OK sounds good. Are the replace by tags in that file, I couldn't see them? Anyway it all looks great. No objections here Val Midori Harris wrote: > 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 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) > >> _______________________________________________ > >> Go mailing list > >> Go@geneontology.org > >> http://fafner.stanford.edu/mailman/listinfo/go > >> > >> > > > > > >