Changes committed on 25th March, 2008

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Working Group Members

Jim Hu
Debby Siegele
Michelle Gwinn-Giglio
Ingrid Keseler
Jen Deegan
Pascale Gaudet

Group e-mail address: electron-transport at geneontology.org

Summary of Edits

We have been working on a branch file of gene_ontology_edit.obo since January 2008. Our first set of changes is to go live on 25th March 2008 and includes the obsoletions listed below. The new terms added are listed in the obsoletion mails, as part of the discussion of why the obsoletions were made.


GO:0006118 : electron transport obsoletion warning

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:0016491 ; oxidoreductase activity.

We have also made a new electron transport chain term. The new term stanzas are included below. 

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

GO:0006125 : thioredoxin pathway obsoletion warning

The proposal has been made to obsolete GO:0006125 : thioredoxin pathway.

There exist today annotations to this term as follows (data from AmiGO):

    * RGD: 3 objects
    * UniProtKB: 4 objects
    * GeneDB: 1 object
    * FlyBase: 1 object
    * MGI: 2 objects

The term is used in the following mapping:
MetaCyc: THIOREDOX-PWY

The term is not found in the generic GO slim set.

The reason for this proposal is that the term is undefined and we are unable 
to fix on a single intended meaning for it based on the current set of annotations.
We suggest that annotators might consider instead 'cell redox homeostasis'. 
If there are other requirements for different replacement terms then we 
can also make further additions.

GO:0000044 : ascorbate stabilization obsoletion warning

The proposal has been made to obsolete GO:0000044 : ascorbate stabilization.

There exist today no annotations to this term.

The term is used in no mappings.

The term is not found in the generic GO slim set.

The reason for this proposal is that the term is defined as a function 
but is placed in the process ontology.

GO:0006133 : 5,10-methylenetetrahydrofolate oxidation obsoletion warning

The proposal has been made to obsolete GO:0006133 :
5,10-methylenetetrahydrofolate oxidation.

There exist today no annotations to this term.

The term is used in no mappings.

The term is not found in the generic GO slim set.

The reason for this proposal is that the term is defined to represent a
function, but is in the process ontology.

GO:0009502 : photosynthetic electron transport chain obsoletion warning

The proposal has been made to obsolete GO:0009502 ; photosynthetic electron transport chain.

There exist today annotations to this term as follows (data from AmiGO):

    * UniProtKB: 6 objects
    * TAIR: 4 objects

The reasons for this proposal are that the term is defined 
as a process term but is in the cellular component ontology.


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