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[go-friends] Proposal to obsolete grouping terms for coenzyme role

Karen Christie Karen.Christie at jax.org
Mon Apr 13 13:49:24 PDT 2020


Dear all,



The proposal has been made to obsolete the coenzyme grouping terms:

  *   GO:0050662 - coenzyme binding
  *   GO:0006732 - coenzyme metabolic process
  *   GO:0009108 - coenzyme biosynthetic process
  *   GO:0009109 - coenzyme catabolic process
  *   GO:0051182 - coenzyme transport
  *   GO:0051185 - coenzyme transmembrane transporter activity
  *   GO:0051196 - regulation of coenzyme metabolic process
  *   GO:0051198 - negative regulation of coenzyme metabolic process
  *   GO:0051197 - positive regulation of coenzyme metabolic process



The reasons for these obsoletions are:

  *   Reasoning over ChEBI role of “coenzyme” is producing many inferences that are not appropriate in GO.
  *   It is not very meaningful to group processes that are not metabolically related by the fact that they produce a compound that may be used as a coenzyme or to group various kinds of binding to chemically unrelated compounds by the fact that they may be used as a coenzyme.

There are 37 annotations to these terms that need to be reviewed and 32 sequence annotations that may need to be reviewed:


Contributor
EXP TAS RCA
SEQ
AspGD
7
0
CAFA
2
0
EcoCyc
2
0
GeneDB
0
1
JCVI
0
4
MGI
1
8
MTBBASE
4
0
PseudoCAP
4
0
Reactome
6
0
RGD
4
6
TIGR
0
1
UniProt
7
12
Grand Total
37
32





There are InterPro2GO & UniRule mappings to these terms:


GO Term
External Mapping
coenzyme binding
InterPro:IPR001509
InterPro:IPR002202
InterPro:IPR003421
InterPro:IPR004553
InterPro:IPR009023
InterPro:IPR009029
InterPro:IPR013118
UniRule:UR000100714
coenzyme biosynthetic process
InterPro:IPR002835
InterPro:IPR005980
InterPro:IPR019939
UniRule:UR000039422
UniRule:UR000039429
UniRule:UR000079254
UniRule:UR000079257
UniRule:UR000092052
UniRule:UR000101490



The term “coenzyme binding” is included in the subset: metagenomics.



Please consider if these annotations can be transferred to a term for some specific type of cofactor. Let me know if you think we may need any new terms.



Any comments can be  added to the issue: https://github.com/geneontology/go-ontology/issues/19243



We are opening a comment period for these proposed obsoletions. We’d like to proceed and obsolete this term on April 27th. Unless objections are received by April 27th, we will assume that you agree to this change.









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