

CGD done

jlewsmith avatar Apr 01 '24 15:04 jlewsmith

FB done

hattrill avatar Apr 02 '24 08:04 hattrill

TAIR done

tberardini avatar Apr 03 '24 21:04 tberardini

EcoCyc done

amandamackie avatar Apr 15 '24 02:04 amandamackie

uniprot done

Antonialock avatar Apr 25 '24 09:04 Antonialock

RGD finished.

slaulederkind avatar Apr 29 '24 19:04 slaulederkind

Hi Pascale,

Thanks for that. I removed the mentioned terms and added GO:0000272 to IPR001547. The changes will be available in InterPro 100.0.

Best, Beatriz

blazaropinto avatar May 01 '24 08:05 blazaropinto

MGI @LiNiMGI ComplexProtal @sandraorchard PseudoCap @glwinsor

Still need to review their annotations.

pgaudet avatar May 01 '24 08:05 pgaudet

Complex Portal done

sandraorchard avatar May 09 '24 05:05 sandraorchard

@pgaudet Should I wait more or go ahead with obsoleting these terms? Thanks.

raymond91125 avatar May 15 '24 22:05 raymond91125

@LiNiMGI Do you want to have a look at the MGI annotations before we go ahead with the obsoletion?

pgaudet avatar Jun 07 '24 08:06 pgaudet

Thanks@pgaudet, I plan to start the review next week (was waiting and trying to get some help), it might take me a while to finish this one; obsolete now will make the review process even hard since I have to switch to graph editor to make all the changes...

LiNiMGI avatar Jun 07 '24 12:06 LiNiMGI

These terms were obsoleted; remaining annotations will appear in GORULES error reports

suzialeksander avatar Aug 13 '24 00:08 suzialeksander