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 > >