From val at sanger.ac.uk Sun Jun 1 02:25:38 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Sun, 1 Jun 2008 09:25:38 UT Subject: [Go] [Gofriends] Gene Ontology Newsletter - May 2008 issue Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Sun Jun 1 09:00:18 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sun, 1 Jun 2008 16:00:18 UT Subject: [Go] SourceForge Update Message-ID: <200806011600.m51G0IY1516101@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Mon Jun 2 02:03:22 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 2 Jun 2008 10:03:22 +0100 (BST) Subject: [Go] Ontology development - May highlights Message-ID: Dear GO, The most recent monthly report on ontology content, for May 2008, is now available at: http://gocwiki.geneontology.org/index.php/May2008_report Ontology development highlights from May: * There has been progress on describing links between GO terms and taxon IDs, as discussed at the meeting in April (http://wiki.geneontology.org/index.php/Implementation_April_2008_onwards). * Function-process links are still being gathered for electron transport and metabolic pathways. Function-process main page: http://wiki.geneontology.org/index.php/Function-Process_Links. * The first F-P links to go live will be 'regulates' links, as announced in this month's newsletter (http://www.geneontology.org/newsletter/archive/200805.shtml) * The overhaul of signal transduction process terms is well under way (http://wiki.geneontology.org/index.php/Signaling). * Work on transport and transporters has resumed, with new experts involved (http://wiki.geneontology.org/index.php/Transporters). * We've done a cleanup of old oustanding SourceForge items, with many closed, still others assigned, and a few closed as out-of-date. As noted last month, the function-process work will continue, as will the signaling overhaul and quality control work connected with the regulation terms. In June, we'll also reorganize the protease activity terms in MF. Our plans for implementing cross-products based on Chris' new suggestion are unchanged (see http://wiki.geneontology.org/index.php/Cross_Product_Guide and files in the go/scratch/xps/ directory), as are plans to improve the metabolism branch with respect to structure and consistency with ChEBI. 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. Ontology Development wiki: http://wiki.geneontology.org/index.php/Ontology_Development SourceForge Curator Requests tracker: https://sourceforge.net/tracker/?group_id=36855&atid=440764 Midori & David on behalf of GO's ontology developers _______________________________________________ Go mailing list Go at geneontology.org http://fafner.stanford.edu/mailman/listinfo/go _______________________________________________ Go mailing list Go at geneontology.org http://fafner.stanford.edu/mailman/listinfo/go From jdeegan at ebi.ac.uk Mon Jun 2 02:07:22 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Mon, 02 Jun 2008 10:07:22 +0100 Subject: [Go] Advocacy and Outreach Message-ID: <4843B84A.3080101@ebi.ac.uk> Hi, Jane and I are writting reports on the advocacy and outreach activity taking place in April and May. If you have done anything to bring on new annotation groups or to help train new users then could you write and let us know? Thanks, Jen -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From midori at ebi.ac.uk Mon Jun 2 09:00:20 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 2 Jun 2008 16:00:20 UT Subject: [Go] SourceForge Update Message-ID: <200806021600.m52G0Ka1284101@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Tue Jun 3 09:00:15 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 3 Jun 2008 16:00:15 UT Subject: [Go] SourceForge Update Message-ID: <200806031600.m53G0GK1053566@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Wed Jun 4 09:00:17 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 4 Jun 2008 16:00:17 UT Subject: [Go] SourceForge Update Message-ID: <200806041600.m54G0I11333815@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Fri Jun 6 09:00:15 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 6 Jun 2008 16:00:15 UT Subject: [Go] SourceForge Update Message-ID: <200806061600.m56G0FI1367891@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Sat Jun 7 09:00:23 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 7 Jun 2008 16:00:23 UT Subject: [Go] SourceForge Update Message-ID: <200806071600.m57G0No1116932@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Mon Jun 9 09:00:16 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 9 Jun 2008 16:00:16 UT Subject: [Go] SourceForge Update Message-ID: <200806091600.m59G0GO1140190@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From jimhu at tamu.edu Mon Jun 9 10:19:59 2008 From: jimhu at tamu.edu (Jim Hu) Date: Mon, 9 Jun 2008 12:19:59 -0500 Subject: [Go] 1 year limit on IEAs Message-ID: <59A99D6E-85D9-4054-9E39-828C5EF660B8@tamu.edu> Hi All, As I recall, this was discussed at the SLC consortium meeting, but I find that I can't reconstruct the rationale for the 1 year expiration date on IEAs. For E. coli, we're importing the IEAs from Uniprot, but most of them will expire almost immediately. I assume that there is a problem in other genomes of too many IEAs. But perhaps a limit on how many per gene or some such might be more flexible. For our E. coli websites, I think it makes sense to display IEAs with appropriate caveats, since we're trying to encourage the community to do quality control on them. But I'm not sure, and I imagine that other mods have thought about this a lot. Jim ===================================== Jim Hu Associate Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054 -------------- next part -------------- An HTML attachment was scrubbed... URL: From maria at genome.stanford.edu Mon Jun 9 10:28:49 2008 From: maria at genome.stanford.edu (Maria Costanzo) Date: Mon, 09 Jun 2008 13:28:49 -0400 Subject: [Go] 1 year limit on IEAs In-Reply-To: <59A99D6E-85D9-4054-9E39-828C5EF660B8@tamu.edu> References: <59A99D6E-85D9-4054-9E39-828C5EF660B8@tamu.edu> Message-ID: <484D6851.3020001@genome.stanford.edu> An HTML attachment was scrubbed... URL: From suzi at berkeleybop.org Mon Jun 9 10:29:44 2008 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Mon, 9 Jun 2008 10:29:44 -0700 Subject: [Go] 1 year limit on IEAs In-Reply-To: <59A99D6E-85D9-4054-9E39-828C5EF660B8@tamu.edu> References: <59A99D6E-85D9-4054-9E39-828C5EF660B8@tamu.edu> Message-ID: <3A3BF814-C564-4A09-B965-CF4FE4306BBC@berkeleybop.org> Hi Jim, Actually the one-year expiration date was decided many years ago at a different meeting. The problem we were/are trying to address is when a group provides a one-time annotation of a genome to us and then, as time drifts by, the ontology changes, the gene models/proteins may change, and the annotations from which the original IEA annotations were based may also have changed. Given all of this drift once a set of annotations are orphaned we didn't feel they would/could remain relevant and useful. As you are actively monitoring the E. coli set of annotations these wouldn't fall under this sunset clause for abandoned annotation sets. -S On Jun 9, 2008, at 10:19 AM, Jim Hu wrote: > Hi All, > > As I recall, this was discussed at the SLC consortium meeting, but I > find that I can't reconstruct the rationale for the 1 year > expiration date on IEAs. For E. coli, we're importing the IEAs from > Uniprot, but most of them will expire almost immediately. I assume > that there is a problem in other genomes of too many IEAs. But > perhaps a limit on how many per gene or some such might be more > flexible. > > For our E. coli websites, I think it makes sense to display IEAs > with appropriate caveats, since we're trying to encourage the > community to do quality control on them. But I'm not sure, and I > imagine that other mods have thought about this a lot. > > Jim > > ===================================== > Jim Hu > Associate Professor > Dept. of Biochemistry and Biophysics > 2128 TAMU > Texas A&M Univ. > College Station, TX 77843-2128 > 979-862-4054 > > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From hjd at informatics.jax.org Mon Jun 9 10:34:16 2008 From: hjd at informatics.jax.org (Harold Drabkin) Date: Mon, 09 Jun 2008 13:34:16 -0400 Subject: [Go] 1 year limit on IEAs In-Reply-To: <59A99D6E-85D9-4054-9E39-828C5EF660B8@tamu.edu> References: <59A99D6E-85D9-4054-9E39-828C5EF660B8@tamu.edu> Message-ID: <484D6998.7080200@informatics.jax.org> Jim, if I'm not mistaken (someone from UniProt chime in please) , the IEAs from UniProt are based on the translation files (ec2go, ip2go and spkw2go) based on information in a uniprot record (ec#, domains, keywords). These change frequently; sometimes domains get added or removed, or the translation files change (mappings that are suddently to recently obsoleted terms, eg.) and so the IEAs go stale, espeically after 1 year. We update daily. I would really worry if they were older than 1 month,l et alone a year. hjd Jim Hu wrote: > Hi All, > > As I recall, this was discussed at the SLC consortium meeting, but I > find that I can't reconstruct the rationale for the 1 year expiration > date on IEAs. For E. coli, we're importing the IEAs from Uniprot, but > most of them will expire almost immediately. I assume that there is a > problem in other genomes of too many IEAs. But perhaps a limit on how > many per gene or some such might be more flexible. > > For our E. coli websites, I think it makes sense to display IEAs with > appropriate caveats, since we're trying to encourage the community to > do quality control on them. But I'm not sure, and I imagine that > other mods have thought about this a lot. > > Jim > > ===================================== > > Jim Hu > > Associate Professor > > Dept. of Biochemistry and Biophysics > > 2128 TAMU > > Texas A&M Univ. > > College Station, TX 77843-2128 > > 979-862-4054 > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From cherry at stanford.edu Mon Jun 9 10:52:13 2008 From: cherry at stanford.edu (Mike Cherry) Date: Mon, 9 Jun 2008 10:52:13 -0700 Subject: [Go] 1 year limit on IEAs In-Reply-To: <484D6998.7080200@informatics.jax.org> References: <59A99D6E-85D9-4054-9E39-828C5EF660B8@tamu.edu> <484D6998.7080200@informatics.jax.org> Message-ID: <50D85AD6-9641-4904-983F-30E584A29E88@stanford.edu> UNIPROTs IEA are updated with each of their monthly releases. So if you get their IEAs at least once a year you're fine. The 1 year limit was set way back. I think back in 2001 for the reasons Suzanna gave. If the IEAs cannot be updated once a year how actuate are they? -Mike On Jun 9, 2008, at 10:34 AM, Harold Drabkin wrote: > Jim, if I'm not mistaken (someone from UniProt chime in please) , > the IEAs from UniProt are based on the translation files (ec2go, > ip2go and spkw2go) based on information in a uniprot record (ec#, > domains, keywords). These change frequently; sometimes domains get > added or removed, or the translation files change (mappings that > are suddently to recently obsoleted terms, eg.) and so the IEAs go > stale, espeically after 1 year. We update daily. I would really > worry if they were older than 1 month,l et alone a year. > > hjd > > Jim Hu wrote: >> Hi All, >> >> As I recall, this was discussed at the SLC consortium meeting, but >> I find that I can't reconstruct the rationale for the 1 year >> expiration date on IEAs. For E. coli, we're importing the IEAs >> from Uniprot, but most of them will expire almost immediately. I >> assume that there is a problem in other genomes of too many IEAs. >> But perhaps a limit on how many per gene or some such might be more >> flexible. >> For our E. coli websites, I think it makes sense to display IEAs >> with appropriate caveats, since we're trying to encourage the >> community to do quality control on them. But I'm not sure, and I >> imagine that other mods have thought about this a lot. >> >> Jim >> >> ===================================== >> >> Jim Hu >> >> Associate Professor >> >> Dept. of Biochemistry and Biophysics >> >> 2128 TAMU >> >> Texas A&M Univ. >> >> College Station, TX 77843-2128 >> >> 979-862-4054 >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From dbarrell at ebi.ac.uk Tue Jun 10 00:34:22 2008 From: dbarrell at ebi.ac.uk (Daniel Barrell) Date: Tue, 10 Jun 2008 08:34:22 +0100 Subject: [Go] 1 year limit on IEAs In-Reply-To: <50D85AD6-9641-4904-983F-30E584A29E88@stanford.edu> References: <59A99D6E-85D9-4054-9E39-828C5EF660B8@tamu.edu> <484D6998.7080200@informatics.jax.org> <50D85AD6-9641-4904-983F-30E584A29E88@stanford.edu> Message-ID: <484E2E7E.5030808@ebi.ac.uk> What Harold and Mike have described is correct. The mapping files (ec2go, hamap2go, interpro2go, etc) are sanity checked on a weekly basis and corrected/extended by curators if needs be. The IEA pipeline is run 3 weekly after each UniProt release (so, realistically, monthly). If you are parsing our files directly you should do it at least annually to conform to the GO 1 year rule, but ideally you'd be taking them far more often. Cheers Dan Mike Cherry wrote: > UNIPROTs IEA are updated with each of their monthly releases. So if you > get their IEAs at least once a year you're fine. > > The 1 year limit was set way back. I think back in 2001 for the reasons > Suzanna gave. If the IEAs cannot be updated once a year how actuate are > they? > > -Mike > > > On Jun 9, 2008, at 10:34 AM, Harold Drabkin wrote: > >> Jim, if I'm not mistaken (someone from UniProt chime in please) , the >> IEAs from UniProt are based on the translation files (ec2go, ip2go and >> spkw2go) based on information in a uniprot record (ec#, domains, >> keywords). These change frequently; sometimes domains get added or >> removed, or the translation files change (mappings that are suddently >> to recently obsoleted terms, eg.) and so the IEAs go stale, espeically >> after 1 year. We update daily. I would really worry if they were older >> than 1 month,l et alone a year. >> >> hjd >> >> Jim Hu wrote: >>> Hi All, >>> >>> As I recall, this was discussed at the SLC consortium meeting, but I >>> find that I can't reconstruct the rationale for the 1 year expiration >>> date on IEAs. For E. coli, we're importing the IEAs from Uniprot, >>> but most of them will expire almost immediately. I assume that there >>> is a problem in other genomes of too many IEAs. But perhaps a limit >>> on how many per gene or some such might be more flexible. >>> For our E. coli websites, I think it makes sense to display IEAs with >>> appropriate caveats, since we're trying to encourage the community to >>> do quality control on them. But I'm not sure, and I imagine that >>> other mods have thought about this a lot. >>> >>> Jim >>> >>> ===================================== >>> >>> Jim Hu >>> >>> Associate Professor >>> >>> Dept. of Biochemistry and Biophysics >>> >>> 2128 TAMU >>> >>> Texas A&M Univ. >>> >>> College Station, TX 77843-2128 >>> >>> 979-862-4054 >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go -- Daniel Barrell EMBL - The EBI Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Phone: +44 (0)1223 492551 Email: dbarrell at ebi.ac.uk From midori at ebi.ac.uk Tue Jun 10 09:00:16 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 10 Jun 2008 16:00:16 UT Subject: [Go] SourceForge Update Message-ID: <200806101600.m5AG0GU1249692@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Wed Jun 11 09:00:15 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 11 Jun 2008 16:00:15 UT Subject: [Go] SourceForge Update Message-ID: <200806111600.m5BG0Fc1532727@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From pj37 at cornell.edu Wed Jun 11 10:12:05 2008 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 11 Jun 2008 13:12:05 -0400 Subject: [Go] Usage of the With/From Column for IEA ? In-Reply-To: <4808C439.3050505@cornell.edu> References: <4808C439.3050505@cornell.edu> Message-ID: <48500765.8040808@cornell.edu> I didn't hear from the group on this. Could you please help. Pankaj Pankaj Jaiswal wrote: > http://www.geneontology.org/GO.evidence.shtml#iea > > Ref: From the above site > > Usage of the With/From Column for IEA > > At the January 2007 GOC meeting, it was agreed that it will be required > to make an entry in the with/from column for all annotations made after > May 1, 2007 when using this evidence code to indicate what individual > sequences, sequence objects, methods, keyword mapping files, etc. are > the basis of the annotation. When multiple entries are placed in the > with/from field, they are separated by pipes. > > ------------ > Based on this rule, would you please suggest, what would be the value > for the 'WITH' column. > > - if we are making a TMHMM prediction for a 'putative tansmembrane' > annotation > - if we have used TargetP/SignalP/Predotar/Psort to predict a putative > cellular localization > > None of the above prediction softwares give appropriate value to be > filled in the 'WITH' column. > > If you agree our suggestion is to relax this rule for IEA's. > > Pankaj > From mgiglio at SOM.UMARYLAND.EDU Wed Jun 11 10:15:16 2008 From: mgiglio at SOM.UMARYLAND.EDU (Gwinn Giglio, Michelle) Date: Wed, 11 Jun 2008 13:15:16 -0400 Subject: [Go] Usage of the With/From Column for IEA ? In-Reply-To: <48500765.8040808@cornell.edu> Message-ID: Hi, Well, considering our new policy for ISS not requiring "with" for the very types of evidence you mention, it seems IEA should not require "with" as well...... Michelle On 6/11/08 1:12 PM, "Pankaj Jaiswal" wrote: > I didn't hear from the group on this. Could you please help. > > Pankaj > > Pankaj Jaiswal wrote: >> http://www.geneontology.org/GO.evidence.shtml#iea >> >> Ref: From the above site >> >> Usage of the With/From Column for IEA >> >> At the January 2007 GOC meeting, it was agreed that it will be required >> to make an entry in the with/from column for all annotations made after >> May 1, 2007 when using this evidence code to indicate what individual >> sequences, sequence objects, methods, keyword mapping files, etc. are >> the basis of the annotation. When multiple entries are placed in the >> with/from field, they are separated by pipes. >> >> ------------ >> Based on this rule, would you please suggest, what would be the value >> for the 'WITH' column. >> >> - if we are making a TMHMM prediction for a 'putative tansmembrane' >> annotation >> - if we have used TargetP/SignalP/Predotar/Psort to predict a putative >> cellular localization >> >> None of the above prediction softwares give appropriate value to be >> filled in the 'WITH' column. >> >> If you agree our suggestion is to relax this rule for IEA's. >> >> Pankaj >> > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go From pj37 at cornell.edu Thu Jun 12 08:48:08 2008 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 12 Jun 2008 11:48:08 -0400 Subject: [Go] Usage of the With/From Column for IEA ? In-Reply-To: References: Message-ID: <48514538.7010002@cornell.edu> Great. Do we need a formal word or voting on this request. We are waiting to submit some of our annotations that didn't make it through due to the mandatory 'with' rule. Pankaj Gwinn Giglio, Michelle wrote: > > Hi, > > Well, considering our new policy for ISS not requiring "with" for the very > types of evidence you mention, it seems IEA should not require "with" as > well...... > > Michelle > > > > > On 6/11/08 1:12 PM, "Pankaj Jaiswal" wrote: > >> I didn't hear from the group on this. Could you please help. >> >> Pankaj >> >> Pankaj Jaiswal wrote: >>> http://www.geneontology.org/GO.evidence.shtml#iea >>> >>> Ref: From the above site >>> >>> Usage of the With/From Column for IEA >>> >>> At the January 2007 GOC meeting, it was agreed that it will be required >>> to make an entry in the with/from column for all annotations made after >>> May 1, 2007 when using this evidence code to indicate what individual >>> sequences, sequence objects, methods, keyword mapping files, etc. are >>> the basis of the annotation. When multiple entries are placed in the >>> with/from field, they are separated by pipes. >>> >>> ------------ >>> Based on this rule, would you please suggest, what would be the value >>> for the 'WITH' column. >>> >>> - if we are making a TMHMM prediction for a 'putative tansmembrane' >>> annotation >>> - if we have used TargetP/SignalP/Predotar/Psort to predict a putative >>> cellular localization >>> >>> None of the above prediction softwares give appropriate value to be >>> filled in the 'WITH' column. >>> >>> If you agree our suggestion is to relax this rule for IEA's. >>> >>> Pankaj >>> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > > -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From midori at ebi.ac.uk Thu Jun 12 09:00:23 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 12 Jun 2008 16:00:23 UT Subject: [Go] SourceForge Update Message-ID: <200806121600.m5CG0N51285969@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From mgiglio at SOM.UMARYLAND.EDU Thu Jun 12 10:02:46 2008 From: mgiglio at SOM.UMARYLAND.EDU (Gwinn Giglio, Michelle) Date: Thu, 12 Jun 2008 13:02:46 -0400 Subject: [Go] Usage of the With/From Column for IEA ? In-Reply-To: <48514538.7010002@cornell.edu> Message-ID: I think we do need some kind of consensus - anyone else want to voice an opinion? Michelel On 6/12/08 11:48 AM, "Pankaj Jaiswal" wrote: > Great. Do we need a formal word or voting on this request. We are > waiting to submit some of our annotations that didn't make it through > due to the mandatory 'with' rule. > > Pankaj > > Gwinn Giglio, Michelle wrote: >> >> Hi, >> >> Well, considering our new policy for ISS not requiring "with" for the very >> types of evidence you mention, it seems IEA should not require "with" as >> well...... >> >> Michelle >> >> >> >> >> On 6/11/08 1:12 PM, "Pankaj Jaiswal" wrote: >> >>> I didn't hear from the group on this. Could you please help. >>> >>> Pankaj >>> >>> Pankaj Jaiswal wrote: >>>> http://www.geneontology.org/GO.evidence.shtml#iea >>>> >>>> Ref: From the above site >>>> >>>> Usage of the With/From Column for IEA >>>> >>>> At the January 2007 GOC meeting, it was agreed that it will be required >>>> to make an entry in the with/from column for all annotations made after >>>> May 1, 2007 when using this evidence code to indicate what individual >>>> sequences, sequence objects, methods, keyword mapping files, etc. are >>>> the basis of the annotation. When multiple entries are placed in the >>>> with/from field, they are separated by pipes. >>>> >>>> ------------ >>>> Based on this rule, would you please suggest, what would be the value >>>> for the 'WITH' column. >>>> >>>> - if we are making a TMHMM prediction for a 'putative tansmembrane' >>>> annotation >>>> - if we have used TargetP/SignalP/Predotar/Psort to predict a putative >>>> cellular localization >>>> >>>> None of the above prediction softwares give appropriate value to be >>>> filled in the 'WITH' column. >>>> >>>> If you agree our suggestion is to relax this rule for IEA's. >>>> >>>> Pankaj >>>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >> >> From pgaudet at northwestern.edu Thu Jun 12 11:21:47 2008 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Thu, 12 Jun 2008 14:21:47 -0400 Subject: [Go] [Annotation] Usage of the With/From Column for IEA ? In-Reply-To: References: Message-ID: <4851693B.6060300@northwestern.edu> An HTML attachment was scrubbed... URL: From mgiglio at SOM.UMARYLAND.EDU Thu Jun 12 11:28:51 2008 From: mgiglio at SOM.UMARYLAND.EDU (Gwinn Giglio, Michelle) Date: Thu, 12 Jun 2008 14:28:51 -0400 Subject: [Go] [Annotation] Usage of the With/From Column for IEA ? In-Reply-To: <4851693B.6060300@northwestern.edu> Message-ID: Yes, that?s what we did before the new documentation came out. That?s what we did at TIGR for years. But I think under the new ISS guidelines the CBS tools would fall under the set of things that don?t get ?with?. That is because the CBS tools are not always as straightforward as being a single HMM. TMHMM is a single HMM and therefore I think using CBS:TMHMM is perfectly appropriate, however SignalP is a combination of a neural network and an HMM, so it is less clear there. But lets say you are doing tRNAscan automatically or the snoRNA predictor, just like in ISS, they would not have a ?with?. Michelle On 6/12/08 2:21 PM, "Pascale Gaudet" wrote: > I wonder why we can't write CBS: TMHMM and CBS: SignalP > Seems accepted by our guidelines > http://geneontology.org/cgi-bin/xrefs.cgi#ref-C > > Pascale > > Gwinn Giglio, Michelle wrote: >> >> >> I think we do need some kind of consensus - anyone else want to voice an >> opinion? >> >> Michelel >> >> >> >> On 6/12/08 11:48 AM, "Pankaj Jaiswal" >> wrote: >> >> >> >>> >>> Great. Do we need a formal word or voting on this request. We are >>> waiting to submit some of our annotations that didn't make it through >>> due to the mandatory 'with' rule. >>> >>> Pankaj >>> >>> Gwinn Giglio, Michelle wrote: >>> >>> >>>> >>>> Hi, >>>> >>>> Well, considering our new policy for ISS not requiring "with" for the very >>>> types of evidence you mention, it seems IEA should not require "with" as >>>> well...... >>>> >>>> Michelle >>>> >>>> >>>> >>>> >>>> On 6/11/08 1:12 PM, "Pankaj Jaiswal" >>>> wrote: >>>> >>>> >>>> >>>>> >>>>> I didn't hear from the group on this. Could you please help. >>>>> >>>>> Pankaj >>>>> >>>>> Pankaj Jaiswal wrote: >>>>> >>>>> >>>>>> >>>>>> http://www.geneontology.org/GO.evidence.shtml#iea >>>>>> >>>>>> Ref: From the above site >>>>>> >>>>>> Usage of the With/From Column for IEA >>>>>> >>>>>> At the January 2007 GOC meeting, it was agreed that it will be required >>>>>> to make an entry in the with/from column for all annotations made after >>>>>> May 1, 2007 when using this evidence code to indicate what individual >>>>>> sequences, sequence objects, methods, keyword mapping files, etc. are >>>>>> the basis of the annotation. When multiple entries are placed in the >>>>>> with/from field, they are separated by pipes. >>>>>> >>>>>> ------------ >>>>>> Based on this rule, would you please suggest, what would be the value >>>>>> for the 'WITH' column. >>>>>> >>>>>> - if we are making a TMHMM prediction for a 'putative tansmembrane' >>>>>> annotation >>>>>> - if we have used TargetP/SignalP/Predotar/Psort to predict a putative >>>>>> cellular localization >>>>>> >>>>>> None of the above prediction softwares give appropriate value to be >>>>>> filled in the 'WITH' column. >>>>>> >>>>>> If you agree our suggestion is to relax this rule for IEA's. >>>>>> >>>>>> Pankaj >>>>>> >>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Go mailing list >>>>> Go at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >> >> >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hitz at genome.stanford.edu Thu Jun 12 11:38:26 2008 From: hitz at genome.stanford.edu (Benjamin Hitz) Date: Thu, 12 Jun 2008 11:38:26 -0700 Subject: [Go] Usage of the With/From Column for IEA ? In-Reply-To: References: Message-ID: <124705FE-F5C6-4D7F-8CBB-7B1A112F32F8@genome.stanford.edu> WITH fields are very important for IEA and "true" ISS where you are inferring an annotation based on sequence similarity. The reason is to prevent circular associations via sequence similarity. That is why the WITH column was made mandatory for IEAs and (old) ISS. From a database/machine loading perspective, the only way to enforce this is to make the with field MANDATORY. Ben On Jun 12, 2008, at 10:02 AM, Gwinn Giglio, Michelle wrote: > > > I think we do need some kind of consensus - anyone else want to > voice an > opinion? > > Michelel > > > > On 6/12/08 11:48 AM, "Pankaj Jaiswal" wrote: > >> Great. Do we need a formal word or voting on this request. We are >> waiting to submit some of our annotations that didn't make it through >> due to the mandatory 'with' rule. >> >> Pankaj >> >> Gwinn Giglio, Michelle wrote: >>> >>> Hi, >>> >>> Well, considering our new policy for ISS not requiring "with" for >>> the very >>> types of evidence you mention, it seems IEA should not require >>> "with" as >>> well...... >>> >>> Michelle >>> >>> >>> >>> >>> On 6/11/08 1:12 PM, "Pankaj Jaiswal" wrote: >>> >>>> I didn't hear from the group on this. Could you please help. >>>> >>>> Pankaj >>>> >>>> Pankaj Jaiswal wrote: >>>>> http://www.geneontology.org/GO.evidence.shtml#iea >>>>> >>>>> Ref: From the above site >>>>> >>>>> Usage of the With/From Column for IEA >>>>> >>>>> At the January 2007 GOC meeting, it was agreed that it will be >>>>> required >>>>> to make an entry in the with/from column for all annotations >>>>> made after >>>>> May 1, 2007 when using this evidence code to indicate what >>>>> individual >>>>> sequences, sequence objects, methods, keyword mapping files, >>>>> etc. are >>>>> the basis of the annotation. When multiple entries are placed in >>>>> the >>>>> with/from field, they are separated by pipes. >>>>> >>>>> ------------ >>>>> Based on this rule, would you please suggest, what would be the >>>>> value >>>>> for the 'WITH' column. >>>>> >>>>> - if we are making a TMHMM prediction for a 'putative >>>>> tansmembrane' >>>>> annotation >>>>> - if we have used TargetP/SignalP/Predotar/Psort to predict a >>>>> putative >>>>> cellular localization >>>>> >>>>> None of the above prediction softwares give appropriate value to >>>>> be >>>>> filled in the 'WITH' column. >>>>> >>>>> If you agree our suggestion is to relax this rule for IEA's. >>>>> >>>>> Pankaj >>>>> >>>> _______________________________________________ >>>> Go mailing list >>>> Go at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/go >>> >>> > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go -- Ben Hitz Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium Stanford University ** hitz at genome.stanford.edu From pj37 at cornell.edu Thu Jun 12 11:50:27 2008 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 12 Jun 2008 14:50:27 -0400 Subject: [Go] [Annotation] Usage of the With/From Column for IEA ? In-Reply-To: <4851693B.6060300@northwestern.edu> References: <4851693B.6060300@northwestern.edu> Message-ID: <48516FF3.1080103@cornell.edu> I see your suggestion a mix and match situation. We always use 'entities' such as accession IDs of genes/proteins in the WITH column, because we are trying to assert an association against reference. Now with this suggestion of using the resource site and method, it consists of a mixed BAG. Ideally there is a need for separate column where even for ISS/any_other_code you can say what method was used e.g. BLAST/BLATN/BLATP/SignalP/TargetP/TMHMM. I don't think we should populate the WITH column with method. Thisi way method column can be asserted for 'mandatory' status, but not 'with'. Pankaj Pascale Gaudet wrote: > I wonder why we can't write CBS: TMHMM and CBS: SignalP > Seems accepted by our guidelines > http://geneontology.org/cgi-bin/xrefs.cgi#ref-C > > Pascale > > Gwinn Giglio, Michelle wrote: >> I think we do need some kind of consensus - anyone else want to voice an >> opinion? >> >> Michelel >> >> >> >> On 6/12/08 11:48 AM, "Pankaj Jaiswal" wrote: >> >> >>> Great. Do we need a formal word or voting on this request. We are >>> waiting to submit some of our annotations that didn't make it through >>> due to the mandatory 'with' rule. >>> >>> Pankaj >>> >>> Gwinn Giglio, Michelle wrote: >>> >>>> Hi, >>>> >>>> Well, considering our new policy for ISS not requiring "with" for the very >>>> types of evidence you mention, it seems IEA should not require "with" as >>>> well...... >>>> >>>> Michelle >>>> >>>> >>>> >>>> >>>> On 6/11/08 1:12 PM, "Pankaj Jaiswal" wrote: >>>> >>>> >>>>> I didn't hear from the group on this. Could you please help. >>>>> >>>>> Pankaj >>>>> >>>>> Pankaj Jaiswal wrote: >>>>> >>>>>> http://www.geneontology.org/GO.evidence.shtml#iea >>>>>> >>>>>> Ref: From the above site >>>>>> >>>>>> Usage of the With/From Column for IEA >>>>>> >>>>>> At the January 2007 GOC meeting, it was agreed that it will be required >>>>>> to make an entry in the with/from column for all annotations made after >>>>>> May 1, 2007 when using this evidence code to indicate what individual >>>>>> sequences, sequence objects, methods, keyword mapping files, etc. are >>>>>> the basis of the annotation. When multiple entries are placed in the >>>>>> with/from field, they are separated by pipes. >>>>>> >>>>>> ------------ >>>>>> Based on this rule, would you please suggest, what would be the value >>>>>> for the 'WITH' column. >>>>>> >>>>>> - if we are making a TMHMM prediction for a 'putative tansmembrane' >>>>>> annotation >>>>>> - if we have used TargetP/SignalP/Predotar/Psort to predict a putative >>>>>> cellular localization >>>>>> >>>>>> None of the above prediction softwares give appropriate value to be >>>>>> filled in the 'WITH' column. >>>>>> >>>>>> If you agree our suggestion is to relax this rule for IEA's. >>>>>> >>>>>> Pankaj >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Go mailing list >>>>> Go at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>>> >>>> >> >> _______________________________________________ >> Annotation mailing list >> Annotation at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/annotation >> >> >> -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From mgiglio at SOM.UMARYLAND.EDU Thu Jun 12 12:02:31 2008 From: mgiglio at SOM.UMARYLAND.EDU (Gwinn Giglio, Michelle) Date: Thu, 12 Jun 2008 15:02:31 -0400 Subject: [Go] [Annotation] Usage of the With/From Column for IEA ? In-Reply-To: <124705FE-F5C6-4D7F-8CBB-7B1A112F32F8@genome.stanford.edu> Message-ID: Ben, No one is disputing the importance of the "with" fields and I think we all know why we have them. However, even making the "with" field always mandatory will not make people annotate correctly. It is easy to get around the spirit of these "rules" if someone wants to. The bottom line is we have had this debate more than once and have reached the decision not to require "with" for all ISS annotations - it only makes sense that the IEAs using the same kinds of information would be treated the same way. Let's think about the people who are trying to do a thoughtful and careful job of annotating using best GO practices. They will read the guidelines and they will try to follow them. As for those who use bad annotation practices, they will produce bad annotation whether or not we make them populate "with". Putting the methods/tools like tRNAscan and snoRNA scan into "with" would be mixing methods and accessions-of-items-found-with-methods in the "with" column. Many GO folks have expressed that they don't want to do this. As Pankaj and others have pointed out, there is always the option of yet another column for this. Or, others have argued it can be captured in the reference field. Anyway, we have a policy in place. Of course we've changed our minds in the past before..... Michelle On 6/12/08 2:38 PM, "Benjamin Hitz" wrote: > > WITH fields are very important for IEA and "true" ISS where you are > inferring an annotation based on sequence similarity. > The reason is to prevent circular associations via sequence similarity. > > That is why the WITH column was made mandatory for IEAs and (old) > ISS. From a database/machine loading perspective, the only way to > enforce this is to make the with field MANDATORY. > > Ben > > On Jun 12, 2008, at 10:02 AM, Gwinn Giglio, Michelle wrote: > >> >> >> I think we do need some kind of consensus - anyone else want to >> voice an >> opinion? >> >> Michelel >> >> >> >> On 6/12/08 11:48 AM, "Pankaj Jaiswal" wrote: >> >>> Great. Do we need a formal word or voting on this request. We are >>> waiting to submit some of our annotations that didn't make it through >>> due to the mandatory 'with' rule. >>> >>> Pankaj >>> >>> Gwinn Giglio, Michelle wrote: >>>> >>>> Hi, >>>> >>>> Well, considering our new policy for ISS not requiring "with" for >>>> the very >>>> types of evidence you mention, it seems IEA should not require >>>> "with" as >>>> well...... >>>> >>>> Michelle >>>> >>>> >>>> >>>> >>>> On 6/11/08 1:12 PM, "Pankaj Jaiswal" wrote: >>>> >>>>> I didn't hear from the group on this. Could you please help. >>>>> >>>>> Pankaj >>>>> >>>>> Pankaj Jaiswal wrote: >>>>>> http://www.geneontology.org/GO.evidence.shtml#iea >>>>>> >>>>>> Ref: From the above site >>>>>> >>>>>> Usage of the With/From Column for IEA >>>>>> >>>>>> At the January 2007 GOC meeting, it was agreed that it will be >>>>>> required >>>>>> to make an entry in the with/from column for all annotations >>>>>> made after >>>>>> May 1, 2007 when using this evidence code to indicate what >>>>>> individual >>>>>> sequences, sequence objects, methods, keyword mapping files, >>>>>> etc. are >>>>>> the basis of the annotation. When multiple entries are placed in >>>>>> the >>>>>> with/from field, they are separated by pipes. >>>>>> >>>>>> ------------ >>>>>> Based on this rule, would you please suggest, what would be the >>>>>> value >>>>>> for the 'WITH' column. >>>>>> >>>>>> - if we are making a TMHMM prediction for a 'putative >>>>>> tansmembrane' >>>>>> annotation >>>>>> - if we have used TargetP/SignalP/Predotar/Psort to predict a >>>>>> putative >>>>>> cellular localization >>>>>> >>>>>> None of the above prediction softwares give appropriate value to >>>>>> be >>>>>> filled in the 'WITH' column. >>>>>> >>>>>> If you agree our suggestion is to relax this rule for IEA's. >>>>>> >>>>>> Pankaj >>>>>> >>>>> _______________________________________________ >>>>> Go mailing list >>>>> Go at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>> >>>> >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go > > -- > Ben Hitz > Senior Scientific Programmer ** Saccharomyces Genome Database ** GO > Consortium > Stanford University ** hitz at genome.stanford.edu > > > > _______________________________________________ > Annotation mailing list > Annotation at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/annotation From jane at ebi.ac.uk Fri Jun 13 04:00:10 2008 From: jane at ebi.ac.uk (Jane Lomax) Date: Fri, 13 Jun 2008 12:00:10 +0100 Subject: [Go] sporulation rearrangement Message-ID: <4852533A.90900@ebi.ac.uk> Hi - the PAMGO group are currently working on some terms to annotate higher fungi and have encountered some problems with the existing placement of the term 'sporulation' and its children in the graph. Essentially the problem is that sporulation is a child of 'cell differentiation' but in higher fungi spores are often multicellular or syncytial structures so this is a tpv. So we'd like to propose some changes to the existing graph to remedy this: NOW: developmental process ---[i] cellular developmental process ------[i] cell differentiation ---------[i] sporulation ; GO:0030435 ------------[i] asexual sporulation ; GO:0030436 ------------[i] sexual sporulation ; GO:0034293 PROPOSED: developmental process ---[i] sporulation ; GO:new ------[i] cellular sporulation ; GO:0030435 ------[i] multicellular or syncytial sporulation ; GO:new ---------[i] multicellular or syncytial sexual sporulation ; GO:new ---------[i] multicellular or syncytial asexual sporulation ; GO:new ------[i] sexual sporulation ; GO:new ---------[i] cellular sexual sporulation ; GO:0034293 ---------[i] multicellular or syncytial sexual sporulation ; GO:new ------[i] asexual sporulation ; GO:new ---------[i] cellular asexual sporulation ; GO:0030436 ---------[i] multicellular or syncytial asexual sporulation ; GO:new developmental process ---[i] cellular developmental process ------[i] cell differentiation ---------[i] cellular sporulation ; GO:0030435 ------------[i] cellular asexual sporulation ; GO:0030436 ------------[i] cellular sexual sporulation ; GO:0034293 how does that sound to you single-celled fungi people? cheers, Jane -- Dr Jane Lomax GO Editorial Office EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridgeshire, UK CB10 1SD p: +44 1223 492516 f: +44 1223 494468 From midori at ebi.ac.uk Fri Jun 13 04:02:39 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 13 Jun 2008 12:02:39 +0100 (BST) Subject: [Go] sporulation rearrangement In-Reply-To: <4852533A.90900@ebi.ac.uk> References: <4852533A.90900@ebi.ac.uk> Message-ID: works for me On Fri, 13 Jun 2008, Jane Lomax wrote: > Hi - the PAMGO group are currently working on some terms to annotate higher > fungi and have encountered some problems with the existing placement of the > term 'sporulation' and its children in the graph. Essentially the problem is > that sporulation is a child of 'cell differentiation' but in higher fungi > spores are often multicellular or syncytial structures so this is a tpv. So > we'd like to propose some changes to the existing graph to remedy this: > > NOW: > > developmental process > ---[i] cellular developmental process > ------[i] cell differentiation > ---------[i] sporulation ; GO:0030435 > ------------[i] asexual sporulation ; GO:0030436 > ------------[i] sexual sporulation ; GO:0034293 > > PROPOSED: > > developmental process > ---[i] sporulation ; GO:new > ------[i] cellular sporulation ; GO:0030435 > ------[i] multicellular or syncytial sporulation ; GO:new > ---------[i] multicellular or syncytial sexual sporulation ; GO:new > ---------[i] multicellular or syncytial asexual sporulation ; GO:new > ------[i] sexual sporulation ; GO:new > ---------[i] cellular sexual sporulation ; GO:0034293 > ---------[i] multicellular or syncytial sexual sporulation ; GO:new > ------[i] asexual sporulation ; GO:new > ---------[i] cellular asexual sporulation ; GO:0030436 > ---------[i] multicellular or syncytial asexual sporulation ; GO:new > > developmental process > ---[i] cellular developmental process > ------[i] cell differentiation > ---------[i] cellular sporulation ; GO:0030435 > ------------[i] cellular asexual sporulation ; GO:0030436 > ------------[i] cellular sexual sporulation ; GO:0034293 > > how does that sound to you single-celled fungi people? > > cheers, > > Jane > > From val at sanger.ac.uk Fri Jun 13 05:03:00 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Fri, 13 Jun 2008 12:03:00 UT Subject: [Go] sporulation rearrangement Message-ID: An embedded and charset-unspecified text was scrubbed... Name: not available URL: From pgaudet at northwestern.edu Fri Jun 13 05:10:21 2008 From: pgaudet at northwestern.edu (Pascale Gaudet) Date: Fri, 13 Jun 2008 08:10:21 -0400 Subject: [Go] sporulation rearrangement In-Reply-To: References: Message-ID: <485263AD.1060006@northwestern.edu> An HTML attachment was scrubbed... URL: From dph at informatics.jax.org Fri Jun 13 05:47:04 2008 From: dph at informatics.jax.org (David Hill) Date: Fri, 13 Jun 2008 08:47:04 -0400 Subject: [Go] sporulation rearrangement In-Reply-To: <4852533A.90900@ebi.ac.uk> References: <4852533A.90900@ebi.ac.uk> Message-ID: <48526C48.2070604@informatics.jax.org> Jane, Based on your comments, this makes sense to me. David Jane Lomax wrote: > Hi - the PAMGO group are currently working on some terms to annotate > higher fungi and have encountered some problems with the existing > placement of the term 'sporulation' and its children in the graph. > Essentially the problem is that sporulation is a child of 'cell > differentiation' but in higher fungi spores are often multicellular or > syncytial structures so this is a tpv. So we'd like to propose some > changes to the existing graph to remedy this: > > NOW: > > developmental process > ---[i] cellular developmental process > ------[i] cell differentiation > ---------[i] sporulation ; GO:0030435 > ------------[i] asexual sporulation ; GO:0030436 > ------------[i] sexual sporulation ; GO:0034293 > > PROPOSED: > > developmental process > ---[i] sporulation ; GO:new > ------[i] cellular sporulation ; GO:0030435 > ------[i] multicellular or syncytial sporulation ; GO:new > ---------[i] multicellular or syncytial sexual sporulation ; GO:new > ---------[i] multicellular or syncytial asexual sporulation ; GO:new > ------[i] sexual sporulation ; GO:new > ---------[i] cellular sexual sporulation ; GO:0034293 > ---------[i] multicellular or syncytial sexual sporulation ; GO:new > ------[i] asexual sporulation ; GO:new > ---------[i] cellular asexual sporulation ; GO:0030436 > ---------[i] multicellular or syncytial asexual sporulation ; GO:new > > developmental process > ---[i] cellular developmental process > ------[i] cell differentiation > ---------[i] cellular sporulation ; GO:0030435 > ------------[i] cellular asexual sporulation ; GO:0030436 > ------------[i] cellular sexual sporulation ; GO:0034293 > > how does that sound to you single-celled fungi people? > > cheers, > > Jane > From pj37 at cornell.edu Fri Jun 13 06:08:21 2008 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 13 Jun 2008 09:08:21 -0400 Subject: [Go] sporulation rearrangement In-Reply-To: <48526C48.2070604@informatics.jax.org> References: <4852533A.90900@ebi.ac.uk> <48526C48.2070604@informatics.jax.org> Message-ID: <48527145.6000406@cornell.edu> Looks good. Suggestions inserted. Pankaj David Hill wrote: > Jane, > > Based on your comments, this makes sense to me. > > David > > Jane Lomax wrote: >> Hi - the PAMGO group are currently working on some terms to annotate >> higher fungi and have encountered some problems with the existing >> placement of the term 'sporulation' and its children in the graph. >> Essentially the problem is that sporulation is a child of 'cell >> differentiation' but in higher fungi spores are often multicellular or >> syncytial structures so this is a tpv. Modify the definition of sporulation ; GO:0030435 to suggest uni & multicellular forms. So we'd like to propose some >> changes to the existing graph to remedy this: >> >> NOW: >> >> developmental process >> ---[i] cellular developmental process >> ------[i] cell differentiation >> ---------[i] sporulation ; GO:0030435 >> ------------[i] asexual sporulation ; GO:0030436 >> ------------[i] sexual sporulation ; GO:0034293 >> >> PROPOSED: >> >> developmental process >> ---[i] sporulation ; GO:new Check this term its ID is not new but GO:0030435 >> ------[i] cellular sporulation ; GO:0030435 Should be a new term. My suggestion would be to make it exclusively 'unicellular sporulation', considering a following new term for 'multicellular sporulation' is also suggested. This will introduce consistency. >> ------[i] multicellular or syncytial sporulation ; GO:new use of OR must be avoided. Call the term 'multicellular sporulation' and add synonym 'syncytial sporulation'. They are synonymous and not single terms. >> ---------[i] multicellular or syncytial sexual sporulation ; GO:new >> ---------[i] multicellular or syncytial asexual sporulation ; GO:new >> ------[i] sexual sporulation ; GO:new >> ---------[i] cellular sexual sporulation ; GO:0034293 ................^^^^^^^ unicellular >> ---------[i] multicellular or syncytial sexual sporulation ; GO:new >> ------[i] asexual sporulation ; GO:new >> ---------[i] cellular asexual sporulation ; GO:0030436 >> ---------[i] multicellular or syncytial asexual sporulation ; GO:new >> >> developmental process >> ---[i] cellular developmental process >> ------[i] cell differentiation >> ---------[i] cellular sporulation ; GO:0030435 >> ------------[i] cellular asexual sporulation ; GO:0030436 ................^^^^^^^ unicellular >> ------------[i] cellular sexual sporulation ; GO:0034293 ................^^^^^^^ unicellular >> >> how does that sound to you single-celled fungi people? >> >> cheers, >> >> Jane >> From midori at ebi.ac.uk Fri Jun 13 06:16:49 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 13 Jun 2008 14:16:49 +0100 (BST) Subject: [Go] sporulation rearrangement In-Reply-To: <48527145.6000406@cornell.edu> References: <4852533A.90900@ebi.ac.uk> <48526C48.2070604@informatics.jax.org> <48527145.6000406@cornell.edu> Message-ID: I much prefer the original proposal over these suggested changes -- GO:0030435 is defined as a cellular process, so it's better to make its name match its meaning than change the meaning. 'Multicellular' and 'syncytial' are not synonymous, so maybe there should be two new sporulation terms, but we certainly shouldn't have one term with 'multicellular' in the name and 'syncytial' in an exact synonym. midori On Fri, 13 Jun 2008, Pankaj Jaiswal wrote: > Looks good. Suggestions inserted. > > Pankaj > > David Hill wrote: >> Jane, >> >> Based on your comments, this makes sense to me. >> >> David >> >> Jane Lomax wrote: >>> Hi - the PAMGO group are currently working on some terms to annotate >>> higher fungi and have encountered some problems with the existing >>> placement of the term 'sporulation' and its children in the graph. >>> Essentially the problem is that sporulation is a child of 'cell >>> differentiation' but in higher fungi spores are often multicellular or >>> syncytial structures so this is a tpv. > > Modify the definition of sporulation ; GO:0030435 to suggest uni & > multicellular forms. > > > So we'd like to propose some >>> changes to the existing graph to remedy this: >>> >>> NOW: >>> >>> developmental process >>> ---[i] cellular developmental process >>> ------[i] cell differentiation >>> ---------[i] sporulation ; GO:0030435 >>> ------------[i] asexual sporulation ; GO:0030436 >>> ------------[i] sexual sporulation ; GO:0034293 >>> >>> PROPOSED: >>> >>> developmental process >>> ---[i] sporulation ; GO:new > > Check this term its ID is not new but GO:0030435 > > >>> ------[i] cellular sporulation ; GO:0030435 > > Should be a new term. > > My suggestion would be to make it exclusively > 'unicellular sporulation', considering a following new term for > 'multicellular sporulation' is also suggested. This will introduce > consistency. > > >>> ------[i] multicellular or syncytial sporulation ; GO:new > > use of OR must be avoided. Call the term 'multicellular sporulation' and add > synonym 'syncytial sporulation'. They are synonymous and not single terms. > > >>> ---------[i] multicellular or syncytial sexual sporulation ; GO:new >>> ---------[i] multicellular or syncytial asexual sporulation ; GO:new >>> ------[i] sexual sporulation ; GO:new >>> ---------[i] cellular sexual sporulation ; GO:0034293 > > ................^^^^^^^ unicellular > > >>> ---------[i] multicellular or syncytial sexual sporulation ; GO:new >>> ------[i] asexual sporulation ; GO:new >>> ---------[i] cellular asexual sporulation ; GO:0030436 >>> ---------[i] multicellular or syncytial asexual sporulation ; GO:new >>> >>> developmental process >>> ---[i] cellular developmental process >>> ------[i] cell differentiation >>> ---------[i] cellular sporulation ; GO:0030435 >>> ------------[i] cellular asexual sporulation ; GO:0030436 > > ................^^^^^^^ unicellular > >>> ------------[i] cellular sexual sporulation ; GO:0034293 > ................^^^^^^^ unicellular >>> >>> how does that sound to you single-celled fungi people? >>> >>> cheers, >>> >>> Jane >>> > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From jane at ebi.ac.uk Fri Jun 13 06:23:58 2008 From: jane at ebi.ac.uk (Jane Lomax) Date: Fri, 13 Jun 2008 14:23:58 +0100 Subject: [Go] sporulation rearrangement In-Reply-To: <48527145.6000406@cornell.edu> References: <4852533A.90900@ebi.ac.uk> <48526C48.2070604@informatics.jax.org> <48527145.6000406@cornell.edu> Message-ID: <485274EE.1060903@ebi.ac.uk> Hi Pankaj - the reason I suggested changing the names of the existing sporulation terms to 'cellular ....' and creating new ids for the new, more general sporulation terms is because the existing terms have been used in the cellular sense and the definitions reflect this. I'll write the more general defs for the new terms and that way I won't need to change the definitions of existing terms. I don't really see a problem using 'or' in the term names - we wanted to be clear that syncytial structures were not excluded - what do others think? I'd be okay with changing 'cellular' to 'unicellular' I *think* - although we've used just 'cellular' elsewhere in the graph - perhaps I should add 'unicellular' synonyms? Jane Pankaj Jaiswal wrote: > Looks good. Suggestions inserted. > > Pankaj > > David Hill wrote: >> Jane, >> >> Based on your comments, this makes sense to me. >> >> David >> >> Jane Lomax wrote: >>> Hi - the PAMGO group are currently working on some terms to annotate >>> higher fungi and have encountered some problems with the existing >>> placement of the term 'sporulation' and its children in the graph. >>> Essentially the problem is that sporulation is a child of 'cell >>> differentiation' but in higher fungi spores are often multicellular >>> or syncytial structures so this is a tpv. > > Modify the definition of sporulation ; GO:0030435 to suggest uni & > multicellular forms. > > > So we'd like to propose some >>> changes to the existing graph to remedy this: >>> >>> NOW: >>> >>> developmental process >>> ---[i] cellular developmental process >>> ------[i] cell differentiation >>> ---------[i] sporulation ; GO:0030435 >>> ------------[i] asexual sporulation ; GO:0030436 >>> ------------[i] sexual sporulation ; GO:0034293 >>> >>> PROPOSED: >>> >>> developmental process >>> ---[i] sporulation ; GO:new > > Check this term its ID is not new but GO:0030435 > > >>> ------[i] cellular sporulation ; GO:0030435 > > Should be a new term. > > My suggestion would be to make it exclusively > 'unicellular sporulation', considering a following new term for > 'multicellular sporulation' is also suggested. This will introduce > consistency. > > >>> ------[i] multicellular or syncytial sporulation ; GO:new > > use of OR must be avoided. Call the term 'multicellular sporulation' > and add synonym 'syncytial sporulation'. They are synonymous and not > single terms. > > >>> ---------[i] multicellular or syncytial sexual sporulation ; GO:new >>> ---------[i] multicellular or syncytial asexual sporulation ; GO:new >>> ------[i] sexual sporulation ; GO:new >>> ---------[i] cellular sexual sporulation ; GO:0034293 > > ................^^^^^^^ unicellular > > >>> ---------[i] multicellular or syncytial sexual sporulation ; GO:new >>> ------[i] asexual sporulation ; GO:new >>> ---------[i] cellular asexual sporulation ; GO:0030436 >>> ---------[i] multicellular or syncytial asexual sporulation ; GO:new >>> >>> developmental process >>> ---[i] cellular developmental process >>> ------[i] cell differentiation >>> ---------[i] cellular sporulation ; GO:0030435 >>> ------------[i] cellular asexual sporulation ; GO:0030436 > > ................^^^^^^^ unicellular > >>> ------------[i] cellular sexual sporulation ; GO:0034293 > ................^^^^^^^ unicellular >>> >>> how does that sound to you single-celled fungi people? >>> >>> cheers, >>> >>> Jane >>> -- Dr Jane Lomax GO Editorial Office EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridgeshire, UK CB10 1SD p: +44 1223 492516 f: +44 1223 494468 From pj37 at cornell.edu Fri Jun 13 06:36:41 2008 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 13 Jun 2008 09:36:41 -0400 Subject: [Go] sporulation rearrangement In-Reply-To: References: <4852533A.90900@ebi.ac.uk> <48526C48.2070604@informatics.jax.org> <48527145.6000406@cornell.edu> Message-ID: <485277E9.8010003@cornell.edu> Midori Harris wrote: > I much prefer the original proposal over these suggested changes -- > GO:0030435 is defined as a cellular process, so it's better to make its > name match its meaning than change the meaning. > At some point majority of BP terms are cellular. In this particular case the tree is being modified/corrected to identify the multicellular form. Therefore the term names must identify cellular (generic) to uni/multi cellular forms. You may want to consult Barry on this. > 'Multicellular' and 'syncytial' are not synonymous, so maybe there > should be two new sporulation terms, but we certainly shouldn't have one > term with 'multicellular' in the name and 'syncytial' in an exact synonym. > Not an exact synonym but a related/narrow synonym considering they are structures with multi-nucleate cells formed by the fusion of neighboring cells. Pankaj From midori at ebi.ac.uk Fri Jun 13 06:39:55 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 13 Jun 2008 14:39:55 +0100 (BST) Subject: [Go] sporulation rearrangement In-Reply-To: <485277E9.8010003@cornell.edu> References: <4852533A.90900@ebi.ac.uk> <48526C48.2070604@informatics.jax.org> <48527145.6000406@cornell.edu> <485277E9.8010003@cornell.edu> Message-ID: On Fri, 13 Jun 2008, Pankaj Jaiswal wrote: > > > Midori Harris wrote: >> I much prefer the original proposal over these suggested changes -- >> GO:0030435 is defined as a cellular process, so it's better to make its >> name match its meaning than change the meaning. >> > > At some point majority of BP terms are cellular. In this particular case the > tree is being modified/corrected to identify the multicellular form. > Therefore the term names must identify cellular (generic) to uni/multi > cellular forms. You may want to consult Barry on this. This is irrelevant to the question of whether to change the name or the definition of a term in cases where the scope or scale don't already match. It is well-established GO practice to preserve meanings and adjust names, not the other way around. m > >> 'Multicellular' and 'syncytial' are not synonymous, so maybe there should >> be two new sporulation terms, but we certainly shouldn't have one term with >> 'multicellular' in the name and 'syncytial' in an exact synonym. >> > Not an exact synonym but a related/narrow synonym considering they are > structures with multi-nucleate cells formed by the fusion of neighboring > cells. > > > Pankaj > From midori at ebi.ac.uk Fri Jun 13 09:00:17 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 13 Jun 2008 16:00:17 UT Subject: [Go] SourceForge Update Message-ID: <200806131600.m5DG0H91562363@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From cjm at fruitfly.org Fri Jun 13 10:28:03 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Fri, 13 Jun 2008 10:28:03 -0700 Subject: [Go] sporulation rearrangement In-Reply-To: <4852533A.90900@ebi.ac.uk> References: <4852533A.90900@ebi.ac.uk> Message-ID: <4D2E0CF7-1E5B-4E61-96C0-D0C0E853827F@fruitfly.org> The fungal_anatomy ontology could be very useful for checking child terms. However, this ontology is marked as quiescent in OBO. Would there be any chance of resurrecting it? On Jun 13, 2008, at 4:00 AM, Jane Lomax wrote: > Hi - the PAMGO group are currently working on some terms to > annotate higher fungi and have encountered some problems with the > existing placement of the term 'sporulation' and its children in > the graph. Essentially the problem is that sporulation is a child > of 'cell differentiation' but in higher fungi spores are often > multicellular or syncytial structures so this is a tpv. So we'd > like to propose some changes to the existing graph to remedy this: > > NOW: > > developmental process > ---[i] cellular developmental process > ------[i] cell differentiation > ---------[i] sporulation ; GO:0030435 > ------------[i] asexual sporulation ; GO:0030436 > ------------[i] sexual sporulation ; GO:0034293 > > PROPOSED: > > developmental process > ---[i] sporulation ; GO:new > ------[i] cellular sporulation ; GO:0030435 > ------[i] multicellular or syncytial sporulation ; GO:new > ---------[i] multicellular or syncytial sexual sporulation ; GO:new > ---------[i] multicellular or syncytial asexual sporulation ; GO:new > ------[i] sexual sporulation ; GO:new > ---------[i] cellular sexual sporulation ; GO:0034293 > ---------[i] multicellular or syncytial sexual sporulation ; GO:new > ------[i] asexual sporulation ; GO:new > ---------[i] cellular asexual sporulation ; GO:0030436 > ---------[i] multicellular or syncytial asexual sporulation ; GO:new > > developmental process > ---[i] cellular developmental process > ------[i] cell differentiation > ---------[i] cellular sporulation ; GO:0030435 > ------------[i] cellular asexual sporulation ; GO:0030436 > ------------[i] cellular sexual sporulation ; GO:0034293 > > how does that sound to you single-celled fungi people? > > cheers, > > Jane > > -- > Dr Jane > Lomax > GO Editorial > Office > EMBL- > EBI > Wellcome Trust Genome > Campus > > Hinxton > Cambridgeshire, > UK > CB10 > 1SD > > > p: +44 1223 > 492516 > f: +44 1223 494468 > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From maria at genome.stanford.edu Fri Jun 13 10:50:02 2008 From: maria at genome.stanford.edu (Maria Costanzo) Date: Fri, 13 Jun 2008 13:50:02 -0400 Subject: [Go] sporulation rearrangement In-Reply-To: <4D2E0CF7-1E5B-4E61-96C0-D0C0E853827F@fruitfly.org> References: <4852533A.90900@ebi.ac.uk> <4D2E0CF7-1E5B-4E61-96C0-D0C0E853827F@fruitfly.org> Message-ID: <4852B34A.7000106@genome.stanford.edu> Hi Chris, I don't think it's likely that SGD will resurrect this project. There wasn't very much interest from the fungal community, and the project is very peripheral to our goals (yeast don't have much anatomy!) so we would not pick it up again without a strong request from fungal scientists who would be willing to help with the scientific content. We'd be happy to hand it over to another group, if anyone is interested in pursuing it. Maria Chris Mungall wrote: > The fungal_anatomy ontology could be very useful for checking child > terms. However, this ontology is marked as quiescent in OBO. Would > there be any chance of resurrecting it? > > On Jun 13, 2008, at 4:00 AM, Jane Lomax wrote: > >> Hi - the PAMGO group are currently working on some terms to annotate >> higher fungi and have encountered some problems with the existing >> placement of the term 'sporulation' and its children in the graph. >> Essentially the problem is that sporulation is a child of 'cell >> differentiation' but in higher fungi spores are often multicellular >> or syncytial structures so this is a tpv. So we'd like to propose >> some changes to the existing graph to remedy this: >> >> NOW: >> >> developmental process >> ---[i] cellular developmental process >> ------[i] cell differentiation >> ---------[i] sporulation ; GO:0030435 >> ------------[i] asexual sporulation ; GO:0030436 >> ------------[i] sexual sporulation ; GO:0034293 >> >> PROPOSED: >> >> developmental process >> ---[i] sporulation ; GO:new >> ------[i] cellular sporulation ; GO:0030435 >> ------[i] multicellular or syncytial sporulation ; GO:new >> ---------[i] multicellular or syncytial sexual sporulation ; GO:new >> ---------[i] multicellular or syncytial asexual sporulation ; GO:new >> ------[i] sexual sporulation ; GO:new >> ---------[i] cellular sexual sporulation ; GO:0034293 >> ---------[i] multicellular or syncytial sexual sporulation ; GO:new >> ------[i] asexual sporulation ; GO:new >> ---------[i] cellular asexual sporulation ; GO:0030436 >> ---------[i] multicellular or syncytial asexual sporulation ; GO:new >> >> developmental process >> ---[i] cellular developmental process >> ------[i] cell differentiation >> ---------[i] cellular sporulation ; GO:0030435 >> ------------[i] cellular asexual sporulation ; GO:0030436 >> ------------[i] cellular sexual sporulation ; GO:0034293 >> >> how does that sound to you single-celled fungi people? >> >> cheers, >> >> Jane >> >> -- >> Dr Jane >> Lomax >> GO Editorial >> Office >> >> EMBL-EBI >> Wellcome Trust Genome >> Campus >> >> Hinxton >> Cambridgeshire, >> UK >> CB10 >> 1SD >> >> >> p: +44 1223 >> 492516 >> f: +44 1223 494468 >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> From pj37 at cornell.edu Fri Jun 13 11:03:39 2008 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 13 Jun 2008 14:03:39 -0400 Subject: [Go] sporulation rearrangement In-Reply-To: <4852B34A.7000106@genome.stanford.edu> References: <4852533A.90900@ebi.ac.uk> <4D2E0CF7-1E5B-4E61-96C0-D0C0E853827F@fruitfly.org> <4852B34A.7000106@genome.stanford.edu> Message-ID: <4852B67B.4050900@cornell.edu> Hi Maria, Assembling the Fungal Tree of Life [AFTOL] project [http://aftol.org/] is currently getting together to work on a similar lines. Just yesterday John A. Crow [crow at umn.edu] from UMN contacted me. I am copying this mail to John and the PI Joey Spatafora. Pankaj Maria Costanzo wrote: > Hi Chris, > > I don't think it's likely that SGD will resurrect this project. There > wasn't very much interest from the fungal community, and the project is > very peripheral to our goals (yeast don't have much anatomy!) so we > would not pick it up again without a strong request from fungal > scientists who would be willing to help with the scientific content. > We'd be happy to hand it over to another group, if anyone is interested > in pursuing it. > > Maria > > > Chris Mungall wrote: >> The fungal_anatomy ontology could be very useful for checking child >> terms. However, this ontology is marked as quiescent in OBO. Would >> there be any chance of resurrecting it? >> >> On Jun 13, 2008, at 4:00 AM, Jane Lomax wrote: >> >>> Hi - the PAMGO group are currently working on some terms to annotate >>> higher fungi and have encountered some problems with the existing >>> placement of the term 'sporulation' and its children in the graph. >>> Essentially the problem is that sporulation is a child of 'cell >>> differentiation' but in higher fungi spores are often multicellular >>> or syncytial structures so this is a tpv. So we'd like to propose >>> some changes to the existing graph to remedy this: >>> >>> NOW: >>> >>> developmental process >>> ---[i] cellular developmental process >>> ------[i] cell differentiation >>> ---------[i] sporulation ; GO:0030435 >>> ------------[i] asexual sporulation ; GO:0030436 >>> ------------[i] sexual sporulation ; GO:0034293 >>> >>> PROPOSED: >>> >>> developmental process >>> ---[i] sporulation ; GO:new >>> ------[i] cellular sporulation ; GO:0030435 >>> ------[i] multicellular or syncytial sporulation ; GO:new >>> ---------[i] multicellular or syncytial sexual sporulation ; GO:new >>> ---------[i] multicellular or syncytial asexual sporulation ; GO:new >>> ------[i] sexual sporulation ; GO:new >>> ---------[i] cellular sexual sporulation ; GO:0034293 >>> ---------[i] multicellular or syncytial sexual sporulation ; GO:new >>> ------[i] asexual sporulation ; GO:new >>> ---------[i] cellular asexual sporulation ; GO:0030436 >>> ---------[i] multicellular or syncytial asexual sporulation ; GO:new >>> >>> developmental process >>> ---[i] cellular developmental process >>> ------[i] cell differentiation >>> ---------[i] cellular sporulation ; GO:0030435 >>> ------------[i] cellular asexual sporulation ; GO:0030436 >>> ------------[i] cellular sexual sporulation ; GO:0034293 >>> >>> how does that sound to you single-celled fungi people? >>> >>> cheers, >>> >>> Jane >>> >>> -- >>> Dr Jane >>> Lomax >>> GO Editorial >>> Office >>> >>> EMBL-EBI >>> Wellcome Trust Genome >>> Campus >>> >>> Hinxton >>> Cambridgeshire, >>> UK >>> CB10 >>> 1SD >>> >>> >>> p: +44 1223 >>> 492516 >>> f: +44 1223 494468 >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From midori at ebi.ac.uk Sat Jun 14 09:00:17 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 14 Jun 2008 16:00:17 UT Subject: [Go] SourceForge Update Message-ID: <200806141600.m5EG0H51310953@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Sun Jun 15 09:00:18 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sun, 15 Jun 2008 16:00:18 UT Subject: [Go] SourceForge Update Message-ID: <200806151600.m5FG0IQ1057493@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Mon Jun 16 08:23:04 2008 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 16 Jun 2008 16:23:04 +0100 (BST) Subject: [Go] Alert: proposal to obsolete GO:0010320 (no annotations affected) Message-ID: Hello, The proposal has been made to obsolete arginine/lysine endopeptidase activity ; GO:0010320 This term is not used in annotations or mappings, and is not included in any subset maintained in GO. The reason is that this term is defined incorrectly: there are no known peptidases using a catalytic mechanism involving arginine and lysine, and the Arabidopsis metacaspases that prompted addition of this term are in fact cysteine-type endopeptidases. Suggested term for annotations: cysteine-type endopeptidase activity ; GO:0004197 SourceForge link: https://sourceforge.net/tracker/index.php?func=detail&aid=1995254&group_id=36855&atid=440764 The comment period ends Monday, June 30, 2008. *** Unless objections are received by June 30, we will assume that you agree to this change. *** Midori _______________________________________________ Go mailing list Go at geneontology.org http://fafner.stanford.edu/mailman/listinfo/go From midori at ebi.ac.uk Mon Jun 16 09:00:26 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 16 Jun 2008 16:00:26 UT Subject: [Go] SourceForge Update Message-ID: <200806161600.m5GG0Qd1333632@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From jdeegan at ebi.ac.uk Tue Jun 17 02:28:19 2008 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Tue, 17 Jun 2008 10:28:19 +0100 Subject: [Go] electron carrier activity Message-ID: <485783B3.8060609@ebi.ac.uk> Hi, A proposal has been made to move 'electron carrier activity' out of under 'oxidoreductase activity' to be a direct child of 'molecular function'. As part of the proposal the terms 'electron donor activity' and 'electron acceptor activity' will be merged into the parent term 'electron carrier activity'. This should not cause any problems for anyone, but I just wanted to make sure people have the opportunity to comment. The sourceforge item is here: [ 1995835 ] electron carrier activity https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1995835&group_id=36855 The changes will be made one the 27th June if no objections are raised. Thanks, Jen -- Jennifer Deegan (nee Clark) EMBL-European Bioinformatics Institute Gene Ontology Consortium From midori at ebi.ac.uk Tue Jun 17 09:00:35 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 17 Jun 2008 16:00:35 UT Subject: [Go] SourceForge Update Message-ID: <200806171600.m5HG0ZY1095093@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Wed Jun 18 09:00:11 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 18 Jun 2008 16:00:11 UT Subject: [Go] SourceForge Update Message-ID: <200806181600.m5IG0B81374762@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Thu Jun 19 09:00:12 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Thu, 19 Jun 2008 16:00:12 UT Subject: [Go] SourceForge Update Message-ID: <200806191600.m5JG0Cv1123108@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Fri Jun 20 09:00:14 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 20 Jun 2008 16:00:14 UT Subject: [Go] SourceForge Update Message-ID: <200806201600.m5KG0E71401211@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From mgiglio at SOM.UMARYLAND.EDU Mon Jun 23 08:56:13 2008 From: mgiglio at SOM.UMARYLAND.EDU (Gwinn Giglio, Michelle) Date: Mon, 23 Jun 2008 11:56:13 -0400 Subject: [Go] [Annotation] Usage of the With/From Column for IEA ? In-Reply-To: <485DBA00.9060607@cornell.edu> Message-ID: Hi all, I think there are two options: 1. We extend the same rules that currently apply to ISS to IEA. Namely, that when tools such as tRNAscan and snoSCAN are used there does not need to be an entry in "with/from". OR 2. We come up with a system to store this information in "with/from" (which would also apply to ISS). Karen proposed such a system way back when this discussion for ISS was first underway and her system would have worked well I think. Votes? Michelle On 6/21/08 10:33 PM, "Pankaj Jaiswal" wrote: > Can we have a resolution on this? We are waiting to checkin the > association file. > > Pankaj > > Gwinn Giglio, Michelle wrote: >> >> Ben, >> >> No one is disputing the importance of the "with" fields and I think we all >> know why we have them. However, even making the "with" field always >> mandatory will not make people annotate correctly. It is easy to get around >> the spirit of these "rules" if someone wants to. >> >> The bottom line is we have had this debate more than once and have reached >> the decision not to require "with" for all ISS annotations - it only makes >> sense that the IEAs using the same kinds of information would be treated the >> same way. >> >> Let's think about the people who are trying to do a thoughtful and careful >> job of annotating using best GO practices. They will read the guidelines >> and they will try to follow them. >> As for those who use bad annotation practices, they will produce bad >> annotation whether or not we make them populate "with". >> >> Putting the methods/tools like tRNAscan and snoRNA scan into "with" would be >> mixing methods and accessions-of-items-found-with-methods in the "with" >> column. Many GO folks have expressed that they don't want to do this. As >> Pankaj and others have pointed out, there is always the option of yet >> another column for this. Or, others have argued it can be captured in the >> reference field. >> >> Anyway, we have a policy in place. Of course we've changed our minds in the >> past before..... >> >> Michelle >> >> >> >> >> >> On 6/12/08 2:38 PM, "Benjamin Hitz" wrote: >> >>> WITH fields are very important for IEA and "true" ISS where you are >>> inferring an annotation based on sequence similarity. >>> The reason is to prevent circular associations via sequence similarity. >>> >>> That is why the WITH column was made mandatory for IEAs and (old) >>> ISS. From a database/machine loading perspective, the only way to >>> enforce this is to make the with field MANDATORY. >>> >>> Ben >>> >>> On Jun 12, 2008, at 10:02 AM, Gwinn Giglio, Michelle wrote: >>> >>>> >>>> I think we do need some kind of consensus - anyone else want to >>>> voice an >>>> opinion? >>>> >>>> Michelel >>>> >>>> >>>> >>>> On 6/12/08 11:48 AM, "Pankaj Jaiswal" wrote: >>>> >>>>> Great. Do we need a formal word or voting on this request. We are >>>>> waiting to submit some of our annotations that didn't make it through >>>>> due to the mandatory 'with' rule. >>>>> >>>>> Pankaj >>>>> >>>>> Gwinn Giglio, Michelle wrote: >>>>>> Hi, >>>>>> >>>>>> Well, considering our new policy for ISS not requiring "with" for >>>>>> the very >>>>>> types of evidence you mention, it seems IEA should not require >>>>>> "with" as >>>>>> well...... >>>>>> >>>>>> Michelle >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 6/11/08 1:12 PM, "Pankaj Jaiswal" wrote: >>>>>> >>>>>>> I didn't hear from the group on this. Could you please help. >>>>>>> >>>>>>> Pankaj >>>>>>> >>>>>>> Pankaj Jaiswal wrote: >>>>>>>> http://www.geneontology.org/GO.evidence.shtml#iea >>>>>>>> >>>>>>>> Ref: From the above site >>>>>>>> >>>>>>>> Usage of the With/From Column for IEA >>>>>>>> >>>>>>>> At the January 2007 GOC meeting, it was agreed that it will be >>>>>>>> required >>>>>>>> to make an entry in the with/from column for all annotations >>>>>>>> made after >>>>>>>> May 1, 2007 when using this evidence code to indicate what >>>>>>>> individual >>>>>>>> sequences, sequence objects, methods, keyword mapping files, >>>>>>>> etc. are >>>>>>>> the basis of the annotation. When multiple entries are placed in >>>>>>>> the >>>>>>>> with/from field, they are separated by pipes. >>>>>>>> >>>>>>>> ------------ >>>>>>>> Based on this rule, would you please suggest, what would be the >>>>>>>> value >>>>>>>> for the 'WITH' column. >>>>>>>> >>>>>>>> - if we are making a TMHMM prediction for a 'putative >>>>>>>> tansmembrane' >>>>>>>> annotation >>>>>>>> - if we have used TargetP/SignalP/Predotar/Psort to predict a >>>>>>>> putative >>>>>>>> cellular localization >>>>>>>> >>>>>>>> None of the above prediction softwares give appropriate value to >>>>>>>> be >>>>>>>> filled in the 'WITH' column. >>>>>>>> >>>>>>>> If you agree our suggestion is to relax this rule for IEA's. >>>>>>>> >>>>>>>> Pankaj >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Go mailing list >>>>>>> Go at geneontology.org >>>>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>>>> >>>> _______________________________________________ >>>> Go mailing list >>>> Go at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/go >>> -- >>> Ben Hitz >>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO >>> Consortium >>> Stanford University ** hitz at genome.stanford.edu >>> >>> >>> >>> _______________________________________________ >>> Annotation mailing list >>> Annotation at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/annotation >> >> _______________________________________________ >> Go mailing list >> Go at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/go >> From midori at ebi.ac.uk Mon Jun 23 09:00:12 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 23 Jun 2008 16:00:12 UT Subject: [Go] SourceForge Update Message-ID: <200806231600.m5NG0Ch1172852@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From rama at genome.stanford.edu Mon Jun 23 15:50:17 2008 From: rama at genome.stanford.edu (Rama Balakrishnan) Date: Mon, 23 Jun 2008 15:50:17 -0700 Subject: [Go] Annotation file format question Message-ID: <9F333797-5E81-4DE9-9FE3-4B12D94D220F@genome.stanford.edu> Hi All, I have a question about allowed characters for Column 15 (Assigned_by) of the gene_association file. We are getting ready to load some predicted GO annotations made for yeast genes from an external source - bioPIXIE/MEFIT (Princeton University). They would like us to enter the source as bioPIXIE/MEFIT (with a slash between biopixie and MEFIT). So far I have not seen anybody enter a DB/group name with punctuation (e.g. slashes or hyphens) and I did not see anything regarding this in the documentation. I would like to know if the source can be entered with a slash in that column? Thanks for your input, Rama From cjm at fruitfly.org Mon Jun 23 17:45:23 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Mon, 23 Jun 2008 17:45:23 -0700 Subject: [Go] Annotation file format question In-Reply-To: <9F333797-5E81-4DE9-9FE3-4B12D94D220F@genome.stanford.edu> References: <9F333797-5E81-4DE9-9FE3-4B12D94D220F@genome.stanford.edu> Message-ID: <63901FAD-C73C-4065-BB34-0D3BE10BC092@fruitfly.org> All entries in col15 should be a registered DB in GO.xrf_abbs[1] - I don't see bioPixie/MEFIT there. bioPixie/MEFIT could ask to be registered as a database in GO.xrf_abbs - but I'm not sure we should add them as it sounds more like a composed description of a method rather than a database or institution. And I think we should avoid slashes anyway. It sounds like bipixie/MEFIT should be a GO_REF referenced in the publication field [1] http://www.geneontology.org/cgi-bin/xrefs.cgi On Jun 23, 2008, at 3:50 PM, Rama Balakrishnan wrote: > Hi All, > > I have a question about allowed characters for Column 15 > (Assigned_by) of the gene_association file. We are getting ready to > load some predicted GO annotations made for yeast genes from an > external source - bioPIXIE/MEFIT (Princeton University). They would > like us to enter the source as bioPIXIE/MEFIT (with a slash between > biopixie and MEFIT). > So far I have not seen anybody enter a DB/group name with > punctuation (e.g. slashes or hyphens) and I did not see anything > regarding this in the documentation. I would like to know if the > source can be entered with a slash in that column? > > Thanks for your input, > > Rama > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From midori at ebi.ac.uk Tue Jun 24 09:00:14 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Tue, 24 Jun 2008 16:00:14 UT Subject: [Go] SourceForge Update Message-ID: <200806241600.m5OG0Eg1460456@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From kchris at genome.stanford.edu Tue Jun 24 13:31:11 2008 From: kchris at genome.stanford.edu (Karen Christie) Date: Tue, 24 Jun 2008 13:31:11 -0700 (PDT) Subject: [Go] [Annotation] Usage of the With/From Column for IEA ? In-Reply-To: References: Message-ID: Hi, I personally don't have a problem with dropping the requirement for the with column for IEAs to be comparable to the rules for ISS, though I am certainly not speaking for all of SGD. However, having tried to come up with a system to store method names in the with column after the decision at the Jan 07 meeting that we would do this, I think this is a bad idea. It is non-trivial to identify the name of a method from many papers, and unless we are going to start keeping some sort of file to control what goes in there, these method names could become a muddle of free text in the with/from column. So between the two options you suggest, I think only the first is feasible. But, I think the best idea is what Kara suggested, that whether or not the annotation is manual vs electronic should be recorded separately. Then the evidence codes can be used as appropriate for either manual or electronic, following the appropriate rules for the with column for that evidence code. I do realize that this would be a big change and won't happen quickly though... -Karen On Mon, 23 Jun 2008, Gwinn Giglio, Michelle wrote: > Hi all, > > I think there are two options: > > 1. We extend the same rules that currently apply to ISS to IEA. Namely, > that when tools such as tRNAscan and snoSCAN are used there does not need to > be an entry in "with/from". > > OR > > 2. We come up with a system to store this information in "with/from" > (which would also apply to ISS). > Karen proposed such a system way back when this discussion for ISS was first > underway and her system would have worked well I think. > > Votes? > > > Michelle > > > > > On 6/21/08 10:33 PM, "Pankaj Jaiswal" wrote: > >> Can we have a resolution on this? We are waiting to checkin the >> association file. >> >> Pankaj >> >> Gwinn Giglio, Michelle wrote: >>> >>> Ben, >>> >>> No one is disputing the importance of the "with" fields and I think we all >>> know why we have them. However, even making the "with" field always >>> mandatory will not make people annotate correctly. It is easy to get around >>> the spirit of these "rules" if someone wants to. >>> >>> The bottom line is we have had this debate more than once and have reached >>> the decision not to require "with" for all ISS annotations - it only makes >>> sense that the IEAs using the same kinds of information would be treated the >>> same way. >>> >>> Let's think about the people who are trying to do a thoughtful and careful >>> job of annotating using best GO practices. They will read the guidelines >>> and they will try to follow them. >>> As for those who use bad annotation practices, they will produce bad >>> annotation whether or not we make them populate "with". >>> >>> Putting the methods/tools like tRNAscan and snoRNA scan into "with" would be >>> mixing methods and accessions-of-items-found-with-methods in the "with" >>> column. Many GO folks have expressed that they don't want to do this. As >>> Pankaj and others have pointed out, there is always the option of yet >>> another column for this. Or, others have argued it can be captured in the >>> reference field. >>> >>> Anyway, we have a policy in place. Of course we've changed our minds in the >>> past before..... >>> >>> Michelle >>> >>> >>> >>> >>> >>> On 6/12/08 2:38 PM, "Benjamin Hitz" wrote: >>> >>>> WITH fields are very important for IEA and "true" ISS where you are >>>> inferring an annotation based on sequence similarity. >>>> The reason is to prevent circular associations via sequence similarity. >>>> >>>> That is why the WITH column was made mandatory for IEAs and (old) >>>> ISS. From a database/machine loading perspective, the only way to >>>> enforce this is to make the with field MANDATORY. >>>> >>>> Ben >>>> >>>> On Jun 12, 2008, at 10:02 AM, Gwinn Giglio, Michelle wrote: >>>> >>>>> >>>>> I think we do need some kind of consensus - anyone else want to >>>>> voice an >>>>> opinion? >>>>> >>>>> Michelel >>>>> >>>>> >>>>> >>>>> On 6/12/08 11:48 AM, "Pankaj Jaiswal" wrote: >>>>> >>>>>> Great. Do we need a formal word or voting on this request. We are >>>>>> waiting to submit some of our annotations that didn't make it through >>>>>> due to the mandatory 'with' rule. >>>>>> >>>>>> Pankaj >>>>>> >>>>>> Gwinn Giglio, Michelle wrote: >>>>>>> Hi, >>>>>>> >>>>>>> Well, considering our new policy for ISS not requiring "with" for >>>>>>> the very >>>>>>> types of evidence you mention, it seems IEA should not require >>>>>>> "with" as >>>>>>> well...... >>>>>>> >>>>>>> Michelle >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 6/11/08 1:12 PM, "Pankaj Jaiswal" wrote: >>>>>>> >>>>>>>> I didn't hear from the group on this. Could you please help. >>>>>>>> >>>>>>>> Pankaj >>>>>>>> >>>>>>>> Pankaj Jaiswal wrote: >>>>>>>>> http://www.geneontology.org/GO.evidence.shtml#iea >>>>>>>>> >>>>>>>>> Ref: From the above site >>>>>>>>> >>>>>>>>> Usage of the With/From Column for IEA >>>>>>>>> >>>>>>>>> At the January 2007 GOC meeting, it was agreed that it will be >>>>>>>>> required >>>>>>>>> to make an entry in the with/from column for all annotations >>>>>>>>> made after >>>>>>>>> May 1, 2007 when using this evidence code to indicate what >>>>>>>>> individual >>>>>>>>> sequences, sequence objects, methods, keyword mapping files, >>>>>>>>> etc. are >>>>>>>>> the basis of the annotation. When multiple entries are placed in >>>>>>>>> the >>>>>>>>> with/from field, they are separated by pipes. >>>>>>>>> >>>>>>>>> ------------ >>>>>>>>> Based on this rule, would you please suggest, what would be the >>>>>>>>> value >>>>>>>>> for the 'WITH' column. >>>>>>>>> >>>>>>>>> - if we are making a TMHMM prediction for a 'putative >>>>>>>>> tansmembrane' >>>>>>>>> annotation >>>>>>>>> - if we have used TargetP/SignalP/Predotar/Psort to predict a >>>>>>>>> putative >>>>>>>>> cellular localization >>>>>>>>> >>>>>>>>> None of the above prediction softwares give appropriate value to >>>>>>>>> be >>>>>>>>> filled in the 'WITH' column. >>>>>>>>> >>>>>>>>> If you agree our suggestion is to relax this rule for IEA's. >>>>>>>>> >>>>>>>>> Pankaj >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Go mailing list >>>>>>>> Go at geneontology.org >>>>>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>>>>> >>>>> _______________________________________________ >>>>> Go mailing list >>>>> Go at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/go >>>> -- >>>> Ben Hitz >>>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO >>>> Consortium >>>> Stanford University ** hitz at genome.stanford.edu >>>> >>>> >>>> >>>> _______________________________________________ >>>> Annotation mailing list >>>> Annotation at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/annotation >>> >>> _______________________________________________ >>> Go mailing list >>> Go at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/go >>> > > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From cjm at fruitfly.org Tue Jun 24 14:51:01 2008 From: cjm at fruitfly.org (Chris Mungall) Date: Tue, 24 Jun 2008 14:51:01 -0700 Subject: [Go] [Annotation] Usage of the With/From Column for IEA ? In-Reply-To: References: Message-ID: <32CC2FF8-41F3-4310-A772-F208D031578E@fruitfly.org> On Jun 24, 2008, at 1:31 PM, Karen Christie wrote: > But, I think the best idea is what Kara suggested, that whether or > not the annotation is manual vs electronic should be recorded > separately. Then the evidence codes can be used as appropriate for > either manual or electronic, following the appropriate rules for > the with column for that evidence code. I do realize that this > would be a big change and won't happen quickly though... Logically it makes no difference if the codes are pre- or post- coordinated. Given that post-coordinating them (ie recording separately) will require massive changes to the GAF, software etc it would seem sensible to pre coordinate them > -Karen From midori at ebi.ac.uk Wed Jun 25 09:00:17 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Wed, 25 Jun 2008 16:00:17 UT Subject: [Go] SourceForge Update Message-ID: <200806251600.m5PG0IM1211343@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From val at sanger.ac.uk Fri Jun 27 01:32:25 2008 From: val at sanger.ac.uk (Valerie Wood) Date: Fri, 27 Jun 2008 09:32:25 +0100 Subject: [Go] Dr Evelyn Camon-McWhinney Message-ID: <4864A599.3050408@sanger.ac.uk> I'm sure you will all want to congratulate Ev who had her PhD viva on Monday. That must be something of a record, writing up and submitting ~10 years after finishing! -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From midori at ebi.ac.uk Fri Jun 27 09:00:11 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Fri, 27 Jun 2008 16:00:11 UT Subject: [Go] SourceForge Update Message-ID: <200806271600.m5RG0BG1204237@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From camon at ebi.ac.uk Fri Jun 27 14:56:39 2008 From: camon at ebi.ac.uk (camon at ebi.ac.uk) Date: Fri, 27 Jun 2008 22:56:39 +0100 (BST) Subject: [Go] Dr Evelyn Camon-McWhinney In-Reply-To: <4864A599.3050408@sanger.ac.uk> References: <4864A599.3050408@sanger.ac.uk> Message-ID: <49384.217.43.213.202.1214603799.squirrel@webmail.ebi.ac.uk> Thanks Val, Its great to finish, the record at UCD is 16 years after submission....those laid back Irish eh! not to be recommended. Fortunately my thesis results were published 10 years ago and to my delight did and still are making an impact on vaccine design, my saving grace.. Hope everyone is doing well. I'm in the middle of a house and county move and then will give one last try to seek out an immune gene GO grant of some sort now that i'm nicely up-to-date with immunological research. have a nice weekend, Evelyn > > I'm sure you will all want to congratulate Ev who had her PhD viva on > Monday. That must be something of a record, writing up and submitting > ~10 years after finishing! > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > _______________________________________________ > Go mailing list > Go at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/go > From midori at ebi.ac.uk Sat Jun 28 09:00:11 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Sat, 28 Jun 2008 16:00:11 UT Subject: [Go] SourceForge Update Message-ID: <200806281600.m5SG0B41475309@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: From midori at ebi.ac.uk Mon Jun 30 09:00:13 2008 From: midori at ebi.ac.uk (midori at ebi.ac.uk) Date: Mon, 30 Jun 2008 16:00:13 UT Subject: [Go] SourceForge Update Message-ID: <200806301600.m5UG0Dk1491382@mozart.ebi.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: