[Go] Alert: proposal to obsolete GO:0006512 that impacts existing annotation

[Midori Harris]

Hello,

The proposal has been made to obsolete

   ubiquitin cycle ; GO:0006512

The reason for making this term obsolete is that it implies that every 
protein that s ubiquitinated is also subsequently deubiquinitated, which 
is not true. Also, the process ontology does not include analogous terms 
for other small modifiers.

Terms suggested for annotation updates:
   protein deubiquitination ; GO:0016597
   protein ubiquitination ; GO:0016567

Annotations to GO:0006512 exist as follows:



gene_association.cgd.gz
IEA	non-IEA	Total
2	0	2

gene_association.dictyBase.gz
IEA	non-IEA	Total
97	0	97

gene_association.fb.gz
IEA	non-IEA	Total
25	33	58

gene_association.GeneDB_Lmajor.gz
IEA	non-IEA	Total
34	0	34

gene_association.GeneDB_Pfalciparum.gz
IEA	non-IEA	Total
25	0	25

gene_association.GeneDB_Spombe.gz
IEA	non-IEA	Total
7	0	7

gene_association.GeneDB_Tbrucei.gz
IEA	non-IEA	Total
31	24	55

gene_association.goa_chicken.gz
IEA	non-IEA	Total
126	0	126

gene_association.goa_cow.gz
IEA	non-IEA	Total
210	0	210

gene_association.goa_human.gz
IEA	non-IEA	Total
502	8	510

gene_association.goa_uniprot.gz
IEA	non-IEA	Total
7372	2	7374

gene_association.gramene_oryza.gz
IEA	non-IEA	Total
0	16	16

gene_association.mgi.gz
IEA	non-IEA	Total
423	34	457

gene_association.rgd.gz
IEA	non-IEA	Total
201	9	210

gene_association.sgd.gz
IEA	non-IEA	Total
137	9	146

gene_association.tair.gz
IEA	non-IEA	Total
7	53	60

gene_association.tigr_Tbrucei_chr2.gz
IEA	non-IEA	Total
0	3	3

gene_association.wb.gz
IEA	non-IEA	Total
28	0	28

gene_association.zfin.gz
IEA	non-IEA	Total
29	0	29

The term is used in the following external mappings:

interpro2go:InterPro:IPR000011 Ubiquitin-activating enzyme, E1 > 
GO:ubiquitin cycle ; GO:0006512
interpro2go:InterPro:IPR000127 Ubiquitin-activating enzyme repeat > 
GO:ubiquitin cycle ; GO:0006512
interpro2go:InterPro:IPR000569 HECT > GO:ubiquitin cycle ; GO:0006512
interpro2go:InterPro:IPR003126 Zinc finger, N-recognin > GO:ubiquitin 
cycle ; GO:0006512
interpro2go:InterPro:IPR003977 Parkin > GO:ubiquitin cycle ; GO:0006512
interpro2go:InterPro:IPR006615 Ubiquitin carboxyl-terminal hydrolase, 
N-terminal region 1 > GO:ubiquitin cycle ; GO:0006512
interpro2go:InterPro:IPR008883 Tumour susceptibility gene 101 > 
GO:ubiquitin cycle ; GO:0006512
interpro2go:InterPro:IPR010309 E3 ubiquitin ligase, region of unknown 
function DUF908 > GO:ubiquitin cycle ; GO:0006512
interpro2go:InterPro:IPR010314 E3 ubiquitin ligase, region of unknown 
function DUF913 > GO:ubiquitin cycle ; GO:0006512
pfam2go:Pfam:PF00632 HECT > GO:ubiquitin cycle ; GO:0006512
pfam2go:Pfam:PF02134 UBACT > GO:ubiquitin cycle ; GO:0006512
pfam2go:Pfam:PF02207 zf-UBR > GO:ubiquitin cycle ; GO:0006512
pfam2go:Pfam:PF05743 UEV > GO:ubiquitin cycle ; GO:0006512
pfam2go:Pfam:PF06012 DUF908 > GO:ubiquitin cycle ; GO:0006512
pfam2go:Pfam:PF06025 DUF913 > GO:ubiquitin cycle ; GO:0006512
pirsf2go:PIRSF:PIRSF037880 Parkin > GO:ubiquitin cycle ; GO:0006512
prints2go:PRINTS:PR01475 PARKIN > GO:ubiquitin cycle ; GO:0006512
prints2go:PRINTS:PR01849 UBIQUITINACT > GO:ubiquitin cycle ; GO:0006512
prosite2go:PROSITE:PS00536 UBIQUITIN_ACTIVAT_1 > GO:ubiquitin cycle ; 
GO:0006512
prosite2go:PROSITE:PS00865 UBIQUITIN_ACTIVAT_2 > GO:ubiquitin cycle ; 
GO:0006512
prosite2go:PROSITE:PS50237 HECT > GO:ubiquitin cycle ; GO:0006512
prosite2go:PROSITE:PS51157 ZF_UBR > GO:ubiquitin cycle ; GO:0006512
smart2go:SMART:SM00119 HECTc > GO:ubiquitin cycle ; GO:0006512
smart2go:SMART:SM00695 DUSP > GO:ubiquitin cycle ; GO:0006512
spkw2go:SP_KW:KW-0833 Ubl conjugation pathway > GO:ubiquitin cycle ; 
GO:0006512

This term is not in any GO slim or subset maintained in the GO .obo files.

SourceForge link:
https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1729553&group_id=36855

The comment period ends Friday, July 25, 2008.

*** Unless objections are received by July 25,
       we will assume that you agree to this change. ***