From midori at ebi.ac.uk Wed Jan 2 11:24:23 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 2 Jan 2008 19:24:23 +0000 (GMT) Subject: [go] Ontology development - December highlights Message-ID: Dear GO, The most recent monthly report on ontology content, for December 2007, is now available at: http://gocwiki.geneontology.org/index.php/Dec2007_ontology_report Ontology development highlights from December: * The first phase of work on regulation terms is essentially done. The 'regulates' relationship will be defined early in January, and deployed soon thereafter (http://gocwiki.geneontology.org/index.php/Regulation_Main_Page). * The content meeting on lung development was held on December 5th-6th; a file is available in go/scratch/ (http://wiki.geneontology.org/index.php/Lung_Development). * Work on 'sensu' terms is almost done, with the latest changes in the go/scratch/directory (main wiki page: http://gocwiki.geneontology.org/index.php/Sensu_Main_Page; outstanding items: http://gocwiki.geneontology.org/index.php/Meeting_Notes_3). * Reorganization of electron transport terms is under way. In January, there will be follow-up work from the lung development meeting, more work on cross-products, including regulation and GO-Cell xps, and work on transport and transporters will resume. As usual, details of small- and medium-scale changes are available in the SourceForge Curator Requests tracker. Please contact us if you want to help out with ontology work in a particular area, or if you have any comments or questions about what's going on. Happy new year! Midori & David on behalf of GO's ontology developers From dhowe at cs.uoregon.edu Fri Jan 4 14:10:54 2008 From: dhowe at cs.uoregon.edu (Doug howe) Date: Fri, 04 Jan 2008 14:10:54 -0800 Subject: [go] Other File Downloads Message-ID: <477EAEEE.8000206@cs.uoregon.edu> The GO website has a section called "Other File Downloads": http://www.geneontology.org/GO.downloads.files.shtml The above url states that the following two files are updated daily, but the files contain date stamps from 12/17/2007. http://www.geneontology.org/doc/GO.terms_and_ids http://www.geneontology.org/doc/GO.terms_alt_ids -Doug From midori at ebi.ac.uk Mon Jan 7 01:53:00 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 7 Jan 2008 09:53:00 +0000 (GMT) Subject: [go] Other File Downloads In-Reply-To: <477EAEEE.8000206@cs.uoregon.edu> References: <477EAEEE.8000206@cs.uoregon.edu> Message-ID: Hi Doug, I've updated both files now. They should be generated automagically (by a script) from the GO database starting Real Soon Now(tm), but at the moment they're still done by a different script and I have to remember to commit them manually. midori On Fri, 4 Jan 2008, Doug howe wrote: > The GO website has a section called "Other File Downloads": > http://www.geneontology.org/GO.downloads.files.shtml > > The above url states that the following two files are updated daily, but the > files contain date stamps from 12/17/2007. > http://www.geneontology.org/doc/GO.terms_and_ids > http://www.geneontology.org/doc/GO.terms_alt_ids > > -Doug > From aji at ebi.ac.uk Mon Jan 7 06:32:26 2008 From: aji at ebi.ac.uk (Amelia Ireland) Date: Mon, 7 Jan 2008 14:32:26 +0000 Subject: [go] AmiGO beta announcement In-Reply-To: <47683AD6.80705@informatics.jax.org> References: <47683AD6.80705@informatics.jax.org> Message-ID: Hi Alex, > [displaying NOT annotations and column ordering] >>> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628&session_id=1458amigo1197932357 >>> >>> the first line of the listed associations reads Qualifier: NOT, >>> Term: GO:0051092 : activation of NF-kappaB transcription factor, >>> link: 63 gene products, I've changed the column so that it is hopefully a little clearer now. Example: http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 Does that work? Cheers, Amelia. -- Amelia Ireland GO Editorial Office, European Bioinformatics Institute, UK. Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp From adiehl at informatics.jax.org Mon Jan 7 07:10:18 2008 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Mon, 07 Jan 2008 15:10:18 +0000 Subject: [go] AmiGO beta announcement In-Reply-To: References: <47683AD6.80705@informatics.jax.org> Message-ID: <478240DA.3070002@informatics.jax.org> Amelia, I like this much more. Thank you very much, and Happy New Year! Alex Amelia Ireland wrote: > Hi Alex, >> > [displaying NOT annotations and column ordering] >>>> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628&session_id=1458amigo1197932357 >>>> >>>> >>>> the first line of the listed associations reads Qualifier: NOT, >>>> Term: GO:0051092 : activation of NF-kappaB transcription factor, >>>> link: 63 gene products, > > I've changed the column so that it is hopefully a little clearer now. > > Example: > http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 > > Does that work? > > Cheers, > Amelia. > > -- > Amelia Ireland > GO Editorial Office, > European Bioinformatics Institute, UK. > Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp > > > -- Alexander Diehl, Ph.D. Senior Scientific Curator Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: adiehl at informatics.jax.org work: +1 (207) 288-6427 fax: +1 (207) 288-6131 From ma11 at gen.cam.ac.uk Mon Jan 7 07:36:58 2008 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Mon, 7 Jan 2008 15:36:58 +0000 Subject: [go] AmiGO beta announcement In-Reply-To: <478240DA.3070002@informatics.jax.org> References: <47683AD6.80705@informatics.jax.org> <478240DA.3070002@informatics.jax.org> Message-ID: Looks good Michael On 7 Jan 2008, at 15:10, Alexander Diehl wrote: > Amelia, > > I like this much more. > > Thank you very much, and Happy New Year! > > Alex > > > Amelia Ireland wrote: >> Hi Alex, >>> >> [displaying NOT annotations and column ordering] >>>>> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi? >>>>> gp=MGI:MGI:2685628&session_id=1458amigo1197932357 >>>>> >>>>> the first line of the listed associations reads Qualifier: NOT, >>>>> Term: GO:0051092 : activation of NF-kappaB transcription >>>>> factor, link: 63 gene products, >> >> I've changed the column so that it is hopefully a little clearer now. >> >> Example: >> http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 >> >> Does that work? >> >> Cheers, >> Amelia. >> >> -- >> Amelia Ireland >> GO Editorial Office, >> European Bioinformatics Institute, UK. >> Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp >> >> >> > > > -- > Alexander Diehl, Ph.D. > Senior Scientific Curator > Mouse Genome Informatics > The Jackson Laboratory > 600 Main Street > Bar Harbor, ME 04609 > > email: adiehl at informatics.jax.org > work: +1 (207) 288-6427 > fax: +1 (207) 288-6131 > From rama at genome.Stanford.EDU Mon Jan 7 13:45:04 2008 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Mon, 7 Jan 2008 13:45:04 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: References: <47683AD6.80705@informatics.jax.org> Message-ID: <89357209-1C66-4995-98A1-7E853BCD2CF5@genome.stanford.edu> Sorry for not piping in earlier on this one. The way you have reordered it (http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi? gp=FB:FBgn0027356) with the NOT next to the evidence code, it looks like the qualifier goes with the evidence code. I think this is misleading.. rama On Jan 7, 2008, at 6:32 AM, Amelia Ireland wrote: > Hi Alex, >> > [displaying NOT annotations and column ordering] >>>> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi? >>>> gp=MGI:MGI:2685628&session_id=1458amigo1197932357 >>>> >>>> the first line of the listed associations reads Qualifier: NOT, >>>> Term: GO:0051092 : activation of NF-kappaB transcription factor, >>>> link: 63 gene products, > > I've changed the column so that it is hopefully a little clearer now. > > Example: > http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 > > Does that work? > > Cheers, > Amelia. > > -- > Amelia Ireland > GO Editorial Office, > European Bioinformatics Institute, UK. > Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp > > From adiehl at informatics.jax.org Mon Jan 7 14:19:04 2008 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Mon, 07 Jan 2008 22:19:04 +0000 Subject: [go] AmiGO beta announcement In-Reply-To: <89357209-1C66-4995-98A1-7E853BCD2CF5@genome.stanford.edu> References: <47683AD6.80705@informatics.jax.org> <89357209-1C66-4995-98A1-7E853BCD2CF5@genome.stanford.edu> Message-ID: <4782A558.5020504@informatics.jax.org> Rama, I'm sorry if you find this misleading now. In my earlier post I explained how I found the previous arrangement (in the beta) misleading. Again, it comes down to trying to convey the maximal amount of information in the least amount of interface space. While I appreciate your concern, I still feel Amelia's new arrangement is less misleading than the previous arrangement of columns, but this is probably quite subjective. If anyone else is wondering what this about, compare these two displays: 1) (current beta) http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 2) (Amelia's new column configuration) http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 or these two: 1) (current beta) http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628 2) (Amelia's new column configuration) http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628 Thanks, Alex Rama Balakrishnan wrote: > Sorry for not piping in earlier on this one. The way you have > reordered it > (http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356) > with the NOT next to the evidence code, it looks like the qualifier > goes with the evidence code. I think this is misleading.. > > rama > > > > On Jan 7, 2008, at 6:32 AM, Amelia Ireland wrote: > >> Hi Alex, >>> >> [displaying NOT annotations and column ordering] >>>>> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628&session_id=1458amigo1197932357 >>>>> >>>>> >>>>> the first line of the listed associations reads Qualifier: NOT, >>>>> Term: GO:0051092 : activation of NF-kappaB transcription factor, >>>>> link: 63 gene products, >> >> I've changed the column so that it is hopefully a little clearer now. >> >> Example: >> http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 >> >> Does that work? >> >> Cheers, >> Amelia. >> >> -- >> Amelia Ireland >> GO Editorial Office, >> European Bioinformatics Institute, UK. >> Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp >> >> > -- Alexander Diehl, Ph.D. Senior Scientific Curator Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: adiehl at informatics.jax.org work: +1 (207) 288-6427 fax: +1 (207) 288-6131 From rama at genome.Stanford.EDU Mon Jan 7 14:40:27 2008 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Mon, 7 Jan 2008 14:40:27 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: <4782A558.5020504@informatics.jax.org> References: <47683AD6.80705@informatics.jax.org> <89357209-1C66-4995-98A1-7E853BCD2CF5@genome.stanford.edu> <4782A558.5020504@informatics.jax.org> Message-ID: <7536504A-9BCE-40A5-B8DB-6A5B690232E1@genome.stanford.edu> Alex, Sorry for not being clear. I agree, the previous arrangement was misleading and I feel the fix we have now is not super clear and since we are still in the testing/commenting mode, we can come up with ways to make it better? For example, one option would be to create a separate table to list gene products annotated to term+qualifier, have anchors on the top and not display all of them in one table. 2 cents. I can go with the majority on this. rama On Jan 7, 2008, at 2:19 PM, Alexander Diehl wrote: > Rama, > > I'm sorry if you find this misleading now. > In my earlier post I explained how I found the previous arrangement > (in the beta) misleading. Again, it comes down to trying to convey > the maximal amount of information in the least amount of interface > space. While I appreciate your concern, I still feel Amelia's new > arrangement is less misleading than the previous arrangement of > columns, but this is probably quite subjective. > > If anyone else is wondering what this about, compare these two > displays: > > 1) (current beta) http://goweb-dev.stanford.edu/cgi-bin/amigo/gp- > assoc.cgi?gp=FB:FBgn0027356 > > 2) (Amelia's new column configuration) http://toy.lbl.gov:9012/cgi- > bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 > > or these two: > > 1) (current beta) http://goweb-dev.stanford.edu/cgi-bin/amigo/gp- > assoc.cgi?gp=MGI:MGI:2685628 > > 2) (Amelia's new column configuration) http://toy.lbl.gov:9012/cgi- > bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628 > > > Thanks, > > Alex > > > > Rama Balakrishnan wrote: >> Sorry for not piping in earlier on this one. The way you have >> reordered it (http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi? >> gp=FB:FBgn0027356) with the NOT next to the evidence code, it >> looks like the qualifier goes with the evidence code. I think this >> is misleading.. >> >> rama >> >> >> >> On Jan 7, 2008, at 6:32 AM, Amelia Ireland wrote: >> >>> Hi Alex, >>>> >>> [displaying NOT annotations and column ordering] >>>>>> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi? >>>>>> gp=MGI:MGI:2685628&session_id=1458amigo1197932357 >>>>>> >>>>>> the first line of the listed associations reads Qualifier: >>>>>> NOT, Term: GO:0051092 : activation of NF-kappaB transcription >>>>>> factor, link: 63 gene products, >>> >>> I've changed the column so that it is hopefully a little clearer >>> now. >>> >>> Example: >>> http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 >>> >>> Does that work? >>> >>> Cheers, >>> Amelia. >>> >>> -- >>> Amelia Ireland >>> GO Editorial Office, >>> European Bioinformatics Institute, UK. >>> Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp >>> >>> >> > > > -- > Alexander Diehl, Ph.D. > Senior Scientific Curator > Mouse Genome Informatics > The Jackson Laboratory > 600 Main Street > Bar Harbor, ME 04609 > > email: adiehl at informatics.jax.org > work: +1 (207) 288-6427 > fax: +1 (207) 288-6131 From eurie at genome.Stanford.EDU Mon Jan 7 15:32:24 2008 From: eurie at genome.Stanford.EDU (Eurie Hong) Date: Mon, 7 Jan 2008 15:32:24 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: <4782A558.5020504@informatics.jax.org> References: <47683AD6.80705@informatics.jax.org> <89357209-1C66-4995-98A1-7E853BCD2CF5@genome.stanford.edu> <4782A558.5020504@informatics.jax.org> Message-ID: I agree with Rama - the new column configuration implies that it's the evidence code that being qualified. And I prefer the organization on the beta, especially with the "contributes_to" and "colocalizes_with" qualifiers. But I agree that counts are misleading. Can the count for the qualified terms be calculated separately from the non-qualified terms? Or just go back to the "view associations" that's currently in production. eurie On Jan 7, 2008, at 2:19 PM, Alexander Diehl wrote: > Rama, > > I'm sorry if you find this misleading now. In my earlier post I > explained how I found the previous arrangement (in the beta) > misleading. Again, it comes down to trying to convey the maximal > amount of information in the least amount of interface space. > While I appreciate your concern, I still feel Amelia's new > arrangement is less misleading than the previous arrangement of > columns, but this is probably quite subjective. > > If anyone else is wondering what this about, compare these two > displays: > > 1) (current beta) http://goweb-dev.stanford.edu/cgi-bin/amigo/gp- > assoc.cgi?gp=FB:FBgn0027356 > > 2) (Amelia's new column configuration) http://toy.lbl.gov:9012/cgi- > bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 > > or these two: > > 1) (current beta) http://goweb-dev.stanford.edu/cgi-bin/amigo/gp- > assoc.cgi?gp=MGI:MGI:2685628 > > 2) (Amelia's new column configuration) http://toy.lbl.gov:9012/cgi- > bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628 > > > Thanks, > > Alex > > > > Rama Balakrishnan wrote: >> Sorry for not piping in earlier on this one. The way you have >> reordered it (http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi? >> gp=FB:FBgn0027356) with the NOT next to the evidence code, it >> looks like the qualifier goes with the evidence code. I think this >> is misleading.. >> >> rama >> >> >> >> On Jan 7, 2008, at 6:32 AM, Amelia Ireland wrote: >> >>> Hi Alex, >>>> >>> [displaying NOT annotations and column ordering] >>>>>> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi? >>>>>> gp=MGI:MGI:2685628&session_id=1458amigo1197932357 >>>>>> >>>>>> the first line of the listed associations reads Qualifier: >>>>>> NOT, Term: GO:0051092 : activation of NF-kappaB transcription >>>>>> factor, link: 63 gene products, >>> >>> I've changed the column so that it is hopefully a little clearer >>> now. >>> >>> Example: >>> http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 >>> >>> Does that work? >>> >>> Cheers, >>> Amelia. >>> >>> -- >>> Amelia Ireland >>> GO Editorial Office, >>> European Bioinformatics Institute, UK. >>> Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp >>> >>> >> > > > -- > Alexander Diehl, Ph.D. > Senior Scientific Curator > Mouse Genome Informatics > The Jackson Laboratory > 600 Main Street > Bar Harbor, ME 04609 > > email: adiehl at informatics.jax.org > work: +1 (207) 288-6427 > fax: +1 (207) 288-6131 From cjm at fruitfly.org Mon Jan 7 17:41:05 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Mon, 7 Jan 2008 17:41:05 -0800 Subject: [go] AmiGO beta announcement In-Reply-To: References: <47683AD6.80705@informatics.jax.org> <89357209-1C66-4995-98A1-7E853BCD2CF5@genome.stanford.edu> <4782A558.5020504@informatics.jax.org> Message-ID: Both displays confused me at first, but I believe this to be because of a bug in the data. FB appear to be submitting a fake non-NOT annotation corresponding to every real NOT annotation. Either that or there are a lot of self-contradictory papers. On Jan 7, 2008, at 3:32 PM, Eurie Hong wrote: > I agree with Rama - the new column configuration implies that it's > the evidence code that being qualified. And I prefer the > organization on the beta, especially with the "contributes_to" and > "colocalizes_with" qualifiers. > > But I agree that counts are misleading. Can the count for the > qualified terms be calculated separately from the non-qualified > terms? Or just go back to the "view associations" that's currently > in production. > > eurie > > On Jan 7, 2008, at 2:19 PM, Alexander Diehl wrote: > >> Rama, >> >> I'm sorry if you find this misleading now. In my earlier post I >> explained how I found the previous arrangement (in the beta) >> misleading. Again, it comes down to trying to convey the maximal >> amount of information in the least amount of interface space. >> While I appreciate your concern, I still feel Amelia's new >> arrangement is less misleading than the previous arrangement of >> columns, but this is probably quite subjective. >> >> If anyone else is wondering what this about, compare these two >> displays: >> >> 1) (current beta) http://goweb-dev.stanford.edu/cgi-bin/amigo/gp- >> assoc.cgi?gp=FB:FBgn0027356 >> >> 2) (Amelia's new column configuration) http://toy.lbl.gov:9012/ >> cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 >> >> or these two: >> >> 1) (current beta) http://goweb-dev.stanford.edu/cgi-bin/amigo/gp- >> assoc.cgi?gp=MGI:MGI:2685628 >> >> 2) (Amelia's new column configuration) http://toy.lbl.gov:9012/ >> cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628 >> >> >> Thanks, >> >> Alex >> >> >> >> Rama Balakrishnan wrote: >>> Sorry for not piping in earlier on this one. The way you have >>> reordered it (http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi? >>> gp=FB:FBgn0027356) with the NOT next to the evidence code, it >>> looks like the qualifier goes with the evidence code. I think >>> this is misleading.. >>> >>> rama >>> >>> >>> >>> On Jan 7, 2008, at 6:32 AM, Amelia Ireland wrote: >>> >>>> Hi Alex, >>>>> >>>> [displaying NOT annotations and column ordering] >>>>>>> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi? >>>>>>> gp=MGI:MGI:2685628&session_id=1458amigo1197932357 >>>>>>> >>>>>>> the first line of the listed associations reads Qualifier: >>>>>>> NOT, Term: GO:0051092 : activation of NF-kappaB transcription >>>>>>> factor, link: 63 gene products, >>>> >>>> I've changed the column so that it is hopefully a little clearer >>>> now. >>>> >>>> Example: >>>> http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi? >>>> gp=FB:FBgn0027356 >>>> >>>> Does that work? >>>> >>>> Cheers, >>>> Amelia. >>>> >>>> -- >>>> Amelia Ireland >>>> GO Editorial Office, >>>> European Bioinformatics Institute, UK. >>>> Carbon neutral driving: http://www.targetneutral.com/TONIC/ >>>> index.jsp >>>> >>>> >>> >> >> >> -- >> Alexander Diehl, Ph.D. >> Senior Scientific Curator >> Mouse Genome Informatics >> The Jackson Laboratory >> 600 Main Street >> Bar Harbor, ME 04609 >> >> email: adiehl at informatics.jax.org >> work: +1 (207) 288-6427 >> fax: +1 (207) 288-6131 > > From sart2 at gen.cam.ac.uk Tue Jan 8 03:28:18 2008 From: sart2 at gen.cam.ac.uk (Susan Tweedie) Date: Tue, 08 Jan 2008 11:28:18 +0000 Subject: [go] AmiGO beta announcement In-Reply-To: References: <47683AD6.80705@informatics.jax.org> <89357209-1C66-4995-98A1-7E853BCD2CF5@genome.stanford.edu> <4782A558.5020504@informatics.jax.org> Message-ID: <1199791698.5314.43.camel@paul.gen.cam.ac.uk> On Mon, 2008-01-07 at 17:41 -0800, Chris Mungall wrote: > Both displays confused me at first, but I believe this to be because > of a bug in the data. FB appear to be submitting a fake non-NOT > annotation corresponding to every real NOT annotation. Either that or > there are a lot of self-contradictory papers. Oh dear.... thanks Chris - there is clearly a bug in the script used to make our ga file which has resulted in a systematic parial duplication of lines with qualiers. I'll get it fixed. However, we do have some genuinely contradictory evidence for the same term based on different papers. Although I would normally prefer to see the qualifier in front of the GO term, I like the way Amelia's new config has each term only once. If there is contradictory evidence for a term, it is important to spot it - this is easier when it is gathered together in a single block rather than under 2 separate term entries. Susan > > On Jan 7, 2008, at 3:32 PM, Eurie Hong wrote: > > > I agree with Rama - the new column configuration implies that it's > > the evidence code that being qualified. And I prefer the > > organization on the beta, especially with the "contributes_to" and > > "colocalizes_with" qualifiers. > > > > But I agree that counts are misleading. Can the count for the > > qualified terms be calculated separately from the non-qualified > > terms? Or just go back to the "view associations" that's currently > > in production. > > > > eurie > > > > On Jan 7, 2008, at 2:19 PM, Alexander Diehl wrote: > > > >> Rama, > >> > >> I'm sorry if you find this misleading now. In my earlier post I > >> explained how I found the previous arrangement (in the beta) > >> misleading. Again, it comes down to trying to convey the maximal > >> amount of information in the least amount of interface space. > >> While I appreciate your concern, I still feel Amelia's new > >> arrangement is less misleading than the previous arrangement of > >> columns, but this is probably quite subjective. > >> > >> If anyone else is wondering what this about, compare these two > >> displays: > >> > >> 1) (current beta) http://goweb-dev.stanford.edu/cgi-bin/amigo/gp- > >> assoc.cgi?gp=FB:FBgn0027356 > >> > >> 2) (Amelia's new column configuration) http://toy.lbl.gov:9012/ > >> cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 > >> > >> or these two: > >> > >> 1) (current beta) http://goweb-dev.stanford.edu/cgi-bin/amigo/gp- > >> assoc.cgi?gp=MGI:MGI:2685628 > >> > >> 2) (Amelia's new column configuration) http://toy.lbl.gov:9012/ > >> cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628 > >> > >> > >> Thanks, > >> > >> Alex > >> > >> > >> > >> Rama Balakrishnan wrote: > >>> Sorry for not piping in earlier on this one. The way you have > >>> reordered it (http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi? > >>> gp=FB:FBgn0027356) with the NOT next to the evidence code, it > >>> looks like the qualifier goes with the evidence code. I think > >>> this is misleading.. > >>> > >>> rama > >>> > >>> > >>> > >>> On Jan 7, 2008, at 6:32 AM, Amelia Ireland wrote: > >>> > >>>> Hi Alex, > >>>>> > >>>> [displaying NOT annotations and column ordering] > >>>>>>> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi? > >>>>>>> gp=MGI:MGI:2685628&session_id=1458amigo1197932357 > >>>>>>> > >>>>>>> the first line of the listed associations reads Qualifier: > >>>>>>> NOT, Term: GO:0051092 : activation of NF-kappaB transcription > >>>>>>> factor, link: 63 gene products, > >>>> > >>>> I've changed the column so that it is hopefully a little clearer > >>>> now. > >>>> > >>>> Example: > >>>> http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi? > >>>> gp=FB:FBgn0027356 > >>>> > >>>> Does that work? > >>>> > >>>> Cheers, > >>>> Amelia. > >>>> > >>>> -- > >>>> Amelia Ireland > >>>> GO Editorial Office, > >>>> European Bioinformatics Institute, UK. > >>>> Carbon neutral driving: http://www.targetneutral.com/TONIC/ > >>>> index.jsp > >>>> > >>>> > >>> > >> > >> > >> -- > >> Alexander Diehl, Ph.D. > >> Senior Scientific Curator > >> Mouse Genome Informatics > >> The Jackson Laboratory > >> 600 Main Street > >> Bar Harbor, ME 04609 > >> > >> email: adiehl at informatics.jax.org > >> work: +1 (207) 288-6427 > >> fax: +1 (207) 288-6131 > > > > > From hjd at informatics.jax.org Tue Jan 8 11:20:53 2008 From: hjd at informatics.jax.org (Harold Drabkin) Date: Tue, 08 Jan 2008 14:20:53 -0500 Subject: [go] AmiGO beta announcement In-Reply-To: References: <47683AD6.80705@informatics.jax.org> <89357209-1C66-4995-98A1-7E853BCD2CF5@genome.stanford.edu> <4782A558.5020504@informatics.jax.org> Message-ID: <4783CD15.9080601@informatics.jax.org> I think the counts are only confusing when the qualifier is a NOT. So, if you want to show # of genes annotated to "nucleus"; if you have a NOT nucleus, reading it one way is confusing. The fact is you do have x number annotated using "nucleus"; but one has a NOT, there are still X annotations using the GO term but the meaning of one of the annotation sis different. This isn't as much of a conflict for the contributes_to and co_localizes_with, since nether are negation statements. The second display does suggest the wrong field is being qualified. The first URL is better in that respect. hjd Eurie Hong wrote: > I agree with Rama - the new column configuration implies that it's the > evidence code that being qualified. And I prefer the organization on > the beta, especially with the "contributes_to" and "colocalizes_with" > qualifiers. > > But I agree that counts are misleading. Can the count for the > qualified terms be calculated separately from the non-qualified > terms? Or just go back to the "view associations" that's currently in > production. > > eurie > > On Jan 7, 2008, at 2:19 PM, Alexander Diehl wrote: > >> Rama, >> >> I'm sorry if you find this misleading now. In my earlier post I >> explained how I found the previous arrangement (in the beta) >> misleading. Again, it comes down to trying to convey the maximal >> amount of information in the least amount of interface space. While >> I appreciate your concern, I still feel Amelia's new arrangement is >> less misleading than the previous arrangement of columns, but this is >> probably quite subjective. >> >> If anyone else is wondering what this about, compare these two displays: >> >> 1) (current beta) >> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 >> >> >> 2) (Amelia's new column configuration) >> http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 >> >> or these two: >> >> 1) (current beta) >> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628 >> >> >> 2) (Amelia's new column configuration) >> http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628 >> >> >> Thanks, >> >> Alex >> >> >> >> Rama Balakrishnan wrote: >>> Sorry for not piping in earlier on this one. The way you have >>> reordered it >>> (http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356) >>> with the NOT next to the evidence code, it looks like the qualifier >>> goes with the evidence code. I think this is misleading.. >>> >>> rama >>> >>> >>> >>> On Jan 7, 2008, at 6:32 AM, Amelia Ireland wrote: >>> >>>> Hi Alex, >>>>> >>>> [displaying NOT annotations and column ordering] >>>>>>> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628&session_id=1458amigo1197932357 >>>>>>> >>>>>>> >>>>>>> the first line of the listed associations reads Qualifier: NOT, >>>>>>> Term: GO:0051092 : activation of NF-kappaB transcription factor, >>>>>>> link: 63 gene products, >>>> >>>> I've changed the column so that it is hopefully a little clearer now. >>>> >>>> Example: >>>> http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356 >>>> >>>> Does that work? >>>> >>>> Cheers, >>>> Amelia. >>>> >>>> -- >>>> Amelia Ireland >>>> GO Editorial Office, >>>> European Bioinformatics Institute, UK. >>>> Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp >>>> >>>> >>> >> >> >> -- >> Alexander Diehl, Ph.D. >> Senior Scientific Curator >> Mouse Genome Informatics >> The Jackson Laboratory >> 600 Main Street >> Bar Harbor, ME 04609 >> >> email: adiehl at informatics.jax.org >> work: +1 (207) 288-6427 >> fax: +1 (207) 288-6131 > From parkinson at ebi.ac.uk Wed Jan 9 00:14:45 2008 From: parkinson at ebi.ac.uk (Helen Parkinson) Date: Wed, 9 Jan 2008 08:14:45 -0000 (GMT) Subject: [go] Message-ID: <58301.84.41.190.196.1199866485.squirrel@webmail.ebi.ac.uk> Dear Colleagues, I'd like to draw your attention to the ISMB call for papers: ISCB ANNOUNCEMENTS AND U P D A T E S :: ISMB 2008, July 19-23, Toronto, Canada Call for Papers Closing in One Week www.iscb.org/ismb2008/sub_papers.php Paper Submission Deadline: January 16, 2008 Robert Stevens and I are co-chairing the databases and ontologies session and we invite you to submit papers on these themes to help us build a stimulating session. We look forward to seeing you in Toronto http://www.iscb.org/ismb2008/ best regards Helen Parkinson and Robert Stevens From pj37 at cornell.edu Wed Jan 9 11:05:26 2008 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 09 Jan 2008 14:05:26 -0500 Subject: [go] International PAG Ontology Workshop 14 January 2008 Message-ID: <47851AF6.8080403@cornell.edu> Dear All, If you are attending the 16th International Plant and Animal Genome meeting to be held in San Diego (USA), everyone is cordially invited to attend the ?Biological Ontologies and Applications? workshop that is scheduled for Monday Afternoon, 14 January 2008 12:50 pm - 3:00 pm. We have a great panel of talks scheduled for this year's workshop, and look forward to see you at the meeting. Thanks Pankaj http://intl-pag.org/16/16-ontology.html Monday Afternoon, 14 January 2008 --- 12:50 pm - 3:00 pm Biological Ontologies and Applications - Royal Palm Salon 1, 2, and 3 Organizer: Pankaj Jaiswal,Cornell University (pj37 at cornell.edu) Workshop Background: The use of various ontologies for biology has been clearly demonstrated in several biological domains e.g., Gene Ontology and Plant Ontology. An Ontology is a common, structured and controlled vocabulary for describing the concepts that exist in an area of knowledge and the relationships that exist between them. Over the last few years a number of ontologies have been developed and implemented for use in the biological databases. However, among the researchers, the enthusiasm for ontologies has been accompanied by a general lack of awareness of what exactly ontologies are and how to use them. In this workshop we are trying to promote awareness and interaction among the researchers (audiences) and the developers of various ontology and/or those developing computational tools for using these ontologies in large/small scale analysis of genomics and genetics datasets. Useful link: OBO Foundry Ontologies Speakers: 12:50pm Michael Ashburner, Department of Genetics, University of Cambridge, UK (ma11 at gen.cam.ac.uk) "GAZ an ENVO: Two new ontologies to help tame data." 1:20pm Bjoern Peters, La Jolla Institute for Allergy and Immunology, USA (bpeters at liai.org) "OBI: Ontology for Biomedical Investigations" 1:45pm Ken Ichiro Fukuda, National Institute of Advanced Industrial Science and Technology, Japan (fukuda-cbrc at aist.go.jp) "Inoh Pathway Event Ontology" 2:10pm Jayesh Pandey, Dept. of Computer Science, Purdue University, USA (jpandey at cs.purdue.edu) "Functional Characterization Of Pathways In Interaction Networks" 2:35pm Neil Sarkar, Encyclopedia of Life, Marine Biological Laboratory, USA (sarkar at mbl.edu) "Towards Developing Practical Taxonomic Ontologies" From BatchelorC at rsc.org Thu Jan 10 06:38:34 2008 From: BatchelorC at rsc.org (Colin Batchelor) Date: Thu, 10 Jan 2008 14:38:34 -0000 Subject: [go] Message-ID: <93B41882A6FB344FA9CEB2A25EE998BD0486EA3D@stamp> subscribe DISCLAIMER: This communication (including any attachments) is intended for the use of the addressee only and may contain confidential, privileged or copyright material. 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From jdeegan at ebi.ac.uk Mon Jan 14 06:24:19 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Mon, 14 Jan 2008 14:24:19 +0000 Subject: [go] editing freeze 15th January 10am GMT Message-ID: <478B7093.5040104@ebi.ac.uk> Hi, I would like to request an editing freeze on gene_ontology_edit.obo to start at 10am GMT on 15th January (tomorrow). I am going to merge in the proteasome changes that we made as part of the sensu effort. Please can you all make sure that if you are editing the file today, you commit your changes tonight before you go? (Or before the freeze starts, if you are editing tomorrow.) After I am finished merging and committing the file I will send an email to announce the fact, and you will need to check out a fresh copy of the file at that point, before you make any new edits. Thanks for your help in this. Best wishes, Jennifer -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From cjm at fruitfly.org Mon Jan 14 07:48:46 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Mon, 14 Jan 2008 07:48:46 -0800 Subject: [go] Fwd: [Obo-discuss] biological processes & molecular functions References: <478981D3.2080601@uchsc.edu> Message-ID: <29554CED-1A6A-4859-B164-8B309312B501@fruitfly.org> For anyone who is interested: the function vs process issue has come up again, this time on the obo-discuss list subscription and archive here: https://lists.sourceforge.net/lists/listinfo/obo-discuss Begin forwarded message: > From: Mike Bada > Date: January 12, 2008 7:13:23 PM PST > To: obo-discuss at lists.sourceforge.net > Subject: [Obo-discuss] biological processes & molecular functions > Reply-To: obo-discuss at lists.sourceforge.net > > Hi all, > > Like Colin Batchelor, who has recently posted to this list, we are > trying to extensively use OBOs in the annotation of journal articles > (i.e., NLP annotation, not annotation in the sense of that done by the > various model-organism databases). And, like Colin, we are > experiencing > issues in trying to use these OBOs (although I won't speak for him!). > > One issue that has caused us trouble is the dichotomy between GO > biological processes and molecular functions, and this leads to a > reexamination of the nature of these concepts. My understanding from > that written by Barry Smith and others is that a biological process is > an actual process and that a molecular function is a functionality > inherent in a gene/gene product that is realized in a corresponding > process. (Please correct me if I'm wrong.) This makes sense, I > think, > when examining the GO transport and transporter terms: The > transporter > terms in the MF subontology are of the form "Enables the transport > of * > into, out of, within or between cells", while the transport terms > in the > BP subontology are of the form "The directed movement of * into, > out of, > within or between cells". So drug transporter activity is the > functionality inherent in a given gene/gene product that is > realized in > a drug-transport process. I assume that this is the reason for so > many > parallel BP transport and MF transporter activity terms. But if > this is > the case, then why isn't there a corresponding BP term for each MF > term? > > Arguing on the other side, most of the MF terms are not defined as > inherent functionalities but rather sound like processes to me: Most > binding terms are defined as "Interacting selectively with *"; most > catalytic-activity terms are defined as "Catalysis of the reaction: > *"; > many enzyme-regulator-activity terms are defined as "Modulates *"; > etc. > Furthermore, on the GO Web site, molecular functions are described as > "activities, such as catalytic or binding activities, that occur at > the > molecular level", which to me sound like processes (at a molecular > level) rather than functionalities inherent in genes/gene products > that > are realized in processes. > > The specific issues we're having and how we deal with them depend > on the > nature of the relationship between BPs and MFs, so I won't go into > more > detail until this is clear. We're hoping someone from GO/OBO could > clear this up for us. > > Cheers, > Mike > > ---------------------------------------------------------------------- > --- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/ > marketplace > _______________________________________________ > Obo-discuss mailing list > Obo-discuss at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/obo-discuss > From cjm at fruitfly.org Mon Jan 14 22:20:46 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Mon, 14 Jan 2008 22:20:46 -0800 Subject: [go] Fwd: [Obo-discuss] 3 forwarded messages on MF vs BP from obo-discuss References: <478C18B8.5030907@uchsc.edu> Message-ID: [redirecting this part to GO, sorry if this confuses the thread, but I want to ask a question of GO folks first] Thanks for responding Jen. I think Mike raises some interesting issues, many of which we've raised internally. I have my ideas on how to answer Mike's question, focusing on the signal transduction/transducer activity example. But I'd like to get feedback, particularly from an annotation perspective, before answering from an ontology-minded perspective. It seems that we should have on the wiki as part of an annotation SOP some rules/guidelines for when to annotate to "signal transducer activity" vs "signal transduction" vs co-annotation of both. (which would of course apply to analagous examples) We also need to start making P<->F links here. If it helps I have added an example query: http://www.berkeleybop.org/goose select from the popup "genes annotated to signal transducer activity but not signal transduction" (and change the DB if you like - it's set to MGI in the example) you can also try swapping the terms around as you can see there is quite a lot Begin forwarded message: > From: Mike Bada > Date: January 14, 2008 6:21:44 PM PST > To: jdeegan at ebi.ac.uk, obo-discuss at lists.sourceforge.net > Subject: Re: [Obo-discuss] 3 forwarded messages on MF vs BP from > obo-discuss > Reply-To: obo-discuss at lists.sourceforge.net > > Thank you for your detailed reply, Jennifer. However, it seems > there's > not even consensus within the GO/OBO Consortium concerning the > relationship between MFs and BPs. I originally asked whether the MFs > were inherent functionalities of genes/gene products that get realized > as processes or as "elementary" processes themselves. What you > describe > agrees with the documentation on the GO Web site and with most of > the MF > term names and their definitions, i.e., with the latter view, while > Barry takes the former view. > > Again, we are most concerned with all of the parallel terms between > the > two subontologies, which makes application toward NLP, among other > tasks, much more difficult. This is not limited to the large > number of > corresponding transporter activity (MF) / transport (BP) terms; some > other examples include: > > signal transducer activity (MF) ; signal transduction (BP) > translation regulator activity (MF) ; regulation of translation (BP) > enzyme regulator activity (MF) ; regulation of catalytic activity (BP) > enzyme activator activity (MF) ; positive regulation of enzyme > activity (BP) > > According to your explanation, all of these pairs of terms seem to > mean > essentially the same thing except for the fact that each of the former > is a single-step process and each of the latter a multi-step process. > It may be relatively easy to divide a metabolic pathway into its > component biochemical reactions, but what constitutes an elementary > single step of a process is often ambiguous. Any process can be > recursively divided into component processes: Even a biochemical > reaction can be divided into component processes of the reaction > mechanism. This ambiguous nature of what an "elementary" step is > makes > it very difficult to determine whether a process mentioned in, say, a > journal article is a single-step or multi-step process (and thus a > MF or > a BP, respectively). > > So there are two views, both of which hamper usability of the > subontologies applied in combination: As to the view that MFs are the > inherent functionalities of genes/gene products that are realized in > BPs, it is often ambiguous whether a natural-language mention > refers to > the inherent functionality or to the process itself. As to the view > that MFs are the "single-step" processes that make up multi-step > BPs, it > is often ambiguous whether a natural-language mention is a "single- > step" > or "multi-step" process. Wouldn't it be easier and clearer if there > were one merged ontology of processes of all granularities and no > parallel terms such as the aforementioned ones? > > Cheers, > Mike > > > Jennifer Deegan (nee Clark) wrote: > >> Hi Mike, >> >> Midori forwarded this e-mail to me as I have been working on an >> extensive overhaul of the transport terms in GO. I think that I >> can help >> clear up at least some of the confusion here, though it might take >> a few >> e-mails to get things completely clear. >> >> In GO, as you have mentioned, we have transport terms in the function >> and process ontologies, and as you mention, they are really quite >> similar. However, this is partly because many of these terms were >> made >> in the early days of GO when we were really not too clear >> ourselves on >> the distinction between function and process. Now that we are much >> clearer about the distinction I have been working through with a >> number >> of expert biologists and improving the terms. >> >> Just to be clear, I will give a nice easy example of some function >> and >> process terms to get the distinction sorted out. We think of a >> molecular >> function as a single step reaction, whilst a process term describes a >> multistep event. You might think of a process term as being made >> up of >> several functions happening one after the other. We currently make no >> distinction between the actual execution of the function and the >> potential execution of the function. >> >> Function terms >> ============== >> An example of a function in GO is when a secondary active transporter >> molecule acts by changing >> shape so as to propel a bound potassium ion across the membrane, in a >> single step chemical reaction. We would consider this reaction to >> be a >> molecular function that belongs in the molecular function >> ontology. The >> term could be 'secondary active potassium transporter activity', >> though >> in fact have the term: >> potassium ion uniporter activity >> def: Catalysis of the active transport of a potassium ion across a >> membrane by a mechanism involving conformational change, where energy >> for active transport is derived from membrane potential if the >> solute is >> charged. >> There is a picture here in case it helps anyone get the biology >> clear: >> http://www.ncbi.nlm.nih.gov/books/bv.fcgi? >> highlight=carrier&rid=mboc4.figgrp.2000 >> >> Process terms >> ============= >> An example of a process that is nice and straightforward is the >> set of >> photochemical reactions that occur in photosynthesis. >> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2589 >> This is currently included in GO as 'photosynthesis, light reaction' >> def: The light reactions of photosynthesis, which take place in >> photosystems II and I. Light energy is harvested and used to power >> the >> transfer of electrons among a series of electron donors and >> acceptors. >> The final electron acceptor is NADP+, which is reduced to NADPH. >> NADPH >> generated from light reactions is used in sugar synthesis in dark >> reactions. Light reactions also generate a proton motive force across >> the thylakoid membrane, and the proton gradient is used to synthesize >> ATP. There are two chemical reactions involved in the light >> reactions: >> water oxidation in photosystem II, and NADP reduction in >> photosystem I. >> >> The thing that I think is confusing you is that we have process terms >> that look really a lot like the transport function terms. The >> thing that >> you need to know is that we have overhauled most of the function >> terms >> and given them proper definitions so that they are no longer carrying >> the very non-specific definitions that you saw before. Most of >> them now >> have very clear defs describing single step reactions as shown above. >> Process transport terms are defined as, for example: >> The directed movement of potassium ions (K+) into, out of, within or >> between cells. (This is clearly a multistep affair, if we could >> think of >> a good example, though I think all these terms need a good looking >> at too. >> For example, do we really need a potassium transport process term? >> This >> is on my list to look at soon. ) >> >> In summary, the function terms are now better defined, to be >> clearly a >> single >> step reaction, and the process terms have much more general >> definitions >> that >> can cover a multistep reaction. >> >> The other thing that I should mention, is that I am currently working >> with several transport experts to re-examine all of the transport >> terms, >> and to improve them to clearly represent the current state of the >> biology. >> I hope to improve the process terms considerably, and we still have a >> lot of work to do on the more granular function terms. If you >> would like >> to be involved in this then I would be very pleased to include you. >> >> Here is a description of what we have done so far: >> http://wiki.geneontology.org/index.php/Transporters >> This is the documentation for the parts that we consider to be >> rigorously logical, and up to date for the field, as it currently >> stands: >> http://wiki.geneontology.org/index.php/Docs >> >> The process and function ontology docs may also help: >> http://www.geneontology.org/GO.process.guidelines.shtml >> http://www.geneontology.org/GO.function.guidelines.shtml >> >> I hope this helps a bit. Please do write back to ask further >> questions. >> It is a tricky subject, and I have had to rattle this e-mail off >> quite >> quickly before diving into a meeting, ironically, with my transport >> experts. Please could you also cc me, as I am not on the obo- >> discuss list. >> >> Thanks, and best wishes, >> >> Jennifer >> >> >> >> >> >> >> >> >> >> >> >> >> >> ---------- Forwarded message ---------- >> Date: Sat, 12 Jan 2008 20:13:23 -0700 >> From: Mike Bada >> Reply-To: obo-discuss at lists.sourceforge.net >> To: obo-discuss at lists.sourceforge.net >> Subject: [Obo-discuss] biological processes & molecular functions >> >> Hi all, >> >> Like Colin Batchelor, who has recently posted to this list, we are >> trying to extensively use OBOs in the annotation of journal articles >> (i.e., NLP annotation, not annotation in the sense of that done by >> the >> various model-organism databases). And, like Colin, we are >> experiencing >> issues in trying to use these OBOs (although I won't speak for him!). >> >> One issue that has caused us trouble is the dichotomy between GO >> biological processes and molecular functions, and this leads to a >> reexamination of the nature of these concepts. My understanding from >> that written by Barry Smith and others is that a biological >> process is >> an actual process and that a molecular function is a functionality >> inherent in a gene/gene product that is realized in a corresponding >> process. (Please correct me if I'm wrong.) This makes sense, I >> think, >> when examining the GO transport and transporter terms: The >> transporter >> terms in the MF subontology are of the form "Enables the transport >> of * >> into, out of, within or between cells", while the transport terms >> in the >> BP subontology are of the form "The directed movement of * into, >> out of, >> within or between cells". So drug transporter activity is the >> functionality inherent in a given gene/gene product that is >> realized in >> a drug-transport process. I assume that this is the reason for so >> many >> parallel BP transport and MF transporter activity terms. But if >> this is >> the case, then why isn't there a corresponding BP term for each MF >> term? >> >> Arguing on the other side, most of the MF terms are not defined as >> inherent functionalities but rather sound like processes to me: Most >> binding terms are defined as "Interacting selectively with *"; most >> catalytic-activity terms are defined as "Catalysis of the >> reaction: *"; >> many enzyme-regulator-activity terms are defined as "Modulates *"; >> etc. >> Furthermore, on the GO Web site, molecular functions are described as >> "activities, such as catalytic or binding activities, that occur >> at the >> molecular level", which to me sound like processes (at a molecular >> level) rather than functionalities inherent in genes/gene products >> that >> are realized in processes. >> >> The specific issues we're having and how we deal with them depend >> on the >> nature of the relationship between BPs and MFs, so I won't go into >> more >> detail until this is clear. We're hoping someone from GO/OBO could >> clear this up for us. >> >> Cheers, >> Mike >> >> --------------------------------------------------------------------- >> ---- >> Check out the new SourceForge.net Marketplace. >> It's the best place to buy or sell services for >> just about anything Open Source. >> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/ >> marketplace >> _______________________________________________ >> Obo-discuss mailing list >> Obo-discuss at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/obo-discuss >> >> >> >> ---------- Forwarded message ---------- >> Date: Sat, 12 Jan 2008 23:24:15 -0400 >> From: "Smith, Barry" >> Reply-To: obo-discuss at lists.sourceforge.net >> To: obo-discuss at lists.sourceforge.net, obo- >> discuss at lists.sourceforge.net >> Subject: Re: [Obo-discuss] biological processes & molecular functions >> >> At 11:13 PM 1/12/2008, Mike Bada wrote: >> >> >>> Hi all, >>> >>> Like Colin Batchelor, who has recently posted to this list, we are >>> trying to extensively use OBOs in the annotation of journal articles >>> (i.e., NLP annotation, not annotation in the sense of that done >>> by the >>> various model-organism databases). And, like Colin, we are >>> experiencing >>> issues in trying to use these OBOs (although I won't speak for >>> him!). >>> >>> One issue that has caused us trouble is the dichotomy between GO >>> biological processes and molecular functions, and this leads to a >>> reexamination of the nature of these concepts. My understanding >>> from >>> that written by Barry Smith and others is that a biological >>> process is >>> an actual process and that a molecular function is a functionality >>> inherent in a gene/gene product that is realized in a corresponding >>> process. (Please correct me if I'm wrong.) >>> >>> >> >> You are not wrong. >> >> >> >>> This makes sense, I think, >>> when examining the GO transport and transporter terms: The >>> transporter >>> terms in the MF subontology are of the form "Enables the >>> transport of * >>> into, out of, within or between cells", while the transport terms >>> in the >>> BP subontology are of the form "The directed movement of * into, >>> out of, >>> within or between cells". So drug transporter activity is the >>> functionality inherent in a given gene/gene product that is >>> realized in >>> a drug-transport process. I assume that this is the reason for >>> so many >>> parallel BP transport and MF transporter activity terms. But if >>> this is >>> the case, then why isn't there a corresponding BP term for each >>> MF term? >>> >>> >> >> I believe that the GO consortium has committed itself to creating >> more consistency here. There are steps, also, to address the issue of >> functions at other (non-molecular) levels of granularity -- for >> example cellular and organ-level functions, reflecting also a more >> careful treatment of the granularities on the process side. >> >> >> >> >>> Arguing on the other side, most of the MF terms are not defined as >>> inherent functionalities but rather sound like processes to me: >>> Most >>> binding terms are defined as "Interacting selectively with *"; most >>> catalytic-activity terms are defined as "Catalysis of the >>> reaction: *"; >>> many enzyme-regulator-activity terms are defined as "Modulates >>> *"; etc. >>> Furthermore, on the GO Web site, molecular functions are >>> described as >>> "activities, such as catalytic or binding activities, that occur >>> at the >>> molecular level", which to me sound like processes (at a molecular >>> level) rather than functionalities inherent in genes/gene >>> products that >>> are realized in processes. >>> >>> >> >> This is a big issue -- resulting from an unfortunate decision to >> label all function terms with the suffix 'activity'. >> When you read 'activity' in GO, try to thing 'function'. >> >> >> >>> The specific issues we're having and how we deal with them depend >>> on the >>> nature of the relationship between BPs and MFs, so I won't go >>> into more >>> detail until this is clear. We're hoping someone from GO/OBO could >>> clear this up for us. >>> >>> >> Hope the above helps, at least somewhat. >> BS >> >> >> >>> Cheers, >>> Mike >>> >>> -------------------------------------------------------------------- >>> ----- >>> Check out the new SourceForge.net Marketplace. >>> It's the best place to buy or sell services for >>> just about anything Open Source. >>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/ >>> marketplace >>> _______________________________________________ >>> Obo-discuss mailing list >>> Obo-discuss at lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>> >>> >> >> >> >> >> --------------------------------------------------------------------- >> ---- >> Check out the new SourceForge.net Marketplace. >> It's the best place to buy or sell services for >> just about anything Open Source. >> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/ >> marketplace >> _______________________________________________ >> Obo-discuss mailing list >> Obo-discuss at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/obo-discuss >> >> >> >> ---------- Forwarded message ---------- >> Date: Sun, 13 Jan 2008 18:21:45 -0700 >> From: Mike Bada >> Reply-To: obo-discuss at lists.sourceforge.net >> To: obo-discuss at lists.sourceforge.net >> Subject: Re: [Obo-discuss] biological processes & molecular functions >> >> Smith, Barry wrote: >> >> >> >>> At 11:13 PM 1/12/2008, Mike Bada wrote: >>> >>> >>> >>> >>>> Hi all, >>>> >>>> Like Colin Batchelor, who has recently posted to this list, we are >>>> trying to extensively use OBOs in the annotation of journal >>>> articles >>>> (i.e., NLP annotation, not annotation in the sense of that done >>>> by the >>>> various model-organism databases). And, like Colin, we are >>>> experiencing >>>> issues in trying to use these OBOs (although I won't speak for >>>> him!). >>>> >>>> One issue that has caused us trouble is the dichotomy between GO >>>> biological processes and molecular functions, and this leads to a >>>> reexamination of the nature of these concepts. My understanding >>>> from >>>> that written by Barry Smith and others is that a biological >>>> process is >>>> an actual process and that a molecular function is a functionality >>>> inherent in a gene/gene product that is realized in a corresponding >>>> process. (Please correct me if I'm wrong.) >>>> >>>> >>>> >>>> >>> You are not wrong. >>> >>> >>> >>> >>> >>>> This makes sense, I think, >>>> when examining the GO transport and transporter terms: The >>>> transporter >>>> terms in the MF subontology are of the form "Enables the >>>> transport of * >>>> into, out of, within or between cells", while the transport >>>> terms in the >>>> BP subontology are of the form "The directed movement of * into, >>>> out of, >>>> within or between cells". So drug transporter activity is the >>>> functionality inherent in a given gene/gene product that is >>>> realized in >>>> a drug-transport process. I assume that this is the reason for >>>> so many >>>> parallel BP transport and MF transporter activity terms. But if >>>> this is >>>> the case, then why isn't there a corresponding BP term for each >>>> MF term? >>>> >>>> >>>> >>>> >>> I believe that the GO consortium has committed itself to creating >>> more consistency here. There are steps, also, to address the >>> issue of >>> functions at other (non-molecular) levels of granularity -- for >>> example cellular and organ-level functions, reflecting also a more >>> careful treatment of the granularities on the process side. >>> >>> >>> >>> >> >> OK, it is as I thought. Does this mean that there will be many more >> parallel BP and MF terms, even a one-to-one correspondence? >> >> The crux of our difficulties is that, when analyzing and >> attempting to >> annotate a typical biological assertion found in a journal article, >> we're often finding it extremely difficult to differentiate whether >> something refers to a BP or a MF. A simple example is "A >> transports B >> to the nucleus." Does this refer to the process "B transport" or >> to the >> corresponding inherent functionality "B transporter activity", >> i.e., to >> the actual process or to the ability to effect the process? (I'm >> using transport/transporter activity examples throughout, but >> there are >> many others.) The use of the simple verb might suggest that it's a >> process, but of course, this is a generic statement about the >> ability of >> A to transport B to the nucleus, not about an actual reporting of the >> transport of a specific B to the nucleus by a specific A, so it >> can be >> seen as a MF as well. Frankly, I'd say that this is an ontological >> distinction about which the large majority of biologists >> understandably >> wouldn't care, but it is something we have to consider because we're >> interested in getting computational systems to be able to >> automatically >> recognize GO (and other OBO) terms in natural-language text, and the >> distinctions between the two in text are often ambiguous to say the >> least, which makes the task that much more difficult. >> >> This leads me to ask, perhaps radically: Do we need both BPs and >> MFs? >> I'm not denying an ontological distinction between BPs and MFs as >> they're defined now; I'm just wondering if it might be a distinction >> that is too subtle to be genuinely useful and too ambiguous to >> differentiate in, for example, natural language. Even applied to GO >> annotations, if a gene or gene product has an annotation that >> indicates >> that it has the functionality to effect a drug-transport process, >> is the >> addition of another annotation that indicates that it participates in >> drug-transport processes useful? Wouldn't it be sufficient to >> have only >> processes or only functionalities in the GO? (I think processes are >> more straightforward and thus more generally useful.) This would >> eliminate a huge amount of ambiguity in the application of terms >> among >> these two subontologies, I think. >> >> Trepidatiously expecting a firestorm, >> Mike >> >> >> >>> >>> >>> >>>> Arguing on the other side, most of the MF terms are not defined as >>>> inherent functionalities but rather sound like processes to me: >>>> Most >>>> binding terms are defined as "Interacting selectively with *"; most >>>> catalytic-activity terms are defined as "Catalysis of the >>>> reaction: *"; >>>> many enzyme-regulator-activity terms are defined as "Modulates >>>> *"; etc. >>>> Furthermore, on the GO Web site, molecular functions are >>>> described as >>>> "activities, such as catalytic or binding activities, that occur >>>> at the >>>> molecular level", which to me sound like processes (at a molecular >>>> level) rather than functionalities inherent in genes/gene >>>> products that >>>> are realized in processes. >>>> >>>> >>>> >>>> >>> This is a big issue -- resulting from an unfortunate decision to >>> label all function terms with the suffix 'activity'. >>> When you read 'activity' in GO, try to thing 'function'. >>> >>> >>> >>> >>> >>>> The specific issues we're having and how we deal with them >>>> depend on the >>>> nature of the relationship between BPs and MFs, so I won't go >>>> into more >>>> detail until this is clear. We're hoping someone from GO/OBO could >>>> clear this up for us. >>>> >>>> >>>> >>>> >>> Hope the above helps, at least somewhat. >>> BS >>> >>> >>> >>> >>> >>>> Cheers, >>>> Mike >>>> >>>> ------------------------------------------------------------------- >>>> ------ >>>> Check out the new SourceForge.net Marketplace. >>>> It's the best place to buy or sell services for >>>> just about anything Open Source. >>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/ >>>> marketplace >>>> _______________________________________________ >>>> Obo-discuss mailing list >>>> Obo-discuss at lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>>> >>>> >>>> >>>> >>> >>> >>> -------------------------------------------------------------------- >>> ----- >>> Check out the new SourceForge.net Marketplace. >>> It's the best place to buy or sell services for >>> just about anything Open Source. >>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/ >>> marketplace >>> _______________________________________________ >>> Obo-discuss mailing list >>> Obo-discuss at lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>> >>> >>> >>> >>> >> >> >> --------------------------------------------------------------------- >> ---- >> Check out the new SourceForge.net Marketplace. >> It's the best place to buy or sell services for >> just about anything Open Source. >> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/ >> marketplace >> _______________________________________________ >> Obo-discuss mailing list >> Obo-discuss at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/obo-discuss >> >> >> >> > > > ---------------------------------------------------------------------- > --- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/ > marketplace > _______________________________________________ > Obo-discuss mailing list > Obo-discuss at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/obo-discuss > From jdeegan at ebi.ac.uk Tue Jan 15 01:53:03 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Tue, 15 Jan 2008 09:53:03 +0000 Subject: [go] editing freeze Message-ID: <478C827F.7000702@ebi.ac.uk> Hi, Just a quick reminder that there will be an editing freeze on gene_ontology_edit.obo starting at 10am GMT this morning. I will write again when it is over. Thanks, Jennifer -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From jdeegan at ebi.ac.uk Tue Jan 15 02:42:19 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Tue, 15 Jan 2008 10:42:19 +0000 Subject: [go] editing freeze Message-ID: <478C8E0B.4000004@ebi.ac.uk> Hi, The editing freeze is now over and the merged file has been committed. Thanks for your patience. Please check out a new copy of the file before making any new edits. Thanks, Jennifer -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From midori at ebi.ac.uk Tue Jan 15 04:21:34 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 15 Jan 2008 12:21:34 +0000 (GMT) Subject: [go] Fwd: [Obo-discuss] 3 forwarded messages on MF vs BP from obo-discuss In-Reply-To: References: <478C18B8.5030907@uchsc.edu> Message-ID: Hi Chris, I'm really glad you're paying attention to this thread, and I agree that the annotators' point of view will be valuable. I have a bit more from the ontology front ... What struck me about Mike's most recent message is that his examples of parallel terms list exactly those terms that have been the subject of the most intense discussions on the GO list and at GOC meetings. I think Jen is working on another detailed response, though, so I'll stick to the bigger picture. I found this exchange from yesterday rather alarming: >>> Mike: My understanding ... is that a biological process is an actual >>> process and that a molecular function is a functionality inherent in a >>> gene/gene product that is realized in a corresponding process. (Please >>> correct me if I'm wrong.) >> >> Barry: >> You are not wrong. [snip] > > Mike: > OK, it is as I thought. Does this mean that there will be many more > parallel BP and MF terms, even a one-to-one correspondence? Although Jen's email has probably got Mike sorted out on this point, I still think it's worth pointing out specifically that we have no intention whatsoever of aking MF and BP parallel each other completely -- I can't see how that would be a sensible use of our time. With respect to Mike's most recent: > However, it seems there's not even consensus within the GO/OBO > Consortium concerning the relationship between MFs and BPs. I originally > asked whether the MFs were inherent functionalities of genes/gene > products that get realized as processes or as "elementary" processes > themselves. What you describe agrees with the documentation on the GO > Web site and with most of the MF term names and their definitions, i.e., > with the latter view, while Barry takes the former view. I think it's quite clear that there is consensus within GO on what the distinction between MF and BP is at present. We've long acknowledged that the split was arbitrary, and done for pragmatic reasons (which Jen might go into). Accordingly, there is still a lot of discussion, sometimes outright argument, about exactly where the boundary lies, and whether a given term/entity belongs in MF or BP, but the inherent functionality vs. actual "process" question hasn't come up. Barry's "you are not wrong" statement was therefore not an accurate description of GO's present content, documentation or practices. Perhaps GO will move towards distinguishing inherent functionalities from molecular-scale processes, but it's early days -- the issue is still very much under discussion, implementation has barely begun (if at all; it's probably fairer to simply say this is not what we're doing now) and it's certainly not what we've done historically. If anything, we have occasionally tried to speak and think of MF terms as events (and annotation could be thought of as making a statement about a particular gene product's inherent functionality). It's been a long, long time since I've done any gene product annotation, so I hope more people chime in. But one thing I can say is that when I was doing annotation, I was definitely among that majority of biologists who (as Mike correctly surmises) don't care about the inherent functionality/execution of function distinction. I might even stick my neck out and say that in many papers Mike's "A transports B to the nucleus" example would refer to both the process "B transport" and to the corresponding inherent functionality "B transporter activity" -- an experiment documents an actual instance of the process, and from that result the authors infer A's ability to do the deed. Sorry to be long-winded -- I thought mine was going to be the brief response! midori On Mon, 14 Jan 2008, Chris Mungall wrote: > [redirecting this part to GO, sorry if this confuses the thread, but I want > to ask a question of GO folks first] > > Thanks for responding Jen. > > I think Mike raises some interesting issues, many of which we've raised > internally. I have my ideas on how to answer Mike's question, focusing on the > signal transduction/transducer activity example. But I'd like to get > feedback, particularly from an annotation perspective, before answering from > an ontology-minded perspective. > > It seems that we should have on the wiki as part of an annotation SOP some > rules/guidelines for when to annotate to "signal transducer activity" vs > "signal transduction" vs co-annotation of both. (which would of course apply > to analagous examples) > > We also need to start making P<->F links here. > > If it helps I have added an example query: > http://www.berkeleybop.org/goose > > select from the popup "genes annotated to signal transducer activity but not > signal transduction" (and change the DB if you like - it's set to MGI in the > example) > > you can also try swapping the terms around > > as you can see there is quite a lot > > Begin forwarded message: > >> From: Mike Bada >> Date: January 14, 2008 6:21:44 PM PST >> To: jdeegan at ebi.ac.uk, obo-discuss at lists.sourceforge.net >> Subject: Re: [Obo-discuss] 3 forwarded messages on MF vs BP from >> obo-discuss >> Reply-To: obo-discuss at lists.sourceforge.net >> >> Thank you for your detailed reply, Jennifer. However, it seems there's >> not even consensus within the GO/OBO Consortium concerning the >> relationship between MFs and BPs. I originally asked whether the MFs >> were inherent functionalities of genes/gene products that get realized >> as processes or as "elementary" processes themselves. What you describe >> agrees with the documentation on the GO Web site and with most of the MF >> term names and their definitions, i.e., with the latter view, while >> Barry takes the former view. >> >> Again, we are most concerned with all of the parallel terms between the >> two subontologies, which makes application toward NLP, among other >> tasks, much more difficult. This is not limited to the large number of >> corresponding transporter activity (MF) / transport (BP) terms; some >> other examples include: >> >> signal transducer activity (MF) ; signal transduction (BP) >> translation regulator activity (MF) ; regulation of translation (BP) >> enzyme regulator activity (MF) ; regulation of catalytic activity (BP) >> enzyme activator activity (MF) ; positive regulation of enzyme activity >> (BP) >> >> According to your explanation, all of these pairs of terms seem to mean >> essentially the same thing except for the fact that each of the former >> is a single-step process and each of the latter a multi-step process. >> It may be relatively easy to divide a metabolic pathway into its >> component biochemical reactions, but what constitutes an elementary >> single step of a process is often ambiguous. Any process can be >> recursively divided into component processes: Even a biochemical >> reaction can be divided into component processes of the reaction >> mechanism. This ambiguous nature of what an "elementary" step is makes >> it very difficult to determine whether a process mentioned in, say, a >> journal article is a single-step or multi-step process (and thus a MF or >> a BP, respectively). >> >> So there are two views, both of which hamper usability of the >> subontologies applied in combination: As to the view that MFs are the >> inherent functionalities of genes/gene products that are realized in >> BPs, it is often ambiguous whether a natural-language mention refers to >> the inherent functionality or to the process itself. As to the view >> that MFs are the "single-step" processes that make up multi-step BPs, it >> is often ambiguous whether a natural-language mention is a "single-step" >> or "multi-step" process. Wouldn't it be easier and clearer if there >> were one merged ontology of processes of all granularities and no >> parallel terms such as the aforementioned ones? >> >> Cheers, >> Mike >> >> >> Jennifer Deegan (nee Clark) wrote: >> >>> Hi Mike, >>> >>> Midori forwarded this e-mail to me as I have been working on an >>> extensive overhaul of the transport terms in GO. I think that I can help >>> clear up at least some of the confusion here, though it might take a few >>> e-mails to get things completely clear. >>> >>> In GO, as you have mentioned, we have transport terms in the function >>> and process ontologies, and as you mention, they are really quite >>> similar. However, this is partly because many of these terms were made >>> in the early days of GO when we were really not too clear ourselves on >>> the distinction between function and process. Now that we are much >>> clearer about the distinction I have been working through with a number >>> of expert biologists and improving the terms. >>> >>> Just to be clear, I will give a nice easy example of some function and >>> process terms to get the distinction sorted out. We think of a molecular >>> function as a single step reaction, whilst a process term describes a >>> multistep event. You might think of a process term as being made up of >>> several functions happening one after the other. We currently make no >>> distinction between the actual execution of the function and the >>> potential execution of the function. >>> >>> Function terms >>> ============== >>> An example of a function in GO is when a secondary active transporter >>> molecule acts by changing >>> shape so as to propel a bound potassium ion across the membrane, in a >>> single step chemical reaction. We would consider this reaction to be a >>> molecular function that belongs in the molecular function ontology. The >>> term could be 'secondary active potassium transporter activity', though >>> in fact have the term: >>> potassium ion uniporter activity >>> def: Catalysis of the active transport of a potassium ion across a >>> membrane by a mechanism involving conformational change, where energy >>> for active transport is derived from membrane potential if the solute is >>> charged. >>> There is a picture here in case it helps anyone get the biology clear: >>> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=carrier&rid=mboc4.figgrp.2000 >>> >>> Process terms >>> ============= >>> An example of a process that is nice and straightforward is the set of >>> photochemical reactions that occur in photosynthesis. >>> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2589 >>> This is currently included in GO as 'photosynthesis, light reaction' >>> def: The light reactions of photosynthesis, which take place in >>> photosystems II and I. Light energy is harvested and used to power the >>> transfer of electrons among a series of electron donors and acceptors. >>> The final electron acceptor is NADP+, which is reduced to NADPH. NADPH >>> generated from light reactions is used in sugar synthesis in dark >>> reactions. Light reactions also generate a proton motive force across >>> the thylakoid membrane, and the proton gradient is used to synthesize >>> ATP. There are two chemical reactions involved in the light reactions: >>> water oxidation in photosystem II, and NADP reduction in photosystem I. >>> >>> The thing that I think is confusing you is that we have process terms >>> that look really a lot like the transport function terms. The thing that >>> you need to know is that we have overhauled most of the function terms >>> and given them proper definitions so that they are no longer carrying >>> the very non-specific definitions that you saw before. Most of them now >>> have very clear defs describing single step reactions as shown above. >>> Process transport terms are defined as, for example: >>> The directed movement of potassium ions (K+) into, out of, within or >>> between cells. (This is clearly a multistep affair, if we could think of >>> a good example, though I think all these terms need a good looking at too. >>> For example, do we really need a potassium transport process term? This >>> is on my list to look at soon. ) >>> >>> In summary, the function terms are now better defined, to be clearly a >>> single >>> step reaction, and the process terms have much more general definitions >>> that >>> can cover a multistep reaction. >>> >>> The other thing that I should mention, is that I am currently working >>> with several transport experts to re-examine all of the transport terms, >>> and to improve them to clearly represent the current state of the biology. >>> I hope to improve the process terms considerably, and we still have a >>> lot of work to do on the more granular function terms. If you would like >>> to be involved in this then I would be very pleased to include you. >>> >>> Here is a description of what we have done so far: >>> http://wiki.geneontology.org/index.php/Transporters >>> This is the documentation for the parts that we consider to be >>> rigorously logical, and up to date for the field, as it currently stands: >>> http://wiki.geneontology.org/index.php/Docs >>> >>> The process and function ontology docs may also help: >>> http://www.geneontology.org/GO.process.guidelines.shtml >>> http://www.geneontology.org/GO.function.guidelines.shtml >>> >>> I hope this helps a bit. Please do write back to ask further questions. >>> It is a tricky subject, and I have had to rattle this e-mail off quite >>> quickly before diving into a meeting, ironically, with my transport >>> experts. Please could you also cc me, as I am not on the obo-discuss list. >>> >>> Thanks, and best wishes, >>> >>> Jennifer >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> ---------- Forwarded message ---------- >>> Date: Sat, 12 Jan 2008 20:13:23 -0700 >>> From: Mike Bada >>> Reply-To: obo-discuss at lists.sourceforge.net >>> To: obo-discuss at lists.sourceforge.net >>> Subject: [Obo-discuss] biological processes & molecular functions >>> >>> Hi all, >>> >>> Like Colin Batchelor, who has recently posted to this list, we are >>> trying to extensively use OBOs in the annotation of journal articles >>> (i.e., NLP annotation, not annotation in the sense of that done by the >>> various model-organism databases). And, like Colin, we are experiencing >>> issues in trying to use these OBOs (although I won't speak for him!). >>> >>> One issue that has caused us trouble is the dichotomy between GO >>> biological processes and molecular functions, and this leads to a >>> reexamination of the nature of these concepts. My understanding from >>> that written by Barry Smith and others is that a biological process is >>> an actual process and that a molecular function is a functionality >>> inherent in a gene/gene product that is realized in a corresponding >>> process. (Please correct me if I'm wrong.) This makes sense, I think, >>> when examining the GO transport and transporter terms: The transporter >>> terms in the MF subontology are of the form "Enables the transport of * >>> into, out of, within or between cells", while the transport terms in the >>> BP subontology are of the form "The directed movement of * into, out of, >>> within or between cells". So drug transporter activity is the >>> functionality inherent in a given gene/gene product that is realized in >>> a drug-transport process. I assume that this is the reason for so many >>> parallel BP transport and MF transporter activity terms. But if this is >>> the case, then why isn't there a corresponding BP term for each MF term? >>> >>> Arguing on the other side, most of the MF terms are not defined as >>> inherent functionalities but rather sound like processes to me: Most >>> binding terms are defined as "Interacting selectively with *"; most >>> catalytic-activity terms are defined as "Catalysis of the reaction: *"; >>> many enzyme-regulator-activity terms are defined as "Modulates *"; etc. >>> Furthermore, on the GO Web site, molecular functions are described as >>> "activities, such as catalytic or binding activities, that occur at the >>> molecular level", which to me sound like processes (at a molecular >>> level) rather than functionalities inherent in genes/gene products that >>> are realized in processes. >>> >>> The specific issues we're having and how we deal with them depend on the >>> nature of the relationship between BPs and MFs, so I won't go into more >>> detail until this is clear. We're hoping someone from GO/OBO could >>> clear this up for us. >>> >>> Cheers, >>> Mike >>> >>> ------------------------------------------------------------------------- >>> Check out the new SourceForge.net Marketplace. >>> It's the best place to buy or sell services for >>> just about anything Open Source. >>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace >>> _______________________________________________ >>> Obo-discuss mailing list >>> Obo-discuss at lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>> >>> >>> >>> ---------- Forwarded message ---------- >>> Date: Sat, 12 Jan 2008 23:24:15 -0400 >>> From: "Smith, Barry" >>> Reply-To: obo-discuss at lists.sourceforge.net >>> To: obo-discuss at lists.sourceforge.net, obo-discuss at lists.sourceforge.net >>> Subject: Re: [Obo-discuss] biological processes & molecular functions >>> >>> At 11:13 PM 1/12/2008, Mike Bada wrote: >>> >>> >>>> Hi all, >>>> >>>> Like Colin Batchelor, who has recently posted to this list, we are >>>> trying to extensively use OBOs in the annotation of journal articles >>>> (i.e., NLP annotation, not annotation in the sense of that done by the >>>> various model-organism databases). And, like Colin, we are experiencing >>>> issues in trying to use these OBOs (although I won't speak for him!). >>>> >>>> One issue that has caused us trouble is the dichotomy between GO >>>> biological processes and molecular functions, and this leads to a >>>> reexamination of the nature of these concepts. My understanding from >>>> that written by Barry Smith and others is that a biological process is >>>> an actual process and that a molecular function is a functionality >>>> inherent in a gene/gene product that is realized in a corresponding >>>> process. (Please correct me if I'm wrong.) >>>> >>>> >>> >>> You are not wrong. >>> >>> >>> >>>> This makes sense, I think, >>>> when examining the GO transport and transporter terms: The transporter >>>> terms in the MF subontology are of the form "Enables the transport of * >>>> into, out of, within or between cells", while the transport terms in the >>>> BP subontology are of the form "The directed movement of * into, out of, >>>> within or between cells". So drug transporter activity is the >>>> functionality inherent in a given gene/gene product that is realized in >>>> a drug-transport process. I assume that this is the reason for so many >>>> parallel BP transport and MF transporter activity terms. But if this is >>>> the case, then why isn't there a corresponding BP term for each MF term? >>>> >>>> >>> >>> I believe that the GO consortium has committed itself to creating >>> more consistency here. There are steps, also, to address the issue of >>> functions at other (non-molecular) levels of granularity -- for >>> example cellular and organ-level functions, reflecting also a more >>> careful treatment of the granularities on the process side. >>> >>> >>> >>> >>>> Arguing on the other side, most of the MF terms are not defined as >>>> inherent functionalities but rather sound like processes to me: Most >>>> binding terms are defined as "Interacting selectively with *"; most >>>> catalytic-activity terms are defined as "Catalysis of the reaction: *"; >>>> many enzyme-regulator-activity terms are defined as "Modulates *"; etc. >>>> Furthermore, on the GO Web site, molecular functions are described as >>>> "activities, such as catalytic or binding activities, that occur at the >>>> molecular level", which to me sound like processes (at a molecular >>>> level) rather than functionalities inherent in genes/gene products that >>>> are realized in processes. >>>> >>>> >>> >>> This is a big issue -- resulting from an unfortunate decision to >>> label all function terms with the suffix 'activity'. >>> When you read 'activity' in GO, try to thing 'function'. >>> >>> >>> >>>> The specific issues we're having and how we deal with them depend on the >>>> nature of the relationship between BPs and MFs, so I won't go into more >>>> detail until this is clear. We're hoping someone from GO/OBO could >>>> clear this up for us. >>>> >>>> >>> Hope the above helps, at least somewhat. >>> BS >>> >>> >>> >>>> Cheers, >>>> Mike >>>> >>>> ------------------------------------------------------------------------- >>>> Check out the new SourceForge.net Marketplace. >>>> It's the best place to buy or sell services for >>>> just about anything Open Source. >>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace >>>> _______________________________________________ >>>> Obo-discuss mailing list >>>> Obo-discuss at lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>>> >>>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------- >>> Check out the new SourceForge.net Marketplace. >>> It's the best place to buy or sell services for >>> just about anything Open Source. >>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace >>> _______________________________________________ >>> Obo-discuss mailing list >>> Obo-discuss at lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>> >>> >>> >>> ---------- Forwarded message ---------- >>> Date: Sun, 13 Jan 2008 18:21:45 -0700 >>> From: Mike Bada >>> Reply-To: obo-discuss at lists.sourceforge.net >>> To: obo-discuss at lists.sourceforge.net >>> Subject: Re: [Obo-discuss] biological processes & molecular functions >>> >>> Smith, Barry wrote: >>> >>> >>> >>>> At 11:13 PM 1/12/2008, Mike Bada wrote: >>>> >>>> >>>> >>>> >>>>> Hi all, >>>>> >>>>> Like Colin Batchelor, who has recently posted to this list, we are >>>>> trying to extensively use OBOs in the annotation of journal articles >>>>> (i.e., NLP annotation, not annotation in the sense of that done by the >>>>> various model-organism databases). And, like Colin, we are experiencing >>>>> issues in trying to use these OBOs (although I won't speak for him!). >>>>> >>>>> One issue that has caused us trouble is the dichotomy between GO >>>>> biological processes and molecular functions, and this leads to a >>>>> reexamination of the nature of these concepts. My understanding from >>>>> that written by Barry Smith and others is that a biological process is >>>>> an actual process and that a molecular function is a functionality >>>>> inherent in a gene/gene product that is realized in a corresponding >>>>> process. (Please correct me if I'm wrong.) >>>>> >>>>> >>>>> >>>>> >>>> You are not wrong. >>>> >>>> >>>> >>>> >>>> >>>>> This makes sense, I think, >>>>> when examining the GO transport and transporter terms: The transporter >>>>> terms in the MF subontology are of the form "Enables the transport of * >>>>> into, out of, within or between cells", while the transport terms in the >>>>> BP subontology are of the form "The directed movement of * into, out of, >>>>> within or between cells". So drug transporter activity is the >>>>> functionality inherent in a given gene/gene product that is realized in >>>>> a drug-transport process. I assume that this is the reason for so many >>>>> parallel BP transport and MF transporter activity terms. But if this is >>>>> the case, then why isn't there a corresponding BP term for each MF term? >>>>> >>>>> >>>>> >>>>> >>>> I believe that the GO consortium has committed itself to creating >>>> more consistency here. There are steps, also, to address the issue of >>>> functions at other (non-molecular) levels of granularity -- for >>>> example cellular and organ-level functions, reflecting also a more >>>> careful treatment of the granularities on the process side. >>>> >>>> >>>> >>>> >>> >>> OK, it is as I thought. Does this mean that there will be many more >>> parallel BP and MF terms, even a one-to-one correspondence? >>> >>> The crux of our difficulties is that, when analyzing and attempting to >>> annotate a typical biological assertion found in a journal article, >>> we're often finding it extremely difficult to differentiate whether >>> something refers to a BP or a MF. A simple example is "A transports B >>> to the nucleus." Does this refer to the process "B transport" or to the >>> corresponding inherent functionality "B transporter activity", i.e., to >>> the actual process or to the ability to effect the process? (I'm >>> using transport/transporter activity examples throughout, but there are >>> many others.) The use of the simple verb might suggest that it's a >>> process, but of course, this is a generic statement about the ability of >>> A to transport B to the nucleus, not about an actual reporting of the >>> transport of a specific B to the nucleus by a specific A, so it can be >>> seen as a MF as well. Frankly, I'd say that this is an ontological >>> distinction about which the large majority of biologists understandably >>> wouldn't care, but it is something we have to consider because we're >>> interested in getting computational systems to be able to automatically >>> recognize GO (and other OBO) terms in natural-language text, and the >>> distinctions between the two in text are often ambiguous to say the >>> least, which makes the task that much more difficult. >>> >>> This leads me to ask, perhaps radically: Do we need both BPs and MFs? >>> I'm not denying an ontological distinction between BPs and MFs as >>> they're defined now; I'm just wondering if it might be a distinction >>> that is too subtle to be genuinely useful and too ambiguous to >>> differentiate in, for example, natural language. Even applied to GO >>> annotations, if a gene or gene product has an annotation that indicates >>> that it has the functionality to effect a drug-transport process, is the >>> addition of another annotation that indicates that it participates in >>> drug-transport processes useful? Wouldn't it be sufficient to have only >>> processes or only functionalities in the GO? (I think processes are >>> more straightforward and thus more generally useful.) This would >>> eliminate a huge amount of ambiguity in the application of terms among >>> these two subontologies, I think. >>> >>> Trepidatiously expecting a firestorm, >>> Mike >>> >>> >>> >>>> >>>> >>>> >>>>> Arguing on the other side, most of the MF terms are not defined as >>>>> inherent functionalities but rather sound like processes to me: Most >>>>> binding terms are defined as "Interacting selectively with *"; most >>>>> catalytic-activity terms are defined as "Catalysis of the reaction: *"; >>>>> many enzyme-regulator-activity terms are defined as "Modulates *"; etc. >>>>> Furthermore, on the GO Web site, molecular functions are described as >>>>> "activities, such as catalytic or binding activities, that occur at the >>>>> molecular level", which to me sound like processes (at a molecular >>>>> level) rather than functionalities inherent in genes/gene products that >>>>> are realized in processes. >>>>> >>>>> >>>>> >>>>> >>>> This is a big issue -- resulting from an unfortunate decision to >>>> label all function terms with the suffix 'activity'. >>>> When you read 'activity' in GO, try to thing 'function'. >>>> >>>> >>>> >>>> >>>> >>>>> The specific issues we're having and how we deal with them depend on the >>>>> nature of the relationship between BPs and MFs, so I won't go into more >>>>> detail until this is clear. We're hoping someone from GO/OBO could >>>>> clear this up for us. >>>>> >>>>> >>>>> >>>>> >>>> Hope the above helps, at least somewhat. >>>> BS >>>> >>>> >>>> >>>> >>>> >>>>> Cheers, >>>>> Mike >>>>> >>>>> ------------------------------------------------------------------------- >>>>> Check out the new SourceForge.net Marketplace. >>>>> It's the best place to buy or sell services for >>>>> just about anything Open Source. >>>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace >>>>> _______________________________________________ >>>>> Obo-discuss mailing list >>>>> Obo-discuss at lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> ------------------------------------------------------------------------- >>>> Check out the new SourceForge.net Marketplace. >>>> It's the best place to buy or sell services for >>>> just about anything Open Source. >>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace >>>> _______________________________________________ >>>> Obo-discuss mailing list >>>> Obo-discuss at lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>>> >>>> >>>> >>>> >>>> >>> >>> >>> ------------------------------------------------------------------------- >>> Check out the new SourceForge.net Marketplace. >>> It's the best place to buy or sell services for >>> just about anything Open Source. >>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace >>> _______________________________________________ >>> Obo-discuss mailing list >>> Obo-discuss at lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>> >>> >>> >>> >> >> >> ------------------------------------------------------------------------- >> Check out the new SourceForge.net Marketplace. >> It's the best place to buy or sell services for >> just about anything Open Source. >> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace >> _______________________________________________ >> Obo-discuss mailing list >> Obo-discuss at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/obo-discuss > From midori at ebi.ac.uk Tue Jan 15 08:24:10 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 15 Jan 2008 16:24:10 +0000 (GMT) Subject: [go] Alert: proposal to obsolete GO:0045192 (cellular component), which affects existing annotation Message-ID: The proposal has been made to obsolete low-density lipoprotein catabolic process ; GO:0045192 Annotations to this term exist at present as follows: UniProtKB:P01130 IEA UniProtKB:Q14162 TAS UniProtKB:Q15036 NAS MGI:96765 IDA, IMP RGD:1306424 ISS RGD:1309330 ISS This term is not used in any external2go mappings, and is not used in any GO slim set maintained within the OBO flat file. The reason for this proposal is that low-density lipoprotein is a macromolecular complex, and its degradation is better represented as a complex disassembly term. SourceForge link: https://sourceforge.net/tracker/index.php?func=detail&aid=1854029&group_id=36855&atid=440764 The two-week comment period ends on Wednesday, January 30, 2008. *** Unless objections are received by January 30, we will assume that you agree to this change. *** From tberardi at acoma.Stanford.EDU Tue Jan 15 12:17:08 2008 From: tberardi at acoma.Stanford.EDU (Tanya Berardini) Date: Tue, 15 Jan 2008 12:17:08 -0800 Subject: [go] Refined is_a relationships for 'regulation' terms Message-ID: <8e22ab960801151217t4ac6ea73m985bd905a1c65459@mail.gmail.com> Dear Everyone, We (Chris, David and I) have just committed a new version of the gene_ontology_edit.obo file that refines the is_a relationships between 'regulation' terms and their is_a parents by placing the terms under more specific parents and deleting the more general parents. This analysis also created is_a links that were missed in the initial term creation phase. For example: OLD: [Term] id: GO:0051799 name: negative regulation of hair follicle development namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of hair follicle development." [GOC:ai] synonym: "down regulation of hair follicle development" EXACT [] synonym: "down-regulation of hair follicle development" EXACT [] synonym: "downregulation of hair follicle development" EXACT [] synonym: "inhibition of hair follicle development" NARROW [] is_a: GO:0051093 ! negative regulation of developmental process is_a: GO:0051797 ! regulation of hair follicle development NEW: [Term] id: GO:0051799 name: negative regulation of hair follicle development namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of hair follicle development." [GOC:ai] synonym: "down regulation of hair follicle development" EXACT [] synonym: "down-regulation of hair follicle development" EXACT [] synonym: "downregulation of hair follicle development" EXACT [] synonym: "inhibition of hair follicle development" NARROW [] is_a: GO:0045683 ! negative regulation of epidermis development is_a: GO:0051241 ! negative regulation of multicellular organismal process is_a: GO:0051797 ! regulation of hair follicle development Statistics: 969 new links 302 deleted links Tanya, Chris and David From midori at ebi.ac.uk Wed Jan 16 05:39:40 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 16 Jan 2008 13:39:40 +0000 (GMT) Subject: [go] Alert: proposal to obsolete GO:0045192 (cellular component), which affects existing annotation In-Reply-To: References: Message-ID: addendum to reason for obsoleting included below On Tue, 15 Jan 2008, Midori Harris wrote: > The proposal has been made to obsolete > > low-density lipoprotein catabolic process ; GO:0045192 > > Annotations to this term exist at present as follows: > > UniProtKB:P01130 IEA > UniProtKB:Q14162 TAS > UniProtKB:Q15036 NAS > > MGI:96765 IDA, IMP > > RGD:1306424 ISS > RGD:1309330 ISS > > This term is not used in any external2go mappings, and is not used in any GO > slim set maintained within the OBO flat file. > The reason for this proposal is that low-density lipoprotein is a macromolecular complex, and its degradation involves the dissociation of non-covalently attached constituents as well as some breaking and reforming of covalent bonds. The process is therefore better represented as a complex disassembly term. > > SourceForge link: > https://sourceforge.net/tracker/index.php?func=detail&aid=1854029&group_id=36855&atid=440764 > > The two-week comment period ends on Wednesday, January 30, 2008. > > *** Unless objections are received by January 30, > we will assume that you agree to this change. *** > From ma11 at gen.cam.ac.uk Wed Jan 16 10:38:54 2008 From: ma11 at gen.cam.ac.uk (Michael Ashburner) Date: Wed, 16 Jan 2008 10:38:54 -0800 Subject: [go] Fwd: [Obo-discuss] 3 forwarded messages on MF vs BP from obo-discuss In-Reply-To: References: <478C18B8.5030907@uchsc.edu> Message-ID: I suggest this to be an agenda item for Salt Lake City. Michael On 15 Jan 2008, at 04:21, Midori Harris wrote: > Hi Chris, > > I'm really glad you're paying attention to this thread, and I agree > that the annotators' point of view will be valuable. I have a bit > more from the ontology front ... > > What struck me about Mike's most recent message is that his > examples of parallel terms list exactly those terms that have been > the subject of the most intense discussions on the GO list and at > GOC meetings. I think Jen is working on another detailed response, > though, so I'll stick to the bigger picture. > > I found this exchange from yesterday rather alarming: > >>>> Mike: My understanding ... is that a biological process is an >>>> actual process and that a molecular function is a functionality >>>> inherent in a gene/gene product that is realized in a >>>> corresponding process. (Please >>>> correct me if I'm wrong.) >>> >>> Barry: >>> You are not wrong. > [snip] >> >> Mike: >> OK, it is as I thought. Does this mean that there will be many >> more parallel BP and MF terms, even a one-to-one correspondence? > > Although Jen's email has probably got Mike sorted out on this > point, I still think it's worth pointing out specifically that we > have no intention whatsoever of aking MF and BP parallel each other > completely -- I can't see how that would be a sensible use of our > time. > > With respect to Mike's most recent: >> However, it seems there's not even consensus within the GO/OBO >> Consortium concerning the relationship between MFs and BPs. I >> originally asked whether the MFs were inherent functionalities of >> genes/gene products that get realized as processes or as >> "elementary" processes themselves. What you describe agrees with >> the documentation on the GO Web site and with most of the MF term >> names and their definitions, i.e., >> with the latter view, while Barry takes the former view. > > I think it's quite clear that there is consensus within GO on what > the distinction between MF and BP is at present. We've long > acknowledged that the split was arbitrary, and done for pragmatic > reasons (which Jen might go into). Accordingly, there is still a > lot of discussion, sometimes outright argument, about exactly where > the boundary lies, and whether a given term/entity belongs in MF or > BP, but the inherent functionality vs. actual "process" question > hasn't come up. > > Barry's "you are not wrong" statement was therefore not an accurate > description of GO's present content, documentation or practices. > Perhaps GO will move towards distinguishing inherent > functionalities from molecular-scale processes, but it's early days > -- the issue is still very much under discussion, implementation > has barely begun (if at all; it's probably fairer to simply say > this is not what we're doing now) and it's certainly not what we've > done historically. If anything, we have occasionally tried to speak > and think of MF terms as events (and annotation could be thought of > as making a statement about a particular gene product's inherent > functionality). > > It's been a long, long time since I've done any gene product > annotation, so I hope more people chime in. But one thing I can say > is that when I was doing annotation, I was definitely among that > majority of biologists who (as Mike correctly surmises) don't care > about the inherent functionality/execution of function distinction. > I might even stick my neck out and say that in many papers Mike's > "A transports B to the nucleus" example would refer to both the > process "B transport" and to the corresponding inherent > functionality "B transporter activity" -- an experiment documents > an actual instance of the process, and from that result the authors > infer A's ability to do the deed. > > Sorry to be long-winded -- I thought mine was going to be the brief > response! > > midori > > On Mon, 14 Jan 2008, Chris Mungall wrote: > >> [redirecting this part to GO, sorry if this confuses the thread, >> but I want to ask a question of GO folks first] >> >> Thanks for responding Jen. >> >> I think Mike raises some interesting issues, many of which we've >> raised internally. I have my ideas on how to answer Mike's >> question, focusing on the signal transduction/transducer activity >> example. But I'd like to get feedback, particularly from an >> annotation perspective, before answering from an ontology-minded >> perspective. >> >> It seems that we should have on the wiki as part of an annotation >> SOP some rules/guidelines for when to annotate to "signal >> transducer activity" vs "signal transduction" vs co-annotation of >> both. (which would of course apply to analagous examples) >> >> We also need to start making P<->F links here. >> >> If it helps I have added an example query: >> http://www.berkeleybop.org/goose >> >> select from the popup "genes annotated to signal transducer >> activity but not signal transduction" (and change the DB if you >> like - it's set to MGI in the example) >> >> you can also try swapping the terms around >> >> as you can see there is quite a lot >> >> Begin forwarded message: >> >>> From: Mike Bada >>> Date: January 14, 2008 6:21:44 PM PST >>> To: jdeegan at ebi.ac.uk, obo-discuss at lists.sourceforge.net >>> Subject: Re: [Obo-discuss] 3 forwarded messages on MF vs BP from >>> obo-discuss >>> Reply-To: obo-discuss at lists.sourceforge.net >>> Thank you for your detailed reply, Jennifer. However, it seems >>> there's >>> not even consensus within the GO/OBO Consortium concerning the >>> relationship between MFs and BPs. I originally asked whether the >>> MFs >>> were inherent functionalities of genes/gene products that get >>> realized >>> as processes or as "elementary" processes themselves. What you >>> describe >>> agrees with the documentation on the GO Web site and with most of >>> the MF >>> term names and their definitions, i.e., with the latter view, while >>> Barry takes the former view. >>> Again, we are most concerned with all of the parallel terms >>> between the >>> two subontologies, which makes application toward NLP, among other >>> tasks, much more difficult. This is not limited to the large >>> number of >>> corresponding transporter activity (MF) / transport (BP) terms; some >>> other examples include: >>> signal transducer activity (MF) ; signal transduction (BP) >>> translation regulator activity (MF) ; regulation of translation (BP) >>> enzyme regulator activity (MF) ; regulation of catalytic activity >>> (BP) >>> enzyme activator activity (MF) ; positive regulation of enzyme >>> activity (BP) >>> According to your explanation, all of these pairs of terms seem >>> to mean >>> essentially the same thing except for the fact that each of the >>> former >>> is a single-step process and each of the latter a multi-step >>> process. >>> It may be relatively easy to divide a metabolic pathway into its >>> component biochemical reactions, but what constitutes an elementary >>> single step of a process is often ambiguous. Any process can be >>> recursively divided into component processes: Even a biochemical >>> reaction can be divided into component processes of the reaction >>> mechanism. This ambiguous nature of what an "elementary" step is >>> makes >>> it very difficult to determine whether a process mentioned in, >>> say, a >>> journal article is a single-step or multi-step process (and thus >>> a MF or >>> a BP, respectively). >>> So there are two views, both of which hamper usability of the >>> subontologies applied in combination: As to the view that MFs >>> are the >>> inherent functionalities of genes/gene products that are realized in >>> BPs, it is often ambiguous whether a natural-language mention >>> refers to >>> the inherent functionality or to the process itself. As to the view >>> that MFs are the "single-step" processes that make up multi-step >>> BPs, it >>> is often ambiguous whether a natural-language mention is a >>> "single-step" >>> or "multi-step" process. Wouldn't it be easier and clearer if there >>> were one merged ontology of processes of all granularities and no >>> parallel terms such as the aforementioned ones? >>> Cheers, >>> Mike >>> Jennifer Deegan (nee Clark) wrote: >>>> Hi Mike, >>>> Midori forwarded this e-mail to me as I have been working on an >>>> extensive overhaul of the transport terms in GO. I think that I >>>> can help >>>> clear up at least some of the confusion here, though it might >>>> take a few >>>> e-mails to get things completely clear. >>>> In GO, as you have mentioned, we have transport terms in the >>>> function >>>> and process ontologies, and as you mention, they are really quite >>>> similar. However, this is partly because many of these terms >>>> were made >>>> in the early days of GO when we were really not too clear >>>> ourselves on >>>> the distinction between function and process. Now that we are much >>>> clearer about the distinction I have been working through with a >>>> number >>>> of expert biologists and improving the terms. >>>> Just to be clear, I will give a nice easy example of some >>>> function and >>>> process terms to get the distinction sorted out. We think of a >>>> molecular >>>> function as a single step reaction, whilst a process term >>>> describes a >>>> multistep event. You might think of a process term as being made >>>> up of >>>> several functions happening one after the other. We currently >>>> make no >>>> distinction between the actual execution of the function and the >>>> potential execution of the function. >>>> Function terms >>>> ============== >>>> An example of a function in GO is when a secondary active >>>> transporter >>>> molecule acts by changing >>>> shape so as to propel a bound potassium ion across the membrane, >>>> in a >>>> single step chemical reaction. We would consider this reaction >>>> to be a >>>> molecular function that belongs in the molecular function >>>> ontology. The >>>> term could be 'secondary active potassium transporter activity', >>>> though >>>> in fact have the term: >>>> potassium ion uniporter activity >>>> def: Catalysis of the active transport of a potassium ion across a >>>> membrane by a mechanism involving conformational change, where >>>> energy >>>> for active transport is derived from membrane potential if the >>>> solute is >>>> charged. >>>> There is a picture here in case it helps anyone get the biology >>>> clear: >>>> http://www.ncbi.nlm.nih.gov/books/bv.fcgi? >>>> highlight=carrier&rid=mboc4.figgrp.2000 >>>> Process terms >>>> ============= >>>> An example of a process that is nice and straightforward is the >>>> set of >>>> photochemical reactions that occur in photosynthesis. >>>> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.2589 >>>> This is currently included in GO as 'photosynthesis, light >>>> reaction' >>>> def: The light reactions of photosynthesis, which take place in >>>> photosystems II and I. Light energy is harvested and used to >>>> power the >>>> transfer of electrons among a series of electron donors and >>>> acceptors. >>>> The final electron acceptor is NADP+, which is reduced to NADPH. >>>> NADPH >>>> generated from light reactions is used in sugar synthesis in dark >>>> reactions. Light reactions also generate a proton motive force >>>> across >>>> the thylakoid membrane, and the proton gradient is used to >>>> synthesize >>>> ATP. There are two chemical reactions involved in the light >>>> reactions: >>>> water oxidation in photosystem II, and NADP reduction in >>>> photosystem I. >>>> The thing that I think is confusing you is that we have process >>>> terms >>>> that look really a lot like the transport function terms. The >>>> thing that >>>> you need to know is that we have overhauled most of the function >>>> terms >>>> and given them proper definitions so that they are no longer >>>> carrying >>>> the very non-specific definitions that you saw before. Most of >>>> them now >>>> have very clear defs describing single step reactions as shown >>>> above. >>>> Process transport terms are defined as, for example: >>>> The directed movement of potassium ions (K+) into, out of, >>>> within or >>>> between cells. (This is clearly a multistep affair, if we could >>>> think of >>>> a good example, though I think all these terms need a good >>>> looking at too. >>>> For example, do we really need a potassium transport process >>>> term? This >>>> is on my list to look at soon. ) >>>> In summary, the function terms are now better defined, to be >>>> clearly a >>>> single >>>> step reaction, and the process terms have much more general >>>> definitions >>>> that >>>> can cover a multistep reaction. >>>> The other thing that I should mention, is that I am currently >>>> working >>>> with several transport experts to re-examine all of the >>>> transport terms, >>>> and to improve them to clearly represent the current state of >>>> the biology. >>>> I hope to improve the process terms considerably, and we still >>>> have a >>>> lot of work to do on the more granular function terms. If you >>>> would like >>>> to be involved in this then I would be very pleased to include you. >>>> Here is a description of what we have done so far: >>>> http://wiki.geneontology.org/index.php/Transporters >>>> This is the documentation for the parts that we consider to be >>>> rigorously logical, and up to date for the field, as it >>>> currently stands: >>>> http://wiki.geneontology.org/index.php/Docs >>>> The process and function ontology docs may also help: >>>> http://www.geneontology.org/GO.process.guidelines.shtml >>>> http://www.geneontology.org/GO.function.guidelines.shtml >>>> I hope this helps a bit. Please do write back to ask further >>>> questions. >>>> It is a tricky subject, and I have had to rattle this e-mail off >>>> quite >>>> quickly before diving into a meeting, ironically, with my transport >>>> experts. Please could you also cc me, as I am not on the obo- >>>> discuss list. >>>> Thanks, and best wishes, >>>> Jennifer >>>> ---------- Forwarded message ---------- >>>> Date: Sat, 12 Jan 2008 20:13:23 -0700 >>>> From: Mike Bada >>>> Reply-To: obo-discuss at lists.sourceforge.net >>>> To: obo-discuss at lists.sourceforge.net >>>> Subject: [Obo-discuss] biological processes & molecular functions >>>> Hi all, >>>> Like Colin Batchelor, who has recently posted to this list, we are >>>> trying to extensively use OBOs in the annotation of journal >>>> articles >>>> (i.e., NLP annotation, not annotation in the sense of that done >>>> by the >>>> various model-organism databases). And, like Colin, we are >>>> experiencing >>>> issues in trying to use these OBOs (although I won't speak for >>>> him!). >>>> One issue that has caused us trouble is the dichotomy between GO >>>> biological processes and molecular functions, and this leads to a >>>> reexamination of the nature of these concepts. My understanding >>>> from >>>> that written by Barry Smith and others is that a biological >>>> process is >>>> an actual process and that a molecular function is a functionality >>>> inherent in a gene/gene product that is realized in a corresponding >>>> process. (Please correct me if I'm wrong.) This makes sense, I >>>> think, >>>> when examining the GO transport and transporter terms: The >>>> transporter >>>> terms in the MF subontology are of the form "Enables the >>>> transport of * >>>> into, out of, within or between cells", while the transport >>>> terms in the >>>> BP subontology are of the form "The directed movement of * into, >>>> out of, >>>> within or between cells". So drug transporter activity is the >>>> functionality inherent in a given gene/gene product that is >>>> realized in >>>> a drug-transport process. I assume that this is the reason for >>>> so many >>>> parallel BP transport and MF transporter activity terms. But if >>>> this is >>>> the case, then why isn't there a corresponding BP term for each >>>> MF term? >>>> Arguing on the other side, most of the MF terms are not defined as >>>> inherent functionalities but rather sound like processes to me: >>>> Most >>>> binding terms are defined as "Interacting selectively with *"; most >>>> catalytic-activity terms are defined as "Catalysis of the >>>> reaction: *"; >>>> many enzyme-regulator-activity terms are defined as "Modulates >>>> *"; etc. >>>> Furthermore, on the GO Web site, molecular functions are >>>> described as >>>> "activities, such as catalytic or binding activities, that occur >>>> at the >>>> molecular level", which to me sound like processes (at a molecular >>>> level) rather than functionalities inherent in genes/gene >>>> products that >>>> are realized in processes. >>>> The specific issues we're having and how we deal with them >>>> depend on the >>>> nature of the relationship between BPs and MFs, so I won't go >>>> into more >>>> detail until this is clear. We're hoping someone from GO/OBO could >>>> clear this up for us. >>>> Cheers, >>>> Mike >>>> ------------------------------------------------------------------- >>>> ------ >>>> Check out the new SourceForge.net Marketplace. >>>> It's the best place to buy or sell services for >>>> just about anything Open Source. >>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/ >>>> marketplace >>>> _______________________________________________ >>>> Obo-discuss mailing list >>>> Obo-discuss at lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>>> ---------- Forwarded message ---------- >>>> Date: Sat, 12 Jan 2008 23:24:15 -0400 >>>> From: "Smith, Barry" >>>> Reply-To: obo-discuss at lists.sourceforge.net >>>> To: obo-discuss at lists.sourceforge.net, obo- >>>> discuss at lists.sourceforge.net >>>> Subject: Re: [Obo-discuss] biological processes & molecular >>>> functions >>>> At 11:13 PM 1/12/2008, Mike Bada wrote: >>>>> Hi all, >>>>> Like Colin Batchelor, who has recently posted to this list, we are >>>>> trying to extensively use OBOs in the annotation of journal >>>>> articles >>>>> (i.e., NLP annotation, not annotation in the sense of that done >>>>> by the >>>>> various model-organism databases). And, like Colin, we are >>>>> experiencing >>>>> issues in trying to use these OBOs (although I won't speak for >>>>> him!). >>>>> One issue that has caused us trouble is the dichotomy between GO >>>>> biological processes and molecular functions, and this leads to a >>>>> reexamination of the nature of these concepts. My >>>>> understanding from >>>>> that written by Barry Smith and others is that a biological >>>>> process is >>>>> an actual process and that a molecular function is a functionality >>>>> inherent in a gene/gene product that is realized in a >>>>> corresponding >>>>> process. (Please correct me if I'm wrong.) >>>> You are not wrong. >>>>> This makes sense, I think, >>>>> when examining the GO transport and transporter terms: The >>>>> transporter >>>>> terms in the MF subontology are of the form "Enables the >>>>> transport of * >>>>> into, out of, within or between cells", while the transport >>>>> terms in the >>>>> BP subontology are of the form "The directed movement of * >>>>> into, out of, >>>>> within or between cells". So drug transporter activity is the >>>>> functionality inherent in a given gene/gene product that is >>>>> realized in >>>>> a drug-transport process. I assume that this is the reason for >>>>> so many >>>>> parallel BP transport and MF transporter activity terms. But >>>>> if this is >>>>> the case, then why isn't there a corresponding BP term for each >>>>> MF term? >>>> I believe that the GO consortium has committed itself to creating >>>> more consistency here. There are steps, also, to address the >>>> issue of >>>> functions at other (non-molecular) levels of granularity -- for >>>> example cellular and organ-level functions, reflecting also a more >>>> careful treatment of the granularities on the process side. >>>>> Arguing on the other side, most of the MF terms are not defined as >>>>> inherent functionalities but rather sound like processes to >>>>> me: Most >>>>> binding terms are defined as "Interacting selectively with *"; >>>>> most >>>>> catalytic-activity terms are defined as "Catalysis of the >>>>> reaction: *"; >>>>> many enzyme-regulator-activity terms are defined as "Modulates >>>>> *"; etc. >>>>> Furthermore, on the GO Web site, molecular functions are >>>>> described as >>>>> "activities, such as catalytic or binding activities, that >>>>> occur at the >>>>> molecular level", which to me sound like processes (at a molecular >>>>> level) rather than functionalities inherent in genes/gene >>>>> products that >>>>> are realized in processes. >>>> This is a big issue -- resulting from an unfortunate decision to >>>> label all function terms with the suffix 'activity'. >>>> When you read 'activity' in GO, try to thing 'function'. >>>>> The specific issues we're having and how we deal with them >>>>> depend on the >>>>> nature of the relationship between BPs and MFs, so I won't go >>>>> into more >>>>> detail until this is clear. We're hoping someone from GO/OBO >>>>> could >>>>> clear this up for us. >>>> Hope the above helps, at least somewhat. >>>> BS >>>>> Cheers, >>>>> Mike >>>>> ------------------------------------------------------------------ >>>>> ------- >>>>> Check out the new SourceForge.net Marketplace. >>>>> It's the best place to buy or sell services for >>>>> just about anything Open Source. >>>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http:// >>>>> sf.net/marketplace >>>>> _______________________________________________ >>>>> Obo-discuss mailing list >>>>> Obo-discuss at lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>>> ------------------------------------------------------------------- >>>> ------ >>>> Check out the new SourceForge.net Marketplace. >>>> It's the best place to buy or sell services for >>>> just about anything Open Source. >>>> http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/ >>>> marketplace >>>> _______________________________________________ >>>> Obo-discuss mailing list >>>> Obo-discuss at lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/obo-discuss >>>> ---------- Forwarded message ---------- >>>> Date: Sun, 13 Jan 2008 18:21:45 -0700 >>>> From: Mike Bada >>>> Reply-To: obo-discuss at lists.sourceforge.net >>>> To: obo-discuss at lists.sourceforge.net >>>> Subject: Re: [Obo-discuss] biological processes & molecular >>>> functions >>>> Smith, Barry wrote: >>>>> At 11:13 PM 1/12/2008, Mike Bada wrote: >>>>>> Hi all, >>>>>> Like Colin Batchelor, who has recently posted to this list, we >>>>>> are >>>>>> trying to extensively use OBOs in the annotation of journal >>>>>> articles >>>>>> (i.e., NLP annotation, not annotation in the sense of that >>>>>> done by the >>>>>> various model-organism databases). And, like Colin, we are >>>>>> experiencing >>>>>> issues in trying to use these OBOs (although I won't speak for >>>>>> him!). >>>>>> One issue that has caused us trouble is the dichotomy between GO >>>>>> biological processes and molecular functions, and this leads to a >>>>>> reexamination of the nature of these concepts. My >>>>>> understanding from >>>>>> that written by Barry Smith and others is that a biological >>>>>> process is >>>>>> an actual process and that a molecular function is a >>>>>> functionality >>>>>> inherent in a gene/gene product that is realized in a >>>>>> corresponding >>>>>> process. (Please correct me if I'm wrong.) >>>>> You are not wrong. >>>>>> This makes sense, I think, >>>>>> when examining the GO transport and transporter terms: The >>>>>> transporter >>>>>> terms in the MF subontology are of the form "Enables the >>>>>> transport of * >>>>>> into, out of, within or between cells", while the transport >>>>>> terms in the >>>>>> BP subontology are of the form "The directed movement of * >>>>>> into, out of, >>>>>> within or between cells". So drug transporter activity is the >>>>>> functionality inherent in a given gene/gene product that is >>>>>> realized in >>>>>> a drug-transport process. I assume that this is the reason >>>>>> for so many >>>>>> parallel BP transport and MF transporter activity terms. But >>>>>> if this is >>>>>> the case, then why isn't there a corresponding BP term for >>>>>> each MF term? >>>>> I believe that the GO consortium has committed itself to creating >>>>> more consistency here. There are steps, also, to address the >>>>> issue of >>>>> functions at other (non-molecular) levels of granu