From midori at ebi.ac.uk Mon Nov 2 02:41:22 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 2 Nov 2009 10:41:22 +0000 (GMT) Subject: [Ontology-editors] Inference of GO BP relationships from CHEBI In-Reply-To: <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> Message-ID: Yes, I think we can make quite a bit more progress with a teleconf -- not just more newlinks; there are a few SF items awaiting GO-Chebi resolution. m On Fri, 30 Oct 2009, Chris Mungall wrote: > > Thanks Midori! > > Looks like a few things still to be resolved. Perhaps a chebi-go telecon to > sort these out? > > On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: > >> Hi all, >> >> A quick update: I've added the last of the links from the second version of >> go/scratch/xps/biological_process_xp_chebi-newlinks.txt that I thought >> looked OK. I've also updated the file of comments that I attached to the SF >> item, and have attached it here as well. >> >> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >> >> Cheers, >> Midori > From midori at ebi.ac.uk Mon Nov 2 05:37:48 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Mon, 2 Nov 2009 13:37:48 +0000 (GMT) Subject: [Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI In-Reply-To: <4AEEC63A.7080907@gmail.com> References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> Message-ID: OK. Paula - by "next Wednesday" do you mean the 4th or 11th? Chris - what's the earliest time of day that works for you? Midori On Mon, 2 Nov 2009, Paula de Matos wrote: > Sorry for the late response but we're currently busy with the new ChEBI > release. > > Yes a teleconf makes sense. Would you like to setup a doodle poll? Anytime > after next Wednesday is most suitable for us. > > Thanks, > Paula > > Midori Harris wrote: >> Yes, I think we can make quite a bit more progress with a teleconf -- not >> just more newlinks; there are a few SF items awaiting GO-Chebi resolution. >> >> m >> >> On Fri, 30 Oct 2009, Chris Mungall wrote: >> >> >>> Thanks Midori! >>> >>> Looks like a few things still to be resolved. Perhaps a chebi-go telecon >>> to sort these out? >>> >>> On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: >>> >>> >>>> Hi all, >>>> >>>> A quick update: I've added the last of the links from the second version >>>> of go/scratch/xps/biological_process_xp_chebi-newlinks.txt that I thought >>>> looked OK. I've also updated the file of comments that I attached to the >>>> SF item, and have attached it here as well. >>>> >>>> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >>>> >>>> Cheers, >>>> Midori >>>> >> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart your >> developing skills, take BlackBerry mobile applications to market and stay >> ahead of the curve. Join us from November 9 - 12, 2009. Register now! >> http://p.sf.net/sfu/devconference >> _______________________________________________ >> Chebi-ontology mailing list >> Chebi-ontology at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/chebi-ontology >> >> From cjm at fruitfly.org Mon Nov 2 09:19:12 2009 From: cjm at fruitfly.org (Chris Mungall) Date: Mon, 2 Nov 2009 09:19:12 -0800 Subject: [Ontology-editors] Demo cross products In-Reply-To: References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> Message-ID: <68F977F7-92CE-4E9D-A375-3577B87CC917@fruitfly.org> Bay bridge still closed. Bart schedule off. May be late. Sent from my iPhone. On Nov 2, 2009, at 2:41 AM, Midori Harris wrote: > Yes, I think we can make quite a bit more progress with a teleconf > -- not just more newlinks; there are a few SF items awaiting GO- > Chebi resolution. > > m > > On Fri, 30 Oct 2009, Chris Mungall wrote: > >> >> Thanks Midori! >> >> Looks like a few things still to be resolved. Perhaps a chebi-go >> telecon to sort these out? >> >> On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: >> >>> Hi all, >>> A quick update: I've added the last of the links from the second >>> version of go/scratch/xps/biological_process_xp_chebi-newlinks.txt >>> that I thought looked OK. I've also updated the file of comments >>> that I attached to the SF item, and have attached it here as well. >>> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >>> Cheers, >>> Midori >> > From paula.dematos at gmail.com Mon Nov 2 03:44:58 2009 From: paula.dematos at gmail.com (Paula de Matos) Date: Mon, 02 Nov 2009 11:44:58 +0000 Subject: [Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI In-Reply-To: References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> Message-ID: <4AEEC63A.7080907@gmail.com> Sorry for the late response but we're currently busy with the new ChEBI release. Yes a teleconf makes sense. Would you like to setup a doodle poll? Anytime after next Wednesday is most suitable for us. Thanks, Paula Midori Harris wrote: > Yes, I think we can make quite a bit more progress with a teleconf -- not > just more newlinks; there are a few SF items awaiting GO-Chebi resolution. > > m > > On Fri, 30 Oct 2009, Chris Mungall wrote: > > >> Thanks Midori! >> >> Looks like a few things still to be resolved. Perhaps a chebi-go telecon to >> sort these out? >> >> On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: >> >> >>> Hi all, >>> >>> A quick update: I've added the last of the links from the second version of >>> go/scratch/xps/biological_process_xp_chebi-newlinks.txt that I thought >>> looked OK. I've also updated the file of comments that I attached to the SF >>> item, and have attached it here as well. >>> >>> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >>> >>> Cheers, >>> Midori >>> > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > Chebi-ontology mailing list > Chebi-ontology at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/chebi-ontology > > From paula.dematos at gmail.com Mon Nov 2 05:42:29 2009 From: paula.dematos at gmail.com (Paula de Matos) Date: Mon, 02 Nov 2009 13:42:29 +0000 Subject: [Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI In-Reply-To: References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> Message-ID: <4AEEE1C5.6020206@gmail.com> Sorry I meant the 11th. P Midori Harris wrote: > OK. > > Paula - by "next Wednesday" do you mean the 4th or 11th? > > Chris - what's the earliest time of day that works for you? > > Midori > > On Mon, 2 Nov 2009, Paula de Matos wrote: > >> Sorry for the late response but we're currently busy with the new >> ChEBI release. >> >> Yes a teleconf makes sense. Would you like to setup a doodle poll? >> Anytime after next Wednesday is most suitable for us. >> >> Thanks, >> Paula >> >> Midori Harris wrote: >>> Yes, I think we can make quite a bit more progress with a teleconf >>> -- not just more newlinks; there are a few SF items awaiting >>> GO-Chebi resolution. >>> >>> m >>> >>> On Fri, 30 Oct 2009, Chris Mungall wrote: >>> >>> >>>> Thanks Midori! >>>> >>>> Looks like a few things still to be resolved. Perhaps a chebi-go >>>> telecon to sort these out? >>>> >>>> On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: >>>> >>>> >>>>> Hi all, >>>>> >>>>> A quick update: I've added the last of the links from the second >>>>> version of go/scratch/xps/biological_process_xp_chebi-newlinks.txt >>>>> that I thought looked OK. I've also updated the file of comments >>>>> that I attached to the SF item, and have attached it here as well. >>>>> >>>>> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >>>>> >>>>> >>>>> Cheers, >>>>> Midori >>>>> >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >>> is the only developer event you need to attend this year. Jumpstart >>> your >>> developing skills, take BlackBerry mobile applications to market and >>> stay ahead of the curve. Join us from November 9 - 12, 2009. >>> Register now! >>> http://p.sf.net/sfu/devconference >>> _______________________________________________ >>> Chebi-ontology mailing list >>> Chebi-ontology at lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/chebi-ontology >>> >>> From midori at ebi.ac.uk Wed Nov 4 03:01:08 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 4 Nov 2009 11:01:08 +0000 (GMT) Subject: [Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI In-Reply-To: <4AEEC63A.7080907@gmail.com> References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> Message-ID: Hi all, I've set up a doodle poll for a phone conference: http://www.doodle.com/dh9gy58q6uu3fwdd It just covers one week; if we can't find a time on the dates in this poll, I'll do a new one for the following week or so. cheers, Midori On Mon, 2 Nov 2009, Paula de Matos wrote: > Sorry for the late response but we're currently busy with the new ChEBI > release. > > Yes a teleconf makes sense. Would you like to setup a doodle poll? Anytime > after next Wednesday is most suitable for us. > > Thanks, > Paula > > Midori Harris wrote: >> Yes, I think we can make quite a bit more progress with a teleconf -- not >> just more newlinks; there are a few SF items awaiting GO-Chebi resolution. >> >> m >> >> On Fri, 30 Oct 2009, Chris Mungall wrote: >> >> >>> Thanks Midori! >>> >>> Looks like a few things still to be resolved. Perhaps a chebi-go telecon >>> to sort these out? >>> >>> On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: >>> >>> >>>> Hi all, >>>> >>>> A quick update: I've added the last of the links from the second version >>>> of go/scratch/xps/biological_process_xp_chebi-newlinks.txt that I thought >>>> looked OK. I've also updated the file of comments that I attached to the >>>> SF item, and have attached it here as well. >>>> >>>> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >>>> >>>> Cheers, >>>> Midori >>>> >> >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart your >> developing skills, take BlackBerry mobile applications to market and stay >> ahead of the curve. Join us from November 9 - 12, 2009. Register now! >> http://p.sf.net/sfu/devconference >> _______________________________________________ >> Chebi-ontology mailing list >> Chebi-ontology at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/chebi-ontology >> >> From cjm at berkeleybop.org Wed Nov 4 10:53:04 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Wed, 4 Nov 2009 10:53:04 -0800 Subject: [Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI In-Reply-To: <4AEEE1C5.6020206@gmail.com> References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> <4AEEE1C5.6020206@gmail.com> Message-ID: <37318F81-BCF3-4221-9CD6-508E6E6FC958@berkeleybop.org> I can do the 11th or some time following week On Nov 2, 2009, at 5:42 AM, Paula de Matos wrote: > Sorry I meant the 11th. > P > > > Midori Harris wrote: >> OK. >> >> Paula - by "next Wednesday" do you mean the 4th or 11th? >> >> Chris - what's the earliest time of day that works for you? >> >> Midori >> >> On Mon, 2 Nov 2009, Paula de Matos wrote: >> >>> Sorry for the late response but we're currently busy with the new >>> ChEBI release. >>> >>> Yes a teleconf makes sense. Would you like to setup a doodle poll? >>> Anytime after next Wednesday is most suitable for us. >>> >>> Thanks, >>> Paula >>> >>> Midori Harris wrote: >>>> Yes, I think we can make quite a bit more progress with a >>>> teleconf -- not just more newlinks; there are a few SF items >>>> awaiting GO-Chebi resolution. >>>> >>>> m >>>> >>>> On Fri, 30 Oct 2009, Chris Mungall wrote: >>>> >>>> >>>>> Thanks Midori! >>>>> >>>>> Looks like a few things still to be resolved. Perhaps a chebi-go >>>>> telecon to sort these out? >>>>> >>>>> On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: >>>>> >>>>> >>>>>> Hi all, >>>>>> >>>>>> A quick update: I've added the last of the links from the >>>>>> second version of go/scratch/xps/biological_process_xp_chebi- >>>>>> newlinks.txt that I thought looked OK. I've also updated the >>>>>> file of comments that I attached to the SF item, and have >>>>>> attached it here as well. >>>>>> >>>>>> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >>>>>> >>>>>> Cheers, >>>>>> Midori >>>>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Come build with us! The BlackBerry(R) Developer Conference in SF, >>>> CA >>>> is the only developer event you need to attend this year. >>>> Jumpstart your >>>> developing skills, take BlackBerry mobile applications to market >>>> and stay ahead of the curve. Join us from November 9 - 12, 2009. >>>> Register now! >>>> http://p.sf.net/sfu/devconference >>>> _______________________________________________ >>>> Chebi-ontology mailing list >>>> Chebi-ontology at lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/chebi-ontology >>>> >>>> > > From midori at ebi.ac.uk Thu Nov 5 03:58:52 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 5 Nov 2009 11:58:52 +0000 (GMT) Subject: [Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI In-Reply-To: <37318F81-BCF3-4221-9CD6-508E6E6FC958@berkeleybop.org> References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> <4AEEE1C5.6020206@gmail.com> <37318F81-BCF3-4221-9CD6-508E6E6FC958@berkeleybop.org> Message-ID: Can you do 8 AM (your time) on the 12th or 13th? Those are looking best on the doodle poll. If not, maybe same day & time the following week -- 19th or 20th? m On Wed, 4 Nov 2009, Chris Mungall wrote: > > I can do the 11th or some time following week > > On Nov 2, 2009, at 5:42 AM, Paula de Matos wrote: > >> Sorry I meant the 11th. >> P >> >> >> Midori Harris wrote: >>> OK. >>> >>> Paula - by "next Wednesday" do you mean the 4th or 11th? >>> >>> Chris - what's the earliest time of day that works for you? >>> >>> Midori >>> >>> On Mon, 2 Nov 2009, Paula de Matos wrote: >>> >>>> Sorry for the late response but we're currently busy with the new ChEBI >>>> release. >>>> >>>> Yes a teleconf makes sense. Would you like to setup a doodle poll? >>>> Anytime after next Wednesday is most suitable for us. >>>> >>>> Thanks, >>>> Paula >>>> >>>> Midori Harris wrote: >>>>> Yes, I think we can make quite a bit more progress with a teleconf -- >>>>> not just more newlinks; there are a few SF items awaiting GO-Chebi >>>>> resolution. >>>>> >>>>> m >>>>> >>>>> On Fri, 30 Oct 2009, Chris Mungall wrote: >>>>> >>>>> >>>>>> Thanks Midori! >>>>>> >>>>>> Looks like a few things still to be resolved. Perhaps a chebi-go >>>>>> telecon to sort these out? >>>>>> >>>>>> On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: >>>>>> >>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> A quick update: I've added the last of the links from the second >>>>>>> version of go/scratch/xps/biological_process_xp_chebi-newlinks.txt >>>>>>> that I thought looked OK. I've also updated the file of comments that >>>>>>> I attached to the SF item, and have attached it here as well. >>>>>>> >>>>>>> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >>>>>>> >>>>>>> Cheers, >>>>>>> Midori >>>>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >>>>> is the only developer event you need to attend this year. Jumpstart your >>>>> developing skills, take BlackBerry mobile applications to market and >>>>> stay ahead of the curve. Join us from November 9 - 12, 2009. Register >>>>> now! >>>>> http://p.sf.net/sfu/devconference >>>>> _______________________________________________ >>>>> Chebi-ontology mailing list >>>>> Chebi-ontology at lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/chebi-ontology >>>>> >>>>> >> > From jane at ebi.ac.uk Thu Nov 5 07:59:04 2009 From: jane at ebi.ac.uk (Jane Lomax) Date: Thu, 05 Nov 2009 15:59:04 +0000 Subject: [Ontology-editors] online working ontology browser? Message-ID: <4AF2F648.2010503@ebi.ac.uk> I'm currently working on an ontology development project with some external experts - as we do. I have a working obo file that I'm editing, and the problem I have is that I want to be able to send it around for comments but I think loading it into OE is a bit hard-core for some external (and possibly internal) folks - there's a bit of a learning threashold getting it up and running etc. Sometimes I think people are just going through looking at the obo stanzas to make comments, which isn't a great way to browse an ontology. Can anyone think of a solution to this? It would be great to have some sort of online resource where you could upload an obo file and it would provide a graph view of the ontology for people to click through. What about an online instantiation of OE, with just the browse features enabled? Is that even remotely feasible? Is is there something like that out there already? Or am I being a bit optimistic here...it's just that we're doing work with external people so much these days it would be good if we could make it easier. cheers, Jane -- Dr Jane Lomax GO Editorial Office EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridgeshire, UK CB10 1SD p: +44 1223 492516 f: +44 1223 494468 From midori at ebi.ac.uk Thu Nov 5 08:25:15 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 5 Nov 2009 16:25:15 +0000 (GMT) Subject: [Ontology-editors] online working ontology browser? In-Reply-To: <4AF2F648.2010503@ebi.ac.uk> References: <4AF2F648.2010503@ebi.ac.uk> Message-ID: I think the OLS technology would work ... if I've got that right, it would be more a question of whether you'd want an ontology to get into OLS if it's at a really early stage of development -- and if not, where we might be able to set up an OLS server that would handle ontologies that you didn't want made public yet. m On Thu, 5 Nov 2009, Jane Lomax wrote: > I'm currently working on an ontology development project with some external > experts - as we do. I have a working obo file that I'm editing, and the > problem I have is that I want to be able to send it around for comments but I > think loading it into OE is a bit hard-core for some external (and possibly > internal) folks - there's a bit of a learning threashold getting it up and > running etc. Sometimes I think people are just going through looking at the > obo stanzas to make comments, which isn't a great way to browse an ontology. > > Can anyone think of a solution to this? It would be great to have some sort > of online resource where you could upload an obo file and it would provide a > graph view of the ontology for people to click through. What about an online > instantiation of OE, with just the browse features enabled? Is that even > remotely feasible? Is is there something like that out there already? > > Or am I being a bit optimistic here...it's just that we're doing work with > external people so much these days it would be good if we could make it > easier. > > cheers, > > Jane > > From jane at ebi.ac.uk Thu Nov 5 08:29:11 2009 From: jane at ebi.ac.uk (Jane Lomax) Date: Thu, 05 Nov 2009 16:29:11 +0000 Subject: [Ontology-editors] online working ontology browser? In-Reply-To: References: <4AF2F648.2010503@ebi.ac.uk> Message-ID: <4AF2FD57.20007@ebi.ac.uk> Yes, that's exactly what I meant...definitely wouldn't want it in the main OLS though. Would have to be on an ontology dev page somewhere... Midori Harris wrote: > I think the OLS technology would work ... if I've got that right, it > would be more a question of whether you'd want an ontology to get into > OLS if it's at a really early stage of development -- and if not, > where we might be able to set up an OLS server that would handle > ontologies that you didn't want made public yet. > > m > > On Thu, 5 Nov 2009, Jane Lomax wrote: > >> I'm currently working on an ontology development project with some >> external experts - as we do. I have a working obo file that I'm >> editing, and the problem I have is that I want to be able to send it >> around for comments but I think loading it into OE is a bit hard-core >> for some external (and possibly internal) folks - there's a bit of a >> learning threashold getting it up and running etc. Sometimes I think >> people are just going through looking at the obo stanzas to make >> comments, which isn't a great way to browse an ontology. >> >> Can anyone think of a solution to this? It would be great to have >> some sort of online resource where you could upload an obo file and >> it would provide a graph view of the ontology for people to click >> through. What about an online instantiation of OE, with just the >> browse features enabled? Is that even remotely feasible? Is is there >> something like that out there already? >> >> Or am I being a bit optimistic here...it's just that we're doing work >> with external people so much these days it would be good if we could >> make it easier. >> >> cheers, >> >> Jane >> >> -- Dr Jane Lomax GO Editorial Office EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridgeshire, UK CB10 1SD p: +44 1223 492516 f: +44 1223 494468 From hjd at informatics.jax.org Thu Nov 5 08:32:37 2009 From: hjd at informatics.jax.org (Harold Drabkin) Date: Thu, 05 Nov 2009 11:32:37 -0500 Subject: [Ontology-editors] online working ontology browser? In-Reply-To: <4AF2F648.2010503@ebi.ac.uk> References: <4AF2F648.2010503@ebi.ac.uk> Message-ID: <4AF2FE25.7060201@informatics.jax.org> Perhaps a special version of OE that's merely a viewer? All other modules (reasoners, id managers, etc.) removed? hd Jane Lomax wrote:I'm currently working on an ontology development project with some external experts - as we do. I have a working obo file that I'm editing, and the problem I have is that I want to be able to send it around for comments but I think loading it into OE is a bit hard-core for some external (and possibly internal) folks - there's a bit of a learning threashold getting it up and running etc. Sometimes I think people are just going through looking at the obo stanzas to make comments, which isn't a great way to browse an ontology. Can anyone think of a solution to this? It would be great to have some sort of online resource where you could upload an obo file and it would provide a graph view of the ontology for people to click through. What about an online instantiation of OE, with just the browse features enabled? Is that even remotely feasible? Is is there something like that out there already? Or am I being a bit optimistic here...it's just that we're doing work with external people so much these days it would be good if we could make it easier. cheers, Jane From genkisugi.net at gmail.com Thu Nov 5 10:15:50 2009 From: genkisugi.net at gmail.com (Seth Carbon) Date: Thu, 05 Nov 2009 10:15:50 -0800 Subject: [Ontology-editors] online working ontology browser? In-Reply-To: <4AF2FE25.7060201@informatics.jax.org> References: <4AF2F648.2010503@ebi.ac.uk> <4AF2FE25.7060201@informatics.jax.org> Message-ID: <4AF31656.3030809@gmail.com> It might also be possible to do this with some of the AmiGO parts that I have around, but it could range from fairly simple to ugly hack (and probably not worth it) depending on your requirements. How big an ontology are you trying to work with and are you interested in a viewer (ontology all displayed at once) or a browser (the ontology is big and complicated enough that having it all at once would be bad). Cheers, -Seth Harold Drabkin wrote: > Perhaps a special version of OE that's merely a viewer? All other > modules (reasoners, id managers, etc.) removed? > > hd > > > Jane Lomax wrote:I'm currently working on an ontology development > project with some external experts - as we do. I have a working obo > file that I'm editing, and the problem I have is that I want to be > able to send it around for comments but I think loading it into OE is > a bit hard-core for some external (and possibly internal) folks - > there's a bit of a learning threashold getting it up and running etc. > Sometimes I think people are just going through looking at the obo > stanzas to make comments, which isn't a great way to browse an ontology. > > Can anyone think of a solution to this? It would be great to have some > sort of online resource where you could upload an obo file and it > would provide a graph view of the ontology for people to click > through. What about an online instantiation of OE, with just the > browse features enabled? Is that even remotely feasible? Is is there > something like that out there already? > > Or am I being a bit optimistic here...it's just that we're doing work > with external people so much these days it would be good if we could > make it easier. > > cheers, > > Jane > > > From cjm at berkeleybop.org Thu Nov 5 10:46:23 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 5 Nov 2009 10:46:23 -0800 Subject: [Ontology-editors] online working ontology browser? In-Reply-To: <4AF31656.3030809@gmail.com> References: <4AF2F648.2010503@ebi.ac.uk> <4AF2FE25.7060201@informatics.jax.org> <4AF31656.3030809@gmail.com> Message-ID: <497C1990-512E-4589-BDB8-155AFB7065E5@berkeleybop.org> We need to rewrite parts of AmiGO anyway, such as the tree-browser. If this is done using the new GOBO code then we can be agnostic about whether there is a database behind the scenes or a file loaded into memory. This means it will be easier to allow people to upload their own ontologies, overlay them, etc On Nov 5, 2009, at 10:15 AM, Seth Carbon wrote: > It might also be possible to do this with some of the AmiGO parts > that I have around, but it could range from fairly simple to ugly > hack (and probably not worth it) depending on your requirements. > > How big an ontology are you trying to work with and are you > interested in a viewer (ontology all displayed at once) or a browser > (the ontology is big and complicated enough that having it all at > once would be bad). > > Cheers, > > -Seth > > > Harold Drabkin wrote: >> Perhaps a special version of OE that's merely a viewer? All other >> modules (reasoners, id managers, etc.) removed? >> >> hd >> >> >> Jane Lomax wrote:I'm currently working on an ontology development >> project with some external experts - as we do. I have a working obo >> file that I'm editing, and the problem I have is that I want to be >> able to send it around for comments but I think loading it into OE >> is a bit hard-core for some external (and possibly internal) folks >> - there's a bit of a learning threashold getting it up and running >> etc. Sometimes I think people are just going through looking at the >> obo stanzas to make comments, which isn't a great way to browse an >> ontology. >> >> Can anyone think of a solution to this? It would be great to have >> some sort of online resource where you could upload an obo file and >> it would provide a graph view of the ontology for people to click >> through. What about an online instantiation of OE, with just the >> browse features enabled? Is that even remotely feasible? Is is >> there something like that out there already? >> >> Or am I being a bit optimistic here...it's just that we're doing >> work with external people so much these days it would be good if we >> could make it easier. >> >> cheers, >> >> Jane >> >> >> > > _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors > From cjm at berkeleybop.org Thu Nov 5 10:46:58 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 5 Nov 2009 10:46:58 -0800 Subject: [Ontology-editors] online working ontology browser? In-Reply-To: <4AF2FE25.7060201@informatics.jax.org> References: <4AF2F648.2010503@ebi.ac.uk> <4AF2FE25.7060201@informatics.jax.org> Message-ID: On Nov 5, 2009, at 8:32 AM, Harold Drabkin wrote: > Perhaps a special version of OE that's merely a viewer? All other > modules (reasoners, id managers, etc.) removed? A webstart OE is one options But rewriting OE to be a true web application would be a monumental task > hd > > > Jane Lomax wrote:I'm currently working on an ontology development > project with some external experts - as we do. I have a working obo > file that I'm editing, and the problem I have is that I want to be > able to send it around for comments but I think loading it into OE > is a bit hard-core for some external (and possibly internal) folks - > there's a bit of a learning threashold getting it up and running > etc. Sometimes I think people are just going through looking at the > obo stanzas to make comments, which isn't a great way to browse an > ontology. > > Can anyone think of a solution to this? It would be great to have > some sort of online resource where you could upload an obo file and > it would provide a graph view of the ontology for people to click > through. What about an online instantiation of OE, with just the > browse features enabled? Is that even remotely feasible? Is is there > something like that out there already? > > Or am I being a bit optimistic here...it's just that we're doing > work with external people so much these days it would be good if we > could make it easier. > > cheers, > > Jane > > > _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors > From cjm at berkeleybop.org Thu Nov 5 11:38:00 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 5 Nov 2009 11:38:00 -0800 Subject: [Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI In-Reply-To: References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> <4AEEE1C5.6020206@gmail.com> <37318F81-BCF3-4221-9CD6-508E6E6FC958@berkeleybop.org> Message-ID: <1602ACC5-53B9-4D98-ABBC-56EBE8CE04B5@berkeleybop.org> The following week. I filled in the poll. On Nov 5, 2009, at 3:58 AM, Midori Harris wrote: > Can you do 8 AM (your time) on the 12th or 13th? Those are looking > best on the doodle poll. > > If not, maybe same day & time the following week -- 19th or 20th? > > m > > On Wed, 4 Nov 2009, Chris Mungall wrote: > >> >> I can do the 11th or some time following week >> >> On Nov 2, 2009, at 5:42 AM, Paula de Matos wrote: >> >>> Sorry I meant the 11th. >>> P >>> Midori Harris wrote: >>>> OK. >>>> Paula - by "next Wednesday" do you mean the 4th or 11th? >>>> Chris - what's the earliest time of day that works for you? >>>> Midori >>>> On Mon, 2 Nov 2009, Paula de Matos wrote: >>>>> Sorry for the late response but we're currently busy with the >>>>> new ChEBI release. >>>>> Yes a teleconf makes sense. Would you like to setup a doodle >>>>> poll? Anytime after next Wednesday is most suitable for us. >>>>> Thanks, >>>>> Paula >>>>> Midori Harris wrote: >>>>>> Yes, I think we can make quite a bit more progress with a >>>>>> teleconf -- not just more newlinks; there are a few SF items >>>>>> awaiting GO-Chebi resolution. >>>>>> m >>>>>> On Fri, 30 Oct 2009, Chris Mungall wrote: >>>>>>> Thanks Midori! >>>>>>> Looks like a few things still to be resolved. Perhaps a chebi- >>>>>>> go telecon to sort these out? >>>>>>> On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: >>>>>>>> Hi all, >>>>>>>> A quick update: I've added the last of the links from the >>>>>>>> second version of go/scratch/xps/biological_process_xp_chebi- >>>>>>>> newlinks.txt that I thought looked OK. I've also updated the >>>>>>>> file of comments that I attached to the SF item, and have >>>>>>>> attached it here as well. >>>>>>>> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >>>>>>>> Cheers, >>>>>>>> Midori >>>>>> ------------------------------------------------------------------------------ >>>>>> Come build with us! The BlackBerry(R) Developer Conference in >>>>>> SF, CA >>>>>> is the only developer event you need to attend this year. >>>>>> Jumpstart your >>>>>> developing skills, take BlackBerry mobile applications to >>>>>> market and stay ahead of the curve. Join us from November 9 - >>>>>> 12, 2009. Register now! >>>>>> http://p.sf.net/sfu/devconference >>>>>> _______________________________________________ >>>>>> Chebi-ontology mailing list >>>>>> Chebi-ontology at lists.sourceforge.net >>>>>> https://lists.sourceforge.net/lists/listinfo/chebi-ontology >> > From sjcarbon at berkeleybop.org Thu Nov 5 15:09:09 2009 From: sjcarbon at berkeleybop.org (Seth Carbon) Date: Thu, 05 Nov 2009 15:09:09 -0800 Subject: [Ontology-editors] online working ontology browser? In-Reply-To: <497C1990-512E-4589-BDB8-155AFB7065E5@berkeleybop.org> References: <4AF2F648.2010503@ebi.ac.uk> <4AF2FE25.7060201@informatics.jax.org> <4AF31656.3030809@gmail.com> <497C1990-512E-4589-BDB8-155AFB7065E5@berkeleybop.org> Message-ID: <4AF35B15.6070807@berkeleybop.org> > > We need to rewrite parts of AmiGO anyway, such as the tree-browser. If > this is done using the new GOBO code then we can be agnostic about > whether there is a database behind the scenes or a file loaded into > memory. This means it will be easier to allow people to upload their > own ontologies, overlay them, etc True, but there are some considerations here. The most important off the top of my head is persistent storage, which is handled automatically by having db on the backend. Having data uploaded and maintaining its connection to the user throughout its life would require plumbing changes to be done consistently with the way that AmiGO has been going recently (everything more servicey and a very thin session layer). Another is the optimizations and proximity to the inner workings which are important to the speed of AmiGO and one of the problems with the old go-perl/go-db-perl way of doing things. This wouldn't be such a big deal in the small case (just like how the new visualization tool stands off to the side) and GOBO would be the way to go, but in a larger and more integrated system I'm not convinced that it would be an improvement. -Seth > > > On Nov 5, 2009, at 10:15 AM, Seth Carbon wrote: > >> It might also be possible to do this with some of the AmiGO parts >> that I have around, but it could range from fairly simple to ugly >> hack (and probably not worth it) depending on your requirements. >> >> How big an ontology are you trying to work with and are you >> interested in a viewer (ontology all displayed at once) or a browser >> (the ontology is big and complicated enough that having it all at >> once would be bad). >> >> Cheers, >> >> -Seth >> >> >> Harold Drabkin wrote: >>> Perhaps a special version of OE that's merely a viewer? All other >>> modules (reasoners, id managers, etc.) removed? >>> >>> hd >>> >>> >>> Jane Lomax wrote:I'm currently working on an ontology development >>> project with some external experts - as we do. I have a working obo >>> file that I'm editing, and the problem I have is that I want to be >>> able to send it around for comments but I think loading it into OE >>> is a bit hard-core for some external (and possibly internal) folks - >>> there's a bit of a learning threashold getting it up and running >>> etc. Sometimes I think people are just going through looking at the >>> obo stanzas to make comments, which isn't a great way to browse an >>> ontology. >>> >>> Can anyone think of a solution to this? It would be great to have >>> some sort of online resource where you could upload an obo file and >>> it would provide a graph view of the ontology for people to click >>> through. What about an online instantiation of OE, with just the >>> browse features enabled? Is that even remotely feasible? Is is there >>> something like that out there already? >>> >>> Or am I being a bit optimistic here...it's just that we're doing >>> work with external people so much these days it would be good if we >>> could make it easier. >>> >>> cheers, >>> >>> Jane >>> >>> >>> >> >> _______________________________________________ >> Ontology-editors mailing list >> Ontology-editors at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >> > > From midori at ebi.ac.uk Fri Nov 6 05:26:37 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 6 Nov 2009 13:26:37 +0000 (GMT) Subject: [Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI In-Reply-To: <1602ACC5-53B9-4D98-ABBC-56EBE8CE04B5@berkeleybop.org> References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> <4AEEE1C5.6020206@gmail.com> <37318F81-BCF3-4221-9CD6-508E6E6FC958@berkeleybop.org> <1602ACC5-53B9-4D98-ABBC-56EBE8CE04B5@berkeleybop.org> Message-ID: Hi, Thanks to all who have responded to the poll. From the results so far, it looks like it would actually be best to schedule the call for November 19th or 20th (even though the poll didn't include those dates). So ... is there anyone who wants to participate but CAN'T make it at 4 PM GMT (11 AM EST; 8 M PST) on Thursday, Nov. 19? Cheers, Midori On Thu, 5 Nov 2009, Chris Mungall wrote: > > The following week. I filled in the poll. > > On Nov 5, 2009, at 3:58 AM, Midori Harris wrote: > >> Can you do 8 AM (your time) on the 12th or 13th? Those are looking best on >> the doodle poll. >> >> If not, maybe same day & time the following week -- 19th or 20th? >> >> m >> >> On Wed, 4 Nov 2009, Chris Mungall wrote: >> >>> >>> I can do the 11th or some time following week >>> >>> On Nov 2, 2009, at 5:42 AM, Paula de Matos wrote: >>> >>>> Sorry I meant the 11th. >>>> P >>>> Midori Harris wrote: >>>>> OK. >>>>> Paula - by "next Wednesday" do you mean the 4th or 11th? >>>>> Chris - what's the earliest time of day that works for you? >>>>> Midori >>>>> On Mon, 2 Nov 2009, Paula de Matos wrote: >>>>>> Sorry for the late response but we're currently busy with the new ChEBI >>>>>> release. >>>>>> Yes a teleconf makes sense. Would you like to setup a doodle poll? >>>>>> Anytime after next Wednesday is most suitable for us. >>>>>> Thanks, >>>>>> Paula >>>>>> Midori Harris wrote: >>>>>>> Yes, I think we can make quite a bit more progress with a teleconf -- >>>>>>> not just more newlinks; there are a few SF items awaiting GO-Chebi >>>>>>> resolution. >>>>>>> m >>>>>>> On Fri, 30 Oct 2009, Chris Mungall wrote: >>>>>>>> Thanks Midori! >>>>>>>> Looks like a few things still to be resolved. Perhaps a chebi-go >>>>>>>> telecon to sort these out? >>>>>>>> On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: >>>>>>>>> Hi all, >>>>>>>>> A quick update: I've added the last of the links from the second >>>>>>>>> version of go/scratch/xps/biological_process_xp_chebi-newlinks.txt >>>>>>>>> that I thought looked OK. I've also updated the file of comments >>>>>>>>> that I attached to the SF item, and have attached it here as well. >>>>>>>>> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >>>>>>>>> Cheers, >>>>>>>>> Midori >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >>>>>>> is the only developer event you need to attend this year. Jumpstart >>>>>>> your >>>>>>> developing skills, take BlackBerry mobile applications to market and >>>>>>> stay ahead of the curve. Join us from November 9 - 12, 2009. Register >>>>>>> now! >>>>>>> http://p.sf.net/sfu/devconference >>>>>>> _______________________________________________ >>>>>>> Chebi-ontology mailing list >>>>>>> Chebi-ontology at lists.sourceforge.net >>>>>>> https://lists.sourceforge.net/lists/listinfo/chebi-ontology >>> > From midori at ebi.ac.uk Fri Nov 6 06:11:41 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 6 Nov 2009 14:11:41 +0000 (GMT) Subject: [Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI In-Reply-To: <4AF42E02.2090105@gmail.com> References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> <4AEEE1C5.6020206@gmail.com> <37318F81-BCF3-4221-9CD6-508E6E6FC958@berkeleybop.org> <1602ACC5-53B9-4D98-ABBC-56EBE8CE04B5@berkeleybop.org> <4AF42E02.2090105@gmail.com> Message-ID: I was kind of hoping the 19th or 20th would just work for enough people, but if not, I'll do another poll. m On Fri, 6 Nov 2009, Paula de Matos wrote: > I'm afraid I would like to participate but am in Italy Nov 18-20. > > Can we just extend the poll? > > Cheers, > Paula > > Midori Harris wrote: >> Hi, >> >> Thanks to all who have responded to the poll. From the results so far, it >> looks like it would actually be best to schedule the call for November 19th >> or 20th (even though the poll didn't include those dates). >> >> So ... is there anyone who wants to participate but CAN'T make it at 4 PM >> GMT (11 AM EST; 8 M PST) on Thursday, Nov. 19? >> >> Cheers, >> Midori >> >> On Thu, 5 Nov 2009, Chris Mungall wrote: >> >>> >>> The following week. I filled in the poll. >>> >>> On Nov 5, 2009, at 3:58 AM, Midori Harris wrote: >>> >>>> Can you do 8 AM (your time) on the 12th or 13th? Those are looking best >>>> on the doodle poll. >>>> >>>> If not, maybe same day & time the following week -- 19th or 20th? >>>> >>>> m >>>> >>>> On Wed, 4 Nov 2009, Chris Mungall wrote: >>>> >>>>> >>>>> I can do the 11th or some time following week >>>>> >>>>> On Nov 2, 2009, at 5:42 AM, Paula de Matos wrote: >>>>> >>>>>> Sorry I meant the 11th. >>>>>> P >>>>>> Midori Harris wrote: >>>>>>> OK. >>>>>>> Paula - by "next Wednesday" do you mean the 4th or 11th? >>>>>>> Chris - what's the earliest time of day that works for you? >>>>>>> Midori >>>>>>> On Mon, 2 Nov 2009, Paula de Matos wrote: >>>>>>>> Sorry for the late response but we're currently busy with the new >>>>>>>> ChEBI release. >>>>>>>> Yes a teleconf makes sense. Would you like to setup a doodle poll? >>>>>>>> Anytime after next Wednesday is most suitable for us. >>>>>>>> Thanks, >>>>>>>> Paula >>>>>>>> Midori Harris wrote: >>>>>>>>> Yes, I think we can make quite a bit more progress with a teleconf >>>>>>>>> -- not just more newlinks; there are a few SF items awaiting >>>>>>>>> GO-Chebi resolution. >>>>>>>>> m >>>>>>>>> On Fri, 30 Oct 2009, Chris Mungall wrote: >>>>>>>>>> Thanks Midori! >>>>>>>>>> Looks like a few things still to be resolved. Perhaps a chebi-go >>>>>>>>>> telecon to sort these out? >>>>>>>>>> On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: >>>>>>>>>>> Hi all, >>>>>>>>>>> A quick update: I've added the last of the links from the second >>>>>>>>>>> version of go/scratch/xps/biological_process_xp_chebi-newlinks.txt >>>>>>>>>>> that I thought looked OK. I've also updated the file of comments >>>>>>>>>>> that I attached to the SF item, and have attached it here as well. >>>>>>>>>>> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >>>>>>>>>>> Cheers, >>>>>>>>>>> Midori >>>>>>>>> >>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >>>>>>>>> is the only developer event you need to attend this year. Jumpstart >>>>>>>>> your >>>>>>>>> developing skills, take BlackBerry mobile applications to market and >>>>>>>>> stay ahead of the curve. Join us from November 9 - 12, 2009. >>>>>>>>> Register now! >>>>>>>>> http://p.sf.net/sfu/devconference >>>>>>>>> _______________________________________________ >>>>>>>>> Chebi-ontology mailing list >>>>>>>>> Chebi-ontology at lists.sourceforge.net >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/chebi-ontology >>>>> >>> >> > From paula.dematos at gmail.com Fri Nov 6 06:09:06 2009 From: paula.dematos at gmail.com (Paula de Matos) Date: Fri, 06 Nov 2009 14:09:06 +0000 Subject: [Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI In-Reply-To: References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> <4AEEE1C5.6020206@gmail.com> <37318F81-BCF3-4221-9CD6-508E6E6FC958@berkeleybop.org> <1602ACC5-53B9-4D98-ABBC-56EBE8CE04B5@berkeleybop.org> Message-ID: <4AF42E02.2090105@gmail.com> I'm afraid I would like to participate but am in Italy Nov 18-20. Can we just extend the poll? Cheers, Paula Midori Harris wrote: > Hi, > > Thanks to all who have responded to the poll. From the results so far, > it looks like it would actually be best to schedule the call for > November 19th or 20th (even though the poll didn't include those dates). > > So ... is there anyone who wants to participate but CAN'T make it at 4 > PM GMT (11 AM EST; 8 M PST) on Thursday, Nov. 19? > > Cheers, > Midori > > On Thu, 5 Nov 2009, Chris Mungall wrote: > >> >> The following week. I filled in the poll. >> >> On Nov 5, 2009, at 3:58 AM, Midori Harris wrote: >> >>> Can you do 8 AM (your time) on the 12th or 13th? Those are looking >>> best on the doodle poll. >>> >>> If not, maybe same day & time the following week -- 19th or 20th? >>> >>> m >>> >>> On Wed, 4 Nov 2009, Chris Mungall wrote: >>> >>>> >>>> I can do the 11th or some time following week >>>> >>>> On Nov 2, 2009, at 5:42 AM, Paula de Matos wrote: >>>> >>>>> Sorry I meant the 11th. >>>>> P >>>>> Midori Harris wrote: >>>>>> OK. >>>>>> Paula - by "next Wednesday" do you mean the 4th or 11th? >>>>>> Chris - what's the earliest time of day that works for you? >>>>>> Midori >>>>>> On Mon, 2 Nov 2009, Paula de Matos wrote: >>>>>>> Sorry for the late response but we're currently busy with the >>>>>>> new ChEBI release. >>>>>>> Yes a teleconf makes sense. Would you like to setup a doodle >>>>>>> poll? Anytime after next Wednesday is most suitable for us. >>>>>>> Thanks, >>>>>>> Paula >>>>>>> Midori Harris wrote: >>>>>>>> Yes, I think we can make quite a bit more progress with a >>>>>>>> teleconf -- not just more newlinks; there are a few SF items >>>>>>>> awaiting GO-Chebi resolution. >>>>>>>> m >>>>>>>> On Fri, 30 Oct 2009, Chris Mungall wrote: >>>>>>>>> Thanks Midori! >>>>>>>>> Looks like a few things still to be resolved. Perhaps a >>>>>>>>> chebi-go telecon to sort these out? >>>>>>>>> On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: >>>>>>>>>> Hi all, >>>>>>>>>> A quick update: I've added the last of the links from the >>>>>>>>>> second version of >>>>>>>>>> go/scratch/xps/biological_process_xp_chebi-newlinks.txt that >>>>>>>>>> I thought looked OK. I've also updated the file of comments >>>>>>>>>> that I attached to the SF item, and have attached it here as >>>>>>>>>> well. >>>>>>>>>> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >>>>>>>>>> >>>>>>>>>> Cheers, >>>>>>>>>> Midori >>>>>>>> ------------------------------------------------------------------------------ >>>>>>>> >>>>>>>> Come build with us! The BlackBerry(R) Developer Conference in >>>>>>>> SF, CA >>>>>>>> is the only developer event you need to attend this year. >>>>>>>> Jumpstart your >>>>>>>> developing skills, take BlackBerry mobile applications to >>>>>>>> market and stay ahead of the curve. Join us from November 9 - >>>>>>>> 12, 2009. Register now! >>>>>>>> http://p.sf.net/sfu/devconference >>>>>>>> _______________________________________________ >>>>>>>> Chebi-ontology mailing list >>>>>>>> Chebi-ontology at lists.sourceforge.net >>>>>>>> https://lists.sourceforge.net/lists/listinfo/chebi-ontology >>>> >> > From jane at ebi.ac.uk Tue Nov 10 03:08:06 2009 From: jane at ebi.ac.uk (Jane Lomax) Date: Tue, 10 Nov 2009 11:08:06 +0000 Subject: [Ontology-editors] online working ontology browser? In-Reply-To: <4AF31656.3030809@gmail.com> References: <4AF2F648.2010503@ebi.ac.uk> <4AF2FE25.7060201@informatics.jax.org> <4AF31656.3030809@gmail.com> Message-ID: <4AF94996.8080901@ebi.ac.uk> It would need to accommodate up to the full GO bp ontology, so that's pretty big I guess. And would therefore need to be a browser... Jane Seth Carbon wrote: > It might also be possible to do this with some of the AmiGO parts that > I have around, but it could range from fairly simple to ugly hack (and > probably not worth it) depending on your requirements. > > How big an ontology are you trying to work with and are you interested > in a viewer (ontology all displayed at once) or a browser (the > ontology is big and complicated enough that having it all at once > would be bad). > > Cheers, > > -Seth > > > Harold Drabkin wrote: >> Perhaps a special version of OE that's merely a viewer? All other >> modules (reasoners, id managers, etc.) removed? >> >> hd >> >> >> Jane Lomax wrote:I'm currently working on an ontology development >> project with some external experts - as we do. I have a working obo >> file that I'm editing, and the problem I have is that I want to be >> able to send it around for comments but I think loading it into OE is >> a bit hard-core for some external (and possibly internal) folks - >> there's a bit of a learning threashold getting it up and running etc. >> Sometimes I think people are just going through looking at the obo >> stanzas to make comments, which isn't a great way to browse an ontology. >> >> Can anyone think of a solution to this? It would be great to have >> some sort of online resource where you could upload an obo file and >> it would provide a graph view of the ontology for people to click >> through. What about an online instantiation of OE, with just the >> browse features enabled? Is that even remotely feasible? Is is there >> something like that out there already? >> >> Or am I being a bit optimistic here...it's just that we're doing work >> with external people so much these days it would be good if we could >> make it easier. >> >> cheers, >> >> Jane >> >> >> -- Dr Jane Lomax GO Editorial Office EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridgeshire, UK CB10 1SD p: +44 1223 492516 f: +44 1223 494468 From midori at ebi.ac.uk Tue Nov 10 06:01:27 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 10 Nov 2009 14:01:27 +0000 (GMT) Subject: [Ontology-editors] [Chebi-ontology] Inference of GO BP relationships from CHEBI In-Reply-To: <4AF42E02.2090105@gmail.com> References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> <4AEEE1C5.6020206@gmail.com> <37318F81-BCF3-4221-9CD6-508E6E6FC958@berkeleybop.org> <1602ACC5-53B9-4D98-ABBC-56EBE8CE04B5@berkeleybop.org> <4AF42E02.2090105@gmail.com> Message-ID: Hi all, In light of the last couple of emails, it looks like we'll have to re-od the poll because we haven't yet found a time that everyone can make. Before I do, though, can I double-check which participants are essential? We may not be able to get everybody, but we should at least make sure that we don't miss anyone who's really deeply involved. I think we really need Chris, and we ought to have at least two, preferably all three, of myself, Jane, and David. Any other GO people would be welcome but aren't indispensable. >From ChEBI, I guess we need Marcus and Paula, but I don't know who else is essential. Thanks, Midori On Fri, 6 Nov 2009, Paula de Matos wrote: > I'm afraid I would like to participate but am in Italy Nov 18-20. > > Can we just extend the poll? > > Cheers, > Paula > > Midori Harris wrote: >> Hi, >> >> Thanks to all who have responded to the poll. From the results so far, it >> looks like it would actually be best to schedule the call for November 19th >> or 20th (even though the poll didn't include those dates). >> >> So ... is there anyone who wants to participate but CAN'T make it at 4 PM >> GMT (11 AM EST; 8 M PST) on Thursday, Nov. 19? >> >> Cheers, >> Midori >> >> On Thu, 5 Nov 2009, Chris Mungall wrote: >> >>> >>> The following week. I filled in the poll. >>> >>> On Nov 5, 2009, at 3:58 AM, Midori Harris wrote: >>> >>>> Can you do 8 AM (your time) on the 12th or 13th? Those are looking best >>>> on the doodle poll. >>>> >>>> If not, maybe same day & time the following week -- 19th or 20th? >>>> >>>> m >>>> >>>> On Wed, 4 Nov 2009, Chris Mungall wrote: >>>> >>>>> >>>>> I can do the 11th or some time following week >>>>> >>>>> On Nov 2, 2009, at 5:42 AM, Paula de Matos wrote: >>>>> >>>>>> Sorry I meant the 11th. >>>>>> P >>>>>> Midori Harris wrote: >>>>>>> OK. >>>>>>> Paula - by "next Wednesday" do you mean the 4th or 11th? >>>>>>> Chris - what's the earliest time of day that works for you? >>>>>>> Midori >>>>>>> On Mon, 2 Nov 2009, Paula de Matos wrote: >>>>>>>> Sorry for the late response but we're currently busy with the new >>>>>>>> ChEBI release. >>>>>>>> Yes a teleconf makes sense. Would you like to setup a doodle poll? >>>>>>>> Anytime after next Wednesday is most suitable for us. >>>>>>>> Thanks, >>>>>>>> Paula >>>>>>>> Midori Harris wrote: >>>>>>>>> Yes, I think we can make quite a bit more progress with a teleconf >>>>>>>>> -- not just more newlinks; there are a few SF items awaiting >>>>>>>>> GO-Chebi resolution. >>>>>>>>> m >>>>>>>>> On Fri, 30 Oct 2009, Chris Mungall wrote: >>>>>>>>>> Thanks Midori! >>>>>>>>>> Looks like a few things still to be resolved. Perhaps a chebi-go >>>>>>>>>> telecon to sort these out? >>>>>>>>>> On Oct 28, 2009, at 10:10 AM, Midori Harris wrote: >>>>>>>>>>> Hi all, >>>>>>>>>>> A quick update: I've added the last of the links from the second >>>>>>>>>>> version of go/scratch/xps/biological_process_xp_chebi-newlinks.txt >>>>>>>>>>> that I thought looked OK. I've also updated the file of comments >>>>>>>>>>> that I attached to the SF item, and have attached it here as well. >>>>>>>>>>> https://sourceforge.net/tracker/?func=detail&aid=2812369&group_id=36855&atid=440764 >>>>>>>>>>> Cheers, >>>>>>>>>>> Midori >>>>>>>>> >>>>>>>>> ------------------------------------------------------------------------------ >>>>>>>>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >>>>>>>>> is the only developer event you need to attend this year. Jumpstart >>>>>>>>> your >>>>>>>>> developing skills, take BlackBerry mobile applications to market and >>>>>>>>> stay ahead of the curve. Join us from November 9 - 12, 2009. >>>>>>>>> Register now! >>>>>>>>> http://p.sf.net/sfu/devconference >>>>>>>>> _______________________________________________ >>>>>>>>> Chebi-ontology mailing list >>>>>>>>> Chebi-ontology at lists.sourceforge.net >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/chebi-ontology >>>>> >>> >> > From sjcarbon at berkeleybop.org Tue Nov 10 09:56:14 2009 From: sjcarbon at berkeleybop.org (Seth Carbon) Date: Tue, 10 Nov 2009 09:56:14 -0800 Subject: [Ontology-editors] online working ontology browser? In-Reply-To: <4AF94996.8080901@ebi.ac.uk> References: <4AF2F648.2010503@ebi.ac.uk> <4AF2FE25.7060201@informatics.jax.org> <4AF31656.3030809@gmail.com> <4AF94996.8080901@ebi.ac.uk> Message-ID: <4AF9A93E.3020001@berkeleybop.org> > It would need to accommodate up to the full GO bp ontology, so that's > pretty big I guess. And would therefore need to be a browser... That sounds a little outside of the range of things that I think could be done easily with current AmiGO parts. Something with OBO-Edit would probably be a better fit. Cheers, -Seth > > Jane > > Seth Carbon wrote: >> It might also be possible to do this with some of the AmiGO parts >> that I have around, but it could range from fairly simple to ugly >> hack (and probably not worth it) depending on your requirements. >> >> How big an ontology are you trying to work with and are you >> interested in a viewer (ontology all displayed at once) or a browser >> (the ontology is big and complicated enough that having it all at >> once would be bad). >> >> Cheers, >> >> -Seth >> >> >> Harold Drabkin wrote: >>> Perhaps a special version of OE that's merely a viewer? All other >>> modules (reasoners, id managers, etc.) removed? >>> >>> hd >>> >>> >>> Jane Lomax wrote:I'm currently working on an ontology development >>> project with some external experts - as we do. I have a working obo >>> file that I'm editing, and the problem I have is that I want to be >>> able to send it around for comments but I think loading it into OE >>> is a bit hard-core for some external (and possibly internal) folks - >>> there's a bit of a learning threashold getting it up and running >>> etc. Sometimes I think people are just going through looking at the >>> obo stanzas to make comments, which isn't a great way to browse an >>> ontology. >>> >>> Can anyone think of a solution to this? It would be great to have >>> some sort of online resource where you could upload an obo file and >>> it would provide a graph view of the ontology for people to click >>> through. What about an online instantiation of OE, with just the >>> browse features enabled? Is that even remotely feasible? Is is there >>> something like that out there already? >>> >>> Or am I being a bit optimistic here...it's just that we're doing >>> work with external people so much these days it would be good if we >>> could make it easier. >>> >>> cheers, >>> >>> Jane >>> >>> >>> > > From midori at ebi.ac.uk Wed Nov 11 08:46:28 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Wed, 11 Nov 2009 16:46:28 +0000 (GMT) Subject: [Ontology-editors] GO-ChEBI call, take 2 (Re: Inference of GO BP relationships from CHEBI) In-Reply-To: <4AFAA247.5060805@ebi.ac.uk> References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> <4AEEE1C5.6020206@gmail.com> <37318F81-BCF3-4221-9CD6-508E6E6FC958@berkeleybop.org> <1602ACC5-53B9-4D98-ABBC-56EBE8CE04B5@berkeleybop.org> <4AF42E02.2090105@gmail.com> <4AFAA247.5060805@ebi.ac.uk> Message-ID: Hi all, Since the first poll didn't find a conf call date and time that was good for all of the essential participants, I've set up a new one with dates later this month (and extending into the beginning of December, but I hope it won't be that long!): http://www.doodle.com/ha7af2vkkd9q9q3a >From emails and the previous poll, the people we really need are Chris, Jane, David, and me from GO, and Paula, Marcus, Nico, and Janna from ChEBI. Anyone else on these lists is welcome, if they can make the time we end up with, but their absence won't stop us. Cheers, Midori From midori at ebi.ac.uk Fri Nov 13 05:06:07 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 13 Nov 2009 13:06:07 +0000 (GMT) Subject: [Ontology-editors] multi-organism process and conjugation In-Reply-To: <8e22ab960911061218p3efb0aa8p4489e7a45c22abe@mail.gmail.com> References: <4AF44810.2030805@ebi.ac.uk> <8e22ab960911061218p3efb0aa8p4489e7a45c22abe@mail.gmail.com> Message-ID: I'm not convinced that we should make these changes. In what way is cell-cell adhesion not a "process that is carried out at the cellular level, but not necessarily restricted to a single cell"? That's my main concern about this proposal. It would take cell-cell adhesion out from under an ancestor whose definition fits it just fine, to solve a non-existent problem. At present, we represent some types of cell-cell adhesion as parts --not types -- of MOPs (e.g. conjugation, flocculation); this maskes sense, avoids path violotions, and permits GO to collect all processes that a cell can carry out under cellular process. m On Fri, 6 Nov 2009, Tanya Berardini wrote: > What are the objections to this move? > >> From the defs of multi-organism process, cellular process and the term in > question, it seems to follow that the changes you propose make sense. > > Tanya > > Tanya Berardini > TAIR Curator > www.arabidopsis.org > > > On Fri, Nov 6, 2009 at 8:00 AM, Jennifer Deegan (nee Clark) < > jdeegan at ebi.ac.uk> wrote: > >> Hi, >> >> I've been asking a few people about an ontology issue, and getting >> conflicting answers. I wondered if others could chip in with views? >> >> I attach a picture of the graph for: >> >> id: GO:0000752 >> name: agglutination involved in conjugation with cellular fusion >> def: During conjugation with cellular fusion, the aggregation or adhesion >> of compatible mating types via complementary cell-cell interactions. An >> example of this process is agglutination in Saccharomyces cerevisiae. >> >> As I understand it, this is a cell-cell adhesion process involving two >> separate individuals of a single celled species. It seems to me that it must >> be a type of multi-organism process and that it cannot be a type of cellular >> process. (Remembering that cellular process and multi-organism process are >> disjoint). To solve this I would like to delete the link between cell >> adhesion and cellular process. Then the descendents of cell adhesion that do >> not involve multiple organisms can have new links made to cellular process. >> >> Could people let me know if they have objections to this? >> >> Thanks, >> >> Jennifer >> >> >> _______________________________________________ >> Ontology-editors mailing list >> Ontology-editors at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >> >> > From dph at informatics.jax.org Fri Nov 13 05:30:29 2009 From: dph at informatics.jax.org (David Hill) Date: Fri, 13 Nov 2009 08:30:29 -0500 Subject: [Ontology-editors] multi-organism process and conjugation In-Reply-To: References: <4AF44810.2030805@ebi.ac.uk> <8e22ab960911061218p3efb0aa8p4489e7a45c22abe@mail.gmail.com> Message-ID: <4AFD5F75.5020905@informatics.jax.org> I have been thinking a lot about his as well, and I agree with Midori. If we follow the same line of reasoning that would remove "agglutination involved in conjugation with cellular fusion" from under cellular process because it is a part of a multi-organism process, then we would also have to remove terms like "cell division" from under cellular process, because something like epidermal cell division occurs in a multicellular organism. David Midori Harris wrote: > I'm not convinced that we should make these changes. > > In what way is cell-cell adhesion not a "process that is carried out > at the cellular level, but not necessarily restricted to a single cell"? > > That's my main concern about this proposal. It would take cell-cell > adhesion out from under an ancestor whose definition fits it just > fine, to solve a non-existent problem. At present, we represent some > types of cell-cell adhesion as parts --not types -- of MOPs (e.g. > conjugation, flocculation); this maskes sense, avoids path violotions, > and permits GO to collect all processes that a cell can carry out > under cellular process. > > m > > On Fri, 6 Nov 2009, Tanya Berardini wrote: > >> What are the objections to this move? >> >>> From the defs of multi-organism process, cellular process and the >>> term in >> question, it seems to follow that the changes you propose make sense. >> >> Tanya >> >> Tanya Berardini >> TAIR Curator >> www.arabidopsis.org >> >> >> On Fri, Nov 6, 2009 at 8:00 AM, Jennifer Deegan (nee Clark) < >> jdeegan at ebi.ac.uk> wrote: >> >>> Hi, >>> >>> I've been asking a few people about an ontology issue, and getting >>> conflicting answers. I wondered if others could chip in with views? >>> >>> I attach a picture of the graph for: >>> >>> id: GO:0000752 >>> name: agglutination involved in conjugation with cellular fusion >>> def: During conjugation with cellular fusion, the aggregation or >>> adhesion >>> of compatible mating types via complementary cell-cell interactions. An >>> example of this process is agglutination in Saccharomyces cerevisiae. >>> >>> As I understand it, this is a cell-cell adhesion process involving two >>> separate individuals of a single celled species. It seems to me that >>> it must >>> be a type of multi-organism process and that it cannot be a type of >>> cellular >>> process. (Remembering that cellular process and multi-organism >>> process are >>> disjoint). To solve this I would like to delete the link between cell >>> adhesion and cellular process. Then the descendents of cell adhesion >>> that do >>> not involve multiple organisms can have new links made to cellular >>> process. >>> >>> Could people let me know if they have objections to this? >>> >>> Thanks, >>> >>> Jennifer >>> >>> >>> _______________________________________________ >>> Ontology-editors mailing list >>> Ontology-editors at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >>> >>> >> > _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors -- David P. Hill, Ph.D. Bioinformatics Scientist: Ontology Development Gene Ontology Consortium The Jackson Laboratory www.geneontology.org www.informatics.jax.org tel:207-288-6430 From midori at ebi.ac.uk Fri Nov 13 08:55:45 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 13 Nov 2009 16:55:45 +0000 (GMT) Subject: [Ontology-editors] GO-ChEBI call, take 2 (Re: Inference of GO BP relationships from CHEBI) In-Reply-To: References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> <4AEEE1C5.6020206@gmail.com> <37318F81-BCF3-4221-9CD6-508E6E6FC958@berkeleybop.org> <1602ACC5-53B9-4D98-ABBC-56EBE8CE04B5@berkeleybop.org> <4AF42E02.2090105@gmail.com> <4AFAA247.5060805@ebi.ac.uk> Message-ID: Hi, We haven't heard yet from Nico, but I hope he can make Thursday, December 3rd, at 4pm BST/11am EST/8am PST -- everyone else can. I'll book a room next week (having come home early because getting rained on once was enough). Midori On Wed, 11 Nov 2009, Midori Harris wrote: > Hi all, > > Since the first poll didn't find a conf call date and time that was good for > all of the essential participants, I've set up a new one with dates later > this month (and extending into the beginning of December, but I hope it won't > be that long!): > > http://www.doodle.com/ha7af2vkkd9q9q3a > >> From emails and the previous poll, the people we really need are Chris, > Jane, David, and me from GO, and Paula, Marcus, Nico, and Janna from ChEBI. > Anyone else on these lists is welcome, if they can make the time we end up > with, but their absence won't stop us. > > Cheers, > Midori > _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors > From paula.dematos at gmail.com Fri Nov 13 10:19:34 2009 From: paula.dematos at gmail.com (Paula de Matos) Date: Fri, 13 Nov 2009 18:19:34 +0000 Subject: [Ontology-editors] GO-ChEBI call, take 2 (Re: Inference of GO BP relationships from CHEBI) In-Reply-To: References: <9A98F1BA-6E20-4282-AADF-AB427C881519@berkeleybop.org> <0107F9DA-9D94-4749-BF8E-C004B0623EED@berkeleybop.org> <4AEEC63A.7080907@gmail.com> <4AEEE1C5.6020206@gmail.com> <37318F81-BCF3-4221-9CD6-508E6E6FC958@berkeleybop.org> <1602ACC5-53B9-4D98-ABBC-56EBE8CE04B5@berkeleybop.org> <4AF42E02.2090105@gmail.com> <4AFAA247.5060805@ebi.ac.uk> Message-ID: <4AFDA336.8060001@gmail.com> Sounds good. Cheers, Paula Midori Harris wrote: > Hi, > > We haven't heard yet from Nico, but I hope he can make Thursday, > December 3rd, at 4pm BST/11am EST/8am PST -- everyone else can. I'll > book a room next week (having come home early because getting rained > on once was enough). > > Midori > > On Wed, 11 Nov 2009, Midori Harris wrote: > >> Hi all, >> >> Since the first poll didn't find a conf call date and time that was >> good for all of the essential participants, I've set up a new one >> with dates later this month (and extending into the beginning of >> December, but I hope it won't be that long!): >> >> http://www.doodle.com/ha7af2vkkd9q9q3a >> >>> From emails and the previous poll, the people we really need are Chris, >> Jane, David, and me from GO, and Paula, Marcus, Nico, and Janna from >> ChEBI. Anyone else on these lists is welcome, if they can make the >> time we end up with, but their absence won't stop us. >> >> Cheers, >> Midori >> _______________________________________________ >> Ontology-editors mailing list >> Ontology-editors at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >> > From jdeegan at ebi.ac.uk Mon Nov 16 12:20:19 2009 From: jdeegan at ebi.ac.uk (Jennifer Deegan (nee Clark)) Date: Mon, 16 Nov 2009 12:20:19 +0000 Subject: [Ontology-editors] multi-organism process and conjugation In-Reply-To: <4AFD5F75.5020905@informatics.jax.org> References: <4AF44810.2030805@ebi.ac.uk> <8e22ab960911061218p3efb0aa8p4489e7a45c22abe@mail.gmail.com> <4AFD5F75.5020905@informatics.jax.org> Message-ID: <4B014383.2070609@ebi.ac.uk> Hi David, In that case could I take you and Tanya up on your offer of a get together on skype and webex to look at some of my implied links in my cross product set? I think they are going to take a bit of serious thought, and might be better done with several heads rather than just one. Thanks, Jennifer David Hill wrote: > I have been thinking a lot about his as well, and I agree with Midori. > If we follow the same line of reasoning that would remove "agglutination > involved in conjugation with cellular fusion" from under cellular > process because it is a part of a multi-organism process, then we would > also have to remove terms like "cell division" from under cellular > process, because something like epidermal cell division occurs in a > multicellular organism. > > David > > Midori Harris wrote: >> I'm not convinced that we should make these changes. >> >> In what way is cell-cell adhesion not a "process that is carried out >> at the cellular level, but not necessarily restricted to a single cell"? >> >> That's my main concern about this proposal. It would take cell-cell >> adhesion out from under an ancestor whose definition fits it just >> fine, to solve a non-existent problem. At present, we represent some >> types of cell-cell adhesion as parts --not types -- of MOPs (e.g. >> conjugation, flocculation); this maskes sense, avoids path violotions, >> and permits GO to collect all processes that a cell can carry out >> under cellular process. >> >> m >> >> On Fri, 6 Nov 2009, Tanya Berardini wrote: >> >>> What are the objections to this move? >>> >>>> From the defs of multi-organism process, cellular process and the >>>> term in >>> question, it seems to follow that the changes you propose make sense. >>> >>> Tanya >>> >>> Tanya Berardini >>> TAIR Curator >>> www.arabidopsis.org >>> >>> >>> On Fri, Nov 6, 2009 at 8:00 AM, Jennifer Deegan (nee Clark) < >>> jdeegan at ebi.ac.uk> wrote: >>> >>>> Hi, >>>> >>>> I've been asking a few people about an ontology issue, and getting >>>> conflicting answers. I wondered if others could chip in with views? >>>> >>>> I attach a picture of the graph for: >>>> >>>> id: GO:0000752 >>>> name: agglutination involved in conjugation with cellular fusion >>>> def: During conjugation with cellular fusion, the aggregation or >>>> adhesion >>>> of compatible mating types via complementary cell-cell interactions. An >>>> example of this process is agglutination in Saccharomyces cerevisiae. >>>> >>>> As I understand it, this is a cell-cell adhesion process involving two >>>> separate individuals of a single celled species. It seems to me that >>>> it must >>>> be a type of multi-organism process and that it cannot be a type of >>>> cellular >>>> process. (Remembering that cellular process and multi-organism >>>> process are >>>> disjoint). To solve this I would like to delete the link between cell >>>> adhesion and cellular process. Then the descendents of cell adhesion >>>> that do >>>> not involve multiple organisms can have new links made to cellular >>>> process. >>>> >>>> Could people let me know if they have objections to this? >>>> >>>> Thanks, >>>> >>>> Jennifer >>>> >>>> >>>> _______________________________________________ >>>> Ontology-editors mailing list >>>> Ontology-editors at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >>>> >>>> >>> >> _______________________________________________ >> Ontology-editors mailing list >> Ontology-editors at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/ontology-editors > From cjm at berkeleybop.org Mon Nov 16 19:08:27 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Mon, 16 Nov 2009 11:08:27 -0800 Subject: [Ontology-editors] NF-kappaB complex Message-ID: I'd like a term representing a NF-kappaB complex This will allow for the logical definition of * GO:0042348 ! NF-kappaB import into nucleus Which in turn will allow us to automatically map reactions such as this: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193691 to the above GO ID. Is the appropriate place to request this GO or PRO? From midori at ebi.ac.uk Tue Nov 17 11:05:23 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 17 Nov 2009 11:05:23 +0000 (GMT) Subject: [Ontology-editors] NF-kappaB complex In-Reply-To: References: Message-ID: Both, I think -- GO should have a term for 'NF-kappaB complex' and PRO should represent the monomers. From a book I found online: "In the majority of cell types NF-kappaB exists in the cytoplasm as homo- or heterodimers of a family of structurally related proteins." I've created an item for GO: https://sourceforge.net/tracker/?func=detail&aid=2898993&group_id=36855&atid=440764 I'll assume you'll take care of a PRO request. cheers, m On Mon, 16 Nov 2009, Chris Mungall wrote: > I'd like a term representing a NF-kappaB complex > > This will allow for the logical definition of > * GO:0042348 ! NF-kappaB import into nucleus > > Which in turn will allow us to automatically map reactions such as this: > > http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193691 > > to the above GO ID. > > Is the appropriate place to request this GO or PRO? > _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors > From dph at informatics.jax.org Tue Nov 17 13:06:20 2009 From: dph at informatics.jax.org (David Hill) Date: Tue, 17 Nov 2009 08:06:20 -0500 Subject: [Ontology-editors] NF-kappaB complex In-Reply-To: References: Message-ID: <4B029FCC.5020307@informatics.jax.org> I'm not sure who is going to end up working on this in the end, but NF-kappaB translocates to the nucleus as a transcription factor as part of it's signaling. David Midori Harris wrote: > Both, I think -- GO should have a term for 'NF-kappaB complex' and PRO > should represent the monomers. From a book I found online: > > "In the majority of cell types NF-kappaB exists in the cytoplasm as > homo- or heterodimers of a family of structurally related proteins." > > I've created an item for GO: > > https://sourceforge.net/tracker/?func=detail&aid=2898993&group_id=36855&atid=440764 > > > I'll assume you'll take care of a PRO request. > > cheers, > m > > On Mon, 16 Nov 2009, Chris Mungall wrote: > >> I'd like a term representing a NF-kappaB complex >> >> This will allow for the logical definition of >> * GO:0042348 ! NF-kappaB import into nucleus >> >> Which in turn will allow us to automatically map reactions such as this: >> >> http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193691 >> >> to the above GO ID. >> >> Is the appropriate place to request this GO or PRO? >> _______________________________________________ >> Ontology-editors mailing list >> Ontology-editors at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >> > _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors -- David P. Hill, Ph.D. Bioinformatics Scientist: Ontology Development Gene Ontology Consortium The Jackson Laboratory www.geneontology.org www.informatics.jax.org tel:207-288-6430 From midori at ebi.ac.uk Tue Nov 17 13:18:57 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 17 Nov 2009 13:18:57 +0000 (GMT) Subject: [Ontology-editors] NF-kappaB complex In-Reply-To: <4B029FCC.5020307@informatics.jax.org> References: <4B029FCC.5020307@informatics.jax.org> Message-ID: yup, noted in teh def that's taking happe On Tue, 17 Nov 2009, David Hill wrote: > I'm not sure who is going to end up working on this in the end, but NF-kappaB > translocates to the nucleus as a transcription factor as part of it's > signaling. > > David > > Midori Harris wrote: >> Both, I think -- GO should have a term for 'NF-kappaB complex' and PRO >> should represent the monomers. From a book I found online: >> >> "In the majority of cell types NF-kappaB exists in the cytoplasm as homo- >> or heterodimers of a family of structurally related proteins." >> >> I've created an item for GO: >> >> https://sourceforge.net/tracker/?func=detail&aid=2898993&group_id=36855&atid=440764 >> >> I'll assume you'll take care of a PRO request. >> >> cheers, >> m >> >> On Mon, 16 Nov 2009, Chris Mungall wrote: >> >>> I'd like a term representing a NF-kappaB complex >>> >>> This will allow for the logical definition of >>> * GO:0042348 ! NF-kappaB import into nucleus >>> >>> Which in turn will allow us to automatically map reactions such as this: >>> >>> http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193691 >>> >>> to the above GO ID. >>> >>> Is the appropriate place to request this GO or PRO? >>> _______________________________________________ >>> Ontology-editors mailing list >>> Ontology-editors at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >>> >> _______________________________________________ >> Ontology-editors mailing list >> Ontology-editors at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/ontology-editors > > From midori at ebi.ac.uk Tue Nov 17 14:43:39 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 17 Nov 2009 14:43:39 +0000 (GMT) Subject: [Ontology-editors] UniProtKB accessions Message-ID: Hi all, After a brief chat with Emily, I'm removing UniProtKB accessions that have been used as definition dbxrefs. The main reason is that a UniProt entry should provide links to other references (e.g. papers) that would be preferable def sources anyway. An additional reason is that the presence of UniProt accessions in the ontology files is confusing some people over here. I would recommend not using UniProtKB accessions as definition dbxrefs in the future, unless an alternative source really can't be found. cheers, m From midori at ebi.ac.uk Tue Nov 17 14:59:02 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 17 Nov 2009 14:59:02 +0000 (GMT) Subject: [Ontology-editors] UniProtKB accessions In-Reply-To: References: Message-ID: p.s. also remember that when you use a curator's initials as a def dbxref, the prefix is *always* GOC: (no matter which db the curator works for) On Tue, 17 Nov 2009, Midori Harris wrote: > Hi all, > > After a brief chat with Emily, I'm removing UniProtKB accessions that have > been used as definition dbxrefs. > > The main reason is that a UniProt entry should provide links to other > references (e.g. papers) that would be preferable def sources anyway. An > additional reason is that the presence of UniProt accessions in the ontology > files is confusing some people over here. > > I would recommend not using UniProtKB accessions as definition dbxrefs in the > future, unless an alternative source really can't be found. > > cheers, > m > _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors > From jane at ebi.ac.uk Tue Nov 17 14:59:32 2009 From: jane at ebi.ac.uk (Jane Lomax) Date: Tue, 17 Nov 2009 14:59:32 +0000 (GMT) Subject: [Ontology-editors] UniProtKB accessions In-Reply-To: References: Message-ID: Please wait! There are definitely cases where I've used UniProtKB as a def dbxref where there isn't a paper...mostly prok stuff. Let me find some examples... On Tue, 17 Nov 2009, Midori Harris wrote: > Hi all, > > After a brief chat with Emily, I'm removing UniProtKB accessions that have > been used as definition dbxrefs. > > The main reason is that a UniProt entry should provide links to other > references (e.g. papers) that would be preferable def sources anyway. An > additional reason is that the presence of UniProt accessions in the ontology > files is confusing some people over here. > > I would recommend not using UniProtKB accessions as definition dbxrefs in the > future, unless an alternative source really can't be found. > > cheers, > m > _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors > -- 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 jane at ebi.ac.uk Tue Nov 17 15:02:13 2009 From: jane at ebi.ac.uk (Jane Lomax) Date: Tue, 17 Nov 2009 15:02:13 +0000 (GMT) Subject: [Ontology-editors] UniProtKB accessions In-Reply-To: References: Message-ID: Okay - here's one: Q8TW31 I've got the subunit composition from the entry - the only paper cited is the genome paper. In this case there's another dbxref (BRENDA) but that's not always the case... Jane On Tue, 17 Nov 2009, Midori Harris wrote: > Hi all, > > After a brief chat with Emily, I'm removing UniProtKB accessions that have > been used as definition dbxrefs. > > The main reason is that a UniProt entry should provide links to other > references (e.g. papers) that would be preferable def sources anyway. An > additional reason is that the presence of UniProt accessions in the ontology > files is confusing some people over here. > > I would recommend not using UniProtKB accessions as definition dbxrefs in the > future, unless an alternative source really can't be found. > > cheers, > m > _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors > -- 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 Tue Nov 17 15:07:39 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 17 Nov 2009 15:07:39 +0000 (GMT) Subject: [Ontology-editors] UniProtKB accessions In-Reply-To: References: Message-ID: PMID: 7026530 >From the MetaCyc entry at http://BioCyc.org/META/NEW-IMAGE?type=ENZYME&object=3-ISOPROPYLMALISOM-CPLX On Tue, 17 Nov 2009, Jane Lomax wrote: > Okay - here's one: Q8TW31 > > I've got the subunit composition from the entry - the only paper cited is the > genome paper. In this case there's another dbxref (BRENDA) but that's not > always the case... > > Jane > > On Tue, 17 Nov 2009, Midori Harris wrote: > >> Hi all, >> >> After a brief chat with Emily, I'm removing UniProtKB accessions that have >> been used as definition dbxrefs. >> >> The main reason is that a UniProt entry should provide links to other >> references (e.g. papers) that would be preferable def sources anyway. An >> additional reason is that the presence of UniProt accessions in the >> ontology files is confusing some people over here. >> >> I would recommend not using UniProtKB accessions as definition dbxrefs in >> the future, unless an alternative source really can't be found. >> >> cheers, >> m >> _______________________________________________ >> Ontology-editors mailing list >> Ontology-editors at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >> > > From jane at ebi.ac.uk Tue Nov 17 16:00:40 2009 From: jane at ebi.ac.uk (Jane Lomax) Date: Tue, 17 Nov 2009 16:00:40 +0000 (GMT) Subject: [Ontology-editors] UniProtKB accessions In-Reply-To: References: Message-ID: Okay - bad example! But I promise there are tonnes of really obscure bacterial complexes and functions that don't have any literature attached to them that I've added for the IMG mapping (hence probably no annotations either) ...also a lot of the time I added a UniProt id dbxref as a sort of example so people could tell what the term meant, as well as getting some info for the def. I know this isn't ideal as a def dbxref, but there's not really another way of capturing it. Maybe we need some field, example annotation? Either way, can we not blanket delete them for now otherwise the info will just be lost... Jane On Tue, 17 Nov 2009, Midori Harris wrote: > PMID: 7026530 > >> From the MetaCyc entry at > http://BioCyc.org/META/NEW-IMAGE?type=ENZYME&object=3-ISOPROPYLMALISOM-CPLX > > On Tue, 17 Nov 2009, Jane Lomax wrote: > >> Okay - here's one: Q8TW31 >> >> I've got the subunit composition from the entry - the only paper cited is >> the genome paper. In this case there's another dbxref (BRENDA) but that's >> not always the case... >> >> Jane >> >> On Tue, 17 Nov 2009, Midori Harris wrote: >> >>> Hi all, >>> >>> After a brief chat with Emily, I'm removing UniProtKB accessions that have >>> been used as definition dbxrefs. >>> >>> The main reason is that a UniProt entry should provide links to other >>> references (e.g. papers) that would be preferable def sources anyway. An >>> additional reason is that the presence of UniProt accessions in the >>> ontology files is confusing some people over here. >>> >>> I would recommend not using UniProtKB accessions as definition dbxrefs in >>> the future, unless an alternative source really can't be found. >>> >>> cheers, >>> m >>> _______________________________________________ >>> Ontology-editors mailing list >>> Ontology-editors at geneontology.org >>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >>> >> >> > -- 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 edimmer at ebi.ac.uk Tue Nov 17 16:09:40 2009 From: edimmer at ebi.ac.uk (Emily Dimmer) Date: Tue, 17 Nov 2009 16:09:40 +0000 Subject: [Ontology-editors] UniProtKB accessions In-Reply-To: References: Message-ID: <4B02CAC4.9020403@ebi.ac.uk> Hi Jane, Your example, Q8TW31, was really interesting. When I first looked at the entry I saw that the subunit composition annotation was tagged with a 'By similarity' tag. So I immediately thought that there had to be a primary source for this annotation line, which we could trace and use instead of the UniProtKB accession number. However, I was unable to find any protein which supplied the source annotation! I've queried this with Michele in UniProtKB, and find out if there is anyway of easily finding the original piece of data that generated such annotation lines! However if there are molecular functions which use a UniProtKB accession as a reference, perhaps we could ask Anne Morgat to ensure such activities are captured by terms in UniPathway - and GO reference UniPathway instead? Cheers, Emily Jane Lomax wrote: > Okay - bad example! But I promise there are tonnes of really obscure > bacterial complexes and functions that don't have any literature attached > to them that I've added for the IMG mapping (hence probably no > annotations either) > > ...also a lot of the time I added a UniProt id dbxref as a sort of > example so people could tell what the term meant, as well as getting > some info for the def. I know this isn't ideal as a def dbxref, but > there's not really > another way of capturing it. Maybe we need some field, example > annotation? > > Either way, can we not blanket delete them for now otherwise the info > will just be lost... > > Jane > > On Tue, 17 Nov 2009, Midori Harris wrote: > >> PMID: 7026530 >> >>> From the MetaCyc entry at >> http://BioCyc.org/META/NEW-IMAGE?type=ENZYME&object=3-ISOPROPYLMALISOM-CPLX >> >> >> On Tue, 17 Nov 2009, Jane Lomax wrote: >> >>> Okay - here's one: Q8TW31 >>> >>> I've got the subunit composition from the entry - the only paper >>> cited is the genome paper. In this case there's another dbxref >>> (BRENDA) but that's not always the case... >>> >>> Jane >>> >>> On Tue, 17 Nov 2009, Midori Harris wrote: >>> >>>> Hi all, >>>> >>>> After a brief chat with Emily, I'm removing UniProtKB accessions >>>> that have been used as definition dbxrefs. >>>> >>>> The main reason is that a UniProt entry should provide links to >>>> other references (e.g. papers) that would be preferable def sources >>>> anyway. An additional reason is that the presence of UniProt >>>> accessions in the ontology files is confusing some people over here. >>>> >>>> I would recommend not using UniProtKB accessions as definition >>>> dbxrefs in the future, unless an alternative source really can't be >>>> found. >>>> >>>> cheers, >>>> m >>>> _______________________________________________ >>>> Ontology-editors mailing list >>>> Ontology-editors at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >>>> >>> >>> >> > -- ------------------------------------------------------------------ Emily Dimmer Ph.D. GOA Coordinator 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 URL: http://www.ebi.ac.uk/goa From midori at ebi.ac.uk Tue Nov 17 16:10:17 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Tue, 17 Nov 2009 16:10:17 +0000 (GMT) Subject: [Ontology-editors] UniProtKB accessions In-Reply-To: References: Message-ID: So far, I haven't had much trouble tracking down references (done about 15-20 so far); if there are any where there really is nothing other than the UniProt entry, those can stay. A definition dbxref is indeed not a place to put an example annotation. I'm really opposed to keeping any def dbxrefs for that purpose -- it muddies the meaning of the def dbxref field. If any are meant as annotations, is there any reason not to pass that info along to UniProt (or whichever group) to be incorporated into the actual annotation datasets? As for losing the info, they will, of course, be in the older revisions in CVS. m On Tue, 17 Nov 2009, Jane Lomax wrote: > Okay - bad example! But I promise there are tonnes of really obscure > bacterial complexes and functions that don't have any literature attached > to them that I've added for the IMG mapping (hence probably no annotations > either) > > ...also a lot of the time I added a UniProt id dbxref as a sort of example so > people could tell what the term meant, as well as getting some info for the > def. I know this isn't ideal as a def dbxref, but there's not really > another way of capturing it. Maybe we need some field, example annotation? > > Either way, can we not blanket delete them for now otherwise the info will > just be lost... > > Jane > > On Tue, 17 Nov 2009, Midori Harris wrote: > >> PMID: 7026530 >> >>> From the MetaCyc entry at >> http://BioCyc.org/META/NEW-IMAGE?type=ENZYME&object=3-ISOPROPYLMALISOM-CPLX >> >> On Tue, 17 Nov 2009, Jane Lomax wrote: >> >>> Okay - here's one: Q8TW31 >>> >>> I've got the subunit composition from the entry - the only paper cited is >>> the genome paper. In this case there's another dbxref (BRENDA) but that's >>> not always the case... >>> >>> Jane >>> >>> On Tue, 17 Nov 2009, Midori Harris wrote: >>> >>>> Hi all, >>>> >>>> After a brief chat with Emily, I'm removing UniProtKB accessions that >>>> have been used as definition dbxrefs. >>>> >>>> The main reason is that a UniProt entry should provide links to other >>>> references (e.g. papers) that would be preferable def sources anyway. An >>>> additional reason is that the presence of UniProt accessions in the >>>> ontology files is confusing some people over here. >>>> >>>> I would recommend not using UniProtKB accessions as definition dbxrefs in >>>> the future, unless an alternative source really can't be found. >>>> >>>> cheers, >>>> m >>>> _______________________________________________ >>>> Ontology-editors mailing list >>>> Ontology-editors at geneontology.org >>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >>>> >>> >>> >> > > From jane at ebi.ac.uk Tue Nov 17 16:15:03 2009 From: jane at ebi.ac.uk (Jane Lomax) Date: Tue, 17 Nov 2009 16:15:03 +0000 (GMT) Subject: [Ontology-editors] UniProtKB accessions In-Reply-To: <4B02CAC4.9020403@ebi.ac.uk> References: <4B02CAC4.9020403@ebi.ac.uk> Message-ID: Oh yes - if you click the 'by similarity' icon, it just tells you what by similarity means! Useful ;) Yes, actually swapping them to UniPathway ids would be fine - they're mostly functions anyhow... Jane On Tue, 17 Nov 2009, Emily Dimmer wrote: > Hi Jane, > > Your example, Q8TW31, was really interesting. When I first looked at the > entry I saw that the subunit composition annotation was tagged with a 'By > similarity' tag. So I immediately thought that there had to be a primary > source for this annotation line, which we could trace and use instead of the > UniProtKB accession number. However, I was unable to find any protein which > supplied the source annotation! I've queried this with Michele in UniProtKB, > and find out if there is anyway of easily finding the original piece of data > that generated such annotation lines! > > However if there are molecular functions which use a UniProtKB accession as a > reference, perhaps we could ask Anne Morgat to ensure such activities are > captured by terms in UniPathway - and GO reference UniPathway instead? > > > Cheers, > Emily > > > > Jane Lomax wrote: >> Okay - bad example! But I promise there are tonnes of really obscure >> bacterial complexes and functions that don't have any literature attached >> to them that I've added for the IMG mapping (hence probably no annotations >> either) >> >> ...also a lot of the time I added a UniProt id dbxref as a sort of example >> so people could tell what the term meant, as well as getting some info for >> the def. I know this isn't ideal as a def dbxref, but there's not really >> another way of capturing it. Maybe we need some field, example annotation? >> >> Either way, can we not blanket delete them for now otherwise the info will >> just be lost... >> >> Jane >> >> On Tue, 17 Nov 2009, Midori Harris wrote: >> >>> PMID: 7026530 >>> >>>> From the MetaCyc entry at >>> http://BioCyc.org/META/NEW-IMAGE?type=ENZYME&object=3-ISOPROPYLMALISOM-CPLX >>> >>> On Tue, 17 Nov 2009, Jane Lomax wrote: >>> >>>> Okay - here's one: Q8TW31 >>>> >>>> I've got the subunit composition from the entry - the only paper cited is >>>> the genome paper. In this case there's another dbxref (BRENDA) but that's >>>> not always the case... >>>> >>>> Jane >>>> >>>> On Tue, 17 Nov 2009, Midori Harris wrote: >>>> >>>>> Hi all, >>>>> >>>>> After a brief chat with Emily, I'm removing UniProtKB accessions that >>>>> have been used as definition dbxrefs. >>>>> >>>>> The main reason is that a UniProt entry should provide links to other >>>>> references (e.g. papers) that would be preferable def sources anyway. An >>>>> additional reason is that the presence of UniProt accessions in the >>>>> ontology files is confusing some people over here. >>>>> >>>>> I would recommend not using UniProtKB accessions as definition dbxrefs >>>>> in the future, unless an alternative source really can't be found. >>>>> >>>>> cheers, >>>>> m >>>>> _______________________________________________ >>>>> Ontology-editors mailing list >>>>> Ontology-editors at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >>>>> >>>> >>>> >>> >> > > > -- 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 jane at ebi.ac.uk Tue Nov 17 16:27:54 2009 From: jane at ebi.ac.uk (Jane Lomax) Date: Tue, 17 Nov 2009 16:27:54 +0000 (GMT) Subject: [Ontology-editors] UniProtKB accessions In-Reply-To: References: Message-ID: I think swapping them for UniPathway ids is the way to go, unless you can find a publication. I could feed back some of those bacterial 'annotations' to UniProt...not sure what evidence code they'd be though, as I get the data from IMG who don't make GO annotations... Jane On Tue, 17 Nov 2009, Midori Harris wrote: > So far, I haven't had much trouble tracking down references (done about 15-20 > so far); if there are any where there really is nothing other than the > UniProt entry, those can stay. > > A definition dbxref is indeed not a place to put an example annotation. I'm > really opposed to keeping any def dbxrefs for that purpose -- it muddies the > meaning of the def dbxref field. If any are meant as annotations, is there > any reason not to pass that info along to UniProt (or whichever group) to be > incorporated into the actual annotation datasets? > > As for losing the info, they will, of course, be in the older revisions in > CVS. > > m > > On Tue, 17 Nov 2009, Jane Lomax wrote: > >> Okay - bad example! But I promise there are tonnes of really obscure >> bacterial complexes and functions that don't have any literature attached >> to them that I've added for the IMG mapping (hence probably no annotations >> either) >> >> ...also a lot of the time I added a UniProt id dbxref as a sort of example >> so people could tell what the term meant, as well as getting some info for >> the def. I know this isn't ideal as a def dbxref, but there's not really >> another way of capturing it. Maybe we need some field, example annotation? >> >> Either way, can we not blanket delete them for now otherwise the info will >> just be lost... >> >> Jane >> >> On Tue, 17 Nov 2009, Midori Harris wrote: >> >>> PMID: 7026530 >>> >>>> From the MetaCyc entry at >>> http://BioCyc.org/META/NEW-IMAGE?type=ENZYME&object=3-ISOPROPYLMALISOM-CPLX >>> >>> On Tue, 17 Nov 2009, Jane Lomax wrote: >>> >>>> Okay - here's one: Q8TW31 >>>> >>>> I've got the subunit composition from the entry - the only paper cited is >>>> the genome paper. In this case there's another dbxref (BRENDA) but that's >>>> not always the case... >>>> >>>> Jane >>>> >>>> On Tue, 17 Nov 2009, Midori Harris wrote: >>>> >>>>> Hi all, >>>>> >>>>> After a brief chat with Emily, I'm removing UniProtKB accessions that >>>>> have been used as definition dbxrefs. >>>>> >>>>> The main reason is that a UniProt entry should provide links to other >>>>> references (e.g. papers) that would be preferable def sources anyway. An >>>>> additional reason is that the presence of UniProt accessions in the >>>>> ontology files is confusing some people over here. >>>>> >>>>> I would recommend not using UniProtKB accessions as definition dbxrefs >>>>> in the future, unless an alternative source really can't be found. >>>>> >>>>> cheers, >>>>> m >>>>> _______________________________________________ >>>>> Ontology-editors mailing list >>>>> Ontology-editors at geneontology.org >>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >>>>> >>>> >>>> >>> >> >> > -- 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 Tue Nov 17 16:31:32 2009 From: kchris at genome.stanford.edu (Karen Christie) Date: Tue, 17 Nov 2009 08:31:32 -0800 (PST) Subject: [Ontology-editors] UniProtKB accessions In-Reply-To: References: Message-ID: these seem more like db cross references indicating a (perhaps rough) correspondance between a GO term and an item in another database, rather than dbxrefs for the definition. -Karen On Tue, 17 Nov 2009, Jane Lomax wrote: > I think swapping them for UniPathway ids is the way to go, unless you can > find a publication. > > I could feed back some of those bacterial 'annotations' to UniProt...not sure > what evidence code they'd be though, as I get the data from IMG who don't > make GO annotations... > > Jane > > On Tue, 17 Nov 2009, Midori Harris wrote: > >> So far, I haven't had much trouble tracking down references (done about >> 15-20 so far); if there are any where there really is nothing other than >> the UniProt entry, those can stay. >> >> A definition dbxref is indeed not a place to put an example annotation. I'm >> really opposed to keeping any def dbxrefs for that purpose -- it muddies >> the meaning of the def dbxref field. If any are meant as annotations, is >> there any reason not to pass that info along to UniProt (or whichever >> group) to be incorporated into the actual annotation datasets? >> >> As for losing the info, they will, of course, be in the older revisions in >> CVS. >> >> m >> >> On Tue, 17 Nov 2009, Jane Lomax wrote: >> >>> Okay - bad example! But I promise there are tonnes of really obscure >>> bacterial complexes and functions that don't have any literature attached >>> to them that I've added for the IMG mapping (hence probably no annotations >>> either) >>> >>> ...also a lot of the time I added a UniProt id dbxref as a sort of example >>> so people could tell what the term meant, as well as getting some info for >>> the def. I know this isn't ideal as a def dbxref, but there's not really >>> another way of capturing it. Maybe we need some field, example annotation? >>> >>> Either way, can we not blanket delete them for now otherwise the info will >>> just be lost... >>> >>> Jane >>> >>> On Tue, 17 Nov 2009, Midori Harris wrote: >>> >>>> PMID: 7026530 >>>> >>>>> From the MetaCyc entry at >>>> http://BioCyc.org/META/NEW-IMAGE?type=ENZYME&object=3-ISOPROPYLMALISOM-CPLX >>>> >>>> On Tue, 17 Nov 2009, Jane Lomax wrote: >>>> >>>>> Okay - here's one: Q8TW31 >>>>> >>>>> I've got the subunit composition from the entry - the only paper cited >>>>> is the genome paper. In this case there's another dbxref (BRENDA) but >>>>> that's not always the case... >>>>> >>>>> Jane >>>>> >>>>> On Tue, 17 Nov 2009, Midori Harris wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> After a brief chat with Emily, I'm removing UniProtKB accessions that >>>>>> have been used as definition dbxrefs. >>>>>> >>>>>> The main reason is that a UniProt entry should provide links to other >>>>>> references (e.g. papers) that would be preferable def sources anyway. >>>>>> An additional reason is that the presence of UniProt accessions in the >>>>>> ontology files is confusing some people over here. >>>>>> >>>>>> I would recommend not using UniProtKB accessions as definition dbxrefs >>>>>> in the future, unless an alternative source really can't be found. >>>>>> >>>>>> cheers, >>>>>> m >>>>>> _______________________________________________ >>>>>> Ontology-editors mailing list >>>>>> Ontology-editors at geneontology.org >>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >>>>>> >>>>> >>>>> >>>> >>> >>> >> > > -- > 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 > _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors > From jane at ebi.ac.uk Tue Nov 17 16:33:17 2009 From: jane at ebi.ac.uk (Jane Lomax) Date: Tue, 17 Nov 2009 16:33:17 +0000 (GMT) Subject: [Ontology-editors] UniProtKB accessions In-Reply-To: References: Message-ID: Yes - they could be general dbxrefs instead... On Tue, 17 Nov 2009, Karen Christie wrote: > these seem more like db cross references indicating a (perhaps rough) > correspondance between a GO term and an item in another database, rather than > dbxrefs for the definition. > > -Karen > > > On Tue, 17 Nov 2009, Jane Lomax wrote: > >> I think swapping them for UniPathway ids is the way to go, unless you can >> find a publication. >> >> I could feed back some of those bacterial 'annotations' to UniProt...not >> sure what evidence code they'd be though, as I get the data from IMG who >> don't make GO annotations... >> >> Jane >> >> On Tue, 17 Nov 2009, Midori Harris wrote: >> >>> So far, I haven't had much trouble tracking down references (done about >>> 15-20 so far); if there are any where there really is nothing other than >>> the UniProt entry, those can stay. >>> >>> A definition dbxref is indeed not a place to put an example annotation. >>> I'm really opposed to keeping any def dbxrefs for that purpose -- it >>> muddies the meaning of the def dbxref field. If any are meant as >>> annotations, is there any reason not to pass that info along to UniProt >>> (or whichever group) to be incorporated into the actual annotation >>> datasets? >>> >>> As for losing the info, they will, of course, be in the older revisions in >>> CVS. >>> >>> m >>> >>> On Tue, 17 Nov 2009, Jane Lomax wrote: >>> >>>> Okay - bad example! But I promise there are tonnes of really obscure >>>> bacterial complexes and functions that don't have any literature attached >>>> to them that I've added for the IMG mapping (hence probably no >>>> annotations either) >>>> >>>> ...also a lot of the time I added a UniProt id dbxref as a sort of >>>> example so people could tell what the term meant, as well as getting some >>>> info for the def. I know this isn't ideal as a def dbxref, but there's >>>> not really >>>> another way of capturing it. Maybe we need some field, example >>>> annotation? >>>> >>>> Either way, can we not blanket delete them for now otherwise the info >>>> will just be lost... >>>> >>>> Jane >>>> >>>> On Tue, 17 Nov 2009, Midori Harris wrote: >>>> >>>>> PMID: 7026530 >>>>> >>>>>> From the MetaCyc entry at >>>>> http://BioCyc.org/META/NEW-IMAGE?type=ENZYME&object=3-ISOPROPYLMALISOM-CPLX >>>>> >>>>> On Tue, 17 Nov 2009, Jane Lomax wrote: >>>>> >>>>>> Okay - here's one: Q8TW31 >>>>>> >>>>>> I've got the subunit composition from the entry - the only paper cited >>>>>> is the genome paper. In this case there's another dbxref (BRENDA) but >>>>>> that's not always the case... >>>>>> >>>>>> Jane >>>>>> >>>>>> On Tue, 17 Nov 2009, Midori Harris wrote: >>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> After a brief chat with Emily, I'm removing UniProtKB accessions that >>>>>>> have been used as definition dbxrefs. >>>>>>> >>>>>>> The main reason is that a UniProt entry should provide links to other >>>>>>> references (e.g. papers) that would be preferable def sources anyway. >>>>>>> An additional reason is that the presence of UniProt accessions in the >>>>>>> ontology files is confusing some people over here. >>>>>>> >>>>>>> I would recommend not using UniProtKB accessions as definition dbxrefs >>>>>>> in the future, unless an alternative source really can't be found. >>>>>>> >>>>>>> cheers, >>>>>>> m >>>>>>> _______________________________________________ >>>>>>> Ontology-editors mailing list >>>>>>> Ontology-editors at geneontology.org >>>>>>> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>> >> >> -- >> 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 >> _______________________________________________ >> Ontology-editors mailing list >> Ontology-editors at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >> > -- 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 cjm at berkeleybop.org Tue Nov 17 17:00:00 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Tue, 17 Nov 2009 09:00:00 -0800 Subject: [Ontology-editors] NF-kappaB complex In-Reply-To: References: Message-ID: Thanks! On Nov 17, 2009, at 3:05 AM, Midori Harris wrote: > Both, I think -- GO should have a term for 'NF-kappaB complex' and > PRO should represent the monomers. From a book I found online: > > "In the majority of cell types NF-kappaB exists in the cytoplasm as > homo- or heterodimers of a family of structurally related proteins." > > I've created an item for GO: > > https://sourceforge.net/tracker/?func=detail&aid=2898993&group_id=36855&atid=440764 > > I'll assume you'll take care of a PRO request. > > cheers, > m > > On Mon, 16 Nov 2009, Chris Mungall wrote: > >> I'd like a term representing a NF-kappaB complex >> >> This will allow for the logical definition of >> * GO:0042348 ! NF-kappaB import into nucleus >> >> Which in turn will allow us to automatically map reactions such as >> this: >> >> http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193691 >> >> to the above GO ID. >> >> Is the appropriate place to request this GO or PRO? >> _______________________________________________ >> Ontology-editors mailing list >> Ontology-editors at geneontology.org >> http://fafner.stanford.edu/mailman/listinfo/ontology-editors >> > From cjm at yuri.lbl.gov Thu Nov 19 15:52:10 2009 From: cjm at yuri.lbl.gov (Chris Mungall) Date: Thu, 19 Nov 2009 07:52:10 -0800 Subject: [Ontology-editors] problem with obo file Message-ID: ERROR: namespace-different-from-is_a-parent: GO:0005262 in molecular_function, GO:0070588 in biological_process From midori at ebi.ac.uk Thu Nov 19 15:53:19 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 19 Nov 2009 15:53:19 +0000 (GMT) Subject: [Ontology-editors] problem with obo file In-Reply-To: References: Message-ID: fixed On Thu, 19 Nov 2009, Chris Mungall wrote: > ERROR: namespace-different-from-is_a-parent: GO:0005262 in molecular_function, GO:0070588 in biological_process From midori at ebi.ac.uk Thu Nov 19 15:57:11 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Thu, 19 Nov 2009 15:57:11 +0000 (GMT) Subject: [Ontology-editors] biogenesis & modification Message-ID: Hi, A quick question (I hope): any objection to expanding the definition of cellular component biogenesis to include modification as well as synthesis of parts (e.g. posttranslational protein modification)? Requested in SF 289887: https://sourceforge.net/tracker/?func=detail&aid=2899887&group_id=36855&atid=440764 thanks, m From cjm at berkeleybop.org Fri Nov 20 02:25:16 2009 From: cjm at berkeleybop.org (Chris Mungall) Date: Thu, 19 Nov 2009 18:25:16 -0800 Subject: [Ontology-editors] enables vs catalysis of Message-ID: <601AE1F6-6AF4-42FA-BD10-D58A0971806D@berkeleybop.org> GO:0022891 ! substrate-specific transmembrane transporter activity *** [DEF: "Catalysis of the transfer of a specific substance or group of related substances from one side of a membrane to the other."] this is *not* under GO:0003824 ! catalytic activity even though it appears to fit the definition the two direct parents say "enables" not "catalysis" GO:0022857 ! transmembrane transporter activity [DEF: "Enables of the transfer of a substance from one side of a membrane to the other."] GO:0022892 ! substrate-specific transporter activity [DEF: "Enables the directed movement of a specific substance or group of related substances (such as macromolecules, small molecules, ions) into, out of, within or between cells."] (also note type in 22857, perhaps there was some half-completed search and replace going on?) From midori at ebi.ac.uk Fri Nov 20 12:00:42 2009 From: midori at ebi.ac.uk (Midori Harris) Date: Fri, 20 Nov 2009 12:00:42 +0000 (GMT) Subject: [Ontology-editors] GO revisability (RE: keeping in touch) (fwd) Message-ID: ---------- Forwarded message ---------- Date: Fri, 20 Nov 2009 11:50:59 +0000 From: "Leonelli, Sabina" To: Midori Harris Subject: RE: keeping in touch Hi Midori, thanks a lot for the quick reply, indeed adding relations is also a key way of shifting ontologies, I got a number of questions yesterday on this from the philosophers at the talk --- it definitely deserves to be put on the list and explored, asking how are these shifts affecting the knowledge represented within the GO. The way to go, in my view, would be to take a couple of specific cases (e.g. one example of adding the relation 'regulates') and see how adding that relation has affected the whole GO network. Has that changed the way in which GO represents the processes in question? In which way -- sharper description of biological process, better fit with available data, better fit with the rest of the GO network? I am really looking forward to hear whether the rest of the team, as well as Chris and David, would be interested in collaborating on this -- thanks for having forwarded the idea to them! You also have a great weekend, and let me know if you get any responses on this, Cheers, Sabina ________________________________________ From: Midori Harris [midori at ebi.ac.uk] Sent: Thursday, November 19, 2009 3:51 PM To: Leonelli, Sabina Subject: RE: keeping in touch Hi Sabina, Yes, it was excellent to catch up. I really enjoyed it, and I'm glad you had the time here. Thanks for the outline/draft -- I think it does look interesting, potentially a route to explain some of what we do and why to the biologists that we want to use the ontology or the annotations (or both). I've really only skimmed it so far, so I'll have to think more about what examples would be good, and whether there are any more categories of changes.One thing I've thought of already -- because we're trying to find the time to write it up anyway -- is the work we've done over the past year or two on regulation. We added three new relationship types so we could do a better job of representing how regulatory processes are related to their targets (which might be other processes, molecular functions, or even biological qualities) ... and I haven't got a quick answer for how to categorize the kind(s) of changes the whole project entailed. Anyway, I'd like to forward the draft around the ontology developers. It wouldn't surprise me if David Hill and Chris Mungall turn out to be interested (in addition to us "go-go girls"). Hope your conference is going well, and have a great weekend. Midori On Thu, 19 Nov 2009, Leonelli, Sabina wrote: > Hi Midori, > > it was really great to see you and catch up a bit, thanks again for making the time (and bringing me to really nice places -- the coffee here is excellent). I am attaching here a very quick outline (well, more a concept really!) for a short reflection piece that we might think of co-writing and sending off to either Bioessayes or some other journal with a reflexive bent (might even try Science, you never know). Let me know whether you think it's in any way workable, or whether you think it's a waste of time and efforts --- it just occurred me over lunch that this would be a productive collaboration towards an interesting piece for your users, but I might be wrong. A lot of it would actually consist of explaining how some of the GO rules have been used in conjunction with biological evidence as ground to decide over ontology shifts -- the key is that we'd do it from the user perspective, in a language that they definitely understand (as it's all about describing biological ! processes). > > All the best and have a good weekend, > Sabina > [snip 'cos it was getting crazy long] From adiehl at informatics.jax.org Fri Nov 20 13:12:24 2009 From: adiehl at informatics.jax.org (Alexander Diehl) Date: Fri, 20 Nov 2009 08:12:24 -0500 Subject: [Ontology-editors] possible publication on "revisability" of GO (RE: keeping in touch) (fwd) In-Reply-To: References: Message-ID: <4B0695B8.809@informatics.jax.org> Midori, I would be happy to contribute to this manuscript, particularly as regards point 1 in Sabina's outline. In fact I'm pretty sure I can come up with examples from the immunology revision that correspond to all five of Sabina's types of changes (not that that's necessarily necessary). Thanks, Alex Midori Harris wrote: > Hi, > > I think some of you are acquainted witth Sabina Leonelli; for those who > aren't, she's a philosopher of science now at the University of Exeter, > interested in quite a few aspects of biological databases and ontologies, > and how people develop and use them. She has worked with TAIR curators > and the GO editorial office, and now has an idea for a publication on > why and how GO changes that I think might dovetail with the kinds of > things we want to do (e.g. in the regulates paper) to help biologists > understand GO more thoroughly. An initial outline is attached, and > I'll also forward a bit of follow-up email. > > Any comments? > > Midori > > ---------- Forwarded message ---------- > Date: Thu, 19 Nov 2009 15:08:16 +0000 > From: "Leonelli, Sabina" > To: Midori Harris > Subject: RE: keeping in touch > > Hi Midori, > > it was really great to see you and catch up a bit, thanks again for > making the time (and bringing me to really nice places -- the coffee > here is excellent). I am attaching here a very quick outline (well, > more a concept really!) for a short reflection piece that we might > think of co-writing and sending off to either Bioessayes or some other > journal with a reflexive bent (might even try Science, you never > know). Let me know whether you think it's in any way workable, or > whether you think it's a waste of time and efforts --- it just > occurred me over lunch that this would be a productive collaboration > towards an interesting piece for your users, but I might be wrong. A > lot of it would actually consist of explaining how some of the GO > rules have been used in conjunction with biological evidence as ground > to decide over ontology shifts -- the key is that we'd do it from the > user perspective, in a language that they definitely understand (as > it's all about describing biological processes). > > All the best and have a good weekend, > Sabina > > ________________________________________ > From: Midori Harris [midori at ebi.ac.uk] > Sent: Friday, November 13, 2009 1:14 PM > To: Leonelli, Sabina > Subject: RE: keeping in touch > > Hi Sabina, > > Thursday lunch would be excellent. Shall we meet at the Corpus Clock > (http://en.wikipedia.org/wiki/Corpus_Clock) and go foraging from there? > There's a nice restaurant just across the street > (http://www.chophouses.co.uk/TheCambridgeChopHouse/), or, if that sounds > too heavy for lunch, there's a decent Thai place nearby, or Italian, > Vietnamese, sandwiches, and a bunch of other options within reasonable > walking distance. > > Midori > > On Thu, 12 Nov 2009, Leonelli, Sabina wrote: > >> Hi Midori, that's really great, thank you for the quick answer! The best >> time for me would probably be Thursday lunch (I have to be at the HPS >> Department at 16, and I am arriving from London at around 11-12 that >> morning). Would that work for you? And do you know any place to meet >> close to Corpus Christi college? I guess anywhere in the centre will be >> close anyhow.. >> Sabina >> >> -----Original Message----- >> From: Midori Harris [mailto:midori at ebi.ac.uk] >> Sent: 12 November 2009 11:59 >> To: Leonelli, Sabina >> Subject: RE: keeping in touch >> >> Hi Sabina, >> >> Great to hear from you again, and congratulations on getting married! >> >> With a week's notice, it should be no problem for me to work from >> home on >> Thursday or Friday next week (especially since GO won't be very busy >> because of the holiday in the US). I think Thursday might be slightly >> better for me, but Friday would work well enough. Which is better for >> you? >> >> Looking forward to catching up! >> >> Midori >> >> On Wed, 11 Nov 2009, Leonelli, Sabina wrote: >> >>> Dear Midori, >>> >>> I hope this finds you and your colleagues very well! I have had a very >>> busy summer (work was a bit crazy, we are feeling the tightening of >>> research funding -- and I got married, which was also a feat) and I am >>> now deep into teaching and trying to finish a couple of papers on >>> bio-ontologies that I hope to be able to send to you soon. I wanted to >>> let you know that I'll be in Cambridge next week, giving a talk (on >>> bio-ontologies!) at the History and Philosophy of Science Seminar. I'll >>> be around during the day on Thursday and on Friday until 5 pm or so -- >>> any chance to meet for a coffee and update? Absolutely no worries if >>> there is no way to do that (I imagine you need to be in your office >>> during the day -- and I'll have to go to post-seminar dinner on >>> Thursday >>> night), I just wanted to check! >>> >>> All the best, >>> Sabina >>> >>> >>> Sabina Leonelli >>> Research Fellow >>> ESRC Centre for Genomics in Society >>> University of Exeter >>> http://huss.exeter.ac.uk/sociology/staff/leonelli/index.php >>> >>> >>> >> > ------------------------------------------------------------------------ > > _______________________________________________ > Ontology-editors mailing list > Ontology-editors at geneontology.org > http://fafner.stanford.edu/mailman/listinfo/ontology-editors -- Alexander D. Diehl, Ph.D. Research Scientist Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 email: adiehl at informatics.jax.org work: +1 (207) 288-6427 fax: +1 (207) 288-6131