From rhee at acoma.Stanford.EDU Mon Feb 2 04:27:27 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 2 Feb 2004 01:27:27 -0800 (PST) Subject: trait ontology on OBO In-Reply-To: <65500.64.169.229.2.1073713528.squirrel@webmail.cornell.edu> Message-ID: Pankaj, It looks like the plant trait ontology at OBO has the contact to be Plant Ontology Consortium and has the status to be 'implementation release'. Since the trait is not something the consortium is tacking currently, perhaps you should change the contact info and the name of the ontology to something like rice or grasses trait ontology? Sue ----------------------------------------------------------------------------- Sue Rhee rhee at acoma.stanford.edu The Arabidopsis Information Resource URL: www.arabidopsis.org Carnegie Institution of Washington FAX: +1-650-325-6857 Department of Plant Biology Tel: +1-650-325-1521 ext. 251 260 Panama St. Stanford, CA 94305 U.S.A. ----------------------------------------------------------------------------- From pj37 at cornell.edu Mon Feb 2 12:26:43 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 02 Feb 2004 12:26:43 -0500 Subject: trait ontology on OBO In-Reply-To: References: Message-ID: <401E8853.1010309@cornell.edu> Hi Sue, I have sent the request for modifications to Suzi. Hopefully it will be done soon. Pankaj Sue Rhee wrote: > Pankaj, > > It looks like the plant trait ontology at OBO has the contact to be Plant > Ontology Consortium and has the status to be 'implementation release'. > > Since the trait is not something the consortium is tacking currently, > perhaps you should change the contact info and the name of the ontology to > something like rice or grasses trait ontology? > > Sue > > ----------------------------------------------------------------------------- > Sue Rhee rhee at acoma.stanford.edu > The Arabidopsis Information Resource URL: www.arabidopsis.org > Carnegie Institution of Washington FAX: +1-650-325-6857 > Department of Plant Biology Tel: +1-650-325-1521 ext. 251 > 260 Panama St. > Stanford, CA 94305 > U.S.A. > ----------------------------------------------------------------------------- > > From rhee at acoma.Stanford.EDU Mon Feb 2 14:31:14 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 2 Feb 2004 11:31:14 -0800 (PST) Subject: trait ontology on OBO In-Reply-To: <401E8853.1010309@cornell.edu> Message-ID: cool thaks, sue On Mon, 2 Feb 2004, Pankaj Jaiswal wrote: > Hi Sue, > > I have sent the request for modifications to Suzi. Hopefully it will be > done soon. > > Pankaj > > Sue Rhee wrote: > > Pankaj, > > > > It looks like the plant trait ontology at OBO has the contact to be Plant > > Ontology Consortium and has the status to be 'implementation release'. > > > > Since the trait is not something the consortium is tacking currently, > > perhaps you should change the contact info and the name of the ontology to > > something like rice or grasses trait ontology? > > > > Sue > > > > ----------------------------------------------------------------------------- > > Sue Rhee rhee at acoma.stanford.edu > > The Arabidopsis Information Resource URL: www.arabidopsis.org > > Carnegie Institution of Washington FAX: +1-650-325-6857 > > Department of Plant Biology Tel: +1-650-325-1521 ext. 251 > > 260 Panama St. > > Stanford, CA 94305 > > U.S.A. > > ----------------------------------------------------------------------------- > > > > > ----------------------------------------------------------------------------- Sue Rhee rhee at acoma.stanford.edu The Arabidopsis Information Resource URL: www.arabidopsis.org Carnegie Institution of Washington FAX: +1-650-325-6857 Department of Plant Biology Tel: +1-650-325-1521 ext. 251 260 Panama St. Stanford, CA 94305 U.S.A. ----------------------------------------------------------------------------- From rhee at acoma.Stanford.EDU Mon Feb 2 14:41:07 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 2 Feb 2004 11:41:07 -0800 (PST) Subject: OBO flat file format documentation (fwd) Message-ID: ---------- Forwarded message ---------- Date: Mon, 02 Feb 2004 14:43:46 +0000 From: JClark To: go at genome.stanford.edu Subject: OBO flat file format documentation Hi, I've put the OBO flat file format documentation onto the website now: http://www.geneontology.org/GO.format.html#oboflat It's just John's proposal e-mail with a very few edits to turn it into documentation instead of a proposal. Also there's a little bit of rearrangement of the page to fit in with the old 'GO' flat file format docs. If people are happy with it then in a week or so we could start to send out announcements to the GO Friends list to warn people that it's coming. Thanks, Jen From katica at acoma.Stanford.EDU Thu Feb 5 12:46:45 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 5 Feb 2004 09:46:45 -0800 (PST) Subject: POC minutes on the POC live site Message-ID: Hi everyone, Final version of the minutes from the POC meeting in San Diego is now posted on the POC live web site: http://www.plantontology.org/docs/minutes/minutes_pag_2004.html Best regards, Katica -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From rhee at acoma.Stanford.EDU Fri Feb 6 16:45:12 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Fri, 6 Feb 2004 13:45:12 -0800 (PST) Subject: a review on bio-ontologies Message-ID: hi, folks jonathan bard at edinburgh and i wrote a review article on ontologies, which will come out in march issue of nature review genetics. here's the proof version in pdf, in case you are interested. sue ----------------------------------------------------------------------------- Sue Rhee rhee at acoma.stanford.edu The Arabidopsis Information Resource URL: www.arabidopsis.org Carnegie Institution of Washington FAX: +1-650-325-6857 Department of Plant Biology Tel: +1-650-325-1521 ext. 251 260 Panama St. Stanford, CA 94305 U.S.A. ----------------------------------------------------------------------------- -------------- next part -------------- A non-text attachment was scrubbed... Name: nrg0304-bard.pdf Type: application/pdf Size: 400493 bytes Desc: URL: From rhee at acoma.Stanford.EDU Mon Feb 9 14:52:43 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 9 Feb 2004 11:52:43 -0800 (PST) Subject: Autogenerating OBO format files (fwd) Message-ID: Hi, all This is a heads up on the switch of Dag-edit to use OBO flat files. There is a script that will convert a GO flat file into OBO flat file and I think this could be done perhaps by Shuly once before we switch to have the curators using the OBO flat file? I will forward a message that describes where the how to run the script. Sue ---------- Forwarded message ---------- Date: Sun, 8 Feb 2004 16:33:46 -0700 (MST) From: John Day-Richter To: Mike Cherry Cc: "go at geneontology.org List" Subject: Re: Autogenerating OBO format files On Sun, 8 Feb 2004, Mike Cherry wrote: > The flat2obo script works great on our Solaris server. I can easily > generate the go.obo file to the go/ontology directory in the CVS > repository as whatever frequency is useful. I'm sending this message to > the GO list for discussion of this topic. Thanks for setting this up! Is it possible to have the script automatically generate the obo file on the server-side every time there's a commit to the cvs repository? If not (or if that's too much of a hassle), I vote to generate the obo file at midnight every night. > The other question is how long should I plan on generating the go.obo > file, before the curators will be switching to committing that > file. Now that the new version of DAG-Edit is out, I am planning to publish some protocols for the obo adapter beta-test I'd like the Cambridge curators to do. (Hopefully I'll send out that document some time tomorrow). Once we've deemed the obo adapter completely stable (which I hope will be done in one or two weeks), I think we should immediately switch to the new format. -John From rhee at acoma.Stanford.EDU Mon Feb 9 14:53:02 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 9 Feb 2004 11:53:02 -0800 (PST) Subject: Autogenerating OBO format files (fwd) Message-ID: ---------- Forwarded message ---------- Date: Sun, 8 Feb 2004 14:03:53 -0800 From: Mike Cherry To: John Day-Richter Cc: "go at geneontology.org List" Subject: Re: Autogenerating OBO format files John, Thanks for the instructions and thanks for a great tool. The flat2obo script works great on our Solaris server. I can easily generate the go.obo file to the go/ontology directory in the CVS repository as whatever frequency is useful. I'm sending this message to the GO list for discussion of this topic. The other question is how long should I plan on generating the go.obo file, before the curators will be switching to committing that file. Obviously, I will need to include checks in my script so that if the go.obo file is newer than the process, function or component files I do not over write. Then after the curators switch to writing go.obo I'll switch to making the flat files from the OBO file for the repository. This is a big change. What other issues does the group need to discuss? -Mike On Feb 7, 2004, at 2:20 PM, John Day-Richter wrote: > > Hi, Mike. I should have gotten to you earlier with this, but I've been > engrossed in some new DAG-Edit features for the last week. > > At the last meeting, we talked about autogenerating the GO files in > OBO format > and posting them on the website. You said you'd be able to write a > script for > that once I sent you some instructions on how to use the conversion > scripts. > Here are those instructions: > > 1) Download DAG-Edit 1.410 from sourceforge.net/projects/geneontology > . I > suggest the .tar.gz format. > > 2) Unpack the archive wherever you'd like. You'll want to be able to > run the > flat2obo script that's in the main installation directory. If you need > to, > you can create a link to the flat2obo script in one of your system path > directories. > > 3) Run flat2obo with the following options: > > flat2obo --gopresets {path-to-component.ontology} > {path-to-process.ontology} > {path-to-function.ontology} -def {path-to-GO.defs} -o > {path-to-create-go.obo} > > The GO ontology files can be listed in any order. > > Let me know if you have any questions. > > Thanks, > > John > J. Michael Cherry, Ph.D. Internet: cherry at stanford.edu Associate Professor (Research) Department of Genetics Medical Center, Room M341 Stanford University School of Medicine Voice: 650-723-7541 Stanford, California 94305-5120 FAX: 650-723-1534 http://genome-www.stanford.edu/~cherry From pj37 at cornell.edu Mon Feb 9 15:27:10 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 09 Feb 2004 15:27:10 -0500 Subject: Autogenerating OBO format files (fwd) In-Reply-To: References: Message-ID: <4027ED1E.9090308@cornell.edu> In one of my earlier mails I suggested on releasing the OBO format with every major release. However, depending on the situation, and user liking we can start having it frequently (once a day), until everything shifts to the OBO format completely. Pankaj Sue Rhee wrote: > ---------- Forwarded message ---------- > Date: Sun, 8 Feb 2004 14:03:53 -0800 > From: Mike Cherry > To: John Day-Richter > Cc: "go at geneontology.org List" > Subject: Re: Autogenerating OBO format files > > John, > > Thanks for the instructions and thanks for a great tool. The flat2obo > script works great on our Solaris server. I can easily generate the > go.obo file to the go/ontology directory in the CVS repository as > whatever frequency is useful. I'm sending this message to the GO list > for discussion of this topic. The other question is how long should I > plan on generating the go.obo file, before the curators will be > switching to committing that file. Obviously, I will need to include > checks in my script so that if the go.obo file is newer than the > process, function or component files I do not over write. > > Then after the curators switch to writing go.obo I'll switch to making > the flat files from the OBO file for the repository. > > This is a big change. What other issues does the group need to discuss? > > -Mike > > On Feb 7, 2004, at 2:20 PM, John Day-Richter wrote: > > >>Hi, Mike. I should have gotten to you earlier with this, but I've been >>engrossed in some new DAG-Edit features for the last week. >> >>At the last meeting, we talked about autogenerating the GO files in >>OBO format >>and posting them on the website. You said you'd be able to write a >>script for >>that once I sent you some instructions on how to use the conversion >>scripts. >>Here are those instructions: >> >>1) Download DAG-Edit 1.410 from sourceforge.net/projects/geneontology >>. I >>suggest the .tar.gz format. >> >>2) Unpack the archive wherever you'd like. You'll want to be able to >>run the >>flat2obo script that's in the main installation directory. If you need >>to, >>you can create a link to the flat2obo script in one of your system path >>directories. >> >>3) Run flat2obo with the following options: >> >>flat2obo --gopresets {path-to-component.ontology} >>{path-to-process.ontology} >>{path-to-function.ontology} -def {path-to-GO.defs} -o >>{path-to-create-go.obo} >> >>The GO ontology files can be listed in any order. >> >>Let me know if you have any questions. >> >> Thanks, >> >> John >> > > J. Michael Cherry, Ph.D. Internet: cherry at stanford.edu > Associate Professor (Research) Department of Genetics > Medical Center, Room M341 Stanford University School of Medicine > Voice: 650-723-7541 Stanford, California 94305-5120 > FAX: 650-723-1534 http://genome-www.stanford.edu/~cherry > > -- ****************************** Pankaj Jaiswal, PhD Gramene Database Department of Plant Breeding G-15 Bradfield Hall Cornell University Ithaca, NY-14853 tel: +1-607-255-3103 fax: +1-607-255-6683 web: http://www.gramene.org ***************************** From rhee at acoma.Stanford.EDU Mon Feb 9 16:17:47 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 9 Feb 2004 13:17:47 -0800 (PST) Subject: Autogenerating OBO format files (fwd) In-Reply-To: <4027ED1E.9090308@cornell.edu> Message-ID: Since we won't be releasing the official PO files until July, I suggest that we release it as OBO. As for the existing spcies-specific files, your suggestion sounds fine to me, though I don't know how frequently these will be updated between now and the PO file release. Sue On Mon, 9 Feb 2004, Pankaj Jaiswal wrote: > In one of my earlier mails I suggested on releasing the OBO format with > every major release. However, depending on the situation, and user > liking we can start having it frequently (once a day), until everything > shifts to the OBO format completely. > > Pankaj > > Sue Rhee wrote: > > > ---------- Forwarded message ---------- > > Date: Sun, 8 Feb 2004 14:03:53 -0800 > > From: Mike Cherry > > To: John Day-Richter > > Cc: "go at geneontology.org List" > > Subject: Re: Autogenerating OBO format files > > > > John, > > > > Thanks for the instructions and thanks for a great tool. The flat2obo > > script works great on our Solaris server. I can easily generate the > > go.obo file to the go/ontology directory in the CVS repository as > > whatever frequency is useful. I'm sending this message to the GO list > > for discussion of this topic. The other question is how long should I > > plan on generating the go.obo file, before the curators will be > > switching to committing that file. Obviously, I will need to include > > checks in my script so that if the go.obo file is newer than the > > process, function or component files I do not over write. > > > > Then after the curators switch to writing go.obo I'll switch to making > > the flat files from the OBO file for the repository. > > > > This is a big change. What other issues does the group need to discuss? > > > > -Mike > > > > On Feb 7, 2004, at 2:20 PM, John Day-Richter wrote: > > > > > >>Hi, Mike. I should have gotten to you earlier with this, but I've been > >>engrossed in some new DAG-Edit features for the last week. > >> > >>At the last meeting, we talked about autogenerating the GO files in > >>OBO format > >>and posting them on the website. You said you'd be able to write a > >>script for > >>that once I sent you some instructions on how to use the conversion > >>scripts. > >>Here are those instructions: > >> > >>1) Download DAG-Edit 1.410 from sourceforge.net/projects/geneontology > >>. I > >>suggest the .tar.gz format. > >> > >>2) Unpack the archive wherever you'd like. You'll want to be able to > >>run the > >>flat2obo script that's in the main installation directory. If you need > >>to, > >>you can create a link to the flat2obo script in one of your system path > >>directories. > >> > >>3) Run flat2obo with the following options: > >> > >>flat2obo --gopresets {path-to-component.ontology} > >>{path-to-process.ontology} > >>{path-to-function.ontology} -def {path-to-GO.defs} -o > >>{path-to-create-go.obo} > >> > >>The GO ontology files can be listed in any order. > >> > >>Let me know if you have any questions. > >> > >> Thanks, > >> > >> John > >> > > > > J. Michael Cherry, Ph.D. Internet: cherry at stanford.edu > > Associate Professor (Research) Department of Genetics > > Medical Center, Room M341 Stanford University School of Medicine > > Voice: 650-723-7541 Stanford, California 94305-5120 > > FAX: 650-723-1534 http://genome-www.stanford.edu/~cherry > > > > > > -- > ****************************** > Pankaj Jaiswal, PhD > Gramene Database > Department of Plant Breeding > G-15 Bradfield Hall > Cornell University > Ithaca, NY-14853 > > tel: +1-607-255-3103 > fax: +1-607-255-6683 > web: http://www.gramene.org > ***************************** > > ----------------------------------------------------------------------------- Sue Rhee rhee at acoma.stanford.edu The Arabidopsis Information Resource URL: www.arabidopsis.org Carnegie Institution of Washington FAX: +1-650-325-6857 Department of Plant Biology Tel: +1-650-325-1521 ext. 251 260 Panama St. Stanford, CA 94305 U.S.A. ----------------------------------------------------------------------------- From peter.stevens at mobot.org Mon Feb 9 15:32:42 2004 From: peter.stevens at mobot.org (Peter Stevens) Date: Mon, 9 Feb 2004 16:32:42 -0400 Subject: glossary for plant phylogeny In-Reply-To: <4027ED1E.9090308@cornell.edu> References: <4027ED1E.9090308@cornell.edu> Message-ID: You should be able to get to the fl. pl. glossary as it stands at http://www.mobot.org/MOBOT/research/APweb/glossary1.html It is designed to go in the vacant space at a flowering plants (subfamilies and above) website, http://www.mobot.org/MOBOT/research/APweb/ Obviously, there are far too many mistakes at present for me not to be other than embarrassed. Note that the hierarchy for the terms is not yet worked out fully, but it will not be a strict hierarchy. That is, it may have terms at a particular hierachical level which is the one that people may be thinking of when they are actually using the site; there is also what may be the "true" hierarchical position. Note that the glossary is for the most part aimed at explicating text that deals with flowering plants and higher level relationships, so many more species level shape, texture and indumentum terms are either absent or only briefly dealt with (but we have Stearn's "Botanical Latin" for that); pollen terms are also particularly incomplete. P. Don't worry about typos, but do let me know of anything you consider more major, whether sins of omission or commission. I will have a plant chemist check that side of things, I have only just started with trial-by-use... From lstein at cshl.edu Thu Feb 12 08:30:52 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 12 Feb 2004 15:30:52 +0200 Subject: glossary for plant phylogeny In-Reply-To: References: <4027ED1E.9090308@cornell.edu> Message-ID: <200402121530.52336.lstein@cshl.edu> Hi Peter, This is quite nice. I do not see the hierarchical nature of the glossary, however. Could you explain? I also see that there are entries that are nothing but synonyms to other terms. Is there a plan to indicate which of several synonyms is the "preferred" one for use with the PO? Lincoln On Monday 09 February 2004 10:32 pm, Peter Stevens wrote: > You should be able to get to the fl. pl. glossary as it stands at > http://www.mobot.org/MOBOT/research/APweb/glossary1.html > > It is designed to go in the vacant space at a flowering plants > (subfamilies and above) website, > http://www.mobot.org/MOBOT/research/APweb/ > > Obviously, there are far too many mistakes at present for me not to > be other than embarrassed. Note that the hierarchy for the terms > is not yet worked out fully, but it will not be a strict hierarchy. > That is, it may have terms at a particular hierachical level which > is the one that people may be thinking of when they are actually > using the site; there is also what may be the "true" hierarchical > position. > > Note that the glossary is for the most part aimed at explicating > text that deals with flowering plants and higher level > relationships, so many more species level shape, texture and > indumentum terms are either absent or only briefly dealt with (but > we have Stearn's "Botanical Latin" for that); pollen terms are also > particularly incomplete. > > P. > > Don't worry about typos, but do let me know of anything you > consider more major, whether sins of omission or commission. I > will have a plant chemist check that side of things, I have only > just started with trial-by-use... -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From rhee at acoma.Stanford.EDU Fri Feb 13 21:24:31 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Fri, 13 Feb 2004 18:24:31 -0800 (PST) Subject: Automatic addition of OBO file to CVS (fwd) Message-ID: ---------- Forwarded message ---------- Date: Fri, 13 Feb 2004 16:37:25 -0800 From: Mike Cherry To: GO List Subject: Automatic addition of OBO file to CVS Hello, I have a script prepared that will automatically generate a new version of the OBO file and commit it to the CVS. A new version of the OBO file is only created if one of the following four files is newer than the OBO file: GO.defs, component.ontology, function.ontology, or process.ontology. This script is for the period before everyone switches to writing the OBO file. Once the switch happens no one should be committing flat files. At that time I will start generating the flat files from the OBO file on the server. The idea is to continue providing the flat files for a long time, but to have the GO Consortium switch to the OBO file in the near future. There were no replies to my earlier message on this topic. If there is no discussion about this I'll start committing the OBO file next week. I was thinking of calling is it gene_ontology.obo. Issues for discussion: 1) Obviously, we need to carefully plan when everyone switches over to committing the OBO file. Once the editorial office is comfortable with the new version of DAG-Edit and confident in the OBO format we need to specify a day for the switch. 2) I can run the OBO building script every hour, although I think that is too much. Once a day should be fine. Initially these OBO files will be useful for testing and to allow everyone to get used to looking at the new files. 3) Once the switch occurs everyone must switch. After the switch if a flat file is committed any changes within that file will be lost because I will be generating flat file parts as the OBO file changes. The alternative would involve some type of merge between out-of-sync flat files and the OBO file. It seems this would require humans to do the merge. I'm open to suggestions how we could easily check for someone doing the wrong thing. -Mike From katica at acoma.Stanford.EDU Tue Feb 17 16:22:58 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Tue, 17 Feb 2004 13:22:58 -0800 (PST) Subject: Trait ontologies In-Reply-To: <402A2741.4050106@arabidopsis.info> Message-ID: Dear Simon, Sorry for the late reply. At the present time, we have no plans for developing Arabidospis trait ontology at TAIR. Instead, we proposed to use combination of the existing ontologies, such as PATO (Phenotype, ATtribute ontology), Gene Ontology, anatomy ontology and developmental stages ontology to annotate Arabidopsis mutant phenotypes. Phenotype description will appear in a free text format, based on the EAV model (Entity - Attribute - Value), where terms for entity, attribute and value come from respective ontologies (e.g., entity term comes from anatomy, developmental stage, GO function, GO process or GO component while attribute term comes from PATO). Please let me know if you need more information on this topic. I can send you more details on the EAV model and also style guidelines for the Allele, Germplasm and Phenotype Curation that we use at TAIR. I hope this helps. Best regards, Katica Ilic TAIR curator On Wed, 11 Feb 2004, Simon Jupp wrote: > Hi Pankaj, > > We are interested in describing some of our Arabidopsis mutant stocks in > Trait ontology terms. Could someone please let me know what is > happening at the moment with regards to arabidopsis TO terms. > > We are very keen to use our current stock data to suggest new terms if > needed. > > Thank you > Simon Jupp > > Nottingham Arabidopsis Stock Centre > Plant Science Division > School of Biosciences > University of Nottingham > Sutton Bonington Campus > Loughborough > LE12 5RD > > -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. --------------------------------------------------------------------------