[Go] Alert: proposal to obsolete GO:0006510 that impacts existing annotations

[Midori Harris]

Dear GO,

The proposal has been made to obsolete

   ATP-dependent proteolysis ; GO:0006510

Annotations to GO:0006510 exist as listed below (tab-delimited):

   DB	IEA	non-IEA	total
   dictyBase.gz	1	2	3
   fb.gz	2	17	19
   GeneDB_Pfalciparum.gz	0	1	1
   GeneDB_Spombe.gz	1	3	4
   GeneDB_Tbrucei.gz	0	1	1
   goa_chicken.gz	7	0	7
   goa_cow.gz	6	0	6
   goa_human.gz	5	4	9
   goa_pdb.gz	2	0	2
   goa_uniprot.gz	2450	0	2450
   mgi.gz	4	0	4
   pseudocap.gz	0	7	7
   rgd.gz	6	1	7
   sgd.gz	1	0	1
   tair.gz	4	32	36
   tigr_Aphagocytophilum.gz	0	4	4
   tigr_Banthracis.gz	0	3	3
   tigr_Cburnetii.gz	0	2	2
   tigr_Chydrogenoformans.gz	0	3	3
   tigr_Cjejuni.gz	0	5	5
   tigr_Cperfringens.gz	0	5	5
   tigr_Cpsychrerythraea.gz	0	6	6
   tigr_Dethenogenes.gz	0	4	4
   tigr_Echaffeensis.gz	0	5	5
   tigr_Gsulfurreducens.gz	0	3	3
   tigr_Hneptunium.gz	0	7	7
   tigr_Lmonocytogenes.gz	0	3	3
   tigr_Mcapsulatus.gz	0	4	4
   tigr_Nsennetsu.gz	0	3	3
   tigr_Pfluorescens.gz	0	2	2
   tigr_Psyringae.gz	0	5	5
   tigr_Psyringae_phaseolicola.gz	0	5	5
   tigr_Soneidensis.gz	0	2	2
   tigr_Spomeroyi.gz	0	7	7
   tigr_Vcholerae.gz	0	2	2
   wb.gz	5	0	5
   zfin.gz	1	0	1

The reason for obsoleting this term is that it represents a molecular 
function, for which a term exists in the MF ontology (see below). Terms 
suggested for annotation updates include the function term and some 
process terms:

    ATP-dependent peptidase activity ; GO:0004176
    proteolysis ; GO:0006508
      proteolysis involved in cellular protein catabolic process ; GO:0051603
      protein maturation via proteolysis ; GO:0051605

This term is in the prokaryote subset, but not in any GO slims maintained 
in the gene_ontology_write.obo file. It is also used in the following 
external mappings:

interpro2go:InterPro:IPR003111 Peptidase S16, lon N-terminal > GO:ATP-dependent proteolysis ; GO:0006510
interpro2go:InterPro:IPR004815 Peptidase S16, ATP-dependent protease La > GO:ATP-dependent proteolysis ; GO:0006510
pfam2go:Pfam:PF02190 LON > GO:ATP-dependent proteolysis ; GO:0006510
smart2go:SMART:SM00464 LON > GO:ATP-dependent proteolysis ; GO:0006510
tigrfams2go:JCVI_TIGRFAMS:TIGR00382 ATP-dependent Clp protease, ATP-binding subunit ClpX > GO:ATP-dependent proteolysis ; GO:0006510
tigrfams2go:JCVI_TIGRFAMS:TIGR00390 heat shock protein HslVU, ATPase subunit HslU > GO:ATP-dependent proteolysis ; GO:0006510
tigrfams2go:JCVI_TIGRFAMS:TIGR00493 ATP-dependent Clp protease, proteolytic subunit ClpP > GO:ATP-dependent proteolysis ; GO:0006510
tigrfams2go:JCVI_TIGRFAMS:TIGR00764 ATP-dependent protease, putative > GO:ATP-dependent proteolysis ; GO:0006510
tigrfams2go:JCVI_TIGRFAMS:TIGR02639 ATP-dependent Clp protease ATP-binding subunit ClpA > GO:ATP-dependent proteolysis ; GO:000651

SourceForge link:
https://sourceforge.net/tracker/index.php?func=detail&aid=2635152&group_id=36855&atid=440764

Comment period ends on March 13, 2009.

*** Unless objections are received by March 13,
       we will assume that you agree to this change. ***

Thanks,
Midori