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.