[go] Alert: Proposal to obsolete GO:0006118 : electron transport that impacts existing annotation

[Jennifer Deegan (nee Clark)]

Hi,

During the discussions  of the electron transport working group the 
proposal has been made to obsolete GO:0006118 : electron transport:
http://tinyurl.com/youuxm

There exist today many annotations to this term as follows (data from 
AmiGO):
http://tinyurl.com/ywhzx7

The term is used in many mappings :
http://tinyurl.com/2x3qln

The term is found in the following GO slim sets or categories:
subset: goslim_candida
subset: goslim_generic
subset: goslim_goa
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok

The reasons for this proposal are as follows. This term is named and 
defined as a function term, along the lines of an oxidoreductase term. 
However, it is placed in the biological process ontology as if it was to 
be used as the respiratory electron transport chain term, or as a more 
general term to include the electron transport involved in the 
photosynthetic light reaction. As a result of this ambiguity the term 
has been used interchangeably to represent any of the roles described 
above.

The term to be obsoleted has a great many annotations. However it is 
likely that each individual database will have always used the term in a 
consistent way.  For example, at TIGR the term has almost always been 
used to represent the respiratory electron transport chain process, and 
so these annotations  can mostly be very quickly updated to refer to a 
new correct term.
As the vast majority of annotations are from TIGR, and other databases 
have tended to use the term in a similarly consistent
way, we anticipate that it may not take too much time to replace 
annotations to this term with annotations to a new alternative term.

As replacement terms we would suggest considering
  GO:0022904 ; respiratory electron transport chain
  GO:0022900 ; electron transport chain.
to be found in our branch file at go/scratch/electron_transport.obo.
(Stanzas pasted below)

Also in the current live graph:  GO:0016491 ; oxidoreductase activity.

We will not implement this obsoletion until 4th April at the earliest, 
to allow for discussion of the request, and for adjustments to be made 
to annotations if the request is agreed.

UNLESS OBJECTIONS ARE RECEIVED BY 4th April WE WILL ASSUME THAT YOU 
AGREE TO THIS CHANGE.

Thank you for taking the time to consider this.

Jennifer




Replacement term stanzas:

[Term]
id: GO:0022900
name: electron transport chain
namespace: biological_process
def: "A process whereby a series of electron carriers operate together 
to transfer electrons from donors to any of
several different terminal electron acceptors to generate a 
transmembrane electrochemical gradient." [GOC:mtg_electron_transport]
is_a: GO:0006091 ! generation of precursor metabolites and energy

[Term]
id: GO:0022904
name: respiratory electron transport chain
namespace: biological_process
def: "A process whereby a series of electron carriers operate together 
to transfer electrons from donors such
as NADH and FADH2 to any of several different terminal electron 
acceptors to generate a transmembrane
electrochemical gradient." [GOC:mtg_electron_transport, 
http://cancerweb.ncl.ac.uk/]
subset: goslim_candida
subset: goslim_generic
subset: goslim_goa
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
synonym: "6-phosphofructokinase reduction" RELATED []
synonym: "dihydrobiopterin reduction" RELATED []
synonym: "dihydrolipoamide reduction" RELATED []
synonym: "dihydrolipoylprotein reduction" RELATED []
synonym: "dihydropteridine reduction" RELATED []
synonym: "electron transfer" EXACT []
synonym: "other pathways of electron transport" RELATED []
synonym: "oxidized glutathione reduction" RELATED []
synonym: "protein-disulfide reduction" RELATED []
is_a: GO:0022900 ! electron transport chain





-- 
Jennifer Deegan (nee Clark)
EMBL-European Bioinformatics Institute
Gene Ontology Consortium