[Go] Alert: proposal to obsolete many peptidase activity terms from the molecular function ontology

[Midori Harris]

Dear GO,

For a few weeks now, a small group of curators from GO, MEROPS, and PRO 
have been working on a substantial reorganization of the peptidase 
activity terms in the molecular function ontology. Background and notes 
from this effort are on the wiki:

   http://wiki.geneontology.org/index.php/Proteases

One important outcome of this work is that many of the existing peptidase 
activity terms will be made obsolete, in most cases because they represent 
gene products. This course of action was readily agreed upon by all of the 
working group, and actively encouraged by the peptidase experts at MEROPS. 
These terms will be made obsolete on August 15, 2008.

The IDs and names of the terms to become obsolete are:

GO:0001509	legumain activity
GO:0003802	coagulation factor VIIa activity
GO:0003803	coagulation factor IXa activity
GO:0003804	coagulation factor Xa activity
GO:0003805	coagulation factor XIa activity
GO:0003806	coagulation factor XIIa activity
GO:0003807	plasma kallikrein activity
GO:0003808	protein C (activated) activity
GO:0003809	thrombin activity
GO:0003812	alternative-complement-pathway C3/C5 convertase activity
GO:0003813	classical-complement-pathway C3/C5 convertase activity
GO:0003815	complement component C1r activity
GO:0003816	complement component C1s activity
GO:0003817	complement factor D activity
GO:0003818	complement factor I activity
GO:0004178	leucyl aminopeptidase activity
GO:0004179	membrane alanyl aminopeptidase activity
GO:0004182	carboxypeptidase A activity
GO:0004183	carboxypeptidase E activity
GO:0004184	lysine carboxypeptidase activity
GO:0004186	carboxypeptidase C activity
GO:0004187	carboxypeptidase D activity
GO:0004188	serine-type Pro-X carboxypeptidase activity
GO:0004189	tubulinyl-Tyr carboxypeptidase activity
GO:0004191	barrierpepsin activity
GO:0004192	cathepsin D activity
GO:0004193	cathepsin E activity
GO:0004194	pepsin A activity
GO:0004195	renin activity
GO:0004196	saccharopepsin activity
GO:0004213	cathepsin B activity
GO:0004214	dipeptidyl-peptidase I activity
GO:0004215	cathepsin H activity
GO:0004216	cathepsin K activity
GO:0004217	cathepsin L activity
GO:0004218	cathepsin S activity
GO:0004219	pyroglutamyl-peptidase I activity
GO:0004226	Gly-X carboxypeptidase activity
GO:0004228	gelatinase A activity
GO:0004229	gelatinase B activity
GO:0004230	glutamyl aminopeptidase activity
GO:0004231	insulysin activity
GO:0004232	interstitial collagenase activity
GO:0004234	macrophage elastase activity
GO:0004235	matrilysin activity
GO:0004237	membrane dipeptidase activity
GO:0004238	meprin A activity
GO:0004239	methionyl aminopeptidase activity
GO:0004240	mitochondrial processing peptidase activity
GO:0004243	mitochondrial intermediate peptidase activity
GO:0004244	mitochondrial inner membrane peptidase activity
GO:0004245	neprilysin activity
GO:0004246	peptidyl-dipeptidase A activity
GO:0004247	saccharolysin activity
GO:0004248	stromelysin 1 activity
GO:0004249	stromelysin 3 activity
GO:0004250	aminopeptidase I activity
GO:0004251	X-Pro dipeptidase activity
GO:0004253	gamma-renin activity
GO:0004254	acylaminoacyl-peptidase activity
GO:0004261	cathepsin G activity
GO:0004262	cerevisin activity
GO:0004263	chymotrypsin activity
GO:0004274	dipeptidyl-peptidase IV activity
GO:0004275	enteropeptidase activity
GO:0004276	furin activity
GO:0004277	granzyme A activity
GO:0004278	granzyme B activity
GO:0004281	pancreatic elastase II activity
GO:0004283	plasmin activity
GO:0004284	acrosin activity
GO:0004285	proprotein convertase 1 activity
GO:0004286	proprotein convertase 2 activity
GO:0004287	prolyl oligopeptidase activity
GO:0004289	subtilase activity
GO:0004290	kexin activity
GO:0004291	subtilisin activity
GO:0004293	tissue kallikrein activity
GO:0004294	tripeptidyl-peptidase II activity
GO:0004295	trypsin activity
GO:0008125	pancreatic elastase I activity
GO:0008129	actinidain activity
GO:0008130	neutrophil collagenase activity
GO:0008132	pancreatic elastase activity
GO:0008133	collagenase activity
GO:0008243	plasminogen activator activity
GO:0008319	prenyl protein specific endopeptidase activity
GO:0008322	Pro-X carboxypeptidase activity
GO:0008423	bleomycin hydrolase activity
GO:0008439	monophenol monooxygenase activator activity
GO:0008450	O-sialoglycoprotein endopeptidase activity
GO:0008451	X-Pro aminopeptidase activity
GO:0008462	endopeptidase Clp activity
GO:0008464	gamma-glutamyl hydrolase activity
GO:0008472	metallocarboxypeptidase D activity
GO:0008487	prenyl-dependent CAAX protease activity
GO:0008533	astacin activity
GO:0008581	ubiquitin-specific protease 5 activity
GO:0008717	D-alanyl-D-alanine endopeptidase activity
GO:0008769	X-His dipeptidase activity
GO:0008846	endopeptidase La activity
GO:0008931	murein DD-endopeptidase activity
GO:0008944	oligopeptidase A activity
GO:0008945	oligopeptidase B activity
GO:0008947	omptin activity
GO:0008956	peptidyl-dipeptidase Dcp activity
GO:0008975	pitrilysin activity
GO:0008978	prepilin peptidase activity
GO:0008981	protease IV activity
GO:0008991	serine-type signal peptidase activity
GO:0008992	repressor LexA activity
GO:0009003	signal peptidase activity
GO:0009004	signal peptidase I activity
GO:0009005	signal peptidase II activity
GO:0009049	aspartic-type signal peptidase activity
GO:0009377	HslUV protease activity
GO:0009980	glutamate carboxypeptidase activity
GO:0009983	tyrosine aminopeptidase activity
GO:0010320	arginine/lysine endopeptidase activity
GO:0016284	alanine aminopeptidase activity
GO:0016285	cytosol alanyl aminopeptidase activity
GO:0016511	endothelin-converting enzyme activity
GO:0016512	endothelin-converting enzyme 1 activity
GO:0016804	prolyl aminopeptidase activity
GO:0016808	proprotein convertase activity
GO:0016919	nardilysin activity
GO:0016921	pyroglutamyl-peptidase II activity
GO:0016946	cathepsin F activity
GO:0017026	procollagen C-endopeptidase activity
GO:0017039	dipeptidyl-peptidase III activity
GO:0017074	procollagen N-endopeptidase activity
GO:0017088	X-Pro dipeptidyl-peptidase activity
GO:0017092	sterol regulatory element-binding protein site 2 protease 
activity
GO:0017093	sterol regulatory element-binding protein protease 
activity
GO:0017094	sterol regulatory element-binding protein site 1 protease 
activity
GO:0017165	dipeptidase E activity
GO:0019131	tripeptidyl-peptidase I activity
GO:0019132	C-terminal processing peptidase activity
GO:0019783	small conjugating protein-specific protease activity
GO:0019784	NEDD8-specific protease activity
GO:0019785	ISG15-specific protease activity
GO:0019786	APG8-specific protease activity
GO:0030019	tryptase activity
GO:0030271	chymase activity
GO:0030303	stromelysin 2 activity
GO:0030402	matrilysin-2 activity
GO:0030403	collagenase 4 activity
GO:0030404	collagenase 3 activity
GO:0030405	matrix metalloproteinase 19 activity
GO:0030406	matrix metalloproteinase 25 activity
GO:0030601	aminopeptidase B activity
GO:0030602	chymosin activity
GO:0030693	caspase activity
GO:0031079	picornain 3C activity
GO:0031368	Pro-X metallocarboxypeptidase activity
GO:0033264	bontoxilysin activity
GO:0042029	fibrolase activity
GO:0042315	cytosol nonspecific dipeptidase activity
GO:0042499	signal peptide peptidase activity
GO:0042576	aspartyl aminopeptidase activity
GO:0042708	elastase activity
GO:0043275	glutamate carboxypeptidase II activity
GO:0043859	cyanophycinase activity
GO:0045024	peptidyl-glutamyl peptide hydrolyzing enzyme activity
GO:0046560	scytalidopepsin B activity
GO:0046561	penicillopepsin activity
GO:0050424	alanine carboxypeptidase activity
GO:0050425	carboxypeptidase B activity
GO:0050426	peptidyl-glycinamidase activity
GO:0051397	N-terminal basic amino acid aminopeptidase activity
GO:0051398	N-terminal lysine aminopeptidase activity
GO:0051399	N-terminal arginine aminopeptidase activity
GO:0051404	clostripain activity
GO:0051405	microbial collagenase activity

Because there are so many terms affected (174), I have not included all of 
the usual details -- specific reasons, annotation counts, and substitute 
terms -- in this email. For a complete list of terms slated to become 
obsolete, in OBO format, with the specific reasons for obsoletion filled 
in, see (this file is also linked to the wiki page):

   http://www.geneontology.org/scratch/peptidase_terms_with_obs_tags.obo

Details of existing annotations to these terms are also on the wiki:

   http://wiki.geneontology.org/index.php/Peptidase_annotations

Every peptidase term that we make obsolete will have at least one 
'replaced_by' tag pointing to a peptidase activity term; these are also 
shown in the .obo file cited above.

A longer term goal is to add new terms to the protein ontology (PRO) 
representing the gene products that have peptidase activity. When the PRO 
terms become available, many of the obsolete GO peptidase activity terms 
will point to PRO terms via 'consider' tags.

Please let us know if you have any questions about this plan, or about the 
files noted above. The comment period ends Friday, August 15, 2008.

*** Unless objections are received by August 15,
       we will assume that you agree to this change. ***

Regards,
Midori

(on behalf of the peptidase activity working group)