From lreiser at acoma.Stanford.EDU Mon Dec 1 14:18:34 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Mon, 1 Dec 2003 11:18:34 -0800 (PST) Subject: agenda In-Reply-To: <3FCB8C52.6060705@cornell.edu> Message-ID: Pankaj asked that I organize the agenda for the call today: 1. Updates on ASPB & BOTANY 2004 (Leonore) 2. Public live website: target release date, content (unified vocabulary vs all vocabularies, update frequency, FTP site content). Comments on site requested by Pankaj. 3.Monsanto collaboration: Unified vocabularies and possible wording of an MTA associated with terms. Dedicated personnel to contribute to the projectin the next year. 4. DB issues/updates from Shuly/Doreen 5.Updates for PAG 2004 if any. 6.tutorial/introductory slideshow comments (or via email) ANything else? Leonore ------------------------------------------------------------------------------- Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------- From Leszek at missouri.edu Mon Dec 1 14:57:38 2003 From: Leszek at missouri.edu (Vincent, Leszek) Date: Mon, 1 Dec 2003 13:57:38 -0600 Subject: agenda Message-ID: <3D4AD7F06881FD42A720D33D8E399DF3AD56BF@COL-EMAIL4.col.missouri.edu> Hi Leonore, Thanks for the agenda info. Are we going to put together an agenda (even a basic one) for our meeting next Monday (Dec. 08) in St. Louis?? I'll be present from the start until 11:30 am so am keen to facilitate a productive contribution from myself during my curtailed 'appearance'. - Leszek > -----Original Message----- > From: owner-po-dev at brie4.cshl.org > [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Leonore Reiser > Sent: Monday, December 01, 2003 1:19 PM > To: POC-dev > Subject: agenda > > > Pankaj asked that I organize the agenda for the call today: > > 1. Updates on ASPB & BOTANY 2004 (Leonore) > 2. Public live website: target release date, content > (unified vocabulary vs all vocabularies, update frequency, > FTP site content). Comments on site requested by Pankaj. > > 3.Monsanto collaboration: Unified vocabularies and possible > wording of an MTA associated with terms. Dedicated personnel > to contribute to the projectin the next year. 4. DB > issues/updates from Shuly/Doreen 5.Updates for PAG 2004 if > any. 6.tutorial/introductory slideshow comments (or via email) > > ANything else? > Leonore > -------------------------------------------------------------- > ----------------- > Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu > The Arabidopsis Information Resource FAX: (650) 325-6857 > Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 > Department of Plant Biology URL: http://arabidopsis.org/ > 260 Panama St. > Stanford, CA 94305 > -------------------------------------------------------------- > ----------------- > > > From lreiser at acoma.Stanford.EDU Mon Dec 1 16:23:50 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Mon, 1 Dec 2003 13:23:50 -0800 (PST) Subject: Minutes In-Reply-To: Message-ID: > Hi Here are the minutes. Feel free to include anything I left out. Leonore > 1. Updates on ASPB & BOTANY 2004 (Leonore) Approved for both. Main will be ASPB and an evening session. Leonore will work with Sue Chambers from ASPB to organize evening users session for 2 hours. Requested BOTANY 2004 shelve for 2005- no response yet. leonore will et everyone know the outcome (and send a copy of the original request). > 2. Public live website: target release date, content (unified vocabulary > vs all vocabularies, update frequency, FTP site content). Comments on site > requested by Pankaj. a.What is the content- how many ontologies to display- all or unified? We want to show 1 ontology not all the components being used to develop. b. Do we need to have a suggestion form for ontologies until we have a unified vocabulary? Remove the existing page for suggestions til later. c. Leonore will make some images for the ontology page and explination of how the ontologies are being merged. d.When to target the release of the website? January 6,2003. e. Comments on the website. Everyone review pages- links, browser compliance, report back the pages. Format- Browser and OS version...then specific comments. f. Will a version of the onotology be included in the release? Prelimiary version will not be included in the January version. By end of December will have started the merge. So conclusion is that we dont need to have the Amigo browser up for January. g.How often to update the public site? start with quarterly update of the ontologies then monthly release schedule. Start with quarterly and then see if we can release on more frequent basis. Just the AMIGO version being updated. h. Contents of FTP site. Mirroring anon CVS everynight. Should Shuly tar up individual vocabularies-NO, only have the PO ontologies, database, create schemas etc. Do not mirror individual ontologies. > 3.Monsanto collaboration: Unified vocabularies and possible wording of an > MTA associated with terms. Dedicated personnel to contribute to the > projectin the next year. Doreen: Outline of the conversation in previous email. THey want to give the vocabularies. Want an MTA for paper trail. Integrate into unified vocabulary but no PUBLIC release of their ontologies. What is the definition of how to be a member of the consortium, rules of membership (Charter), for all developers to integrate. As long as restrictions do not apply to unified vocabulary. Main concern no paper trail. Could someone look at the source term and back fill a Montasnto Ontology? Not if the terms are NOT explicitly identified as contributed by them so no one can trace back what they are doing. They dont care about being able to identify their own terms within the vocabulary. They dont want anyone else to be able to see their entire organized vocabulary. Who has signing authority of signing the MTA? Get final wording on MTA and then sign off on it (Lincoln?). If pioneer developers are POC collaborators they can have access to the POC,and to Monsanto's vocabulary. AS collaborators, they are bound by the MTA. Developer members- applies to current member, discuss in monthly conference call, accept application- CVS repositiry mailing list, monthly minutes- expectation of contribution. Have to provide substatial and meaningful contribution to the POC. Should we have a POC interest groups page publicly available? Monsanto:Will contribute one FTE next year for Soy anatomy and traits in Gramene... Can use the same MTA for Gramene and POC - do not need a separate agreement. ACTION ITEM: Lincoln will write 'charter' for POC. what constitutes membership - what roles and resposibilities for members in terms of access, editing ontologies,behaviors etc... 4. DB issues/updates from Shuly/Doreen a.Issue- getting Amigo to read ontology from POC website. Amigo browser is reading from Gramene database now.Test version is up (http://brie.cshl.org:8080/amigo/go.cgi). Problem with the datasource- options list- is hard coded. Cannot take the headers and footers for POC. Lincoln:Modify the amigo software to take the URL /html and inserts it into the header and footers which is the mod perl. Comment out the associations links for now as we have no associations to display. Table development for the moment as Shuly will focus on other issues since the first website release will not include the merged ontologies. > 5.Updates for PAG 2004 if any. a. should we open the developers session to potential collaborators? Doreen suggests having others join in at the second session. Have potential collaborators coming, Jag, Paulein coming to the meeting. Decided that will open the last half hour of the evening session. b.What is the agenda for this meeting? Introductions, logistics for merging ontologies, timelines etc... > 6.tutorial/introductory slideshow comments (or via email) URL for powerpoint has been sent out. Make commments by the end of the week and send them back to Pankaj/Leonore 7.Next meetings a.In person, December (development meeting) and January (developers meetign at PAG). b. Conference calls. January 2, prior to website release January 6, 2004. Tentatively schedule others for first friday of the month in February and March > > ANything else? > Leonore > ------------------------------------------------------------------------------- > Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu > The Arabidopsis Information Resource FAX: (650) 325-6857 > Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 > Department of Plant Biology URL: http://arabidopsis.org/ > 260 Panama St. > Stanford, CA 94305 > ------------------------------------------------------------------------------- > > > ------------------------------------------------------------------------------- Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------- From lreiser at acoma.Stanford.EDU Tue Dec 23 18:53:09 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Tue, 23 Dec 2003 15:53:09 -0800 (PST) Subject: Plant Ontology symposium (fwd) Message-ID: sounds like thanks to Toby- we are out for Botany2004 workshop- I checked the 'call for discussions' site which is currently empty-seems like that would be a good venue? Toby, Felipe & Peter, what are your thoughts on this? Leonore ------------------------------------------------------------------------------- Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu The Arabidopsis Information Resource FAX: (650) 325-6857 Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 ------------------------------------------------------------------------------- ---------- Forwarded message ---------- Date: Tue, 23 Dec 2003 13:07:35 -0600 From: Jeffrey M. Osborn To: Leonore Reiser , Toby Kellogg Cc: Andi Wolfe , elisens at ou.edu Subject: Plant Ontology symposium Dear Leonore and Toby, Thanks for the messages about the Plant Ontology symposium. I apologize for the delay in return correspondence; I've been conducting field work for the last five weeks and have just returned. We'll go ahead and withdraw the symposium from the program for Botany 2004 in Snowbird, UT, but will expect some "contributed papers" and/or "contributed posters" on the topic. Your authors will need to select a disciplinary Section for their contributions when they submit, and then the Program Chair of that Section will incorporate the talks and/or posters into their program. In addition, if you would like to engage some attendees in a more general discussion about the interdisciplinary nature of your initiative, etc., you might consider submitting a proposal for a one-hour "Discussion Session." The Call for Discussion Sessions, and all relevant info about these, is posted on the Botany 2004 web site (www.botanyconference.org). The submission site will open in mid- to late January. Otherwise, I'll look forward to a symposium proposal for the Botany 2005 conference, which will be held in Austin, Texas. The Call for Symposia for Botany 2005 will be available sometime in the late spring of 2005. Best wishes for the holidays. Jeff Jeffrey M. Osborn, Program Director Botanical Society of America / Botany 2004 -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jeffrey M. Osborn Division of Science Truman State University 100 E. Normal Street Kirksville, MO 63501-4221, USA Tele: (660) 785-4017 Fax: (660) 785-4045 E-mail: josborn at truman.edu Internet: http://www2.truman.edu/~josborn/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~