[go] Alert: Proposal to obsolete three biological process terms that impacts existing annotations

Midori Harris midori at ebi.ac.uk
Thu Feb 21 04:08:17 PST 2008 

Dear GO,

The proposal has been made to obsolete

   reproductive sporulation ; GO:0048622
   sporulation (sensu Bacteria) ; GO:0030436
   spore wall assembly (sensu Bacteria) ; GO:0042243

Annotations to these terms exist at present as follows:

   reproductive sporulation ; GO:0048622
 	None

   sporulation (sensu Bacteria) ; GO:0030436
 	DB		total
 	goa_uniprot	248 (all IEA)
 	tigr_Banthracis	154 (147 ISS, 7 TAS)
 	tigr_Chydrogenoformans	65 (all ISS)
 	tigr_Cperfringens	67 (all ISS)
 	tigr_Cpsychrerythraea	1 (all ISS)
 	tigr_Gsulfurreducens	1 (all ISS)
 	tigr_Lmonocytogenes	2 (all ISS)

   spore wall assembly (sensu Bacteria) ; GO:0042243
 	DB		total
 	goa_pdb	11 (all IEA)
 	goa_uniprot	33 (all IEA)
 	tigr_Cperfringens	3 (all IEA)
 	tigr_Mcapsulatus	1 (all IEA)

These terms are used in any external2go mappings noted as an appendix to 
this message; GO:0030436 and GO:0042243 are in the prokaryote GO subset 
maintained within the OBO flat file.

The reasons for making these terms obsolete are:

reproductive sporulation GO:0048622

   This term is ill defined, so much so that we don't know what it was 
intended to mean; it also has a parent (reproductive process in 
single-celled organism) that isn't consistent with the 'sporulation whose 
primary biological objective is reproduction' meaning (true path violation 
- cf ferns, mosses, mushrooms). No gene products are annotated directly to 
GO:0048622

sporulation (sensu Bacteria) GO:0030436

   This is a grouping term that isn't useful -- there are several different 
types of spore formed by different species/genera/etc. of bacteria, and 
there is neither a need nor a good basis for grouping them with each 
other.

spore wall assembly (sensu Bacteria) GO:0042243
   Reasons analogous to those given for GO:0030436 above.

The proposal is part of the work on 'sensu' terms, documented on the wiki:

   http://gocwiki.geneontology.org/index.php/Sporulation_Meeting_Notes

The comment period ends on Friday, March 7, 2008.

*** Unless objections are received by March 7,
     we will assume that you agree to this change. ***

Midori


Appendix: external2go mappings:

interpro2go:InterPro:IPR001615 Delta-endotoxin CytB > GO:spore wall assembly (sensu Bacteria) ; GO:0042243
pfam2go:Pfam:PF01338 Bac_thur_toxin > GO:spore wall assembly (sensu Bacteria) ; GO:0042243
prodom2go:ProDom:PD009844 Endotoxin_CytB > GO:spore wall assembly (sensu Bacteria) ; GO:0042243

hamap2go:HAMAP:MF_00637 > GO:sporulation (sensu Bacteria) ; GO:0030436
hamap2go:HAMAP:MF_00665 > GO:sporulation (sensu Bacteria) ; GO:0030436
hamap2go:HAMAP:MF_00666 > GO:sporulation (sensu Bacteria) ; GO:0030436
hamap2go:HAMAP:MF_00667 > GO:sporulation (sensu Bacteria) ; GO:0030436
hamap2go:HAMAP:MF_00669 > GO:sporulation (sensu Bacteria) ; GO:0030436
hamap2go:HAMAP:MF_01504 > GO:sporulation (sensu Bacteria) ; GO:0030436
hamap2go:HAMAP:MF_01505 > GO:sporulation (sensu Bacteria) ; GO:0030436
interpro2go:InterPro:IPR005081 Peptidase U4, sporulation factor SpoIIGA > GO:sporulation (sensu Bacteria) ; GO:0030436
interpro2go:InterPro:IPR012610 Small acid-soluble spore H > GO:sporulation (sensu Bacteria) ; GO:0030436
interpro2go:InterPro:IPR012611 Small acid-soluble spore K > GO:sporulation (sensu Bacteria) ; GO:0030436
interpro2go:InterPro:IPR012612 Small acid-soluble spore N > GO:sporulation (sensu Bacteria) ; GO:0030436
interpro2go:InterPro:IPR012613 Small acid-soluble spore O > GO:sporulation (sensu Bacteria) ; GO:0030436
mips2go:MIPS_funcat:43.01.02.05.01 development of endospore > GO:sporulation (sensu Bacteria) ; GO:0030436
pfam2go:Pfam:PF03419 Peptidase_U4 > GO:sporulation (sensu Bacteria) ; GO:0030436
pfam2go:Pfam:PF08141 SspH > GO:sporulation (sensu Bacteria) ; GO:0030436
pfam2go:Pfam:PF08175 SspO > GO:sporulation (sensu Bacteria) ; GO:0030436
pfam2go:Pfam:PF08176 SspK > GO:sporulation (sensu Bacteria) ; GO:0030436
pfam2go:Pfam:PF08177 SspN > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR01441 spore protease > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR01925 anti-sigma F factor > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02214 stage V sporulation protein D > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02615 stage V sporulation protein E > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02728 spore coat protein GerQ > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02764 polysaccharide deacetylase family sporulation protein PdaB > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02829 stage III sporulation protein AE > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02830 stage III sporulation protein AG > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02831 stage II sporulation protein M > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02832 sporulation protein YunB > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02833 stage III sporulation protein AB > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02834 putative sporulation protein YtxC > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02836 stage IV sporulation protein A > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02837 stage II sporulation protein R > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02838 stage V sporulation protein AC > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02839 stage V sporulation protein AE > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02840 putative sporulation protein YtaF > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02844 sporulation transcriptional regulator SpoIIID > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02845 stage V sporulation protein AD > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02848 stage III sporulation protein AC > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02849 stage III sporulation protein AD > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02851 stage V sporulation protein T > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02852 dipicolinic acid synthetase, B subunit > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02853 dipicolinic acid synthetase, A subunit > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02854 sigma-E processing peptidase SpoIIGA > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02855 sporulation peptidase YabG > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02856 sporulation protein YqfC > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02858 stage III sporulation protein AA > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02860 stage IV sporulation protein B > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02861 small acid-soluble spore protein, H-type > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02862 pro-sigmaK processing inhibitor BofA > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02863 small, acid-soluble spore protein, SspJ family > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02864 small, acid-soluble spore protein O > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02865 stage II sporulation protein E > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02867 stage II sporulation protein P > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02870 stage II sporulation protein D > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02871 sporulation integral membrane protein YlbJ > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02872 sporulation integral membrane protein YtvI > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02873 probable sporulation protein, polysaccharide deacetylase family > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02874 sporulation protein YtfJ > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02875 sporulation transcription factor Spo0A > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02876 sporulation protein YqfD > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02877 sporulation protein YhbH > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02878 sporulation protein YpjB > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02881 stage V sporulation protein K > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02883 N-acetylmuramoyl-L-alanine amidase CwlD > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02885 RNA polymerase sigma-F factor > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02886 anti-sigma F factor antagonist > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02887 germination protein, Ger(x)C family > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02888 sporulation protein, YlmC/YmxH family > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02889 germination protein YpeB > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02890 sporulation protein, yteA family > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02892 sporulation protein YabP > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02893 spore cortex biosynthesis protein YabQ > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02896 stage III sporulation protein AF > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02898 sporulation lipoprotein,  YhcN/YlaJ family > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02899 spore coat assembly protein SafA > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02900 stage V sporulation protein B > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02902 ATP-dependent protease LonB > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02903 ATP-dependent protease, Lon family > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02904 spore coat protein YsxE > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02905 spore coat protein YutH > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02906 spore coat protein, CotS family > GO:sporulation (sensu Bacteria) ; GO:0030436
tigrfams2go:TIGR_TIGRFAMS:TIGR02907 stage VI sporulation protein D > GO:sporulation (sensu Bacteria) ; GO:0030436

More information about the Go mailing list