From jane at ebi.ac.uk Thu Mar 1 03:20:51 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Thu, 1 Mar 2007 11:20:51 +0000 Subject: missing GOIDs In-Reply-To: <93035998-ED1D-42FD-8D86-EE791C6AD544@stanford.edu> References: <93035998-ED1D-42FD-8D86-EE791C6AD544@stanford.edu> Message-ID: <60BA0B9C-F4B0-4BDB-876E-A2C88D5E7559@ebi.ac.uk> Hi - sorry, these were my fault - it was when I was merging in those hundreds of PAMGO terms, they weren't supposed to go in at all so I removed them - as they were only in so briefly I didn't think there was much value in recording them as obsolete terms, but I can if people think there's value in doing that. Jane On 1 Mar 2007, at 04:05, Mike Cherry wrote: > Should the following GOIDs be missing? Was it a mistake to add > them? They should not have been deleted, rather made obsolete. > > There are four GOIDs that were created on January 22nd (version > 5.111 with the PAMGO terms) that have gone missing. They were not > mentioned in any of the go-diff messages and are not mentioned at > all in the current OBO file. It would seem that some check has > failed or that some dandy hand edit has deleted these entries. > GOIDs should never be completely deleted from the OBO file! > > -Mike > > Here is what was in the OBO file with version 5.113, and gone now. > > [Term] > id: GO:0052461 > name: modulation by organism of pathogen-associated molecular > pattern-induced symbiont innate immunity > namespace: biological_process > is_a: GO:0052296 ! modulation by organism of pathogen-associated > molecular pattern-induced innate immunity in other organism during > symbiotic interaction > is_a: GO:0052452 ! modulation by organism of symbiont innate immunity > > [Term] > id: GO:0052488 > name: negative regulation by organism of pathogen-associated > molecular pattern-induced symbiont innate immunity > namespace: biological_process > synonym: "suppression of general elicitor induced symbiont innate > immunity" EXACT [] > synonym: "suppression of general elicitor-induced symbiont innate > immunity" EXACT [] > synonym: "suppression of MAMP induced symbiont innate immunity" > EXACT [] > synonym: "suppression of MAMP-induced symbiont innate immunity" > EXACT [] > synonym: "suppression of PAMP induced symbiont innate immunity" > EXACT [] > synonym: "suppression of PAMP-induced symbiont innate immunity" > EXACT [] > synonym: "suppression of pathogen-associated molecular pattern- > induced symbiont innate immunity" EXACT [] > is_a: GO:0052258 ! negative regulation by organism of pathogen- > associated molecular pattern-induced innate immunity of other > organism during symbiotic interaction > is_a: GO:0052461 ! modulation by organism of pathogen-associated > molecular pattern-induced symbiont innate immunity > is_a: GO:0052486 ! negative regulation by organism of symbiont > innate immunity > > [Term] > id: GO:0052498 > name: pathogen-associated molecular pattern dependent induction by > organism of symbiont innate immunity > namespace: biological_process > synonym: "general elicitor-dependent activation of symbiont innate > immunity" EXACT [] > synonym: "general elicitor-dependent induction of symbiont innate > immunity" EXACT [] > synonym: "MAMP dependent activation of symbiont innate immunity" > EXACT [] > synonym: "MAMP dependent induction of symbiont innate immunity" > EXACT [] > synonym: "PAMP dependent activation of symbiont innate immunity" > EXACT [] > synonym: "PAMP dependent induction of symbiont innate immunity" > EXACT [] > synonym: "pathogen-associated molecular pattern dependent > activation by organism of symbiont innate immunity" EXACT [] > is_a: GO:0052257 ! pathogen-associated molecular pattern dependent > induction by organism of innate immunity of other organism during > symbiotic interaction > is_a: GO:0052499 ! pathogen-associated molecular pattern dependent > modulation by organism of symbiont innate immunity > is_a: GO:0052515 ! positive regulation by organism of symbiont > innate immunity > > [Term] > id: GO:0052499 > name: pathogen-associated molecular pattern dependent modulation by > organism of symbiont innate immunity > namespace: biological_process > is_a: GO:0052308 ! pathogen-associated molecular pattern dependent > modulation by organism of innate immunity in other organism during > symbiotic interaction > is_a: GO:0052452 ! modulation by organism of symbiont innate immunity > From r-chisholm at northwestern.edu Thu Mar 1 04:29:22 2007 From: r-chisholm at northwestern.edu (Chisholm, Rex FSM) Date: Thu, 1 Mar 2007 06:29:22 -0600 Subject: cell projection In-Reply-To: <5D6600C8-673E-411D-8A18-D96A94EE2CB3@genome.stanford.edu> References: <5D6600C8-673E-411D-8A18-D96A94EE2CB3@genome.stanford.edu> Message-ID: Hi Ben, Microvilli, pseudopodia, filopodia, cilia and flagella are all membrane bounded, what is an example of a non-membrane bounded projection? Rex -----Original Message----- From: owner-go at genome.stanford.edu [mailto:owner-go at genome.stanford.edu] On Behalf Of Ben Hitz Sent: Wednesday, February 28, 2007 5:55 PM To: gene ontology Subject: cell projection OK, clearly no one has a problem with it. I just think that microvilli/psuedopodia and other "membrane" projects are fundamentally distinct from big chunks of protein like cillia or flagella. To me it's like "arms" and "fingernails" both being "body projections" Maybe we would just need 2 children of cell projection. - membrane bounded and non-membrane bounded. Ben -- Ben Hitz Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium Stanford University ** hitz at genome.stanford.edu From dph at informatics.jax.org Thu Mar 1 04:42:02 2007 From: dph at informatics.jax.org (David Hill) Date: Thu, 01 Mar 2007 07:42:02 -0500 Subject: cell projection In-Reply-To: References: <5D6600C8-673E-411D-8A18-D96A94EE2CB3@genome.stanford.edu> Message-ID: <45E6CA1A.6020505@informatics.jax.org> A bacetrial flagellum? David Chisholm, Rex FSM wrote: > Hi Ben, > > Microvilli, pseudopodia, filopodia, cilia and flagella are all membrane > bounded, what is an example of a non-membrane bounded projection? > > Rex > > -----Original Message----- > From: owner-go at genome.stanford.edu [mailto:owner-go at genome.stanford.edu] > On Behalf Of Ben Hitz > Sent: Wednesday, February 28, 2007 5:55 PM > To: gene ontology > Subject: cell projection > > OK, clearly no one has a problem with it. > I just think that microvilli/psuedopodia and other "membrane" > projects are fundamentally distinct from big chunks of protein like > cillia or flagella. > > To me it's like "arms" and "fingernails" both being "body projections" > > Maybe we would just need 2 children of cell projection. - membrane > bounded and non-membrane bounded. > > Ben > -- > Ben Hitz > Senior Scientific Programmer ** Saccharomyces Genome Database ** GO > Consortium > Stanford University ** hitz at genome.stanford.edu > > > > > From r-chisholm at northwestern.edu Thu Mar 1 04:57:11 2007 From: r-chisholm at northwestern.edu (Chisholm, Rex FSM) Date: Thu, 1 Mar 2007 06:57:11 -0600 Subject: cell projection In-Reply-To: <45E6CA1A.6020505@informatics.jax.org> References: <5D6600C8-673E-411D-8A18-D96A94EE2CB3@genome.stanford.edu> <45E6CA1A.6020505@informatics.jax.org> Message-ID: Oh...shows my eukaryotic orientation. Another sensu issue? -----Original Message----- From: David Hill [mailto:dph at informatics.jax.org] Sent: Thursday, March 01, 2007 6:42 AM To: Chisholm, Rex FSM Cc: Ben Hitz; gene ontology Subject: Re: cell projection A bacetrial flagellum? David Chisholm, Rex FSM wrote: > Hi Ben, > > Microvilli, pseudopodia, filopodia, cilia and flagella are all membrane > bounded, what is an example of a non-membrane bounded projection? > > Rex > > -----Original Message----- > From: owner-go at genome.stanford.edu [mailto:owner-go at genome.stanford.edu] > On Behalf Of Ben Hitz > Sent: Wednesday, February 28, 2007 5:55 PM > To: gene ontology > Subject: cell projection > > OK, clearly no one has a problem with it. > I just think that microvilli/psuedopodia and other "membrane" > projects are fundamentally distinct from big chunks of protein like > cillia or flagella. > > To me it's like "arms" and "fingernails" both being "body projections" > > Maybe we would just need 2 children of cell projection. - membrane > bounded and non-membrane bounded. > > Ben > -- > Ben Hitz > Senior Scientific Programmer ** Saccharomyces Genome Database ** GO > Consortium > Stanford University ** hitz at genome.stanford.edu > > > > > From dph at informatics.jax.org Thu Mar 1 04:59:07 2007 From: dph at informatics.jax.org (David Hill) Date: Thu, 01 Mar 2007 07:59:07 -0500 Subject: cell projection In-Reply-To: References: <5D6600C8-673E-411D-8A18-D96A94EE2CB3@genome.stanford.edu> <45E6CA1A.6020505@informatics.jax.org> Message-ID: <45E6CE1B.7040103@informatics.jax.org> No, we sorted it out in sensu already. I think it was just a question from Ben. David Chisholm, Rex FSM wrote: > Oh...shows my eukaryotic orientation. Another sensu issue? > > -----Original Message----- > From: David Hill [mailto:dph at informatics.jax.org] > Sent: Thursday, March 01, 2007 6:42 AM > To: Chisholm, Rex FSM > Cc: Ben Hitz; gene ontology > Subject: Re: cell projection > > A bacetrial flagellum? > > David > > Chisholm, Rex FSM wrote: > >> Hi Ben, >> >> Microvilli, pseudopodia, filopodia, cilia and flagella are all >> > membrane > >> bounded, what is an example of a non-membrane bounded projection? >> >> Rex >> >> -----Original Message----- >> From: owner-go at genome.stanford.edu >> > [mailto:owner-go at genome.stanford.edu] > >> On Behalf Of Ben Hitz >> Sent: Wednesday, February 28, 2007 5:55 PM >> To: gene ontology >> Subject: cell projection >> >> OK, clearly no one has a problem with it. >> I just think that microvilli/psuedopodia and other "membrane" >> projects are fundamentally distinct from big chunks of protein like >> cillia or flagella. >> >> To me it's like "arms" and "fingernails" both being "body projections" >> >> Maybe we would just need 2 children of cell projection. - membrane >> bounded and non-membrane bounded. >> >> Ben >> -- >> Ben Hitz >> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO >> Consortium >> Stanford University ** hitz at genome.stanford.edu >> >> >> >> >> >> > > > > From jclark at ebi.ac.uk Thu Mar 1 05:34:53 2007 From: jclark at ebi.ac.uk (Jennifer Clark) Date: Thu, 01 Mar 2007 13:34:53 +0000 Subject: ATP-binding cassette (ABC) transporter complex Message-ID: <45E6D67D.2050502@ebi.ac.uk> Hi, During the sensu work in the last few days we merged the two terms: ATP-binding cassette (ABC) transporter complex (sensu Bacteria and Archaea) ; GO:0043192 and ATP-binding cassette (ABC) transporter complex (sensu Eukaryota) ; GO:0043191 into the existing term: ATP-binding cassette (ABC) transporter complex ; GO:0043190 Since this merge, Michelle has correctly pointed out that there is a way to differentiate between these two terms, and it is likely that the merge will be reverted. If you have not changed your annotations to relect this merge then we would suggest that you leave the annotations to the subsumed terms pointing to the secondary ids. so that they will be correct if we revert the merge in the next few days. Thank you for your help in this. Best wishes, The sensu working group. From val at sanger.ac.uk Thu Mar 1 06:12:36 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 01 Mar 2007 14:12:36 +0000 Subject: ATP-binding cassette (ABC) transporter complex In-Reply-To: <45E6D67D.2050502@ebi.ac.uk> References: <45E6D67D.2050502@ebi.ac.uk> Message-ID: <45E6DF54.1000502@sanger.ac.uk> Hi, I'm presuming that we would not create a new complex term if for example the pombe xxx complex differed by one subunit from the S. cerevisiae, or the human complex if these are considered to be analogous. Usually (but not always) when we create an additional complex with a different composition, it is because the complex has a subunit composition which is both a 'within' and 'between' organism difference, and the 'new' complex has different functional properties. The gamma tubulin complexes are a good example. There are various complexes with different compositions (large/small/ ring). These have the same core subunits but some complexes have additional subunits. The exact subunit composition of each complex varies slightly between species. However, the different complexes have specific functions and broadly conserved between species, and considered to be analogous. They also need specific child terms because of TPVs caused by centrosomes vs spindle pole bodies. I guess what I'm trying to say is with the existing annotations, is the merge such a bad thing?. You only need the species specific child terms a) if you are trying to distinguish between the 'different' ABC transporter complexes within your organism, or in another organism, and the existing sensu terms did not specifically do this. or b) if the term causes TPVs with the existing hierarchy Val Jennifer Clark wrote: > Hi, > > During the sensu work in the last few days we merged the two terms: > > ATP-binding cassette (ABC) transporter complex (sensu Bacteria and > Archaea) ; GO:0043192 > and > ATP-binding cassette (ABC) transporter complex (sensu Eukaryota) ; > GO:0043191 > into the existing term: > > ATP-binding cassette (ABC) transporter complex ; GO:0043190 > > Since this merge, Michelle has correctly pointed out that there is a > way to differentiate between these two terms, and it is likely that > the merge will be reverted. If you have not changed your annotations > to relect this merge then we would suggest that you leave the > annotations to the subsumed terms pointing to the secondary ids. so > that they will be correct if we revert the merge in the next few days. > > Thank you for your help in this. > > Best wishes, > > The sensu working group. > > > > -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at sanger.ac.uk Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe From dph at informatics.jax.org Thu Mar 1 06:45:34 2007 From: dph at informatics.jax.org (David Hill) Date: Thu, 01 Mar 2007 09:45:34 -0500 Subject: ATP-binding cassette (ABC) transporter complex In-Reply-To: <45E6DF54.1000502@sanger.ac.uk> References: <45E6D67D.2050502@ebi.ac.uk> <45E6DF54.1000502@sanger.ac.uk> Message-ID: <45E6E70E.7000007@informatics.jax.org> Hi Val, It seems that the decision of when to create a complex and when not to is still under heavy discussion and we can't solve it here. The main issue here is that we did have two types of ABC transporter complexes in the GO. As part of the project to replace terms with 'sensu' designations, we do not want to simply change the GO at will and merge terms because it gets rid of the sensu. Instead we prefer to replace those terms with new term names and definitions that really describe the differences. In some cases we decide that the only difference is that the process or component or function occurs in two different organisms. If this is the case, we merge the terms. I think it is still out there for the community to discuss when it is worth having separate complex types and it really comes down to discussions among experts about the differences between types and whether it is worth representing those differences in the GO. Clearly in some cases we have decided to add separate complexes and in some cases we haven't. I think we really need (perhaps at a GOC meeting) to discuss some rules for when to add a complex to GO. David Valerie Wood wrote: > Hi, > > I'm presuming that we would not create a new complex term if for > example the pombe xxx complex differed by one subunit from the S. > cerevisiae, or the human complex if these are considered to be analogous. > > Usually (but not always) when we create an additional complex with a > different composition, it is because the complex has a subunit > composition which is both a 'within' and 'between' organism > difference, and the 'new' complex has different functional properties. > > The gamma tubulin complexes are a good example. There are various > complexes with different compositions (large/small/ ring). These have > the same core subunits but some complexes have additional subunits. > The exact subunit composition of each complex varies slightly between > species. However, the different complexes have specific functions and > broadly conserved between species, and considered to be analogous. > They also need specific child terms because of TPVs caused by > centrosomes vs spindle pole bodies. > > I guess what I'm trying to say is with the existing annotations, is > the merge such a bad thing?. You only need the species specific child > terms > a) if you are trying to distinguish between the 'different' ABC > transporter complexes within your organism, or in another organism, > and the existing sensu terms did not specifically do this. > or b) if the term causes TPVs with the existing hierarchy > > > Val > > > > Jennifer Clark wrote: > >> Hi, >> >> During the sensu work in the last few days we merged the two terms: >> >> ATP-binding cassette (ABC) transporter complex (sensu Bacteria and >> Archaea) ; GO:0043192 >> and >> ATP-binding cassette (ABC) transporter complex (sensu Eukaryota) ; >> GO:0043191 >> into the existing term: >> >> ATP-binding cassette (ABC) transporter complex ; GO:0043190 >> >> Since this merge, Michelle has correctly pointed out that there is a >> way to differentiate between these two terms, and it is likely that >> the merge will be reverted. If you have not changed your annotations >> to relect this merge then we would suggest that you leave the >> annotations to the subsumed terms pointing to the secondary ids. so >> that they will be correct if we revert the merge in the next few days. >> >> Thank you for your help in this. >> >> Best wishes, >> >> The sensu working group. >> >> >> >> > > From val at sanger.ac.uk Thu Mar 1 07:20:33 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 01 Mar 2007 15:20:33 +0000 Subject: transporter substrates In-Reply-To: <0C123BA1-B923-47DC-9C1C-E269B8DB78A2@twcny.rr.com> References: <45E3FDE0.3050803@ebi.ac.uk> <45E407F8.7090200@sanger.ac.uk> <45E41CFB.4090703@ebi.ac.uk> <0C123BA1-B923-47DC-9C1C-E269B8DB78A2@twcny.rr.com> Message-ID: <45E6EF41.1090005@sanger.ac.uk> This is the current scenario for the high level substrate terms. Does anybody know of any examples where 1 or 2 are not transmembrane (particularly odorant/neurotransmitter and chlorophyll catabolite which I know nothing about) Of the high level substrate terms: 1. I can't find any examples where these are NOT transmembrane transporters: Does anybody know of any? alcohol transporter activity amide transporter activity amine transporter activity/ possibly not, includes serotonin (is this also vesicle mediated?) ammonia transporter activity boron transporter activity drug transporter activity group translocator activity lactone transporter activity nitric oxide transporter activity nucleobase, nucleoside, nucleotide and nucleic acid transporter activity (possibly not nucleic acid) organic acid transporter activity peptide transporter activity peptidoglycan transporter activity water transporter activity 2. These I'm not sure: Can anybody help with these? ATPase activity, coupled to movement of substances (this is an odd one) carbohydrate transporter activity (possibly, not sure) chlorophyll catabolite transporter activity neurotransmitter transporter activity odorant transporter activity siderophore transporter activity toxin transporter activity xenobiotic transporter activity vitamin transporter activity 3. These terms include transporters which are not transmembrane transporters (although some of their child terms may be able to move directly under 'transmembrane transporter' cofactor transporter activity (heme binding serum proteins like hemopexin) intracellular transporter activity (i.e. intracellular trafficking/ nucleocytoplasmic transport) ion transporter activity (includes metallochaperones) lipid transporter activity (i.e. intracellular trafficking of sterol) oxygen transporter activity (globin etc) protein transporter activity (i.e. intracellular trafficking/ nucleocytoplasmic transport) If we can ascertain that there is no possibility that a term could refer to anything other than transmembrane transport, then it can can be moved under the new 'transmembrane transporter' term. If not they will need to stay as a sibling of 'transmembrane transporter' and new term created for 'substrate transmembrane transporter' . However, in this case the granularity of the existing annotation would be lost if the existing term can only refer to a transmembrane transporter, as curators will need to annotate to the more granular term. Cheers Val Maria Costanzo wrote: > Hi Jen, > > 'ion transporter activity' has 'metallochaperone activity' and > 'copper chaperone activity' as children, but these terms don't > represent transport across a membrane; they represent protein binding > to metal ions with the result of sequestering the ions, or delivering > them to a particular enzyme complex. > > There may be other examples like this but these are all I can see at > the moment - I'll keep thinking! > > Maria -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at sanger.ac.uk Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe From cherry at stanford.edu Thu Mar 1 07:23:12 2007 From: cherry at stanford.edu (Mike Cherry) Date: Thu, 1 Mar 2007 07:23:12 -0800 Subject: missing GOIDs In-Reply-To: <60BA0B9C-F4B0-4BDB-876E-A2C88D5E7559@ebi.ac.uk> References: <93035998-ED1D-42FD-8D86-EE791C6AD544@stanford.edu> <60BA0B9C-F4B0-4BDB-876E-A2C88D5E7559@ebi.ac.uk> Message-ID: <01EEEAF2-8FF8-4EF9-9571-5849C4AFABE6@stanford.edu> Jane, If its in CVS at all then there is a good change the it has been loaded a multiple sites. The rule should be that GOIDs are never deleted, even if added by mistake. Could you please add those to the OBO file as obsolete? -Mike On Mar 1, 2007, at 3:20 AM, Jane Lomax wrote: > Hi - sorry, these were my fault - it was when I was merging in > those hundreds of PAMGO terms, they weren't supposed to go in at > all so I removed them - as they were only in so briefly I didn't > think there was much value in recording them as obsolete terms, but > I can if people think there's value in doing that. > > Jane > > > On 1 Mar 2007, at 04:05, Mike Cherry wrote: > >> Should the following GOIDs be missing? Was it a mistake to add >> them? They should not have been deleted, rather made obsolete. >> >> There are four GOIDs that were created on January 22nd (version >> 5.111 with the PAMGO terms) that have gone missing. They were not >> mentioned in any of the go-diff messages and are not mentioned at >> all in the current OBO file. It would seem that some check has >> failed or that some dandy hand edit has deleted these entries. >> GOIDs should never be completely deleted from the OBO file! >> >> -Mike >> >> Here is what was in the OBO file with version 5.113, and gone now. >> >> [Term] >> id: GO:0052461 >> name: modulation by organism of pathogen-associated molecular >> pattern-induced symbiont innate immunity >> namespace: biological_process >> is_a: GO:0052296 ! modulation by organism of pathogen-associated >> molecular pattern-induced innate immunity in other organism during >> symbiotic interaction >> is_a: GO:0052452 ! modulation by organism of symbiont innate immunity >> >> [Term] >> id: GO:0052488 >> name: negative regulation by organism of pathogen-associated >> molecular pattern-induced symbiont innate immunity >> namespace: biological_process >> synonym: "suppression of general elicitor induced symbiont innate >> immunity" EXACT [] >> synonym: "suppression of general elicitor-induced symbiont innate >> immunity" EXACT [] >> synonym: "suppression of MAMP induced symbiont innate immunity" >> EXACT [] >> synonym: "suppression of MAMP-induced symbiont innate immunity" >> EXACT [] >> synonym: "suppression of PAMP induced symbiont innate immunity" >> EXACT [] >> synonym: "suppression of PAMP-induced symbiont innate immunity" >> EXACT [] >> synonym: "suppression of pathogen-associated molecular pattern- >> induced symbiont innate immunity" EXACT [] >> is_a: GO:0052258 ! negative regulation by organism of pathogen- >> associated molecular pattern-induced innate immunity of other >> organism during symbiotic interaction >> is_a: GO:0052461 ! modulation by organism of pathogen-associated >> molecular pattern-induced symbiont innate immunity >> is_a: GO:0052486 ! negative regulation by organism of symbiont >> innate immunity >> >> [Term] >> id: GO:0052498 >> name: pathogen-associated molecular pattern dependent induction by >> organism of symbiont innate immunity >> namespace: biological_process >> synonym: "general elicitor-dependent activation of symbiont innate >> immunity" EXACT [] >> synonym: "general elicitor-dependent induction of symbiont innate >> immunity" EXACT [] >> synonym: "MAMP dependent activation of symbiont innate immunity" >> EXACT [] >> synonym: "MAMP dependent induction of symbiont innate immunity" >> EXACT [] >> synonym: "PAMP dependent activation of symbiont innate immunity" >> EXACT [] >> synonym: "PAMP dependent induction of symbiont innate immunity" >> EXACT [] >> synonym: "pathogen-associated molecular pattern dependent >> activation by organism of symbiont innate immunity" EXACT [] >> is_a: GO:0052257 ! pathogen-associated molecular pattern dependent >> induction by organism of innate immunity of other organism during >> symbiotic interaction >> is_a: GO:0052499 ! pathogen-associated molecular pattern dependent >> modulation by organism of symbiont innate immunity >> is_a: GO:0052515 ! positive regulation by organism of symbiont >> innate immunity >> >> [Term] >> id: GO:0052499 >> name: pathogen-associated molecular pattern dependent modulation >> by organism of symbiont innate immunity >> namespace: biological_process >> is_a: GO:0052308 ! pathogen-associated molecular pattern dependent >> modulation by organism of innate immunity in other organism during >> symbiotic interaction >> is_a: GO:0052452 ! modulation by organism of symbiont innate immunity >> From jane at ebi.ac.uk Thu Mar 1 07:40:19 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Thu, 1 Mar 2007 15:40:19 +0000 Subject: transporter substrates In-Reply-To: <45E6EF41.1090005@sanger.ac.uk> References: <45E3FDE0.3050803@ebi.ac.uk> <45E407F8.7090200@sanger.ac.uk> <45E41CFB.4090703@ebi.ac.uk> <0C123BA1-B923-47DC-9C1C-E269B8DB78A2@twcny.rr.com> <45E6EF41.1090005@sanger.ac.uk> Message-ID: <8B9D4C45-F224-41D6-98E2-79A53F64E757@ebi.ac.uk> > ATPase activity, coupled to movement of substances (this is an odd > one) This is for ABC transporters, which as far as I know always transport across a membrane. Jane From jane at ebi.ac.uk Thu Mar 1 07:43:18 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Thu, 1 Mar 2007 15:43:18 +0000 Subject: missing GOIDs In-Reply-To: <01EEEAF2-8FF8-4EF9-9571-5849C4AFABE6@stanford.edu> References: <93035998-ED1D-42FD-8D86-EE791C6AD544@stanford.edu> <60BA0B9C-F4B0-4BDB-876E-A2C88D5E7559@ebi.ac.uk> <01EEEAF2-8FF8-4EF9-9571-5849C4AFABE6@stanford.edu> Message-ID: I can, but there are about 80 in total - is that still okay? Jane On 1 Mar 2007, at 15:23, Mike Cherry wrote: > Jane, > > If its in CVS at all then there is a good change the it has been > loaded a multiple sites. The rule should be that GOIDs are never > deleted, even if added by mistake. Could you please add those to > the OBO file as obsolete? > > -Mike > > On Mar 1, 2007, at 3:20 AM, Jane Lomax wrote: > >> Hi - sorry, these were my fault - it was when I was merging in >> those hundreds of PAMGO terms, they weren't supposed to go in at >> all so I removed them - as they were only in so briefly I didn't >> think there was much value in recording them as obsolete terms, >> but I can if people think there's value in doing that. >> >> Jane >> >> >> On 1 Mar 2007, at 04:05, Mike Cherry wrote: >> >>> Should the following GOIDs be missing? Was it a mistake to add >>> them? They should not have been deleted, rather made obsolete. >>> >>> There are four GOIDs that were created on January 22nd (version >>> 5.111 with the PAMGO terms) that have gone missing. They were >>> not mentioned in any of the go-diff messages and are not >>> mentioned at all in the current OBO file. It would seem that >>> some check has failed or that some dandy hand edit has deleted >>> these entries. GOIDs should never be completely deleted from the >>> OBO file! >>> >>> -Mike >>> >>> Here is what was in the OBO file with version 5.113, and gone now. >>> >>> [Term] >>> id: GO:0052461 >>> name: modulation by organism of pathogen-associated molecular >>> pattern-induced symbiont innate immunity >>> namespace: biological_process >>> is_a: GO:0052296 ! modulation by organism of pathogen-associated >>> molecular pattern-induced innate immunity in other organism >>> during symbiotic interaction >>> is_a: GO:0052452 ! modulation by organism of symbiont innate >>> immunity >>> >>> [Term] >>> id: GO:0052488 >>> name: negative regulation by organism of pathogen-associated >>> molecular pattern-induced symbiont innate immunity >>> namespace: biological_process >>> synonym: "suppression of general elicitor induced symbiont innate >>> immunity" EXACT [] >>> synonym: "suppression of general elicitor-induced symbiont innate >>> immunity" EXACT [] >>> synonym: "suppression of MAMP induced symbiont innate immunity" >>> EXACT [] >>> synonym: "suppression of MAMP-induced symbiont innate immunity" >>> EXACT [] >>> synonym: "suppression of PAMP induced symbiont innate immunity" >>> EXACT [] >>> synonym: "suppression of PAMP-induced symbiont innate immunity" >>> EXACT [] >>> synonym: "suppression of pathogen-associated molecular pattern- >>> induced symbiont innate immunity" EXACT [] >>> is_a: GO:0052258 ! negative regulation by organism of pathogen- >>> associated molecular pattern-induced innate immunity of other >>> organism during symbiotic interaction >>> is_a: GO:0052461 ! modulation by organism of pathogen-associated >>> molecular pattern-induced symbiont innate immunity >>> is_a: GO:0052486 ! negative regulation by organism of symbiont >>> innate immunity >>> >>> [Term] >>> id: GO:0052498 >>> name: pathogen-associated molecular pattern dependent induction >>> by organism of symbiont innate immunity >>> namespace: biological_process >>> synonym: "general elicitor-dependent activation of symbiont >>> innate immunity" EXACT [] >>> synonym: "general elicitor-dependent induction of symbiont innate >>> immunity" EXACT [] >>> synonym: "MAMP dependent activation of symbiont innate immunity" >>> EXACT [] >>> synonym: "MAMP dependent induction of symbiont innate immunity" >>> EXACT [] >>> synonym: "PAMP dependent activation of symbiont innate immunity" >>> EXACT [] >>> synonym: "PAMP dependent induction of symbiont innate immunity" >>> EXACT [] >>> synonym: "pathogen-associated molecular pattern dependent >>> activation by organism of symbiont innate immunity" EXACT [] >>> is_a: GO:0052257 ! pathogen-associated molecular pattern >>> dependent induction by organism of innate immunity of other >>> organism during symbiotic interaction >>> is_a: GO:0052499 ! pathogen-associated molecular pattern >>> dependent modulation by organism of symbiont innate immunity >>> is_a: GO:0052515 ! positive regulation by organism of symbiont >>> innate immunity >>> >>> [Term] >>> id: GO:0052499 >>> name: pathogen-associated molecular pattern dependent modulation >>> by organism of symbiont innate immunity >>> namespace: biological_process >>> is_a: GO:0052308 ! pathogen-associated molecular pattern >>> dependent modulation by organism of innate immunity in other >>> organism during symbiotic interaction >>> is_a: GO:0052452 ! modulation by organism of symbiont innate >>> immunity >>> From cherry at stanford.edu Thu Mar 1 07:44:54 2007 From: cherry at stanford.edu (Mike Cherry) Date: Thu, 1 Mar 2007 07:44:54 -0800 Subject: missing GOIDs In-Reply-To: References: <93035998-ED1D-42FD-8D86-EE791C6AD544@stanford.edu> <60BA0B9C-F4B0-4BDB-876E-A2C88D5E7559@ebi.ac.uk> <01EEEAF2-8FF8-4EF9-9571-5849C4AFABE6@stanford.edu> Message-ID: <5111BD81-A691-45C8-AA2E-84B43A49231A@stanford.edu> YES. If a GOID is EVER committed to the CVS it should NEVER be removed/deleted. -Mike On Mar 1, 2007, at 7:43 AM, Jane Lomax wrote: > I can, but there are about 80 in total - is that still okay? > > Jane > > > On 1 Mar 2007, at 15:23, Mike Cherry wrote: > >> Jane, >> >> If its in CVS at all then there is a good change the it has been >> loaded a multiple sites. The rule should be that GOIDs are never >> deleted, even if added by mistake. Could you please add those to >> the OBO file as obsolete? >> >> -Mike >> >> On Mar 1, 2007, at 3:20 AM, Jane Lomax wrote: >> >>> Hi - sorry, these were my fault - it was when I was merging in >>> those hundreds of PAMGO terms, they weren't supposed to go in at >>> all so I removed them - as they were only in so briefly I didn't >>> think there was much value in recording them as obsolete terms, >>> but I can if people think there's value in doing that. >>> >>> Jane >>> >>> >>> On 1 Mar 2007, at 04:05, Mike Cherry wrote: >>> >>>> Should the following GOIDs be missing? Was it a mistake to add >>>> them? They should not have been deleted, rather made obsolete. >>>> >>>> There are four GOIDs that were created on January 22nd (version >>>> 5.111 with the PAMGO terms) that have gone missing. They were >>>> not mentioned in any of the go-diff messages and are not >>>> mentioned at all in the current OBO file. It would seem that >>>> some check has failed or that some dandy hand edit has deleted >>>> these entries. GOIDs should never be completely deleted from >>>> the OBO file! >>>> >>>> -Mike >>>> >>>> Here is what was in the OBO file with version 5.113, and gone now. >>>> >>>> [Term] >>>> id: GO:0052461 >>>> name: modulation by organism of pathogen-associated molecular >>>> pattern-induced symbiont innate immunity >>>> namespace: biological_process >>>> is_a: GO:0052296 ! modulation by organism of pathogen-associated >>>> molecular pattern-induced innate immunity in other organism >>>> during symbiotic interaction >>>> is_a: GO:0052452 ! modulation by organism of symbiont innate >>>> immunity >>>> >>>> [Term] >>>> id: GO:0052488 >>>> name: negative regulation by organism of pathogen-associated >>>> molecular pattern-induced symbiont innate immunity >>>> namespace: biological_process >>>> synonym: "suppression of general elicitor induced symbiont >>>> innate immunity" EXACT [] >>>> synonym: "suppression of general elicitor-induced symbiont >>>> innate immunity" EXACT [] >>>> synonym: "suppression of MAMP induced symbiont innate immunity" >>>> EXACT [] >>>> synonym: "suppression of MAMP-induced symbiont innate immunity" >>>> EXACT [] >>>> synonym: "suppression of PAMP induced symbiont innate immunity" >>>> EXACT [] >>>> synonym: "suppression of PAMP-induced symbiont innate immunity" >>>> EXACT [] >>>> synonym: "suppression of pathogen-associated molecular pattern- >>>> induced symbiont innate immunity" EXACT [] >>>> is_a: GO:0052258 ! negative regulation by organism of pathogen- >>>> associated molecular pattern-induced innate immunity of other >>>> organism during symbiotic interaction >>>> is_a: GO:0052461 ! modulation by organism of pathogen-associated >>>> molecular pattern-induced symbiont innate immunity >>>> is_a: GO:0052486 ! negative regulation by organism of symbiont >>>> innate immunity >>>> >>>> [Term] >>>> id: GO:0052498 >>>> name: pathogen-associated molecular pattern dependent induction >>>> by organism of symbiont innate immunity >>>> namespace: biological_process >>>> synonym: "general elicitor-dependent activation of symbiont >>>> innate immunity" EXACT [] >>>> synonym: "general elicitor-dependent induction of symbiont >>>> innate immunity" EXACT [] >>>> synonym: "MAMP dependent activation of symbiont innate immunity" >>>> EXACT [] >>>> synonym: "MAMP dependent induction of symbiont innate immunity" >>>> EXACT [] >>>> synonym: "PAMP dependent activation of symbiont innate immunity" >>>> EXACT [] >>>> synonym: "PAMP dependent induction of symbiont innate immunity" >>>> EXACT [] >>>> synonym: "pathogen-associated molecular pattern dependent >>>> activation by organism of symbiont innate immunity" EXACT [] >>>> is_a: GO:0052257 ! pathogen-associated molecular pattern >>>> dependent induction by organism of innate immunity of other >>>> organism during symbiotic interaction >>>> is_a: GO:0052499 ! pathogen-associated molecular pattern >>>> dependent modulation by organism of symbiont innate immunity >>>> is_a: GO:0052515 ! positive regulation by organism of symbiont >>>> innate immunity >>>> >>>> [Term] >>>> id: GO:0052499 >>>> name: pathogen-associated molecular pattern dependent modulation >>>> by organism of symbiont innate immunity >>>> namespace: biological_process >>>> is_a: GO:0052308 ! pathogen-associated molecular pattern >>>> dependent modulation by organism of innate immunity in other >>>> organism during symbiotic interaction >>>> is_a: GO:0052452 ! modulation by organism of symbiont innate >>>> immunity >>>> From val at sanger.ac.uk Thu Mar 1 08:01:41 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 01 Mar 2007 16:01:41 +0000 Subject: transporter substrates In-Reply-To: <8B9D4C45-F224-41D6-98E2-79A53F64E757@ebi.ac.uk> References: <45E3FDE0.3050803@ebi.ac.uk> <45E407F8.7090200@sanger.ac.uk> <45E41CFB.4090703@ebi.ac.uk> <0C123BA1-B923-47DC-9C1C-E269B8DB78A2@twcny.rr.com> <45E6EF41.1090005@sanger.ac.uk> <8B9D4C45-F224-41D6-98E2-79A53F64E757@ebi.ac.uk> Message-ID: <45E6F8E5.4040407@sanger.ac.uk> thats this term (its child): ATPase activity, coupled to transmembrane movement of substances ATPase activity, coupled to movement of substances has an additional child DNA translocase activity which we think is a group translocator and is_a transmembrane complex involved in transformation therefore is_a transmembrane transporter (However, I just checked, it only has 2 annotations and these might not be transporters at all). But we think this is what the term is for. So we aren't sure whether we still need this or not. Maybe there are things which are transporters, and ATPases but not transmembrane transporters....can't think of any.... Jane Lomax wrote: >> ATPase activity, coupled to movement of substances (this is an odd one) > > > This is for ABC transporters, which as far as I know always transport > across a membrane. > > Jane > -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at sanger.ac.uk Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe From jane at ebi.ac.uk Thu Mar 1 08:10:26 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Thu, 1 Mar 2007 16:10:26 +0000 Subject: transporter substrates In-Reply-To: <45E6F8E5.4040407@sanger.ac.uk> References: <45E3FDE0.3050803@ebi.ac.uk> <45E407F8.7090200@sanger.ac.uk> <45E41CFB.4090703@ebi.ac.uk> <0C123BA1-B923-47DC-9C1C-E269B8DB78A2@twcny.rr.com> <45E6EF41.1090005@sanger.ac.uk> <8B9D4C45-F224-41D6-98E2-79A53F64E757@ebi.ac.uk> <45E6F8E5.4040407@sanger.ac.uk> Message-ID: Oh yes - I think when I made that term I must have had some reason to think that DNA translocases weren't always transmembrane - let me see what I can dig out... Jane On 1 Mar 2007, at 16:01, Valerie Wood wrote: > thats this term (its child): > ATPase activity, coupled to transmembrane movement of substances > > ATPase activity, coupled to movement of substances > has an additional child > DNA translocase activity > > which we think is a group translocator and is_a transmembrane > complex involved in transformation therefore is_a transmembrane > transporter > > (However, I just checked, it only has 2 annotations and these might > not be transporters at all). But we think this is what the term is > for. > > So we aren't sure whether we still need this or not. Maybe there > are things which are transporters, and ATPases but not > transmembrane transporters....can't think of any.... > > > > > Jane Lomax wrote: > >>> ATPase activity, coupled to movement of substances (this is an >>> odd one) >> >> >> This is for ABC transporters, which as far as I know always >> transport across a membrane. >> >> Jane >> > > > -- > ---------------------------------------------------------------------- > ----- > Valerie Wood Tel: 01223 496909 > S. pombe Genome Project Fax: 01223 494919 Wellcome Trust > Sanger Institute email: val at sanger.ac.uk > Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe > Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe From jane at ebi.ac.uk Thu Mar 1 08:23:54 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Thu, 1 Mar 2007 16:23:54 +0000 Subject: transporter substrates In-Reply-To: References: <45E3FDE0.3050803@ebi.ac.uk> <45E407F8.7090200@sanger.ac.uk> <45E41CFB.4090703@ebi.ac.uk> <0C123BA1-B923-47DC-9C1C-E269B8DB78A2@twcny.rr.com> <45E6EF41.1090005@sanger.ac.uk> <8B9D4C45-F224-41D6-98E2-79A53F64E757@ebi.ac.uk> <45E6F8E5.4040407@sanger.ac.uk> Message-ID: <1167C0B4-4A85-4A8F-B9E6-8BE24384788E@ebi.ac.uk> Can't find anything in SF - but in this paper they suggest that DNA helicases have DNA translocase activity...in which case I'm not sure DNA helicase should be a child of transporter at all: http://nar.oxfordjournals.org/cgi/content/full/34/13/3731 ? Jane On 1 Mar 2007, at 16:10, Jane Lomax wrote: > Oh yes - I think when I made that term I must have had some reason > to think that DNA translocases weren't always transmembrane - let > me see what I can dig out... > > Jane > > > On 1 Mar 2007, at 16:01, Valerie Wood wrote: > >> thats this term (its child): >> ATPase activity, coupled to transmembrane movement of substances >> >> ATPase activity, coupled to movement of substances >> has an additional child >> DNA translocase activity >> >> which we think is a group translocator and is_a transmembrane >> complex involved in transformation therefore is_a transmembrane >> transporter >> >> (However, I just checked, it only has 2 annotations and these >> might not be transporters at all). But we think this is what the >> term is for. >> >> So we aren't sure whether we still need this or not. Maybe there >> are things which are transporters, and ATPases but not >> transmembrane transporters....can't think of any.... >> >> >> >> >> Jane Lomax wrote: >> >>>> ATPase activity, coupled to movement of substances (this is an >>>> odd one) >>> >>> >>> This is for ABC transporters, which as far as I know always >>> transport across a membrane. >>> >>> Jane >>> >> >> >> -- >> --------------------------------------------------------------------- >> ------ >> Valerie Wood Tel: 01223 496909 >> S. pombe Genome Project Fax: 01223 494919 Wellcome >> Trust Sanger Institute email: val at sanger.ac.uk >> Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe >> Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/ >> S_pombe From val at sanger.ac.uk Thu Mar 1 08:49:49 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 01 Mar 2007 16:49:49 +0000 Subject: transporter substrates In-Reply-To: <1167C0B4-4A85-4A8F-B9E6-8BE24384788E@ebi.ac.uk> References: <45E3FDE0.3050803@ebi.ac.uk> <45E407F8.7090200@sanger.ac.uk> <45E41CFB.4090703@ebi.ac.uk> <0C123BA1-B923-47DC-9C1C-E269B8DB78A2@twcny.rr.com> <45E6EF41.1090005@sanger.ac.uk> <8B9D4C45-F224-41D6-98E2-79A53F64E757@ebi.ac.uk> <45E6F8E5.4040407@sanger.ac.uk> <1167C0B4-4A85-4A8F-B9E6-8BE24384788E@ebi.ac.uk> Message-ID: <45E7042D.10701@sanger.ac.uk> That makes sense. This is an alternative use of the word 'translocate'. it appears that this refers to ATP-dependent DNA helicase activity I think we can merge this DNA translocase activity with DNA-dependent ATPase activity or ATP-dependent DNA helicase activity and make DNA translocase activity some sort of synonym and remove the transporter parentage. This sounds more like the existing annotations which are this family http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF01580 Then we need a new term for the DNA group translocase Although I'm not sure about the exisiting def Catalysis of the reaction: ATP + H2O = ADP + phosphate to drive the transport of DNA. I think this is capturing the chromosome segregation (porcess) aspect.....Michelle? Jane Lomax wrote: > Can't find anything in SF - but in this paper they suggest that DNA > helicases have DNA translocase activity...in which case I'm not sure > DNA helicase should be a child of transporter at all: > > http://nar.oxfordjournals.org/cgi/content/full/34/13/3731 > > ? > > Jane > > > On 1 Mar 2007, at 16:10, Jane Lomax wrote: > >> Oh yes - I think when I made that term I must have had some reason >> to think that DNA translocases weren't always transmembrane - let me >> see what I can dig out... >> >> Jane >> >> >> On 1 Mar 2007, at 16:01, Valerie Wood wrote: >> >>> thats this term (its child): >>> ATPase activity, coupled to transmembrane movement of substances >>> >>> ATPase activity, coupled to movement of substances >>> has an additional child >>> DNA translocase activity >>> >>> which we think is a group translocator and is_a transmembrane >>> complex involved in transformation therefore is_a transmembrane >>> transporter >>> >>> (However, I just checked, it only has 2 annotations and these might >>> not be transporters at all). But we think this is what the term is >>> for. >>> >>> So we aren't sure whether we still need this or not. Maybe there >>> are things which are transporters, and ATPases but not >>> transmembrane transporters....can't think of any.... >>> >>> >>> >>> >>> Jane Lomax wrote: >>> >>>>> ATPase activity, coupled to movement of substances (this is an >>>>> odd one) >>>> >>>> >>>> >>>> This is for ABC transporters, which as far as I know always >>>> transport across a membrane. >>>> >>>> Jane >>>> >>> >>> >>> -- >>> --------------------------------------------------------------------- >>> ------ >>> Valerie Wood Tel: 01223 496909 >>> S. pombe Genome Project Fax: 01223 494919 >>> Wellcome Trust Sanger Institute email: val at sanger.ac.uk >>> Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe >>> Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/ >>> S_pombe >> > > -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at sanger.ac.uk Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe From jane at ebi.ac.uk Thu Mar 1 09:52:17 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Thu, 1 Mar 2007 17:52:17 +0000 Subject: missing GOIDs In-Reply-To: <5111BD81-A691-45C8-AA2E-84B43A49231A@stanford.edu> References: <93035998-ED1D-42FD-8D86-EE791C6AD544@stanford.edu> <60BA0B9C-F4B0-4BDB-876E-A2C88D5E7559@ebi.ac.uk> <01EEEAF2-8FF8-4EF9-9571-5849C4AFABE6@stanford.edu> <5111BD81-A691-45C8-AA2E-84B43A49231A@stanford.edu> Message-ID: Okay - they're now added as obsoletes. There were 99 so expect a big diff (1000 new lines). Jane On 1 Mar 2007, at 15:44, Mike Cherry wrote: > YES. If a GOID is EVER committed to the CVS it should NEVER be > removed/deleted. > > -Mike > > On Mar 1, 2007, at 7:43 AM, Jane Lomax wrote: > >> I can, but there are about 80 in total - is that still okay? >> >> Jane >> >> >> On 1 Mar 2007, at 15:23, Mike Cherry wrote: >> >>> Jane, >>> >>> If its in CVS at all then there is a good change the it has been >>> loaded a multiple sites. The rule should be that GOIDs are never >>> deleted, even if added by mistake. Could you please add those to >>> the OBO file as obsolete? >>> >>> -Mike >>> >>> On Mar 1, 2007, at 3:20 AM, Jane Lomax wrote: >>> >>>> Hi - sorry, these were my fault - it was when I was merging in >>>> those hundreds of PAMGO terms, they weren't supposed to go in at >>>> all so I removed them - as they were only in so briefly I didn't >>>> think there was much value in recording them as obsolete terms, >>>> but I can if people think there's value in doing that. >>>> >>>> Jane >>>> >>>> >>>> On 1 Mar 2007, at 04:05, Mike Cherry wrote: >>>> >>>>> Should the following GOIDs be missing? Was it a mistake to add >>>>> them? They should not have been deleted, rather made obsolete. >>>>> >>>>> There are four GOIDs that were created on January 22nd (version >>>>> 5.111 with the PAMGO terms) that have gone missing. They were >>>>> not mentioned in any of the go-diff messages and are not >>>>> mentioned at all in the current OBO file. It would seem that >>>>> some check has failed or that some dandy hand edit has deleted >>>>> these entries. GOIDs should never be completely deleted from >>>>> the OBO file! >>>>> >>>>> -Mike >>>>> >>>>> Here is what was in the OBO file with version 5.113, and gone now. >>>>> >>>>> [Term] >>>>> id: GO:0052461 >>>>> name: modulation by organism of pathogen-associated molecular >>>>> pattern-induced symbiont innate immunity >>>>> namespace: biological_process >>>>> is_a: GO:0052296 ! modulation by organism of pathogen- >>>>> associated molecular pattern-induced innate immunity in other >>>>> organism during symbiotic interaction >>>>> is_a: GO:0052452 ! modulation by organism of symbiont innate >>>>> immunity >>>>> >>>>> [Term] >>>>> id: GO:0052488 >>>>> name: negative regulation by organism of pathogen-associated >>>>> molecular pattern-induced symbiont innate immunity >>>>> namespace: biological_process >>>>> synonym: "suppression of general elicitor induced symbiont >>>>> innate immunity" EXACT [] >>>>> synonym: "suppression of general elicitor-induced symbiont >>>>> innate immunity" EXACT [] >>>>> synonym: "suppression of MAMP induced symbiont innate immunity" >>>>> EXACT [] >>>>> synonym: "suppression of MAMP-induced symbiont innate immunity" >>>>> EXACT [] >>>>> synonym: "suppression of PAMP induced symbiont innate immunity" >>>>> EXACT [] >>>>> synonym: "suppression of PAMP-induced symbiont innate immunity" >>>>> EXACT [] >>>>> synonym: "suppression of pathogen-associated molecular pattern- >>>>> induced symbiont innate immunity" EXACT [] >>>>> is_a: GO:0052258 ! negative regulation by organism of pathogen- >>>>> associated molecular pattern-induced innate immunity of other >>>>> organism during symbiotic interaction >>>>> is_a: GO:0052461 ! modulation by organism of pathogen- >>>>> associated molecular pattern-induced symbiont innate immunity >>>>> is_a: GO:0052486 ! negative regulation by organism of symbiont >>>>> innate immunity >>>>> >>>>> [Term] >>>>> id: GO:0052498 >>>>> name: pathogen-associated molecular pattern dependent induction >>>>> by organism of symbiont innate immunity >>>>> namespace: biological_process >>>>> synonym: "general elicitor-dependent activation of symbiont >>>>> innate immunity" EXACT [] >>>>> synonym: "general elicitor-dependent induction of symbiont >>>>> innate immunity" EXACT [] >>>>> synonym: "MAMP dependent activation of symbiont innate >>>>> immunity" EXACT [] >>>>> synonym: "MAMP dependent induction of symbiont innate immunity" >>>>> EXACT [] >>>>> synonym: "PAMP dependent activation of symbiont innate >>>>> immunity" EXACT [] >>>>> synonym: "PAMP dependent induction of symbiont innate immunity" >>>>> EXACT [] >>>>> synonym: "pathogen-associated molecular pattern dependent >>>>> activation by organism of symbiont innate immunity" EXACT [] >>>>> is_a: GO:0052257 ! pathogen-associated molecular pattern >>>>> dependent induction by organism of innate immunity of other >>>>> organism during symbiotic interaction >>>>> is_a: GO:0052499 ! pathogen-associated molecular pattern >>>>> dependent modulation by organism of symbiont innate immunity >>>>> is_a: GO:0052515 ! positive regulation by organism of symbiont >>>>> innate immunity >>>>> >>>>> [Term] >>>>> id: GO:0052499 >>>>> name: pathogen-associated molecular pattern dependent >>>>> modulation by organism of symbiont innate immunity >>>>> namespace: biological_process >>>>> is_a: GO:0052308 ! pathogen-associated molecular pattern >>>>> dependent modulation by organism of innate immunity in other >>>>> organism during symbiotic interaction >>>>> is_a: GO:0052452 ! modulation by organism of symbiont innate >>>>> immunity >>>>> From rama at genome.Stanford.EDU Thu Mar 1 13:52:15 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Thu, 1 Mar 2007 13:52:15 -0800 Subject: Requirements for GO tools In-Reply-To: <800332C0-8D35-41FA-A9DD-6BDD8701FD82@ebi.ac.uk> References: <81326AFD-C946-4648-98E4-8F6897799B0A@ebi.ac.uk> <45E45203.9080506@ebi.ac.uk> <800332C0-8D35-41FA-A9DD-6BDD8701FD82@ebi.ac.uk> Message-ID: This is great. For the essential part, are we going to rely on the tool developers answers or are we going to test the tool for those criteria? Rama On Feb 27, 2007, at 9:41 AM, Jane Lomax wrote: > Yes that's a good point. I think we might be too late asking these > people because they already have a finished tool, but maybe we > could add something to the tools page? > > Jane > > > > On 27 Feb 2007, at 15:45, Evelyn Camon wrote: > >> Hi Jane, >> >> Should we ask if they have asked a GO Consortium member to review >> the tool or would we at least like to advise that they do that???? >> >> It would be nice to hear from these tool developers before reading >> mis-information in publications.... >> >> cheers, >> >> Evelyn >> >> Jane Lomax wrote: >>> Oh yes - that's not very clear is it, I meant how often they >>> update the GO files within their tool, not how often the tool is >>> improved. I'll make that clearer... >>> Jane >>> On 27 Feb 2007, at 13:39, Michael Ashburner (Genetics) wrote: >>>> Looks good Jane and colleagues. The one thing I take exception >>>> to on the wiki >>>> is: >>>> >>>> 'Update frequency minimum, monthly?' >>>> >>>> For a database, yes, but for a tool ? (When was NCBI Blast last >>>> updated ?). >>>> I think that this is covered by the next point: >>>> 'Actively maintained ...' >>>> >>>> Michael >>>> >>>>> Envelope-to: ma11 at gen.cam.ac.uk >>>>> Delivery-date: Tue, 27 Feb 2007 11:58:07 +0000 >>>>> X-Cam-SpamDetails: scanned, SpamAssassin-3.1.7 (score=0) >>>>> X-Cam-AntiVirus: No virus found >>>>> X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ >>>>> X-Authentication-Warning: fafner.Stanford.EDU: majordom set >>>>> sender to >>>> >>>> owner-go-managers at genome-mail.stanford.edu using -f >>>> >>>>> Mime-Version: 1.0 (Apple Message framework v752.3) >>>>> Content-Transfer-Encoding: 7bit >>>>> To: GO Managers List >>>>> From: Jane Lomax >>>>> Subject: Requirements for GO tools >>>>> Date: Tue, 27 Feb 2007 11:57:22 +0000 >>>>> >>>>> Hi - Eurie, Jen and I have been looking at the tools listed on the >>>>> website. We've come up with a draft list of requirements for the >>>>> tools to meet, which is on the wiki: >>>>> >>>>> http://gocwiki.geneontology.org/index.php/Tools_standards >>>>> >>>>> In order that they're listed on the website, the tools will >>>>> have to >>>>> meet all of the essential requirements stated, and the desirable >>>>> requirements could be used in addition to give a score to the tool >>>>> (possibly in addition to some user rankings - we haven't worked >>>>> out >>>>> the details of this yet). The set of questions on the wiki was put >>>>> together by Amelia, and is an extension of what we already ask the >>>>> developers to encompass these extra requirements. >>>>> >>>>> The idea is that we'd send an initial email out to all the tools >>>>> developers (this is easy because they're all subscribed to GO >>>>> friends) with these questions, and any tools for which we haven't >>>>> received a response in a certain time period we'll remove from the >>>>> website (this is a good way to get rid of all of the tools that >>>>> are >>>>> no longer being developed/deprecated tools). We'd warn them >>>>> that any >>>>> tools that don't meet the essential requirements would also be >>>>> removed from the website (harsh!) at some fixed point in the >>>>> future >>>>> to give them a chance to modify their tools. And if by the date >>>>> given >>>>> the tools hadn't been modified, we remove them. >>>>> >>>>> So how does that sound? How about the requirements - too strict/ >>>>> slack? Have we missed anything? >>>>> >>>>> We should add this to the agenda for the meeting tomorrow. >>>>> >>>>> thanks, >>>>> >>>>> Jane and Eurie >>>> >> >> >> -- >> Evelyn Camon >> GOA Coordinator >> Senior Scientific Curator >> European Bioinformatics Institute >> Tel:01223-494465 >> Fax:01223-494468 >> E-mail: camon at ebi.ac.uk >> URL: http://www.ebi.ac.uk/goa From jane at ebi.ac.uk Fri Mar 2 03:06:25 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Fri, 2 Mar 2007 11:06:25 +0000 Subject: GO tools requirements Message-ID: Hi - it seems that this email got cc'ed on to the GO list half way through the thread, but it was probably a bit out of context and confusing, so here's the original email: Eurie, Jen and I have been looking at the tools listed on the website. We've come up with a draft list of requirements for the tools to meet, which is on the wiki: http://gocwiki.geneontology.org/index.php/Tools_standards In order that they're listed on the website, the tools will have to meet all of the essential requirements stated, and the desirable requirements could be used in addition to give a score to the tool (possibly in addition to some user rankings - we haven't worked out the details of this yet). The set of questions on the wiki was put together by Amelia, and is an extension of what we already ask the developers to encompass these extra requirements. The idea is that we'd send an initial email out to all the tools developers (this is easy because they're all subscribed to GO friends) with these questions, and any tools for which we haven't received a response in a certain time period we'll remove from the website (this is a good way to get rid of all of the tools that are no longer being developed/deprecated tools). We'd warn them that any tools that don't meet the essential requirements would also be removed from the website (harsh!) at some fixed point in the future to give them a chance to modify their tools. And if by the date given the tools hadn't been modified, we remove them. So how does that sound? How about the requirements - too strict/ slack? Have we missed anything? thanks, Jane and Eurie From jane at ebi.ac.uk Fri Mar 2 03:07:56 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Fri, 2 Mar 2007 11:07:56 +0000 Subject: Requirements for GO tools In-Reply-To: References: <81326AFD-C946-4648-98E4-8F6897799B0A@ebi.ac.uk> <45E45203.9080506@ebi.ac.uk> <800332C0-8D35-41FA-A9DD-6BDD8701FD82@ebi.ac.uk> Message-ID: <177F9B75-A8A2-47BD-A76D-76AB19BA402C@ebi.ac.uk> Hi Rama - I don't know - although testing all those tools would be a pretty big task, so perhaps we should just trust the developers? Do you think that's wise? Jane On 1 Mar 2007, at 21:52, Rama Balakrishnan wrote: > This is great. > For the essential part, are we going to rely on the tool developers > answers or are we going to test the tool for those criteria? > > Rama > > On Feb 27, 2007, at 9:41 AM, Jane Lomax wrote: > >> Yes that's a good point. I think we might be too late asking these >> people because they already have a finished tool, but maybe we >> could add something to the tools page? >> >> Jane >> >> >> >> On 27 Feb 2007, at 15:45, Evelyn Camon wrote: >> >>> Hi Jane, >>> >>> Should we ask if they have asked a GO Consortium member to review >>> the tool or would we at least like to advise that they do that???? >>> >>> It would be nice to hear from these tool developers before >>> reading mis-information in publications.... >>> >>> cheers, >>> >>> Evelyn >>> >>> Jane Lomax wrote: >>>> Oh yes - that's not very clear is it, I meant how often they >>>> update the GO files within their tool, not how often the tool >>>> is improved. I'll make that clearer... >>>> Jane >>>> On 27 Feb 2007, at 13:39, Michael Ashburner (Genetics) wrote: >>>>> Looks good Jane and colleagues. The one thing I take exception >>>>> to on the wiki >>>>> is: >>>>> >>>>> 'Update frequency minimum, monthly?' >>>>> >>>>> For a database, yes, but for a tool ? (When was NCBI Blast >>>>> last updated ?). >>>>> I think that this is covered by the next point: >>>>> 'Actively maintained ...' >>>>> >>>>> Michael >>>>> >>>>>> Envelope-to: ma11 at gen.cam.ac.uk >>>>>> Delivery-date: Tue, 27 Feb 2007 11:58:07 +0000 >>>>>> X-Cam-SpamDetails: scanned, SpamAssassin-3.1.7 (score=0) >>>>>> X-Cam-AntiVirus: No virus found >>>>>> X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ >>>>>> X-Authentication-Warning: fafner.Stanford.EDU: majordom set >>>>>> sender to >>>>> >>>>> owner-go-managers at genome-mail.stanford.edu using -f >>>>> >>>>>> Mime-Version: 1.0 (Apple Message framework v752.3) >>>>>> Content-Transfer-Encoding: 7bit >>>>>> To: GO Managers List >>>>>> From: Jane Lomax >>>>>> Subject: Requirements for GO tools >>>>>> Date: Tue, 27 Feb 2007 11:57:22 +0000 >>>>>> >>>>>> Hi - Eurie, Jen and I have been looking at the tools listed on >>>>>> the >>>>>> website. We've come up with a draft list of requirements for the >>>>>> tools to meet, which is on the wiki: >>>>>> >>>>>> http://gocwiki.geneontology.org/index.php/Tools_standards >>>>>> >>>>>> In order that they're listed on the website, the tools will >>>>>> have to >>>>>> meet all of the essential requirements stated, and the desirable >>>>>> requirements could be used in addition to give a score to the >>>>>> tool >>>>>> (possibly in addition to some user rankings - we haven't >>>>>> worked out >>>>>> the details of this yet). The set of questions on the wiki was >>>>>> put >>>>>> together by Amelia, and is an extension of what we already ask >>>>>> the >>>>>> developers to encompass these extra requirements. >>>>>> >>>>>> The idea is that we'd send an initial email out to all the tools >>>>>> developers (this is easy because they're all subscribed to GO >>>>>> friends) with these questions, and any tools for which we haven't >>>>>> received a response in a certain time period we'll remove from >>>>>> the >>>>>> website (this is a good way to get rid of all of the tools >>>>>> that are >>>>>> no longer being developed/deprecated tools). We'd warn them >>>>>> that any >>>>>> tools that don't meet the essential requirements would also be >>>>>> removed from the website (harsh!) at some fixed point in the >>>>>> future >>>>>> to give them a chance to modify their tools. And if by the >>>>>> date given >>>>>> the tools hadn't been modified, we remove them. >>>>>> >>>>>> So how does that sound? How about the requirements - too strict/ >>>>>> slack? Have we missed anything? >>>>>> >>>>>> We should add this to the agenda for the meeting tomorrow. >>>>>> >>>>>> thanks, >>>>>> >>>>>> Jane and Eurie >>>>> >>> >>> >>> -- >>> Evelyn Camon >>> GOA Coordinator >>> Senior Scientific Curator >>> European Bioinformatics Institute >>> Tel:01223-494465 >>> Fax:01223-494468 >>> E-mail: camon at ebi.ac.uk >>> URL: http://www.ebi.ac.uk/goa From jclark at ebi.ac.uk Fri Mar 2 08:41:39 2007 From: jclark at ebi.ac.uk (J Clark) Date: Fri, 02 Mar 2007 16:41:39 +0000 Subject: Annotation outreach group report for February Message-ID: <45E853C3.1020708@ebi.ac.uk> Hi, The annotation outreach working group report is now available on the wiki: http://gocwiki.geneontology.org/index.php/February_2007_Monthly_Report Thanks, Jennifer -- Gene Ontology Consortium EMBL-European Bioinformatics Institute From ma11 at gen.cam.ac.uk Mon Mar 5 05:20:19 2007 From: ma11 at gen.cam.ac.uk (Michael Ashburner (Genetics)) Date: Mon, 5 Mar 2007 13:20:19 +0000 (GMT) Subject: Annotation outreach group report for February Message-ID: Great, thanks Jen. Michael From rama at genome.Stanford.EDU Mon Mar 5 11:45:25 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Mon, 5 Mar 2007 11:45:25 -0800 Subject: Requirements for GO tools In-Reply-To: <177F9B75-A8A2-47BD-A76D-76AB19BA402C@ebi.ac.uk> References: <81326AFD-C946-4648-98E4-8F6897799B0A@ebi.ac.uk> <45E45203.9080506@ebi.ac.uk> <800332C0-8D35-41FA-A9DD-6BDD8701FD82@ebi.ac.uk> <177F9B75-A8A2-47BD-A76D-76AB19BA402C@ebi.ac.uk> Message-ID: <45162204-13B9-4A75-9809-827BC7651064@genome.stanford.edu> Jane, I know, it is a huge task to test the tool. I guess we could trust the answers that the developers provide. For the documentation part, can we insist that they give test cases/ examples of data types, IDs etc that work? Thanks, Rama On Mar 2, 2007, at 3:07 AM, Jane Lomax wrote: > Hi Rama - I don't know - although testing all those tools would be > a pretty big task, so perhaps we should just trust the developers? > Do you think that's wise? > > Jane > > > On 1 Mar 2007, at 21:52, Rama Balakrishnan wrote: > >> This is great. >> For the essential part, are we going to rely on the tool >> developers answers or are we going to test the tool for those >> criteria? >> >> Rama >> >> On Feb 27, 2007, at 9:41 AM, Jane Lomax wrote: >> >>> Yes that's a good point. I think we might be too late asking >>> these people because they already have a finished tool, but maybe >>> we could add something to the tools page? >>> >>> Jane >>> >>> >>> >>> On 27 Feb 2007, at 15:45, Evelyn Camon wrote: >>> >>>> Hi Jane, >>>> >>>> Should we ask if they have asked a GO Consortium member to >>>> review the tool or would we at least like to advise that they do >>>> that???? >>>> >>>> It would be nice to hear from these tool developers before >>>> reading mis-information in publications.... >>>> >>>> cheers, >>>> >>>> Evelyn >>>> >>>> Jane Lomax wrote: >>>>> Oh yes - that's not very clear is it, I meant how often they >>>>> update the GO files within their tool, not how often the tool >>>>> is improved. I'll make that clearer... >>>>> Jane >>>>> On 27 Feb 2007, at 13:39, Michael Ashburner (Genetics) wrote: >>>>>> Looks good Jane and colleagues. The one thing I take exception >>>>>> to on the wiki >>>>>> is: >>>>>> >>>>>> 'Update frequency minimum, monthly?' >>>>>> >>>>>> For a database, yes, but for a tool ? (When was NCBI Blast >>>>>> last updated ?). >>>>>> I think that this is covered by the next point: >>>>>> 'Actively maintained ...' >>>>>> >>>>>> Michael >>>>>> >>>>>>> Envelope-to: ma11 at gen.cam.ac.uk >>>>>>> Delivery-date: Tue, 27 Feb 2007 11:58:07 +0000 >>>>>>> X-Cam-SpamDetails: scanned, SpamAssassin-3.1.7 (score=0) >>>>>>> X-Cam-AntiVirus: No virus found >>>>>>> X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ >>>>>>> X-Authentication-Warning: fafner.Stanford.EDU: majordom set >>>>>>> sender to >>>>>> >>>>>> owner-go-managers at genome-mail.stanford.edu using -f >>>>>> >>>>>>> Mime-Version: 1.0 (Apple Message framework v752.3) >>>>>>> Content-Transfer-Encoding: 7bit >>>>>>> To: GO Managers List >>>>>>> From: Jane Lomax >>>>>>> Subject: Requirements for GO tools >>>>>>> Date: Tue, 27 Feb 2007 11:57:22 +0000 >>>>>>> >>>>>>> Hi - Eurie, Jen and I have been looking at the tools listed >>>>>>> on the >>>>>>> website. We've come up with a draft list of requirements for the >>>>>>> tools to meet, which is on the wiki: >>>>>>> >>>>>>> http://gocwiki.geneontology.org/index.php/Tools_standards >>>>>>> >>>>>>> In order that they're listed on the website, the tools will >>>>>>> have to >>>>>>> meet all of the essential requirements stated, and the desirable >>>>>>> requirements could be used in addition to give a score to the >>>>>>> tool >>>>>>> (possibly in addition to some user rankings - we haven't >>>>>>> worked out >>>>>>> the details of this yet). The set of questions on the wiki >>>>>>> was put >>>>>>> together by Amelia, and is an extension of what we already >>>>>>> ask the >>>>>>> developers to encompass these extra requirements. >>>>>>> >>>>>>> The idea is that we'd send an initial email out to all the tools >>>>>>> developers (this is easy because they're all subscribed to GO >>>>>>> friends) with these questions, and any tools for which we >>>>>>> haven't >>>>>>> received a response in a certain time period we'll remove >>>>>>> from the >>>>>>> website (this is a good way to get rid of all of the tools >>>>>>> that are >>>>>>> no longer being developed/deprecated tools). We'd warn them >>>>>>> that any >>>>>>> tools that don't meet the essential requirements would also be >>>>>>> removed from the website (harsh!) at some fixed point in the >>>>>>> future >>>>>>> to give them a chance to modify their tools. And if by the >>>>>>> date given >>>>>>> the tools hadn't been modified, we remove them. >>>>>>> >>>>>>> So how does that sound? How about the requirements - too strict/ >>>>>>> slack? Have we missed anything? >>>>>>> >>>>>>> We should add this to the agenda for the meeting tomorrow. >>>>>>> >>>>>>> thanks, >>>>>>> >>>>>>> Jane and Eurie >>>>>> >>>> >>>> >>>> -- >>>> Evelyn Camon >>>> GOA Coordinator >>>> Senior Scientific Curator >>>> European Bioinformatics Institute >>>> Tel:01223-494465 >>>> Fax:01223-494468 >>>> E-mail: camon at ebi.ac.uk >>>> URL: http://www.ebi.ac.uk/goa From midori at ebi.ac.uk Tue Mar 6 07:30:15 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 6 Mar 2007 15:30:15 +0000 (GMT) Subject: ontology development reports Message-ID: Hi all, I've put monthly reports on ontology development (well, prior to last Novembre they were GO Editorial Office reports, but there's a lot of overlap) on the internal wiki: http://gocwiki.geneontology.org/index.php/Ontology_Development#Reports cheers, midori From rama at genome.Stanford.EDU Tue Mar 6 11:13:31 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Tue, 6 Mar 2007 11:13:31 -0800 Subject: missing GOID Message-ID: <3CF6E8C1-FE41-4D0E-B7AB-0F00908CBF77@genome.stanford.edu> HI All, The following GOID is missing from the gene_ontology_edit.obo file. According to the cvs log file, 51842 'evasion or tolerance of symbiont immune response' was obsoleted on 2007/02/22, in version 5.181, but this term was not there in the previous version 5.180. This term was added to the obo file on 2005/12/07 in version 3.1234 of the gene_ontology.obo file. This term is there in 3.1235 version. Thanks, Rama From rama at genome.Stanford.EDU Tue Mar 6 11:31:59 2007 From: rama at genome.Stanford.EDU (Rama Balakrishnan) Date: Tue, 6 Mar 2007 11:31:59 -0800 Subject: missing GOID In-Reply-To: <3CF6E8C1-FE41-4D0E-B7AB-0F00908CBF77@genome.stanford.edu> References: <3CF6E8C1-FE41-4D0E-B7AB-0F00908CBF77@genome.stanford.edu> Message-ID: Sorry, two more. According the log file, in version 5.198 these should have been obsoleted. 52478 negative regulation by organism of defense-related symbiont cell wall callose deposition 52476 negative regulation by organism of defense-related symbiont MAP kinase-mediated signal transduction pathway are also missing from the obo file. rama On Mar 6, 2007, at 11:13 AM, Rama Balakrishnan wrote: > HI All, > > The following GOID is missing from the gene_ontology_edit.obo file. > > According to the cvs log file, 51842 'evasion or tolerance of > symbiont immune response' was obsoleted on 2007/02/22, in version > 5.181, but this term was not there in the previous version 5.180. > > This term was added to the obo file on 2005/12/07 in version 3.1234 > of the gene_ontology.obo file. This term is there in 3.1235 version. > > Thanks, > > Rama From suzi at berkeleybop.org Tue Mar 6 14:33:20 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Tue, 6 Mar 2007 14:33:20 -0800 Subject: Requirements for GO tools In-Reply-To: <45162204-13B9-4A75-9809-827BC7651064@genome.stanford.edu> References: <81326AFD-C946-4648-98E4-8F6897799B0A@ebi.ac.uk> <45E45203.9080506@ebi.ac.uk> <800332C0-8D35-41FA-A9DD-6BDD8701FD82@ebi.ac.uk> <177F9B75-A8A2-47BD-A76D-76AB19BA402C@ebi.ac.uk> <45162204-13B9-4A75-9809-827BC7651064@genome.stanford.edu> Message-ID: <1C52837E-DC0C-4D8F-9862-2B0829C5DD4C@berkeleybop.org> For some of the tests (e.g. takes NOT into consideration) one can envision testing scripts that could be run. Chris, developing this test suite should be included somewhere on the software group's to-do list (priority TBD) For others (e.g. "good" documentation) it is more subjective. Maybe we should remove the adjective and simply say whether or not the authors can provide a a URL to a documentation page/pdf/wiki -S On Mar 5, 2007, at 11:45 AM, Rama Balakrishnan wrote: > Jane, > > I know, it is a huge task to test the tool. I guess we could trust > the answers that the developers provide. > For the documentation part, can we insist that they give test cases/ > examples of data types, IDs etc that work? > > Thanks, > > Rama > > > > On Mar 2, 2007, at 3:07 AM, Jane Lomax wrote: > >> Hi Rama - I don't know - although testing all those tools would be >> a pretty big task, so perhaps we should just trust the developers? >> Do you think that's wise? >> >> Jane >> >> >> On 1 Mar 2007, at 21:52, Rama Balakrishnan wrote: >> >>> This is great. >>> For the essential part, are we going to rely on the tool >>> developers answers or are we going to test the tool for those >>> criteria? >>> >>> Rama >>> >>> On Feb 27, 2007, at 9:41 AM, Jane Lomax wrote: >>> >>>> Yes that's a good point. I think we might be too late asking >>>> these people because they already have a finished tool, but >>>> maybe we could add something to the tools page? >>>> >>>> Jane >>>> >>>> >>>> >>>> On 27 Feb 2007, at 15:45, Evelyn Camon wrote: >>>> >>>>> Hi Jane, >>>>> >>>>> Should we ask if they have asked a GO Consortium member to >>>>> review the tool or would we at least like to advise that they >>>>> do that???? >>>>> >>>>> It would be nice to hear from these tool developers before >>>>> reading mis-information in publications.... >>>>> >>>>> cheers, >>>>> >>>>> Evelyn >>>>> >>>>> Jane Lomax wrote: >>>>>> Oh yes - that's not very clear is it, I meant how often they >>>>>> update the GO files within their tool, not how often the tool >>>>>> is improved. I'll make that clearer... >>>>>> Jane >>>>>> On 27 Feb 2007, at 13:39, Michael Ashburner (Genetics) wrote: >>>>>>> Looks good Jane and colleagues. The one thing I take >>>>>>> exception to on the wiki >>>>>>> is: >>>>>>> >>>>>>> 'Update frequency minimum, monthly?' >>>>>>> >>>>>>> For a database, yes, but for a tool ? (When was NCBI Blast >>>>>>> last updated ?). >>>>>>> I think that this is covered by the next point: >>>>>>> 'Actively maintained ...' >>>>>>> >>>>>>> Michael >>>>>>> >>>>>>>> Envelope-to: ma11 at gen.cam.ac.uk >>>>>>>> Delivery-date: Tue, 27 Feb 2007 11:58:07 +0000 >>>>>>>> X-Cam-SpamDetails: scanned, SpamAssassin-3.1.7 (score=0) >>>>>>>> X-Cam-AntiVirus: No virus found >>>>>>>> X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ >>>>>>>> X-Authentication-Warning: fafner.Stanford.EDU: majordom set >>>>>>>> sender to >>>>>>> >>>>>>> owner-go-managers at genome-mail.stanford.edu using -f >>>>>>> >>>>>>>> Mime-Version: 1.0 (Apple Message framework v752.3) >>>>>>>> Content-Transfer-Encoding: 7bit >>>>>>>> To: GO Managers List >>>>>>>> From: Jane Lomax >>>>>>>> Subject: Requirements for GO tools >>>>>>>> Date: Tue, 27 Feb 2007 11:57:22 +0000 >>>>>>>> >>>>>>>> Hi - Eurie, Jen and I have been looking at the tools listed >>>>>>>> on the >>>>>>>> website. We've come up with a draft list of requirements for >>>>>>>> the >>>>>>>> tools to meet, which is on the wiki: >>>>>>>> >>>>>>>> http://gocwiki.geneontology.org/index.php/Tools_standards >>>>>>>> >>>>>>>> In order that they're listed on the website, the tools will >>>>>>>> have to >>>>>>>> meet all of the essential requirements stated, and the >>>>>>>> desirable >>>>>>>> requirements could be used in addition to give a score to >>>>>>>> the tool >>>>>>>> (possibly in addition to some user rankings - we haven't >>>>>>>> worked out >>>>>>>> the details of this yet). The set of questions on the wiki >>>>>>>> was put >>>>>>>> together by Amelia, and is an extension of what we already >>>>>>>> ask the >>>>>>>> developers to encompass these extra requirements. >>>>>>>> >>>>>>>> The idea is that we'd send an initial email out to all the >>>>>>>> tools >>>>>>>> developers (this is easy because they're all subscribed to GO >>>>>>>> friends) with these questions, and any tools for which we >>>>>>>> haven't >>>>>>>> received a response in a certain time period we'll remove >>>>>>>> from the >>>>>>>> website (this is a good way to get rid of all of the tools >>>>>>>> that are >>>>>>>> no longer being developed/deprecated tools). We'd warn them >>>>>>>> that any >>>>>>>> tools that don't meet the essential requirements would also be >>>>>>>> removed from the website (harsh!) at some fixed point in the >>>>>>>> future >>>>>>>> to give them a chance to modify their tools. And if by the >>>>>>>> date given >>>>>>>> the tools hadn't been modified, we remove them. >>>>>>>> >>>>>>>> So how does that sound? How about the requirements - too >>>>>>>> strict/ >>>>>>>> slack? Have we missed anything? >>>>>>>> >>>>>>>> We should add this to the agenda for the meeting tomorrow. >>>>>>>> >>>>>>>> thanks, >>>>>>>> >>>>>>>> Jane and Eurie >>>>>>> >>>>> >>>>> >>>>> -- >>>>> Evelyn Camon >>>>> GOA Coordinator >>>>> Senior Scientific Curator >>>>> European Bioinformatics Institute >>>>> Tel:01223-494465 >>>>> Fax:01223-494468 >>>>> E-mail: camon at ebi.ac.uk >>>>> URL: http://www.ebi.ac.uk/goa > > From suzi at berkeleybop.org Tue Mar 6 16:07:20 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Tue, 6 Mar 2007 16:07:20 -0800 Subject: ontology development reports In-Reply-To: References: Message-ID: <741F791B-FA21-46B3-8A76-684D063A0BC9@berkeleybop.org> nice. at first I was sad, I liked those monthly text reports, but this is very nice and a definite improvement -S On Mar 6, 2007, at 7:30 AM, Midori Harris wrote: > Hi all, > > I've put monthly reports on ontology development (well, prior to > last Novembre they were GO Editorial Office reports, but there's a > lot of overlap) on the internal wiki: > > http://gocwiki.geneontology.org/index.php/Ontology_Development#Reports > > cheers, > midori > From suzi at berkeleybop.org Tue Mar 6 19:23:27 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Tue, 6 Mar 2007 19:23:27 -0800 Subject: Fwd: sensu++ References: <45B152E3.5060909@idi.ntnu.no> Message-ID: <91874821-A292-432B-9D24-CB1CB1DFFAE5@berkeleybop.org> Did anyone every answer Waclaw?? -S Begin forwarded message: > From: Waclaw Kusnierczyk > Date: January 19, 2007 3:23:15 PM PST > To: Jane Lomax , Jennifer Clark > Cc: GO Friends > Subject: Re: sensu++ > >> this discussion may not apply, however, to the cases where the >> same term is used to represent different things rather than >> different versions of the same thing ('bud', even if not in go >> right now). in this cases it may still be reasonable to use >> 'sensu ... research community' (and much more this than >> 'sensu ...'), at least temporarily. > > > on second thought: even in these cases (say, 'bud'; there is > 'bud' in go in the sense of an emerging daughter cell, and there > are terms that refer to 'bud' in a completely different sense, > e.g., 'ureteric bud branching', 'golgi vesicle bud') it might be > better to have just 'bud' as the name of different nodes (terms; > 'term name' is an ugly terminological convention, by the way) > associated with different taxa (and having different definitions). > for even if two such nodes have the same name, there does not need > to be a confusion. for the computer, the nodes are ditinct (by > id). for a human user, term names may be modified on-the-fly to > contain the corresponding (and easily kept up to date) taxon > names. searching for a bud, the user is kindly asked whether he > means bud as in cell budding, or as something else. > > otherwise, 'bud' should perhaps be renamed to some '... bud', as it > unfairly uses a name that should be reserved for a much more > general node. (surely out of the scope of go). > > but this solution is unrealistic with the current go specification > that requires terms to have unique names. this may never come to > be changed. > > vQ > > -- > This message is from the GOFriends moderated mailing list. A list > of public > announcements and discussion of the Gene Ontology (GO) project. > Problems with the list? E-mail: owner- > gofriends at geneontology.org > Subscribing send "subscribe" to gofriends- > request at geneontology.org > Unsubscribing send "unsubscribe" to gofriends- > request at geneontology.org > Web: http://www.geneontology.org/ > From suzi at berkeleybop.org Tue Mar 6 19:51:15 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Tue, 6 Mar 2007 19:51:15 -0800 Subject: GOC meeting minutes v3 query AI 49 In-Reply-To: <45E447C7.6040007@sanger.ac.uk> References: <8035F1A3-8954-4689-8B5E-C617CCD70F9B@stanford.edu> <2E812441-8679-4056-B378-9F742E5D74F3@stanford.edu> <8F860E54-A3C4-41A8-95AE-0F958BB880A4@berkeleybop.org> <45E447C7.6040007@sanger.ac.uk> Message-ID: <329411C5-15C6-4345-9423-17E2690E5C92@berkeleybop.org> I have changed this to state: Pipes are treated as AND operations, that is: x|y| == x AND y AND z and means that xyz are all members of the complex that the thing interacts with Commas are treated as OR operations, that is: x,y,z == x OR y OR z and means that any of these 3 may be what is interacted with Is this okay? On Feb 27, 2007, at 7:01 AM, Valerie Wood wrote: > Re. Action item 49, > > This wasn't quite clear to me, but I might have misunderstood. I'm > not sure about the wording: > > 'Pipes mean intersection (or complex), commas mean union (or a > collection of possibilities) > > I came away with the impression that for IPI the new comma > separator will mean multiple independent binary interactions (from > the same Pubmed ID), and the existing pipe separator will refer to > a complex where the specific interactor cannot be distinguished. > > I'm not sure this is analogus to union and intersect. Isn't the > complex a collection of possibilities? (i.e. we don't know the > specific interactor). Also, I thought MGI used IPI for binary > interactions but action item 50 says "MGI change all pipes to > commas" wich also makes me think that something isn't quite correct. > > We also discussed this syntax for genetic interactions. I have used > pipe for multiple deletions (in a single strain), is this correct, > or will this change to comma? I don't remember the outcome. > > > Val > > > > > > Suzanna Lewis wrote: > >> Now with another change from Mike >> >> >> >> > > > -- > ---------------------------------------------------------------------- > ----- > Valerie Wood Tel: 01223 496909 > S. pombe Genome Project Fax: 01223 494919 Wellcome Trust > Sanger Institute email: val at sanger.ac.uk > Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe > Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe > > From suzi at berkeleybop.org Tue Mar 6 23:50:50 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Tue, 6 Mar 2007 23:50:50 -0800 Subject: Fwd: [Go-database] loading FASTA and references References: <44255ea80702230248s5ee1cc96nc0a127ff4f4aca94@mail.gmail.com> Message-ID: <182248B9-1B63-4D70-B37D-73A76C33AAD8@berkeleybop.org> another help question that I don't think (?) got answer. sorry if i'm wrong, but like to make sure our follow-up is good. Begin forwarded message: > From: "Thiago Venancio" > Date: February 23, 2007 2:48:50 AM PST > To: go-database at fruitfly.org > Subject: [Go-database] loading FASTA and references > > Dear Colleagues, > > I have a local AmiGO implementation with gene associations and > terms. Now I would like to insert tow more types of data: > > - sequences (FASTA format) of the annotated gene products. > - references (links) to other local custom database. > > The questions are: > 1) How to insert FASTA sequences in the database using go-dev > scripts ? > 2) How to create generic references and set up links in the place > of SGD or medline ones ? > > Any help is appreciated. > Thanks in advance. > > Thiago > > > -- > "The way to get started is to quit talking and begin doing." > Walt Disney > > ======================== > Thiago Motta Venancio, MSc > PhD student in Bioinformatics > University of Sao Paulo > ======================== > _______________________________________________ > Go-database mailing list > Go-database at fruitfly.org > http://mail.fruitfly.org/mailman/listinfo/go-database From jane at ebi.ac.uk Wed Mar 7 02:55:36 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Wed, 7 Mar 2007 10:55:36 +0000 (GMT) Subject: Fwd: [Go-database] loading FASTA and references In-Reply-To: <182248B9-1B63-4D70-B37D-73A76C33AAD8@berkeleybop.org> References: <44255ea80702230248s5ee1cc96nc0a127ff4f4aca94@mail.gmail.com> <182248B9-1B63-4D70-B37D-73A76C33AAD8@berkeleybop.org> Message-ID: Hi Suzi - no, I don't think this one has had an answer yet...it went to go-database rather than GO help, so it missed the usual go-help mechanisms for making sure everything gets answered. I think we should change the links on the GO database site so everything goes through go-help... Jane On Tue, 6 Mar 2007, Suzanna Lewis wrote: > another help question that I don't think (?) got answer. > > sorry if i'm wrong, but like to make sure our follow-up is good. > > > Begin forwarded message: > >> From: "Thiago Venancio" >> Date: February 23, 2007 2:48:50 AM PST >> To: go-database at fruitfly.org >> Subject: [Go-database] loading FASTA and references >> >> Dear Colleagues, >> >> I have a local AmiGO implementation with gene associations and terms. Now I >> would like to insert tow more types of data: >> >> - sequences (FASTA format) of the annotated gene products. >> - references (links) to other local custom database. >> >> The questions are: >> 1) How to insert FASTA sequences in the database using go-dev scripts ? >> 2) How to create generic references and set up links in the place of SGD or >> medline ones ? >> >> Any help is appreciated. >> Thanks in advance. >> >> Thiago >> >> >> -- >> "The way to get started is to quit talking and begin doing." >> Walt Disney >> >> ======================== >> Thiago Motta Venancio, MSc >> PhD student in Bioinformatics >> University of Sao Paulo >> ======================== >> _______________________________________________ >> Go-database mailing list >> Go-database at fruitfly.org >> http://mail.fruitfly.org/mailman/listinfo/go-database > 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 Wed Mar 7 02:57:04 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 7 Mar 2007 10:57:04 +0000 (GMT) Subject: Fwd: sensu++ In-Reply-To: <91874821-A292-432B-9D24-CB1CB1DFFAE5@berkeleybop.org> References: <45B152E3.5060909@idi.ntnu.no> <91874821-A292-432B-9D24-CB1CB1DFFAE5@berkeleybop.org> Message-ID: I believe Jane and David (and maybe also Jen) have responded; they took it off-list because it was getting rather involved and a bit esoteric. m On Tue, 6 Mar 2007, Suzanna Lewis wrote: > Did anyone every answer Waclaw?? > > -S > > Begin forwarded message: > >> From: Waclaw Kusnierczyk >> Date: January 19, 2007 3:23:15 PM PST >> To: Jane Lomax , Jennifer Clark >> Cc: GO Friends >> Subject: Re: sensu++ >> >>> this discussion may not apply, however, to the cases where the same term >>> is used to represent different things rather than different versions of >>> the same thing ('bud', even if not in go right now). in this cases it may >>> still be reasonable to use 'sensu ... research community' (and much more >>> this than 'sensu ...'), at least temporarily. >> >> >> on second thought: even in these cases (say, 'bud'; there is 'bud' in go >> in the sense of an emerging daughter cell, and there are terms that refer >> to 'bud' in a completely different sense, e.g., 'ureteric bud branching', >> 'golgi vesicle bud') it might be better to have just 'bud' as the name of >> different nodes (terms; 'term name' is an ugly terminological convention, >> by the way) associated with different taxa (and having different >> definitions). for even if two such nodes have the same name, there does >> not need to be a confusion. for the computer, the nodes are ditinct (by >> id). for a human user, term names may be modified on-the-fly to contain >> the corresponding (and easily kept up to date) taxon names. searching for >> a bud, the user is kindly asked whether he means bud as in cell budding, or >> as something else. >> >> otherwise, 'bud' should perhaps be renamed to some '... bud', as it >> unfairly uses a name that should be reserved for a much more general node. >> (surely out of the scope of go). >> >> but this solution is unrealistic with the current go specification that >> requires terms to have unique names. this may never come to be changed. >> >> vQ >> >> -- >> This message is from the GOFriends moderated mailing list. A list of >> public >> announcements and discussion of the Gene Ontology (GO) project. >> Problems with the list? E-mail: owner-gofriends at geneontology.org >> Subscribing send "subscribe" to gofriends-request at geneontology.org >> Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org >> Web: http://www.geneontology.org/ > From jane at ebi.ac.uk Wed Mar 7 05:46:24 2007 From: jane at ebi.ac.uk (Jane Lomax) Date: Wed, 7 Mar 2007 13:46:24 +0000 (GMT) Subject: missing GOID In-Reply-To: References: <3CF6E8C1-FE41-4D0E-B7AB-0F00908CBF77@genome.stanford.edu> Message-ID: Added those 3 terms to the file as obsoletes, Jane On Tue, 6 Mar 2007, Rama Balakrishnan wrote: > Sorry, two more. According the log file, in version 5.198 these should have > been obsoleted. > > 52478 > negative regulation by organism of defense-related symbiont cell wall callose > deposition > > 52476 > negative regulation by organism of defense-related symbiont MAP > kinase-mediated signal transduction > pathway > > are also missing from the obo file. > > rama > > On Mar 6, 2007, at 11:13 AM, Rama Balakrishnan wrote: > >> HI All, >> >> The following GOID is missing from the gene_ontology_edit.obo file. >> >> According to the cvs log file, 51842 'evasion or tolerance of symbiont >> immune response' was obsoleted on 2007/02/22, in version 5.181, but this >> term was not there in the previous version 5.180. >> >> This term was added to the obo file on 2005/12/07 in version 3.1234 of the >> gene_ontology.obo file. This term is there in 3.1235 version. >> >> Thanks, >> >> Rama > 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 val at sanger.ac.uk Wed Mar 7 06:53:49 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Wed, 07 Mar 2007 14:53:49 +0000 Subject: GOC meeting minutes v3 query AI 49 In-Reply-To: <329411C5-15C6-4345-9423-17E2690E5C92@berkeleybop.org> References: <8035F1A3-8954-4689-8B5E-C617CCD70F9B@stanford.edu> <2E812441-8679-4056-B378-9F742E5D74F3@stanford.edu> <8F860E54-A3C4-41A8-95AE-0F958BB880A4@berkeleybop.org> <45E447C7.6040007@sanger.ac.uk> <329411C5-15C6-4345-9423-17E2690E5C92@berkeleybop.org> Message-ID: <45EED1FD.7040008@sanger.ac.uk> Suzanna Lewis wrote: > I have changed this to state: > > Pipes are treated as AND operations, that is: x|y| == x AND y AND z > and means that xyz are all members of the complex that the thing > interacts with > > Commas are treated as OR operations, that is: x,y,z == x OR y OR z > and means that any of these 3 may be what is interacted with > > Is this okay? I think I have got it but I still have a little bit of confusion. To clarify the pipes and the commas are only used when a protein interacts with a complex? Commas are used when you have information that gene a interacts with a complex v|w|x|y|z but because of the nature of the experiment you cannot conclude that the interaction is a direct interaction with any particular subunit ? So we say gene 'a' interacts with some member of complex 'v,w,x,y,z' but we don't know which specifically. Pipes are used when a protein interacts with *specific* members of the complex. Therefore I am likely to have something like 'a interacts with v|z' (a is unlikely to interact directly with every member of the complex). So I would use pipes for direct interactions and commas to represent the entire complex when the direct interactor is not known. Have I understood this correctly? It follows that, if in a single paper you have multiple 2-hybrid interactions a interacts with l,m,n,o,p (which may not be members of the same complex) you cannot use a pipe and MUST curate these as separate interactions? Is this correct? I don't think everybody has done this. I have a couple of instances where I have used the pipe with the term 'protein binding, bridging' where the 2 interactors are NOT members of the same complex, according to the above, these would no longer be allowed, because this is no longer the meaning of the pipe. Is this correct? Sorry to labour this, Val From edimmer at ebi.ac.uk Wed Mar 7 07:16:40 2007 From: edimmer at ebi.ac.uk (Emily Dimmer) Date: Wed, 07 Mar 2007 15:16:40 +0000 Subject: GOC meeting minutes v3 query AI 49 In-Reply-To: <45EED1FD.7040008@sanger.ac.uk> References: <8035F1A3-8954-4689-8B5E-C617CCD70F9B@stanford.edu> <2E812441-8679-4056-B378-9F742E5D74F3@stanford.edu> <8F860E54-A3C4-41A8-95AE-0F958BB880A4@berkeleybop.org> <45E447C7.6040007@sanger.ac.uk> <329411C5-15C6-4345-9423-17E2690E5C92@berkeleybop.org> <45EED1FD.7040008@sanger.ac.uk> Message-ID: <45EED758.1000407@ebi.ac.uk> Hi Val, From that I understood: a. IPI - use commas to list *all* the *direct* binding partners for the identifier in field 2 which were investigated in the cited paper. This format only provides the user with a list of all the direct interactors that a protein has been found to have bound in all the experiments of one paper. This list of accessions may have resulted from multiple, independent binding experiments and therefore the annotation does not inform the user on the composition of any one specific binding interaction. -- Alternatively in this situation, multiple lines of annotations to the same GO term, same PMID but different contents of the 'with' field could be made to indicate the separate protein binding interactions shown in each the different experiments in the one paper (where groups' database setups allow this). b. From the discussion at the GOC, it became clear that an instance where a curator could use pipes with the IPI code would be very rare. Only protein identifiers in the 'with' column should be those found to bind directly to the identifier in field 2. Therefore the interactors in a one-to-many type of interaction should *not* be annotated, as curators cannot be sure which of the interactors bound directly to each other. In this case, if the one-to-many interaction is found to be a functional complex, then you can annotate to the relevant protein complex GO term (probably using the IDA evidence code, with nothing in the 'with column), but if this is not suitable then don't annotate at all. c. IGI - where the curator is only listing in the 'with' column the genes involved in *all* genetic interaction experiments from one paper which indicated the same function, then the gene identifiers in the 'with' field should be separated with commas (as for IPI). d. IGI - where a curator would like to indicate what *specific* combination of genes in a particular experiment produced functional information, then the gene identifiers in the 'with' field of an annotation can be delimited with the pipe symbol. -- Alternatively in this situation, multiple lines of annotations to the same GO term, same PMID but different contents of the 'with' field can be made to indicate the different gene combinations involved in the separate experiments in the paper (where groups' database setups allow this). cheers, Emily Valerie Wood wrote: > Suzanna Lewis wrote: > >> I have changed this to state: >> >> Pipes are treated as AND operations, that is: x|y| == x AND y AND z >> and means that xyz are all members of the complex that the thing >> interacts with >> >> Commas are treated as OR operations, that is: x,y,z == x OR y OR z >> and means that any of these 3 may be what is interacted with >> >> Is this okay? > > > > I think I have got it but I still have a little bit of confusion. To > clarify the pipes and the commas are only used when a protein > interacts with a complex? > > Commas are used when you have information that gene a interacts with a > complex v|w|x|y|z but because of the nature of the experiment you > cannot conclude that the interaction is a direct interaction with any > particular subunit ? So we say gene 'a' interacts with some member of > complex 'v,w,x,y,z' but we don't know which specifically. > > Pipes are used when a protein interacts with *specific* members of the > complex. Therefore I am likely to have something like > 'a interacts with v|z' (a is unlikely to interact directly with every > member of the complex). > So I would use pipes for direct interactions and commas to represent > the entire complex when the direct interactor is not known. > Have I understood this correctly? > > It follows that, if in a single paper you have multiple 2-hybrid > interactions a interacts with l,m,n,o,p (which may not be members of > the same complex) you cannot use a pipe and MUST curate these as > separate interactions? Is this correct? I don't think everybody has > done this. > > I have a couple of instances where I have used the pipe with the term > 'protein binding, bridging' where the 2 interactors are NOT members of > the same complex, according to the above, these would no longer be > allowed, because this is no longer the meaning of the pipe. Is this > correct? > > Sorry to labour this, > > Val > > > > > > > > > > > -- ************************************ Emily Dimmer GOA and IntAct Database Curator EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD, U.K. Tel: +44 1223 494654 Fax: +44 1223 494468 email: edimmer at ebi.ac.uk ************************************ From dph at informatics.jax.org Wed Mar 7 08:28:57 2007 From: dph at informatics.jax.org (David Hill) Date: Wed, 07 Mar 2007 11:28:57 -0500 Subject: neuroblast division (obsolete of change?) Message-ID: <45EEE849.5050607@informatics.jax.org> PLEASE READ IF YOU HAVE ANNOTATED TO NEUROBLAST DIVISION OR ITS CHILDREN. I am trying to address a sourceforge item from last year about neuroblast division GO:0045034. The current def of the term is: The asymmetrical division of a neuroblast, the neural precursor in the central nervous system, giving rise to another neuroblast and a ganglion mother cell. This definition is not correct because neuroblasts don't always divide like this. Instead it refers to a a specific type of neuroblast division that occurs in flies. Unfortunately we have two children of this term, neuroblast division (sensu Nematoda and Protostomia) and neuroblast division (sensu Vertebrata), whose definitions are all based on this incorrect definition. There are two solutions to this problem: 1) I can redefine neuroblast division to be correct: "The process resulting in the physical partitioning and separation of a neuroblast into daughter cells". Then I could change the name of 'neuroblast division (sensu Nematoda and Protostomia)' to be 'asymmetric neuroblast division' and define it as "The process resulting in the physical partitioning and separation of a neuroblast into daughter cells with different developmental potential". This assumes that every occurrence of neuroblast division in flies and worms is asymmetric. If not, I would merge 'neuroblast division (sensu Nematoda and Protostomia)' into 'neuroblast division'. I would then merge neuroblast division (sensu Vertebrata) into 'neuroblast division' because both symmetric and asymmetric neuroblast divisions occur in vertebrates. This process would make all annotations to these terms remain correct as long as we make the right choice with the (sensu Nematoda and Protostomia) term. Finally, I will create terms for symmetric and asymmetric neuroblast division and then correct all the part-of parentages. 2) I can obsolete the current neuroblast division terms and recreate the graph with new terms describing the actual types of neuroblast division that occur. This would require all of us reannotating our genes. I think fly has the most! Please give me feedback on this especially if you use or have used these terms. David From suzi at berkeleybop.org Wed Mar 7 17:13:08 2007 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Wed, 7 Mar 2007 17:13:08 -0800 Subject: [Go-database] loading FASTA and references In-Reply-To: References: <44255ea80702230248s5ee1cc96nc0a127ff4f4aca94@mail.gmail.com> <182248B9-1B63-4D70-B37D-73A76C33AAD8@berkeleybop.org> Message-ID: I agree, Chris, can you please see that this happens. -S On Mar 7, 2007, at 2:55 AM, Jane Lomax wrote: > Hi Suzi - no, I don't think this one has had an answer yet...it > went to go-database rather than GO help, so it missed the usual go- > help mechanisms > for making sure everything gets answered. I think we should change > the links > on the GO database site so everything goes through go-help... > > Jane > > On Tue, 6 Mar 2007, Suzanna Lewis wrote: > >> another help question that I don't think (?) got answer. >> >> sorry if i'm wrong, but like to make sure our follow-up is good. >> >> >> Begin forwarded message: >> >>> From: "Thiago Venancio" >>> Date: February 23, 2007 2:48:50 AM PST >>> To: go-database at fruitfly.org >>> Subject: [Go-database] loading FASTA and references >>> Dear Colleagues, >>> I have a local AmiGO implementation with gene associations and >>> terms. Now I would like to insert tow more types of data: >>> - sequences (FASTA format) of the annotated gene products. >>> - references (links) to other local custom database. >>> The questions are: >>> 1) How to insert FASTA sequences in the database using go-dev >>> scripts ? >>> 2) How to create generic references and set up links in the place >>> of SGD or medline ones ? >>> Any help is appreciated. >>> Thanks in advance. >>> Thiago >>> -- >>> "The way to get started is to quit talking and begin doing." >>> Walt Disney >>> ======================== >>> Thiago Motta Venancio, MSc >>> PhD student in Bioinformatics >>> University of Sao Paulo >>> ======================== >>> _______________________________________________ >>> Go-database mailing list >>> Go-database at fruitfly.org >>> http://mail.fruitfly.org/mailman/listinfo/go-database >> > > 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 kchris at genome.Stanford.EDU Wed Mar 7 17:53:07 2007 From: kchris at genome.Stanford.EDU (Karen Christie) Date: Wed, 7 Mar 2007 17:53:07 -0800 (PST) Subject: GOC meeting minutes v3 query AI 49 In-Reply-To: <45EED758.1000407@ebi.ac.uk> References: <8035F1A3-8954-4689-8B5E-C617CCD70F9B@stanford.edu> <2E812441-8679-4056-B378-9F742E5D74F3@stanford.edu> <8F860E54-A3C4-41A8-95AE-0F958BB880A4@berkeleybop.org> <45E447C7.6040007@sanger.ac.uk> <329411C5-15C6-4345-9423-17E2690E5C92@berkeleybop.org> <45EED1FD.7040008@sanger.ac.uk> <45EED758.1000407@ebi.ac.uk> Message-ID: I think my take on it was quite similar to Emily's. Basically, using pipes, for either IPI or IGI, means that you are specifying that all things in the piped list are interacting at the same time. For IGI, this syntax could be used when you want to indicate multiple mutations occurring in the same strain. For IPI, with the additional requirement that the with field is supposed to indicate direct interactions, it may turn out in practice that it is very rare that one would be certain that more than 2 things are interacting directly at the same time. For commas, it is just a list of things that interact with the annotated object, without any indication of whether they are all occurring at the same time or not. The comma syntax can be used for older annotations made by groups that did not track whether the interactions occurred pairwise or in higher order multiples. -Karen On Wed, 7 Mar 2007, Emily Dimmer wrote: > Hi Val, > > From that I understood: > > a. IPI - use commas to list *all* the *direct* binding partners for the > identifier in field 2 which were investigated in the cited paper. > This format only provides the user with a list of all the direct interactors > that a protein has been found to have bound in all the experiments of one > paper. This list of accessions may have resulted from multiple, independent > binding experiments and therefore the annotation does not inform the user on > the composition of any one specific binding interaction. > -- Alternatively in this situation, multiple lines of annotations to the same > GO term, same PMID but different contents of the 'with' field could be made > to indicate the separate protein binding interactions shown in each the > different experiments in the one paper (where groups' database setups allow > this). > > b. From the discussion at the GOC, it became clear that an instance where a > curator could use pipes with the IPI code would be very rare. Only protein > identifiers in the 'with' column should be those found to bind directly to > the identifier in field 2. Therefore the interactors in a one-to-many type > of interaction should *not* be annotated, as curators cannot be sure which of > the interactors bound directly to each other. In this case, if the > one-to-many interaction is found to be a functional complex, then you can > annotate to the relevant protein complex GO term (probably using the IDA > evidence code, with nothing in the 'with column), but if this is not suitable > then don't annotate at all. > > c. IGI - where the curator is only listing in the 'with' column the genes > involved in *all* genetic interaction experiments from one paper which > indicated the same function, then the gene identifiers in the 'with' field > should be separated with commas (as for IPI). > > d. IGI - where a curator would like to indicate what *specific* combination > of genes in a particular experiment produced functional information, then > the gene identifiers in the 'with' field of an annotation can be delimited > with the pipe symbol. > -- Alternatively in this situation, multiple lines of annotations to the same > GO term, same PMID but different contents of the 'with' field can be made to > indicate the different gene combinations involved in the separate experiments > in the paper (where groups' database setups allow this). > > cheers, > Emily > > > Valerie Wood wrote: > >> Suzanna Lewis wrote: >> >>> I have changed this to state: >>> >>> Pipes are treated as AND operations, that is: x|y| == x AND y AND z and >>> means that xyz are all members of the complex that the thing interacts >>> with >>> >>> Commas are treated as OR operations, that is: x,y,z == x OR y OR z and >>> means that any of these 3 may be what is interacted with >>> >>> Is this okay? >> >> >> >> I think I have got it but I still have a little bit of confusion. To >> clarify the pipes and the commas are only used when a protein interacts >> with a complex? >> >> Commas are used when you have information that gene a interacts with a >> complex v|w|x|y|z but because of the nature of the experiment you cannot >> conclude that the interaction is a direct interaction with any particular >> subunit ? So we say gene 'a' interacts with some member of complex >> 'v,w,x,y,z' but we don't know which specifically. >> >> Pipes are used when a protein interacts with *specific* members of the >> complex. Therefore I am likely to have something like >> 'a interacts with v|z' (a is unlikely to interact directly with every >> member of the complex). >> So I would use pipes for direct interactions and commas to represent the >> entire complex when the direct interactor is not known. >> Have I understood this correctly? >> >> It follows that, if in a single paper you have multiple 2-hybrid >> interactions a interacts with l,m,n,o,p (which may not be members of the >> same complex) you cannot use a pipe and MUST curate these as separate >> interactions? Is this correct? I don't think everybody has done this. >> >> I have a couple of instances where I have used the pipe with the term >> 'protein binding, bridging' where the 2 interactors are NOT members of the >> same complex, according to the above, these would no longer be allowed, >> because this is no longer the meaning of the pipe. Is this correct? >> >> Sorry to labour this, >> >> Val >> >> >> >> >> >> >> >> >> >> >> > > > -- > ************************************ > Emily Dimmer > GOA and IntAct Database Curator > EMBL-EBI > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD, U.K. > Tel: +44 1223 494654 > Fax: +44 1223 494468 > email: edimmer at ebi.ac.uk > ************************************ > From val at sanger.ac.uk Thu Mar 8 03:16:55 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 08 Mar 2007 11:16:55 +0000 Subject: GOC meeting minutes v3 query AI 49 In-Reply-To: References: <8035F1A3-8954-4689-8B5E-C617CCD70F9B@stanford.edu> <2E812441-8679-4056-B378-9F742E5D74F3@stanford.edu> <8F860E54-A3C4-41A8-95AE-0F958BB880A4@berkeleybop.org> <45E447C7.6040007@sanger.ac.uk> <329411C5-15C6-4345-9423-17E2690E5C92@berkeleybop.org> <45EED1FD.7040008@sanger.ac.uk> <45EED758.1000407@ebi.ac.uk> Message-ID: <45EFF0A7.8050405@sanger.ac.uk> Ok.... I tried to restate the existing comments in the minutes taking into account Karen and Emily's summaries (both of which I agree with). I don't think we have quite unambiguously defined each usage see <<>>. So instead of: Pipes are treated as AND operations, that is: x|y| == x AND y AND z and means that xyz are all members of the complex that the thing interacts with Commas are treated as OR operations, that is: x,y,z == x OR y OR z and means that any of these 3 may be what is interacted with I got: Pipes are treated as AND operations, that is: x|y|z == x AND y AND z and means that xyz are interacting at the same time. For IGI, this syntax should be used when you want to indicate multiple mutations occurring in the same strain. For IPI, this would indicate that the interactions are occurring simultaneously, with the additional requirement that the 'with' field indicate only direct interactions. In practice, the use of the pipe for IPI annotations will be vary rare. Commas are treated as OR operations, that is: x,y,z == x OR y OR z and means that all of these 3 are interacted with without any indication of whether the interactions are occurring simultaneously. The comma syntax can be used for older annotations made by groups that did not track whether the interactions occurred pairwise or in higher order multiples <<<<**note I'm still not sure about this bit what does 'higher order multiple mean here? this implies to me that commas can be used for older interactions which might not be 'direct interactions' is that correct? This implies the comma separator has 2 different interpretations i) for multiple direct interactions ii) for a group of interactors where you don't know if the interactions are direct or indirect....***this is the bit that bothers me, see also comment below****>>>. Alternatively to indicate multiple 'direct' interactions' from a single publication, independent annotations can be made to the same GO term, but with different contents of the 'with' field (where groups' database setups allow this) <<<<>>>> Commas are used for IGI - where the curator is only listing in the 'with' column the genes involved in *all* genetic interaction experiments from one paper which indicated the same function, then the gene identifiers in the 'with' field should be separated with commas (as for IPI) <<>>> The interactors in a one-to-many type of interaction should *not* be annotated, as curators cannot be sure which of the interactors bound directly to each other. In this case, if the one-to-many interaction is found to be a functional complex, then you can annotate to (or create) the relevant protein complex GO term (using the IDA evidence code, with nothing in the 'with column). If a complex term is not suitable then don't annotate at all. ? Val Karen Christie wrote: > I think my take on it was quite similar to Emily's. Basically, using > pipes, for either IPI or IGI, means that you are specifying that all > things in the piped list are interacting at the same time. For IGI, > this syntax could be used when you want to indicate multiple mutations > occurring in the same strain. For IPI, with the additional requirement > that the with field is supposed to indicate direct interactions, it > may turn out in practice that it is very rare that one would be > certain that more than 2 things are interacting directly at the same > time. > > For commas, it is just a list of things that interact with the > annotated object, without any indication of whether they are all > occurring at the same time or not. The comma syntax can be used for > older annotations made by groups that did not track whether the > interactions occurred pairwise or in higher order multiples. > > -Karen > > > On Wed, 7 Mar 2007, Emily Dimmer wrote: > >> Hi Val, >> >> From that I understood: >> >> a. IPI - use commas to list *all* the *direct* binding partners for >> the identifier in field 2 which were investigated in the cited paper. >> This format only provides the user with a list of all the direct >> interactors that a protein has been found to have bound in all the >> experiments of one paper. This list of accessions may have resulted >> from multiple, independent binding experiments and therefore the >> annotation does not inform the user on the composition of any one >> specific binding interaction. >> -- Alternatively in this situation, multiple lines of annotations to >> the same GO term, same PMID but different contents of the 'with' >> field could be made to indicate the separate protein binding >> interactions shown in each the different experiments in the one paper >> (where groups' database setups allow this). >> >> b. From the discussion at the GOC, it became clear that an instance >> where a curator could use pipes with the IPI code would be very rare. >> Only protein identifiers in the 'with' column should be those found >> to bind directly to the identifier in field 2. Therefore the >> interactors in a one-to-many type of interaction should *not* be >> annotated, as curators cannot be sure which of the interactors bound >> directly to each other. In this case, if the one-to-many interaction >> is found to be a functional complex, then you can annotate to the >> relevant protein complex GO term (probably using the IDA evidence >> code, with nothing in the 'with column), but if this is not suitable >> then don't annotate at all. >> >> c. IGI - where the curator is only listing in the 'with' column the >> genes involved in *all* genetic interaction experiments from one >> paper which indicated the same function, then the gene identifiers in >> the 'with' field should be separated with commas (as for IPI). >> >> d. IGI - where a curator would like to indicate what *specific* >> combination of genes in a particular experiment produced functional >> information, then the gene identifiers in the 'with' field of an >> annotation can be delimited with the pipe symbol. >> -- Alternatively in this situation, multiple lines of annotations to >> the same GO term, same PMID but different contents of the 'with' >> field can be made to indicate the different gene combinations >> involved in the separate experiments in the paper (where groups' >> database setups allow this). >> >> cheers, >> Emily >> >> >> Valerie Wood wrote: >> >>> Suzanna Lewis wrote: >>> >>>> I have changed this to state: >>>> >>>> Pipes are treated as AND operations, that is: x|y| == x AND y AND >>>> z and means that xyz are all members of the complex that the >>>> thing interacts with >>>> >>>> Commas are treated as OR operations, that is: x,y,z == x OR y OR z >>>> and means that any of these 3 may be what is interacted with >>>> >>>> Is this okay? >>> >>> >>> >>> >>> I think I have got it but I still have a little bit of confusion. To >>> clarify the pipes and the commas are only used when a protein >>> interacts with a complex? >>> >>> Commas are used when you have information that gene a interacts with >>> a complex v|w|x|y|z but because of the nature of the experiment you >>> cannot conclude that the interaction is a direct interaction with >>> any particular subunit ? So we say gene 'a' interacts with some >>> member of complex 'v,w,x,y,z' but we don't know which specifically. >>> >>> Pipes are used when a protein interacts with *specific* members of >>> the complex. Therefore I am likely to have something like >>> 'a interacts with v|z' (a is unlikely to interact directly with >>> every member of the complex). >>> So I would use pipes for direct interactions and commas to >>> represent the entire complex when the direct interactor is not known. >>> Have I understood this correctly? >>> >>> It follows that, if in a single paper you have multiple 2-hybrid >>> interactions a interacts with l,m,n,o,p (which may not be members of >>> the same complex) you cannot use a pipe and MUST curate these as >>> separate interactions? Is this correct? I don't think everybody has >>> done this. >>> >>> I have a couple of instances where I have used the pipe with the >>> term 'protein binding, bridging' where the 2 interactors are NOT >>> members of the same complex, according to the above, these would no >>> longer be allowed, because this is no longer the meaning of the >>> pipe. Is this correct? >>> >>> Sorry to labour this, >>> >>> Val >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> >> -- >> ************************************ >> Emily Dimmer >> GOA and IntAct Database Curator >> EMBL-EBI >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD, U.K. >> Tel: +44 1223 494654 >> Fax: +44 1223 494468 >> email: edimmer at ebi.ac.uk >> ************************************ >> > -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at sanger.ac.uk Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe From val at sanger.ac.uk Thu Mar 8 03:41:54 2007 From: val at sanger.ac.uk (Valerie Wood) Date: Thu, 08 Mar 2007 11:41:54 +0000 Subject: Transporter interest group Message-ID: <45EFF682.5050802@sanger.ac.uk> The transporter overhaul covers 890 function terms and is likely to generate a number of questions over the next few weeks. These will usually be annotation based questions about the usage of current terms which are not defined, or appear to have ambiguous usage and can't be addressed by our recruited transport expert Ian Paulsen. Rather than post all of the queries to the big list, it would be useful if we could initially post these to the transport interest group (currently Michelle G-Gwinn, Diana Fisk and me). As there are already a number of transporters in the reference genome list which will potentially be affected by the changes, it would be useful of one person from each ref genome could subscribe to this 'interest group'. Willing participants please e-mail me (don't worry, you don't need to be interested in transporters to join- I'm not). Thanks Val -- --------------------------------------------------------------------------- Valerie Wood Tel: 01223 496909 S. pombe Genome Project Fax: 01223 494919 Wellcome Trust Sanger Institute email: val at sanger.ac.uk Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe From midori at ebi.ac.uk Thu Mar 8 03:46:12 2007 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 8 Mar 2007 11:46:12 +0000 (GMT) Subject: Transporter interest group In-Reply-To: <45EFF682.5050802@sanger.ac.uk> References: <45EFF682.5050802@sanger.ac.uk> Message-ID: The transporter interest group doesn't have a mailing list of its own -- would this be a good time to create one (i.e. now it seems likely that a list would actually get used)? I'll join, just to keep up with what's going on; I doubt that I'll actually be able to help with many of the questions. m On Thu, 8 Mar 2007, Valerie Wood wrote: > > > The transporter overhaul covers 890 function terms and is likely to generate > a number of questions over the next few weeks. These will usually be > annotation based questions about the usage of current terms which are not > defined, or appear to have ambiguous usage and can't be addressed by our > recruited transport expert Ian Paulsen. > > Rather than post all of the queries to the big list, it would be useful if we > could initially post these to the transport interest group (currently > Michelle G-Gwinn, Diana Fisk and me). As there are already a number of > transporters in the reference genome list which will potentially be affected > by the changes, it would be useful of one person from each ref genome could > subscribe to this 'interest group'. > > Willing participants please e-mail me (don't worry, you don't need to be > interested in transporters to join- I'm not). > > > > Thanks > > Val > > > > From jclark at ebi.ac.uk Thu Mar 8 03:48:08 2007 From: jclark at ebi.ac.uk (J Clark) Date: Thu, 08 Mar 2007 11:48:08 +0000 Subject: Transporter interest group In-Reply-To: References: <45EFF682.5050802@sanger.ac.uk> Message-ID: <45EFF7F8.4060800@ebi.ac.uk> I have met a lot of people at conferences who I know would want to be signed up to that. I can get in touch with them and i