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

Fri Jul 25 04:36:39 PDT 2008

Hi Val,

In the vast majority of cases the reason not to merge is that the term 
represents a gene product, and if we did merges we'd end up with a few 
terms, each with a ton of narrow synonyms and alt_ids. People already 
often get confused by the alt_ids even when a term has just one or two. 
Gene products are clearly outside the scope of GO, so for those terms 
obsoleting is more appropriate.

The small-conjugating-etc. terms are a bit different, in that they're not 
just obviously gene product names with 'activity' slapped on the end. But 
we're leaning towards making them obsolete as well, mainly because one of 
the conclusions the working group reached is that trying to use substrate 
specificity to sub-divide peptidases wouldn't work, except for the endo- 
vs. exo- and dipeptidase/tripeptidase cases.

m

On Fri, 25 Jul 2008, Valerie Wood wrote:

> Midori,
>
> Its looks great, a lot of work.
>
> Only one question, a number seem to have single parents (like the small 
> conjugating protein specific protease terms and children), so I'm 
> assuming the pointer will just be to the parent. Any reason why these 
> can't be merges? Or are the resolutions always more complicated?
>
> I did look in the obo file for 'conjugating' and I couldn't see the 
> replace by tages for this term (or for any terms close by in the file) 
> just is_obsolete: true
>
> Val
>
> Midori Harris <midori at ebi.ac.uk> wrote:
>> 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)
>> _______________________________________________
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>> Go at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/go
>>
>>
>
>