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

Karen Christie Karen.Christie at jax.org
Mon Apr 13 13:49:20 PDT 2020


Dear all,



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

  *   GO:0051186 - cofactor metabolic process
  *   GO:0051188 - cofactor biosynthetic process
  *   GO:0051187 - cofactor catabolic process
  *   GO:0018065 - protein-cofactor linkage
  *   GO:0048037 - cofactor binding
  *   GO:0051181 - cofactor transport
  *   GO:0051184 - cofactor transmembrane transporter activity
  *   GO:0051193 - regulation of cofactor metabolic process
  *   GO:0051195 - negative regulation of cofactor metabolic process
  *   GO:0051194 - positive regulation of cofactor metabolic process



The reasons for these obsoletions are:

  *   Reasoning over the ChEBI role of “cofactor” 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 cofactor or to group various kinds of binding to chemically unrelated compounds by the fact that they may be used as a cofactor.



There are 60 annotations to these terms that need to be reviewed and 33 sequence annotations that may need to be reviewed:


Contributor
EXP + AS
SEQ
AgBase
0
2
BHF-UCL
1
0
CGD
1
0
EcoCyc
3
0
EcoliWiki
1
0
GeneDB
4
0
MGI
0
2
PomBase
0
1
PseudoCAP
0
2
Reactome
9
0
RGD
7
2
SGD
3
0
UniProt
31
23
ZFIN
0
1
Grand Total
60
33





There are InterPro2GO & UniRule mappings to these terms:


GO_term
external mappings
cofactor metabolic process
InterPro:IPR010722
InterPro:IPR017678
InterPro:IPR017680
cofactor biosynthetic process
InterPro:IPR003203
InterPro:IPR008225
InterPro:IPR010115
InterPro:IPR011774
InterPro:IPR013477
InterPro:IPR013480
InterPro:IPR023659
InterPro:IPR023661
UniRule:UR000028575
UniRule:UR000195377
UniRule:UR000195519
UniRule:UR000375818
protein-cofactor linkage
InterPro:IPR016614
cofactor binding
InterPro:IPR003781
InterPro:IPR006140
InterPro:IPR011159
InterPro:IPR012349
InterPro:IPR015761
UniRule:UR000171791
UniRule:UR000638782 UniRule:UR000925792





These terms are included in these subset(s).


GO_term
subset
cofactor metabolic process
chembl drosophila generic            pir         pombe     yeast
cofactor binding
pir
cofactor transport
pir





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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