From pj37 at cornell.edu Mon Nov 3 11:34:15 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 03 Nov 2003 11:34:15 -0500 Subject: First meeting of POC - CONFIRMATION In-Reply-To: References: Message-ID: <3FA68387.8060005@cornell.edu> Hi I just got a confirmation from Darrin Scherago on phone for our meeting place. The hotel will provide us with a room on Sunday - January 11, 2004. Since there will be seminars going on, we are going to hold it in 2 sessions 8:30-11.00 am and 3.00-6:30 pm. We are required to pay for any facilities we require. Pankaj Sue Rhee wrote: > ok, how about: > > 8:30-11 and 3-6:30? > > sue > > On Fri, 31 Oct 2003, Pankaj Jaiswal wrote: > > >>The only options left are to have it in 2 parts >>Part-I: Morning 9-11 am >>Part-II 3.00pm-whatever time it takes >> >>We can have a break during the rice workshop from 12:00 noon - 2:40 pm >> >>Pankaj From fzqhd at studentmail.umsl.edu Mon Nov 3 12:21:48 2003 From: fzqhd at studentmail.umsl.edu (Felipe Zapata) Date: Mon, 3 Nov 2003 11:21:48 -0600 Subject: POC: Tech issues In-Reply-To: <3F983FBF.5080901@cornell.edu> References: <3F983FBF.5080901@cornell.edu> Message-ID: <1067880108.3fa68eacad5c3@studentmail.umsl.edu> Hi Pankaj, Well something weird is happening. We have to switch to an earlier version of DAG-Edit as the two latest ones did not work properly in MacOS X 10.2 (when one is loading the terms it does not recognize the file path). Dag Edit 1.405 was working correctly before but now is misbehaving with gremene.anatomy. When we are loading the terms (we have to load them every time) the following message shows up: file:/Users/kellogg/Desktop/sandbox/Poc/anatomy/anatomy_gramene.ontology:10: Unrecognized type character '%plant' found. condition 1 %plant anatomy ontology ; GRO:0005297 ^ file:/Users/kellogg/Desktop/sandbox/Poc/anatomy/anatomy_gramene.ontology:11: Unrecognized type character '%whole' found. condition 1 %whole plant ; GRO:0005000 ^ file:/Users/kellogg/Desktop/sandbox/Poc/anatomy/anatomy_gramene.ontology:12: Unrecognized type character '%embryo' found. condition 1 %embryo ; GRO:0005343 < seed ; GRO:0005339 ^ file:/Users/kellogg/Desktop/sandbox/Poc/anatomy/anatomy_gramene.ontology:13: Unrecognized type character ' References: <3F983FBF.5080901@cornell.edu> <1067880108.3fa68eacad5c3@studentmail.umsl.edu> Message-ID: <3FA7C578.6040107@cornell.edu> Hi Felipe, Try with ver. 1.407. There were some known bugs in the program. It was not recognizing the relationship types from a flat file. It is fixed now. I have also introduced the relationship types comments in my flat files. I have updated the flat files on CVS. Please do a fresh update before you start. About executing Dag edit twice, I am going to ask John Richter the program developer. In the meantime try installing it twice in 2 different directories. It may work. Pankaj Felipe Zapata wrote: > Hi Pankaj, > > Well something weird is happening. We have to switch to an earlier version of > DAG-Edit as the two latest ones did not work properly in MacOS X 10.2 (when one > is loading the terms it does not recognize the file path). Dag Edit 1.405 was > working correctly before but now is misbehaving with gremene.anatomy. When we > are loading the terms (we have to load them every time) the following message > shows up: > > file:/Users/kellogg/Desktop/sandbox/Poc/anatomy/anatomy_gramene.ontology:10: > Unrecognized type character '%plant' found. condition 1 > %plant anatomy ontology ; GRO:0005297 > ^ > > file:/Users/kellogg/Desktop/sandbox/Poc/anatomy/anatomy_gramene.ontology:11: > Unrecognized type character '%whole' found. condition 1 > %whole plant ; GRO:0005000 > ^ > > file:/Users/kellogg/Desktop/sandbox/Poc/anatomy/anatomy_gramene.ontology:12: > Unrecognized type character '%embryo' found. condition 1 > %embryo ; GRO:0005343 < seed ; GRO:0005339 > ^ > > file:/Users/kellogg/Desktop/sandbox/Poc/anatomy/anatomy_gramene.ontology:13: > Unrecognized type character ' ^ > > file:/Users/kellogg/Desktop/sandbox/Poc/anatomy/anatomy_gramene.ontology:14: > Unrecognized type character ' ^ > > 5 errors > > What is that??? this was not happening before.... We got the files through CVS > and we have them in a folder in desktop. > > On the other hand, DAG Edit cannot be oppened twice in Mac...it seems to be > only a PC feature (when I emailed you a couple of weeks ago, it worked in PC, > but not in Mac...our lab runs with Mac...maybe we will have to change the > roots) > > Hope you can help me with these latest issues. > > Thanks > > Felipe > From pj37 at cornell.edu Tue Nov 4 16:57:36 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 04 Nov 2003 16:57:36 -0500 Subject: [Fwd: Launching multiple copies of DAG-Edit from Mac OS] Message-ID: <3FA820D0.908@cornell.edu> Just FYI. I will add this to the docs. Pankaj -------- Original Message -------- From: John Richter Subject: Launching multiple copies of DAG-Edit from Mac OS To: Felipe Zapata CC: Pankaj Jaiswal Hello, Felipe. I've done some research into launching multiple instances of DAG-Edit on Mac OS. It turns out that the problem is not DAG-Edit, it is the way the Mac OS Finder wants to treat java applications. The finder sees that DAG-Edit is already running, and just never sends DAG-Edit the signal to start up. However, I think I have a solution that will trick Mac OS... I've created a Mac OS Application (actually a compiled AppleScript) called "macos_multilauncher" which I've attached to this email. Put the macos_multilauncher file into the folder where you installed DAG-Edit (probably Applications:DAG-Edit). Once you've done that, double-clicking the macos_multilauncher should cause DAG-Edit to start up. The macos_multilauncher should be able to start up as many copies of DAG-Edit as you want. Also, you can drop the macos_multilauncher onto the Mac OS Dock, and it should still work properly. Some notes: --------------- * You have to put macos_multilauncher into your DAG-Edit installation directory! If you put it anywhere else, it won't know how to find DAG-Edit, and it won't work. * Because of the way macos_multilauncher starts DAG-Edit, DAG-Edit will NOT generate the .dagedit.stderr and .dagedit.stdout files used for debugging. So if you encounter a bug while using the macos_multilauncher, you will have no way of sending me the details of your problem. * The preferred way to launch multiple instances of DAG-Edit is to launch the first instance using the normal DAG-Edit shortcut, and then launch additional instances using macos_multilauncher. That way, at least one of the DAG-Edit instances will be correctly writing out debugging information. * All the instances of DAG-Edit you run will share a single configuration file. This means that DAG-Edit will remember your preferences FOR ONLY ONE of the DAG-Edit instances you are running, and there's no way to be sure which instance of DAG-Edit will actually store it's preferences. So, if you are wanting to set up DAG-Edit preferences, or create file loading profiles, or something like that, run only one instance of DAG-Edit. Let me know of the macos_multilauncher file works for you. If it does, I'll start including it in the standard Mac OS installer for DAG-Edit. -John -------------- next part -------------- A non-text attachment was scrubbed... Name: macos_multilauncher Type: application/octet-stream Size: 13780 bytes Desc: not available URL: From pj37 at cornell.edu Tue Nov 4 17:51:55 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 04 Nov 2003 17:51:55 -0500 Subject: DBXrefs Message-ID: <3FA82D8B.4080908@cornell.edu> Hi Everyone, Can you all go through the attached file and sort out the list of DBXrefs which are relevant to POC. We need this as a DBXref documentation for POC Delete any irrelevant ones. Pankaj -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: PO_DBXref.txt URL: From PolaccoM at missouri.edu Tue Nov 4 18:33:51 2003 From: PolaccoM at missouri.edu (Mary Polacco) Date: Tue, 04 Nov 2003 17:33:51 -0600 Subject: DBXrefs In-Reply-To: <3FA82D8B.4080908@cornell.edu> Message-ID: Hi Pankaj, The NCBI listing for MaizeDB has yet to be updated, although Plant Genome section is now linking to MaizeGDB. I will contact NCBI on this, but in the meantime, the list as it stands now is incorrect and the corrrection is provided below. Also, to make the list useful for Phenotype XREF, not just locus, I've added url_syntax for the phenotype objects in MaizeGDB that will be directly linked to POC terms. Does the group think this might be useful? Another question, what is the purpose of the list? -mary On 11/4/03 4:51 PM, "Pankaj Jaiswal" wrote: > abbreviation: MaizeDB > database: Maize Genome Database. > object: Canonical name of gene. > example: MaizeDB:apb1 > generic_url: http://www.agron.missouri.edu/ > url_syntax: > > abbreviation: MaizeDBID > database: Maize Genome Database. > object: Identifier. > example: MaizeDBID:12008 > generic_url: http://www.agron.missouri.edu/ > url_syntax: abbreviation: MaizeGDB database: Maize Genetics and Genome Database. object: Canonical name of gene. example: MaizeGDB:apb1 generic_url: http://www.maizegdb.org/ url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term= object: Phenotype of gene variant example: MaizeGDB:liguleless url_syntax: http://www.maizegdb.org/cgi-bin/displayphenoresults.cgi?term= abbreviation: MaizeGDBID database: Maize Genome Database. object: locus Identifier. example: MaizeGDBID:12008 generic_url: http://www.maizegdb.org/ url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id= object: phenotype identifier example:MaizeGDBID:61504 url_syntax:http://www.maizegdb.org/cgi-bin/displayphenorecord.cgi?id= From pj37 at cornell.edu Tue Nov 4 18:57:17 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 04 Nov 2003 18:57:17 -0500 Subject: DBXrefs In-Reply-To: References: Message-ID: <3FA83CDD.8020808@cornell.edu> Hi Mary Mary Polacco wrote: > Hi Pankaj, > > > The NCBI listing for MaizeDB has yet to be updated, although Plant Genome > section is now linking to MaizeGDB. I will contact NCBI on this, but in the > meantime, the list as it stands now is incorrect and the corrrection is > provided below. > > Also, to make the list useful for Phenotype XREF, not just locus, I've added > url_syntax for the phenotype objects in MaizeGDB that will be directly > linked to POC terms. Does the group think this might be useful? > Strategy would be that each DB builds their own set of mappings to the POC terms and contributes them to POC. The POC DB will act as a central repository to give a summary of all the associations to an ontology term based on a passport info it will store. For further info the associated object will direct a link to the reference db. > Another question, what is the purpose of the list? the objective is to have a list of standardized Xrefs in POC Db. These xrefs are used by the #1 Ontology developers as xrefs to the -definitions of the terms -synonyms to the terms -any generic xrefs #2 In the near future when we start having the associations, from contributing DBs, then in the Ontology DB, we require these Xrefs to link back to the objects (proteins/genes/phenotypes/etc) to their source DB by using the standardized list of Xrefs and formats. #3 This is something in common with the GO application. Also its a better way of assigning the unique identifiers/abbreviations to the DBs and objects. > > -mary > > On 11/4/03 4:51 PM, "Pankaj Jaiswal" wrote: > > >>abbreviation: MaizeDB >>database: Maize Genome Database. >>object: Canonical name of gene. >>example: MaizeDB:apb1 >>generic_url: http://www.agron.missouri.edu/ >>url_syntax: >> >>abbreviation: MaizeDBID >>database: Maize Genome Database. >>object: Identifier. >>example: MaizeDBID:12008 >>generic_url: http://www.agron.missouri.edu/ >>url_syntax: > > > > abbreviation: MaizeGDB > database: Maize Genetics and Genome Database. > object: Canonical name of gene. > example: MaizeGDB:apb1 > generic_url: http://www.maizegdb.org/ > url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term= > object: Phenotype of gene variant > example: MaizeGDB:liguleless > url_syntax: http://www.maizegdb.org/cgi-bin/displayphenoresults.cgi?term= > > abbreviation: MaizeGDBID > database: Maize Genome Database. > object: locus Identifier. > example: MaizeGDBID:12008 > generic_url: http://www.maizegdb.org/ > url_syntax: http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id= > object: phenotype identifier > example:MaizeGDBID:61504 > url_syntax:http://www.maizegdb.org/cgi-bin/displayphenorecord.cgi?id= > > From pj37 at cornell.edu Tue Nov 4 19:15:51 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 04 Nov 2003 19:15:51 -0500 Subject: Unique identifiers assigned to Plant Ontology developer groups Message-ID: <3FA84137.6010204@cornell.edu> Unique identifiers assigned to Plant Ontology developer groups Every term in the anatomy or developmental stage ontology is identified by a unique identifier. Under the conventions that we have already established, the syntax of a PO identifier is PO:nnnnnnn, where nnnnnnn is a zero-padded unique integer of seven digits. In order to ensure database integrity, identifiers are never removed. Terms that are retired(deleted) from the ontology are moved into the obsolete category. To ensure that the same identifier is not used twice, each participating group will be assigned non-overlapping ID ranges and listed on this page for documentation purposes. These ranges will automatically act as (internal) identifiers for the group that submitted the term. If you want the identifiers assigned to your group, please send and e mail to po-dev at plantontology.org Group identifier range (from-to) TAIR 0000001-0005000 Gramene 0005001-0010000 IRRI 0010001-0015000 MaizeDB 0015001-0020000-->Change group name to MaizeGDB For the above 4 groups, the range was assigned prior to the award of this project http://www.plantontology.org/doc/poc_project.html Toby Kellogg 0020001-0025000 Open 0025001-0030000 Open 0030001-0035000 Open 0035001-0040000 Open 0040001-0045000 Open 0045001-0050000 Open 0050001-0055000 Setting your range of numbers within DAG-Edit. Once you have claimed a set of numbers from the ontology numbers file, you must also set these numbers within the configuration file of DAG-Edit. To do this you should open DAG-Edit, and chose from the 'plugins' menu the 'DAG-Edit Configuration Manager'. Within this window you can now fill in your range of numbers, starting in the 'start of id range' line and finishing in the 'End of id range' line. Press 'Save Configuration' to save your changes. In order to avoid conflicts, any new term contributed by the group should carry the Ontology term identifier from the assigned range. It is also an easy way to track the contribution. Pankaj From PolaccoM at missouri.edu Wed Nov 5 11:08:34 2003 From: PolaccoM at missouri.edu (Mary Polacco) Date: Wed, 05 Nov 2003 10:08:34 -0600 Subject: Unique identifiers assigned to Plant Ontology developer groups In-Reply-To: <3FA84137.6010204@cornell.edu> Message-ID: Pankaj, Is there an easy way to get a table of the terms and their POC identifiers other than writing a parser for the flat file that shows also the heirarchy? -mary On 11/4/03 6:15 PM, "Pankaj Jaiswal" wrote: > Unique identifiers assigned to Plant Ontology developer groups > > Every term in the anatomy or developmental stage ontology is identified by a > unique identifier. Under the conventions that we have already established, the > syntax of a PO identifier is PO:nnnnnnn, where nnnnnnn is a zero-padded unique > integer of seven digits. > > In order to ensure database integrity, identifiers are never removed. Terms > that > are retired(deleted) from the ontology are moved into the obsolete category. > To > ensure that the same identifier is not used twice, each participating group > will > be assigned non-overlapping ID ranges and listed on this page for > documentation > purposes. These ranges will automatically act as (internal) identifiers for > the > group that submitted the term. If you want the identifiers assigned to your > group, please send and e mail to po-dev at plantontology.org > > Group identifier range (from-to) > TAIR 0000001-0005000 > Gramene 0005001-0010000 > IRRI 0010001-0015000 > MaizeDB 0015001-0020000-->Change group name to MaizeGDB > > For the above 4 groups, the range was assigned prior to the award of this > project http://www.plantontology.org/doc/poc_project.html > > Toby Kellogg 0020001-0025000 > Open 0025001-0030000 > Open 0030001-0035000 > Open 0035001-0040000 > Open 0040001-0045000 > Open 0045001-0050000 > Open 0050001-0055000 > > Setting your range of numbers within DAG-Edit. > > Once you have claimed a set of numbers from the ontology numbers file, you > must > also set these numbers within the configuration file of DAG-Edit. To do this > you > should open DAG-Edit, and chose from the 'plugins' menu the 'DAG-Edit > Configuration Manager'. Within this window you can now fill in your range of > numbers, starting in the 'start of id range' line and finishing in the 'End of > id range' line. Press 'Save Configuration' to save your changes. > > In order to avoid conflicts, any new term contributed by the group should > carry > the Ontology term identifier from the assigned range. > > > > It is also an easy way to track the contribution. > > > Pankaj > > From pj37 at cornell.edu Wed Nov 5 11:29:34 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 05 Nov 2003 11:29:34 -0500 Subject: Unique identifiers assigned to Plant Ontology developer groups In-Reply-To: References: Message-ID: <3FA9256E.1010201@cornell.edu> Hi Mary, I am copying this message to Liya. I guess this can be pulled out from the Ontology DB tables. I am not so sure about the hierarchy, but here is what I did. By using the Dag-EDIT ver 1.407, I saved the gramene ontology+definition file by using the OBO adapter and I can get a complete record of terms as following. I hope this will work. Earlier versions of Dag-EDIT used to have an adapter for generating an RDF format, but this one seems better. [Typedef] id: part_of name: Part of [Typedef] id: develops_from name: develops from [Term] id: GRO:0005050 name: phelloderm is_a: GRO:0005047 is_a: GRO:0005048 [Term] id: GRO:0005279 name: floral primordium is_a: GRO:0000136 [Term] id: GRO:0005598 name: vascular cambium is_a: GRO:0005597 [Term] id: GRO:0005580 name: floral nectary is_a: GRO:0005659 [Term] id: GRO:0006107 name: microspore mother cell is_a: GRO:0005825 [Term] id: GRO:0005352 name: xylem relationship: part_of GRO:0005369 Pankaj Mary Polacco wrote: > Pankaj, > Is there an easy way to get a table of the terms and their POC identifiers > other than writing a parser for the flat file that shows also the heirarchy? > > -mary > > On 11/4/03 6:15 PM, "Pankaj Jaiswal" wrote: > > >>Unique identifiers assigned to Plant Ontology developer groups >> >>Every term in the anatomy or developmental stage ontology is identified by a >>unique identifier. Under the conventions that we have already established, the >>syntax of a PO identifier is PO:nnnnnnn, where nnnnnnn is a zero-padded unique >>integer of seven digits. >> >>In order to ensure database integrity, identifiers are never removed. Terms >>that >>are retired(deleted) from the ontology are moved into the obsolete category. >>To >>ensure that the same identifier is not used twice, each participating group >>will >>be assigned non-overlapping ID ranges and listed on this page for >>documentation >>purposes. These ranges will automatically act as (internal) identifiers for >>the >>group that submitted the term. If you want the identifiers assigned to your >>group, please send and e mail to po-dev at plantontology.org >> >>Group identifier range (from-to) >>TAIR 0000001-0005000 >>Gramene 0005001-0010000 >>IRRI 0010001-0015000 >>MaizeDB 0015001-0020000-->Change group name to MaizeGDB >> >>For the above 4 groups, the range was assigned prior to the award of this >>project http://www.plantontology.org/doc/poc_project.html >> >>Toby Kellogg 0020001-0025000 >>Open 0025001-0030000 >>Open 0030001-0035000 >>Open 0035001-0040000 >>Open 0040001-0045000 >>Open 0045001-0050000 >>Open 0050001-0055000 >> >>Setting your range of numbers within DAG-Edit. >> >>Once you have claimed a set of numbers from the ontology numbers file, you >>must >>also set these numbers within the configuration file of DAG-Edit. To do this >>you >>should open DAG-Edit, and chose from the 'plugins' menu the 'DAG-Edit >>Configuration Manager'. Within this window you can now fill in your range of >>numbers, starting in the 'start of id range' line and finishing in the 'End of >>id range' line. Press 'Save Configuration' to save your changes. >> >>In order to avoid conflicts, any new term contributed by the group should >>carry >>the Ontology term identifier from the assigned range. >> >> >> >>It is also an easy way to track the contribution. >> >> >>Pankaj >> >> > > > -- ****************************************** Pankaj Jaiswal, Ph.D. Research Associate Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel:+1-607-255-3103 / Fax:+1-607-255-6683 E mail: pj37 at cornell.edu http://www.gramene.org ****************************************** From pj37 at cornell.edu Wed Nov 5 11:35:27 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 05 Nov 2003 11:35:27 -0500 Subject: [Fwd: Botany 2004 symposia]--ACTION required Message-ID: <3FA926CF.1050504@cornell.edu> Action item required. Pankaj -------- Original Message -------- From: Brent Mishler Subject: Botany 2004 symposia To: Leonore Reiser CC: Pankaj Jaiswal , Susan McCouch , Elizabeth Kellogg , Sue Rhee , Lincoln Stein , Doreen Ware Hi all, Jeff Osborne forwarded this proposal to me -- it looks great! I would really like for Deep Gene to be a co-sponsor. One problem is the kind of support needed. Our funds aren't really for paying for big-ticket foreign speakers; I'd rather give student/postdoc support. We do pitch in for faculty travel too, but NSF frowns on paying for foreign faculty from developed countries (going on the assumption that they can generate their own funds and shouldn't be relying on the US NSF). Foreign students they don't seem to mind too much. So if you can cover the "big guys" somehow else, I'd be willing to support some student travel to attend your symposium. Could that work? All the best, Brent > > ******************** > > Symposium Title: Biological Ontologies for Plant Biology: Development > and Applications > ----- > Organizer(s): Contact person: Leonore Reiser > lreiser at acoma.stanford.edu Carnegie Institution, Department of Plant > Biology 260 Panama St Stanford,CA 94305 (T) 650-325-1521X311 (F) > (650) 325-6857 Other organizers (Name/email) Pankaj Jaiswal > pj37 at cornell.edu Susan McCouch srm4 at cornell.edu Elizabeth Kellogg > kellogge at msx.umsl.edu Sue Rhee rhee at acoma.stanford.edu Lincoln Stein > steinl at cshl.edu Doreen Ware ware at cshl.edu > ----- > Sponsoring Sections: > Developmental and Structural Section, Genetics Section, Physiological > Section, Systematics Section > ----- > List of speakers: 1.Lincoln Stein Plant Ontology Consortium/Cold > Spring Harbor Lab "Introductory Remarks" 2.Midori Harris Gene > Ontology Consortium "The Gene Ontology Consortium" 3. Pankaj Jaiswal > Gramene/Cornell University "Anatomy, Trait and Developmental Stage > ontologies for rice" 4.Leszek Vincent University of Missouri-Columbia > "Development of ontologies for maize." 5. Tanya Berardini Carnegie > Institution, Department of Plant Biology and The Arabidopsis > Information Resource (TAIR) " Anatomy and developmental stage > ontologies Arabidopsis" 6.Doreen Ware Cold Spring Harbor Labs/USDA > "Informatics for the Plant Ontology Consortium: Database and tools" > 7.Tanya Berardini/Pankaj Jaiswal TAIR/Gramene "Standards and Methods > for Annotation" 8.Elizabeth Kellogg University of > Missouri-Columbia/Deep Gene "Adaptation of ontologies for diverse > plant taxa: integration and validation". 9.TBD Gramene "Community > Curation at Gramene Database" 10. Rupali Bhalerao, PoplarDB "Annotation > of the Poplar genome: the first sequenced tree genome" and 11.Yukiko > Yamakazi , Oryzabase " Rice Phenotype > Annotation". > > Discussion Topic(s): Expansion and > adaptation of POC for other plant species and integration of > community input for tool development and curation/ontology validation. > ----- > Duration: Half Day > ----- > Nature of sponsorship: Financial support requested > ----- > Amount requested: $2500 to cover the cost of airfare for Dr. Yamakazi > (Japan) and Dr. Bhalerao (Sweden). We feel it is very important to include > Dr Bhalerao as the poplar genome sequence will be released soon. Dr. > Yamakazi's group curates rice phenotypes in Japan. Integration of > information from diverse species as well as diverse groups working on the > same organism is critical to improve access to these resources by the > research community. > > ----- > Requests for sponsorship submitted to: BSA Sections: Developmental > and Structural Section, Genetics Section, Physiological Section, > Systematics Section, Other Sources: Deep Gene Research Coordination > Network, Gene Ontology Consortium, Gramene Community Consortium > > -- > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > 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/ > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ********************************************************** Brent D. Mishler Professor, Department of Integrative Biology Director, University and Jepson Herbaria Associate Director, California Biodiversity Center Mailing address: UNIVERSITY OF CALIFORNIA, BERKELEY UNIVERSITY AND JEPSON HERBARIA 1001 VALLEY LIFE SCIENCES BLDG # 2465 BERKELEY, CA 94720-2465 USA Phone: (510) 642-6810 FAX: (510) 643-5390 E-mail: bmishler at socrates.berkeley.edu WWW: http://ucjeps.berkeley.edu/people/mishler.html ********************************************************** -- ****************************************** Pankaj Jaiswal, Ph.D. Research Associate Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel:+1-607-255-3103 / Fax:+1-607-255-6683 E mail: pj37 at cornell.edu http://www.gramene.org ****************************************** From pj37 at cornell.edu Wed Nov 5 12:15:57 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 05 Nov 2003 12:15:57 -0500 Subject: POC development website Message-ID: <3FA9304D.6030609@cornell.edu> Hi Everyone, Shuly and myself invite you to have a look at the POC-DEV website (http://brie.cshl.org:8080/). It is still UNDER CONSTRUCTION. If you have any questions/suggestions please feel free to send your questions by writing to po-dev at plantontology.org Once everything is in place it will replace the existing live site at http://www.plantontology.org Pankaj From lreiser at acoma.Stanford.EDU Wed Nov 5 14:47:11 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Wed, 5 Nov 2003 11:47:11 -0800 (PST) Subject: [Fwd: Botany 2004 symposia]--ACTION required In-Reply-To: <3FA926CF.1050504@cornell.edu> Message-ID: Thanks for forwarding that- be good to discuss today. I also heard from another group we asked to sponsor- but no specifics yet. Ill update at the phone call in a few minutes. Leonore On Wed, 5 Nov 2003, Pankaj Jaiswal wrote: > Action item required. > > Pankaj > > -------- Original Message -------- > From: Brent Mishler > Subject: Botany 2004 symposia > To: Leonore Reiser > CC: Pankaj Jaiswal , Susan McCouch > , Elizabeth Kellogg , Sue Rhee > , Lincoln Stein , Doreen Ware > > > > > Hi all, > > Jeff Osborne forwarded this proposal to me -- it looks great! I would > really like for Deep Gene to be a co-sponsor. One problem is the kind > of support needed. Our funds aren't really for paying for big-ticket > foreign speakers; I'd rather give student/postdoc support. We do pitch > in for faculty travel too, but NSF frowns on paying for foreign faculty > from developed countries (going on the assumption that they can generate > their own funds and shouldn't be relying on the US NSF). Foreign > students they don't seem to mind too much. So if you can cover the "big > guys" somehow else, I'd be willing to support some student travel to > attend your symposium. Could that work? > > All the best, > > Brent > > > > > > ******************** > > > > > Symposium Title: Biological Ontologies for Plant Biology: Development > > and Applications > > ----- > > > Organizer(s): Contact person: Leonore Reiser > > lreiser at acoma.stanford.edu Carnegie Institution, Department of Plant > > Biology 260 Panama St Stanford,CA 94305 (T) 650-325-1521X311 (F) > > (650) 325-6857 Other organizers (Name/email) Pankaj Jaiswal > > pj37 at cornell.edu Susan McCouch srm4 at cornell.edu Elizabeth Kellogg > > > kellogge at msx.umsl.edu Sue Rhee rhee at acoma.stanford.edu Lincoln Stein > > > steinl at cshl.edu Doreen Ware ware at cshl.edu > > ----- > > > Sponsoring Sections: > > Developmental and Structural Section, Genetics Section, Physiological > > Section, Systematics Section > > ----- > > > List of speakers: 1.Lincoln Stein Plant Ontology Consortium/Cold > > Spring Harbor Lab "Introductory Remarks" 2.Midori Harris Gene > > Ontology Consortium "The Gene Ontology Consortium" 3. Pankaj Jaiswal > > Gramene/Cornell University "Anatomy, Trait and Developmental Stage > > ontologies for rice" 4.Leszek Vincent University of Missouri-Columbia > > "Development of ontologies for maize." 5. Tanya Berardini Carnegie > > Institution, Department of Plant Biology and The Arabidopsis > > Information Resource (TAIR) " Anatomy and developmental stage > > ontologies Arabidopsis" 6.Doreen Ware Cold Spring Harbor Labs/USDA > > "Informatics for the Plant Ontology Consortium: Database and tools" > > 7.Tanya Berardini/Pankaj Jaiswal TAIR/Gramene "Standards and Methods > > for Annotation" 8.Elizabeth Kellogg University of > > Missouri-Columbia/Deep Gene "Adaptation of ontologies for diverse > > > plant taxa: integration and validation". 9.TBD Gramene "Community > > Curation at Gramene Database" 10. Rupali Bhalerao, PoplarDB "Annotation > > of the Poplar genome: the first sequenced tree genome" and 11.Yukiko > > Yamakazi , Oryzabase " Rice Phenotype > > Annotation". > > > > Discussion Topic(s): Expansion and > > adaptation of POC for other plant species and integration of > > community input for tool development and curation/ontology validation. > > ----- > > > Duration: Half Day > > ----- > > > Nature of sponsorship: Financial support requested > > ----- > > > Amount requested: $2500 to cover the cost of airfare for Dr. Yamakazi > > (Japan) and Dr. Bhalerao (Sweden). We feel it is very important to include > > > Dr Bhalerao as the poplar genome sequence will be released soon. Dr. > > Yamakazi's group curates rice phenotypes in Japan. Integration of > > information from diverse species as well as diverse groups working on the > > same organism is critical to improve access to these resources by the > > research community. > > > > ----- > > > Requests for sponsorship submitted to: BSA Sections: Developmental > > and Structural Section, Genetics Section, Physiological Section, > > > Systematics Section, Other Sources: Deep Gene Research Coordination > > > Network, Gene Ontology Consortium, Gramene Community Consortium > > > > > -- > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > 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/ > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > -- > > > ********************************************************** > Brent D. Mishler > Professor, Department of Integrative Biology > Director, University and Jepson Herbaria > Associate Director, California Biodiversity Center > Mailing address: > UNIVERSITY OF CALIFORNIA, BERKELEY > UNIVERSITY AND JEPSON HERBARIA > 1001 VALLEY LIFE SCIENCES BLDG # 2465 > BERKELEY, CA 94720-2465 USA > Phone: (510) 642-6810 > FAX: (510) 643-5390 > E-mail: bmishler at socrates.berkeley.edu > WWW: http://ucjeps.berkeley.edu/people/mishler.html > ********************************************************** > > -- > ****************************************** > Pankaj Jaiswal, Ph.D. > Research Associate > Dept. of Plant Breeding > Cornell University > Ithaca, NY-14853, USA > > Tel:+1-607-255-3103 / Fax:+1-607-255-6683 > E mail: pj37 at cornell.edu > http://www.gramene.org > ****************************************** > > > ------------------------------------------------------------------------------- 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 Wed Nov 5 16:46:32 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Wed, 5 Nov 2003 13:46:32 -0800 (PST) Subject: BSA symposia (fwd) Message-ID: Hi Here is the response from Pam Diggle who is the head of the Developmental and Structural Section. Certainly getting enthusiastic (-$$) support from folks involved in Botany 2004. I'll nudge Susanne Chambers from ASPB some more. -Leonore (Please excuse any unintended omissions in my email to her- I was frantically doing what I thought was damage control- turns out we did follow 'protocol'). ------------------------------------------------------------------------------- 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: Wed, 5 Nov 2003 14:42:15 -0700 From: Pamela Diggle To: Leonore Reiser Subject: Re: BSA symposia Leonore, Apparently, you did follow the instructions! It's just that it's been so long since anyone did, that I didn't even know it. We (the Developmental and Structural Section) typically discuss symposium proposals at the business meeting that's held at the BSA meetings and then accept proposals from members and approve them before they are submitted to the society. As a result, our section has already committed all of its funds to other symposia. I discussed this with the executive committee, and we are willing to add our sponsorship, but we can't offer financial support. If this is agreeable to you, I'll let Jeff Osborn know that we will be a sponsor. Best wishes, Pam Diggle >Dear Dr. Diggle, >I apologize. I clearly was not on top of things with respect to how to set >up the symposium and request sponsorship. I am representing the Plant >Ontology Consortium, which was just funded by the National Science >Foundation to develop controlled vocabularies to describe plant anatomy >and developmental/growth stages. These controlled vocabularies will be >used by databases/genomic resources to describe patterns of gene >expression, mutant phenotypes and QTLs among other data types. The project >follows the paradigm of the Gene Ontology Consortium, which has created >ontologies (structured controlled vocabularies) to describe gene functions >with three aspects: biological process, molecular function and >sub-cellular localization. >The Plant Ontology Consortium (POC) is an 'open source' project and all >tools/data etc... will be freely available to the plant research/breeding >community. It is our hope that by developing and using these ontologies >this will facilitate cross taxa queries (find all mutants with abnormal >inflorescences in all taxa)- and assist in finding correlations between >phenotypes and the underlying genetic basis for these phenotypes. > >The POC collaborators include TAIR (Arabidopsis), Gramene (rice and other >grasses),Maize GDB and Dr. Toby Kellogs lab at Missouri.The website >(www.plantontology.org) has more information about the participants >program. > >We felt that Botany 2004 was an excellent venue for a first 'users' >meeting, where we could present the concepts, tools and data that are >being developed -and most importantly to solicit the feedback and >involvement of the plant biology community in developing/refining the >ontologies and for specifications on the type and format of tools that >will be developed to access and use the data. > >Because the project ties together many disciplines, we hoped to have the >support from a variety of participating groups at Botany 2004. > >I apologize for not contacting you first to ask for your approval. I am >sure I misunderstood the process by which one requests support. Do you >think your group would be interested in being a sponsor for this workshop? >I am happy to provide whatever information you require to assist you in >making your decision. > >Thank you so much for your time and attention. >Best Regards, >Leonore Reiser > >On Fri, 31 Oct 2003, Pamela Diggle wrote: > >> Leonore, >> >> I understand that you have listed the Developmental and Structural >> Section as a sponsor of the symposium on Ontology that you have >> proposed to the BSA. We were not contacted for our approval. >> >> Pam Diggle >> Chair, Developmental and Structural Section >> -- >> ***************************************************************** >> Pamela K. Diggle >> Associate Professor >> Department of Ecology and Evolutionary Biology >> University of Colorado >> Boulder, CO 80309-0334 >> USA >> >> http://spot.colorado.edu/~diggle/ >> >> > >------------------------------------------------------------------------------- >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 >------------------------------------------------------------------------------- -- ***************************************************************** Pamela K. Diggle Associate Professor Department of Ecology and Evolutionary Biology University of Colorado Boulder, CO 80309-0334 USA http://spot.colorado.edu/~diggle/ From lreiser at acoma.Stanford.EDU Wed Nov 5 18:43:52 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Wed, 5 Nov 2003 15:43:52 -0800 (PST) Subject: calendar In-Reply-To: <3FA9672E.2050703@cornell.edu> Message-ID: Hi The URL for the calendar software we use is: www.htmlcal.com might be useful. ------------------------------------------------------------------------------- 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 rhee at acoma.Stanford.EDU Thu Nov 6 00:04:49 2003 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Wed, 5 Nov 2003 21:04:49 -0800 (PST) Subject: POC development website In-Reply-To: <3FA9304D.6030609@cornell.edu> Message-ID: It looks nice. Besides the suggestions that came up during the phone conference, I have the following minor commnets. Front page seems a bit busy. i would move everything except the intro text bit to another section perhaps called 'About' It would be good to add 'breaking news' section on the front page. The other pages look good. I presume the site map will be updated after the development stablizes? It might be nice to have a link in the header called 'Internal Use' or something to that effect where we can get access to under development stuff and the calender, etc with password access. It might be good to add 'Home' as one of the links in the header. It's not always obvious that one should click on the logo to go to the home page. Cheers, Sue On Wed, 5 Nov 2003, Pankaj Jaiswal wrote: > > Hi Everyone, > > Shuly and myself invite you to have a look at the POC-DEV website > (http://brie.cshl.org:8080/). It is still UNDER CONSTRUCTION. If you have any > questions/suggestions please feel free to send your questions by writing to > po-dev at plantontology.org > > Once everything is in place it will replace the existing live site at > http://www.plantontology.org > > Pankaj > > ----------------------------------------------------------------------------- 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 lstein at cshl.edu Thu Nov 6 15:38:44 2003 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 6 Nov 2003 15:38:44 -0500 Subject: calendar In-Reply-To: References: Message-ID: <200311061538.44816.lstein@cshl.edu> It doesn't seem to handle time of day. Am I missing something? Lincoln On Wednesday 05 November 2003 06:43 pm, Leonore Reiser wrote: > Hi > The URL for the calendar software we use is: > www.htmlcal.com > might be useful. > > > --------------------------------------------------------------------------- >---- 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 > --------------------------------------------------------------------------- >---- -- ======================================================================== Lincoln D. Stein Cold Spring Harbor Laboratory lstein at cshl.org Cold Spring Harbor, NY ======================================================================== From lreiser at acoma.Stanford.EDU Thu Nov 6 15:47:21 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Thu, 6 Nov 2003 12:47:21 -0800 (PST) Subject: calendar In-Reply-To: <200311061538.44816.lstein@cshl.edu> Message-ID: You have to input that when you add something e.g. to add POC conference call at 3 pm November 5 something like: 3-4 PM POC developers conference call. Leonore On Thu, 6 Nov 2003, Lincoln Stein wrote: > It doesn't seem to handle time of day. Am I missing something? > > Lincoln > > On Wednesday 05 November 2003 06:43 pm, Leonore Reiser wrote: > > Hi > > The URL for the calendar software we use is: > > www.htmlcal.com > > might be useful. > > > > > > --------------------------------------------------------------------------- > >---- 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 > > --------------------------------------------------------------------------- > >---- > > -- > ======================================================================== > Lincoln D. Stein Cold Spring Harbor Laboratory > lstein at cshl.org Cold Spring Harbor, NY > ======================================================================== > > > ------------------------------------------------------------------------------- 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 lstein at cshl.edu Thu Nov 6 16:25:51 2003 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 6 Nov 2003 16:25:51 -0500 Subject: calendar In-Reply-To: References: Message-ID: <200311061625.51788.lstein@cshl.edu> How simple and sensible! Lincoln On Thursday 06 November 2003 03:47 pm, Leonore Reiser wrote: > You have to input that when you add something > > e.g. to add POC conference call at 3 pm November 5 something like: > 3-4 PM POC developers conference call. > > Leonore > > On Thu, 6 Nov 2003, Lincoln Stein wrote: > > It doesn't seem to handle time of day. Am I missing something? > > > > Lincoln > > > > On Wednesday 05 November 2003 06:43 pm, Leonore Reiser wrote: > > > Hi > > > The URL for the calendar software we use is: > > > www.htmlcal.com > > > might be useful. > > > > > > > > > ----------------------------------------------------------------------- > > >---- ---- 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 > > > ----------------------------------------------------------------------- > > >---- ---- > > > > -- > > ======================================================================== > > Lincoln D. Stein Cold Spring Harbor Laboratory > > lstein at cshl.org Cold Spring Harbor, NY > > ======================================================================== > > --------------------------------------------------------------------------- >---- 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 > --------------------------------------------------------------------------- >---- -- ======================================================================== Lincoln D. Stein Cold Spring Harbor Laboratory lstein at cshl.org Cold Spring Harbor, NY ======================================================================== From lreiser at acoma.Stanford.EDU Thu Nov 6 17:03:46 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Thu, 6 Nov 2003 14:03:46 -0800 (PST) Subject: ASPB 2004 (fwd) Message-ID: Hmm- seems like we are very popular. One thing about ASPB workshops is that they do tend to be short (1.5 hours or so) we could do this in two parts. We did also request a half day for Botany 2004 so it runs about the same. 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: Thu, 6 Nov 2003 16:04:40 -0500 From: Susan Chambers To: Leonore Reiser Cc: Edgar Spalding Subject: RE: ASPB 2004 Hi Leonore: Sorry for the delay in responding. It seems that the TAIR workshops have been very popular at our last two meetings and well attended. So we would be happy to provide you that venue again at the Plant Biology 2004 meeting. Please let me know more specifically about the length of workshops and a/v that you would need sometime in the next couple of months. Best regards, Susan Susan K. Rosenberry Director of Finance & Administration American Society of Plant Biologists 15501 Monona Drive Rockville, MD 20855 USA phone: 301-251-0560, x. 111 fax: 301-279-2996 e-mail: chambers at aspb.org http://www.aspb.org -----Original Message----- From: Leonore Reiser [mailto:lreiser at acoma.Stanford.EDU] Sent: Wednesday, November 05, 2003 4:50 PM To: Susan Chambers Subject: Re: ASPB 2004 Dear Susan: I dont know if you have had a chance to look into this issue yet. At our phone conference today (the POC group) we were discussing our plans for a workshop. We have made some inquiries with the organizers of Botany 2004 which does have some overlapping dates with the ASPB meeting. I think we would prefer to present at ASPB if that is at all possible. Best Regards Leonore On Fri, 24 Oct 2003, Leonore Reiser wrote: > Dear Susan > Thank you so much for all your help with organizing the TAIR workshops at > the Hawaii meeting this year. > I am writing to inquire about a new workshop for next year. TAIR is part > of a collaboration funded by the NSF to develop controlled vocabularies > for plant anatomy and development. This project will result in a database > and query tools for analyzing gene expression , mutant phenotypes and > quantitative traits. Th ecollaboration incldues Gramene database,Maize GDB > and the Solanaceae Genome Network among others. It is an international > collaboration. > > We are wondering if it would be possible to have a workshop or two on this > new project. This is likely to be a smaller event - geared towards > researchers with functial genomics projects, breeders and other genome > groups. > > What would be the best way to proceed towards arranging a workshop. > Best > Leonore Reiser > > ------------------------------------------------------------------------ ------- > 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 pj37 at cornell.edu Thu Nov 6 17:12:03 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 06 Nov 2003 17:12:03 -0500 Subject: ASPB 2004 (fwd) In-Reply-To: References: Message-ID: <3FAAC733.7080901@cornell.edu> Great ! Just make sure they don't confuse POC with TAIR. Although POC will be equally interesting ! Pankaj Leonore Reiser wrote: > Hmm- seems like we are very popular. > One thing about ASPB workshops is that they do tend to be short (1.5 hours > or so) we could do this in two parts. We did also request a half day for > Botany 2004 so it runs about the same. > Leonore From lreiser at acoma.Stanford.EDU Thu Nov 6 19:17:26 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Thu, 6 Nov 2003 16:17:26 -0800 (PST) Subject: ASPB 2004 (fwd) In-Reply-To: <3FAAC733.7080901@cornell.edu> Message-ID: Yes- that does need clarification. What do people think about having a 'POC introductory' workshop durning the regular workshop time and then having an evening session where potential colloaborators would meet (e.g. people such as Paulein). Leonore On Thu, 6 Nov 2003, Pankaj Jaiswal wrote: > Great ! > Just make sure they don't confuse POC with TAIR. Although POC will be equally > interesting ! > > Pankaj > > Leonore Reiser wrote: > > > Hmm- seems like we are very popular. > > One thing about ASPB workshops is that they do tend to be short (1.5 hours > > or so) we could do this in two parts. We did also request a half day for > > Botany 2004 so it runs about the same. > > 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 ware at cshl.edu Fri Nov 7 09:59:36 2003 From: ware at cshl.edu (Ware, Doreen) Date: Fri, 7 Nov 2003 09:59:36 -0500 Subject: ASPB 2004 (fwd) Message-ID: <39FDE54A4920D411AE0C0090274602F202D0A1C1@exch01> I think that sounds great! -----Original Message----- From: Leonore Reiser [mailto:lreiser at acoma.Stanford.EDU] Sent: Thursday, November 06, 2003 7:17 PM To: po-dev at plantontology.org Subject: Re: ASPB 2004 (fwd) Yes- that does need clarification. What do people think about having a 'POC introductory' workshop durning the regular workshop time and then having an evening session where potential colloaborators would meet (e.g. people such as Paulein). Leonore On Thu, 6 Nov 2003, Pankaj Jaiswal wrote: > Great ! > Just make sure they don't confuse POC with TAIR. Although POC will be equally > interesting ! > > Pankaj > > Leonore Reiser wrote: > > > Hmm- seems like we are very popular. > > One thing about ASPB workshops is that they do tend to be short (1.5 hours > > or so) we could do this in two parts. We did also request a half day for > > Botany 2004 so it runs about the same. > > 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 Fri Nov 7 14:11:38 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Fri, 7 Nov 2003 11:11:38 -0800 (PST) Subject: ASPB 2004 (fwd) Message-ID: Well some positive feedback from ASPB as well- so we seem to have interseted both Botany 2004 and ASPB. Given Toby's comments during the phone conference (willingness to present at Botany2004)- do we refine our request to them (not the wide list of speakers) and ask for a shorter workshop period. Some dates/locations to consider Botany 2004 Snowbird,UTAH July 31- August 5, 2004 ASPB Florida July 24-28, 2004 ISMB Glasgow, Scotland July31-August 4, 2004 Crop Functional Genomics April 7-10, 2004 (Sue speaking) Comparative Genomics of Plants (Keystone) Taos,New Mexico March 4-9,2004 So- how shall we proceed with the two sets of workshops currently on the table? Go for both /divvy up people going to one or the other to present but all meeting for collaborator meeting in Fla? Leonore ---------- Forwarded message ---------- Date: Thu, 06 Nov 2003 21:27:26 -0600 From: EDGAR P SPALDING To: Leonore Reiser Cc: chambers at aspb.org Subject: ASPB 2004 Dear Leonore, Thanks for re-explaining your thoughts about workshops at Plant Biology 2004. The miscommunication was my fault, not Susan's, because I let some email slide last month, quite a lot actually! Anyway, I am enthusiastic about your plan to explain the POC to our attendees. The second workshop lines up well with ASPB's desire to present a conference with broad appeal. Also, it will be possible to arrange a meeting room at the site for your group to meet. You may not have known this, but PI's of NSF genome and 2010 grants have been sent such an offer. If members of groups are coming to ASPB 2004 anyway, they may as well get some work done too. Lunch could be arranged in the rooms for a modest fee so your members won't have to miss any of the program. Susan Chambers will help you with the room arrangements. Thanks for your continued interest in our conference. Let us know if we can help in any other ways. Best regards, Edgar Spalding ----- Original Message ----- From: Leonore Reiser Date: Thursday, November 6, 2003 7:05 pm Subject: RE: ASPB 2004 > Dear Susan > Thank you for getting back to me about this. Actually, my original > messagehad to do with holding a Plant Ontology Consortium > Workshop. This is in > addition to presenting a TAIR workshop at the coming meeting. The > POC is a > new project, a collaboration with TAIR, Gramene, MaizeDB/MaizeGDB > and SGN > and Toby Kellogs lab. So in fact I am really asking to hold 2 > separateworkshops. > > I was thinking that perhaps this year we would do the following > > 1.TAIR Advanced Workshop (the latest data/tools) > 2.Intro to the Plant Ontology Consortium Workshop > > In addition- we may want to schedule a collaborators meeting > (similar to > Deep Gene meeting). So the workshop would be targeted towards > users of the > database/tools and the collaborator meeting would be for current and > future developers of the resource. If we could arrange some > space/time at > the meeting for that it would be excellent. > > I hope this clarifies my request. > > Best > Leonore Reiser > > > On Thu, 6 Nov 2003, Susan Chambers wrote: > > > Hi Leonore: Sorry for the delay in responding. It seems that the > TAIR> workshops have been very popular at our last two meetings > and well > > attended. So we would be happy to provide you that venue again > at the > > Plant Biology 2004 meeting. Please let me know more specifically > about> the length of workshops and a/v that you would need > sometime in the next > > couple of months. > > Best regards, > > Susan > > > > Susan K. Rosenberry > > Director of Finance & Administration > > American Society of Plant Biologists > > 15501 Monona Drive > > Rockville, MD 20855 USA > > phone: 301-251-0560, x. 111 > > fax: 301-279-2996 > > e-mail: chambers at aspb.org > > http://www.aspb.org > > > > > > -----Original Message----- > > From: Leonore Reiser [lreiser at acoma.Stanford.EDU] > > Sent: Wednesday, November 05, 2003 4:50 PM > > To: Susan Chambers > > Subject: Re: ASPB 2004 > > > > > > Dear Susan: > > I dont know if you have had a chance to look into this issue > yet. At our > > phone conference today (the POC group) we were discussing our > plans for > > a > > workshop. We have made some inquiries with the organizers of Botany > > 2004 > > which does have some overlapping dates with the ASPB meeting. > > I think we would prefer to present at ASPB if that is at all > possible.> Best Regards > > Leonore > > On Fri, 24 Oct 2003, Leonore Reiser wrote: > > > > > Dear Susan > > > Thank you so much for all your help with organizing the TAIR > workshops> at > > > the Hawaii meeting this year. > > > I am writing to inquire about a new workshop for next year. > TAIR is > > part > > > of a collaboration funded by the NSF to develop controlled > > vocabularies > > > for plant anatomy and development. This project will result in a > > database > > > and query tools for analyzing gene expression , mutant > phenotypes and > > > quantitative traits. Th ecollaboration incldues Gramene > database,Maize> GDB > > > and the Solanaceae Genome Network among others. It is an > international> > collaboration. > > > > > > We are wondering if it would be possible to have a workshop or > two on > > this > > > new project. This is likely to be a smaller event - geared towards > > > researchers with functial genomics projects, breeders and > other genome > > > groups. > > > > > > What would be the best way to proceed towards arranging a > workshop.> > Best > > > Leonore Reiser > > > > > > > > ----------------------------------------------------------------- > ------- > > ------- > > > 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 > > ----------------------------------------------------------------- > ------- > > ------- > > > > > > > > ------------------------------------------------------------------- > ------------ > 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 pj37 at cornell.edu Fri Nov 7 14:43:41 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 07 Nov 2003 14:43:41 -0500 Subject: ASPB 2004 (fwd) In-Reply-To: References: Message-ID: <3FABF5ED.5000309@cornell.edu> I am flexible, except that I have to be in Ithaca on Wed. evening. If Mon and Tuesday can work, I can fly out on Sunday afternoon and take a return flight either Tuesday evening/Wed. morning. Pankaj Leonore Reiser wrote: > Well some positive feedback from ASPB as well- so we seem to have > interseted both Botany 2004 and ASPB. Given Toby's comments during the > phone conference (willingness to present at Botany2004)- do we refine our > request to them (not the wide list of speakers) and ask for a shorter > workshop period. > > Some dates/locations to consider > > Botany 2004 Snowbird,UTAH July 31- August 5, 2004 > > ASPB Florida July 24-28, 2004 > > ISMB Glasgow, Scotland July31-August 4, 2004 > > Crop Functional Genomics April 7-10, 2004 (Sue speaking) > > Comparative Genomics of Plants (Keystone) Taos,New Mexico March 4-9,2004 > > So- how shall we proceed with the two sets of workshops currently on the > table? Go for both /divvy up people going to one or the other to present > but all meeting for collaborator meeting in Fla? > > > Leonore > > ---------- Forwarded message ---------- > Date: Thu, 06 Nov 2003 21:27:26 -0600 > From: EDGAR P SPALDING > To: Leonore Reiser > Cc: chambers at aspb.org > Subject: ASPB 2004 > > > Dear Leonore, > > Thanks for re-explaining your thoughts about workshops at Plant Biology 2004. The miscommunication was my fault, not Susan's, because > I let some email slide last month, quite a lot actually! Anyway, I am enthusiastic about your plan to explain the POC to our > attendees. The second workshop lines up well with ASPB's desire to present a conference with broad appeal. Also, it will be possible > to arrange a meeting room at the site for your group to meet. You may not have known this, but PI's of NSF genome and 2010 grants have > been sent such an offer. If members of groups are coming to ASPB 2004 anyway, they may as well get some work done too. Lunch could be > arranged in the rooms for a modest fee so your members won't have to miss any of the program. Susan Chambers will help you with the > room arrangements. > > Thanks for your continued interest in our conference. Let us know if we can help in any other ways. > > Best regards, > > Edgar Spalding > > ----- Original Message ----- > > From: Leonore Reiser > > Date: Thursday, November 6, 2003 7:05 pm > > Subject: RE: ASPB 2004 > > >>Dear Susan >>Thank you for getting back to me about this. Actually, my original >>messagehad to do with holding a Plant Ontology Consortium >>Workshop. This is in >>addition to presenting a TAIR workshop at the coming meeting. The >>POC is a >>new project, a collaboration with TAIR, Gramene, MaizeDB/MaizeGDB >>and SGN >>and Toby Kellogs lab. So in fact I am really asking to hold 2 >>separateworkshops. >> >>I was thinking that perhaps this year we would do the following >> >>1.TAIR Advanced Workshop (the latest data/tools) >>2.Intro to the Plant Ontology Consortium Workshop >> >>In addition- we may want to schedule a collaborators meeting >>(similar to >>Deep Gene meeting). So the workshop would be targeted towards >>users of the >>database/tools and the collaborator meeting would be for current and >>future developers of the resource. If we could arrange some >>space/time at >>the meeting for that it would be excellent. >> >>I hope this clarifies my request. >> >>Best >>Leonore Reiser >> >> >>On Thu, 6 Nov 2003, Susan Chambers wrote: >> >> >>>Hi Leonore: Sorry for the delay in responding. It seems that the >> >>TAIR> workshops have been very popular at our last two meetings >>and well >> >>>attended. So we would be happy to provide you that venue again >> >>at the >> >>>Plant Biology 2004 meeting. Please let me know more specifically >> >>about> the length of workshops and a/v that you would need >>sometime in the next >> >>>couple of months. >>>Best regards, >>>Susan >>> >>>Susan K. Rosenberry >>>Director of Finance & Administration >>>American Society of Plant Biologists >>>15501 Monona Drive >>>Rockville, MD 20855 USA >>>phone: 301-251-0560, x. 111 >>>fax: 301-279-2996 >>>e-mail: chambers at aspb.org >>>http://www.aspb.org >>> >>> >>>-----Original Message----- >>>From: Leonore Reiser [lreiser at acoma.Stanford.EDU] >>>Sent: Wednesday, November 05, 2003 4:50 PM >>>To: Susan Chambers >>>Subject: Re: ASPB 2004 >>> >>> >>>Dear Susan: >>>I dont know if you have had a chance to look into this issue >> >>yet. At our >> >>>phone conference today (the POC group) we were discussing our >> >>plans for >> >>>a >>>workshop. We have made some inquiries with the organizers of Botany >>>2004 >>>which does have some overlapping dates with the ASPB meeting. >>>I think we would prefer to present at ASPB if that is at all >> >>possible.> Best Regards >> >>>Leonore >>>On Fri, 24 Oct 2003, Leonore Reiser wrote: >>> >>> >>>>Dear Susan >>>>Thank you so much for all your help with organizing the TAIR >> >>workshops> at >> >>>>the Hawaii meeting this year. >>>>I am writing to inquire about a new workshop for next year. >> >>TAIR is >> >>>part >>> >>>>of a collaboration funded by the NSF to develop controlled >>> >>>vocabularies >>> >>>>for plant anatomy and development. This project will result in a >>> >>>database >>> >>>>and query tools for analyzing gene expression , mutant >> >>phenotypes and >> >>>>quantitative traits. Th ecollaboration incldues Gramene >> >>database,Maize> GDB >> >>>>and the Solanaceae Genome Network among others. It is an >> >>international> > collaboration. >> >>>>We are wondering if it would be possible to have a workshop or >> >>two on >> >>>this >>> >>>>new project. This is likely to be a smaller event - geared towards >>>>researchers with functial genomics projects, breeders and >> >>other genome >> >>>>groups. >>>> >>>>What would be the best way to proceed towards arranging a >> >>workshop.> > Best >> >>>>Leonore Reiser >>>> >>>> >>> >>>----------------------------------------------------------------- >> >>------- >> >>>------- >>> >>>>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 >>>----------------------------------------------------------------- >> >>------- >> >>>------- >>> >>> >>> >> >>------------------------------------------------------------------- >>------------ >>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 >>------------------------------------------------------------------- >>------------ >> >> > > > > -- ****************************************** Pankaj Jaiswal, Ph.D. Research Associate Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel:+1-607-255-3103 / Fax:+1-607-255-6683 E mail: pj37 at cornell.edu http://www.gramene.org ****************************************** From pj37 at cornell.edu Fri Nov 7 16:39:20 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 07 Nov 2003 16:39:20 -0500 Subject: keystone symposia In-Reply-To: References: Message-ID: <3FAC1108.10609@cornell.edu> > > Comparative Genomics of Plants (Keystone) Taos,New Mexico March 4-9,2004 > http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=688 I guess Susan is speaking at the symposia, though on a different topic. Susan would you like to present a small talk on POC if at all possible and a slot is available. Pankaj From feedback_submission at brie.cshl.org Wed Nov 5 13:47:28 2003 From: feedback_submission at brie.cshl.org (feedback_submission at brie.cshl.org) Date: Wed, 5 Nov 2003 13:47:28 -0500 Subject: Feedback Submission from the Live Site Message-ID: <200311051847.hA5IlSPO016736@brie.cshl.org> *** Feedback from the Live Site *** refer_to_url: http://brie.cshl.org:8080/index.html comments: test name: Shuly email: shuly at cshl.org organization: CSHL send_feedback: Send your feedback From pj37 at cornell.edu Tue Nov 11 14:32:42 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 11 Nov 2003 14:32:42 -0500 Subject: Query examples Message-ID: <3FB1395A.90306@cornell.edu> Hi Everyone, Can you give me some interesting queries that people would like to make. I need to put them on demo page. Thanks Pankaj Here is a starter.. Show all the genes that are expressed in leaf (anatomy) Show all the genes that are expressed in anthers (anatomy) Show all the genes that are expressed in phloem tissue (anatomy) Show all the genes that are expressed in bundle sheath cells (anatomy) Show all the genes from that are expressed at inflorescence initiation stage (growth stage) Show all the genes that are expressed at embryo development stage (growth stage) Show all the genes from rice that are expressed in embryo (anatomy) at mature grain stage (growth stage) Show all the genes from Arabidopsis that are expressed in hypocotyl (anatomy) at germination (growth stage) Show all the genes from Arabidopsis that are expressed in stamen primordium (anatomy) at stage 7 flower (growth stage) Show all the genes from maize that are expressed in male florets (anatomy) but not in female florets (anatomy) Show all the Mutants from Maize, rice and Arabidopsis associated with a phenotype for leaf (anatomy) color (trait) Show all the Mutants from Maize and rice associated with a phenotype for seed (anatomy) shattering (trait) From PolaccoM at missouri.edu Wed Nov 12 11:17:11 2003 From: PolaccoM at missouri.edu (Mary Polacco) Date: Wed, 12 Nov 2003 10:17:11 -0600 Subject: Unique identifiers assigned to Plant Ontology developer groups In-Reply-To: <3FA9256E.1010201@cornell.edu> Message-ID: Hi Pankaj, This is very useful! What does it take to post this on the downloads section so that other folks who wish to import the terms into databases could have this without having to figure out DAG EDIT? -mary On 11/5/03 10:29 AM, "Pankaj Jaiswal" wrote: > Hi Mary, > > I am copying this message to Liya. I guess this can be pulled out from the > Ontology DB tables. I am not so sure about the hierarchy, but here is what I > did. By using the Dag-EDIT ver 1.407, I saved the gramene ontology+definition > file by using the OBO adapter and I can get a complete record of terms as > following. I hope this will work. Earlier versions of Dag-EDIT used to have an > adapter for generating an RDF format, but this one seems better. > > > [Typedef] > id: part_of > name: Part of > > [Typedef] > id: develops_from > name: develops from > > [Term] > id: GRO:0005050 > name: phelloderm > is_a: GRO:0005047 > is_a: GRO:0005048 > > [Term] > id: GRO:0005279 > name: floral primordium > is_a: GRO:0000136 > > [Term] > id: GRO:0005598 > name: vascular cambium > is_a: GRO:0005597 > > [Term] > id: GRO:0005580 > name: floral nectary > is_a: GRO:0005659 > > [Term] > id: GRO:0006107 > name: microspore mother cell > is_a: GRO:0005825 > > [Term] > id: GRO:0005352 > name: xylem > relationship: part_of GRO:0005369 > > > > > Pankaj > > Mary Polacco wrote: > >> Pankaj, >> Is there an easy way to get a table of the terms and their POC identifiers >> other than writing a parser for the flat file that shows also the heirarchy? >> >> -mary >> >> On 11/4/03 6:15 PM, "Pankaj Jaiswal" wrote: >> >> >>> Unique identifiers assigned to Plant Ontology developer groups >>> >>> Every term in the anatomy or developmental stage ontology is identified by a >>> unique identifier. Under the conventions that we have already established, >>> the >>> syntax of a PO identifier is PO:nnnnnnn, where nnnnnnn is a zero-padded >>> unique >>> integer of seven digits. >>> >>> In order to ensure database integrity, identifiers are never removed. Terms >>> that >>> are retired(deleted) from the ontology are moved into the obsolete category. >>> To >>> ensure that the same identifier is not used twice, each participating group >>> will >>> be assigned non-overlapping ID ranges and listed on this page for >>> documentation >>> purposes. These ranges will automatically act as (internal) identifiers for >>> the >>> group that submitted the term. If you want the identifiers assigned to your >>> group, please send and e mail to po-dev at plantontology.org >>> >>> Group identifier range (from-to) >>> TAIR 0000001-0005000 >>> Gramene 0005001-0010000 >>> IRRI 0010001-0015000 >>> MaizeDB 0015001-0020000-->Change group name to MaizeGDB >>> >>> For the above 4 groups, the range was assigned prior to the award of this >>> project http://www.plantontology.org/doc/poc_project.html >>> >>> Toby Kellogg 0020001-0025000 >>> Open 0025001-0030000 >>> Open 0030001-0035000 >>> Open 0035001-0040000 >>> Open 0040001-0045000 >>> Open 0045001-0050000 >>> Open 0050001-0055000 >>> >>> Setting your range of numbers within DAG-Edit. >>> >>> Once you have claimed a set of numbers from the ontology numbers file, you >>> must >>> also set these numbers within the configuration file of DAG-Edit. To do this >>> you >>> should open DAG-Edit, and chose from the 'plugins' menu the 'DAG-Edit >>> Configuration Manager'. Within this window you can now fill in your range of >>> numbers, starting in the 'start of id range' line and finishing in the 'End >>> of >>> id range' line. Press 'Save Configuration' to save your changes. >>> >>> In order to avoid conflicts, any new term contributed by the group should >>> carry >>> the Ontology term identifier from the assigned range. >>> >>> >>> >>> It is also an easy way to track the contribution. >>> >>> >>> Pankaj >>> >>> >> >> >> From pj37 at cornell.edu Wed Nov 12 14:23:25 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 12 Nov 2003 14:23:25 -0500 Subject: Unique identifiers assigned to Plant Ontology developer groups In-Reply-To: References: Message-ID: <3FB288AD.1080208@cornell.edu> Doreen and Lincoln, please correct me here. I think for the purpose of DB, we will be putting up our complete poc-DB up for download same as Gene Ontology DB. Right ! As far as what Mary is asking, I don't mind putting up another file with a dump using OBO adapter. Perhaps, this can be scheduled only with the DB release and not every time we modify the flat files in the CVS. Pankaj Mary Polacco wrote: > Hi Pankaj, > This is very useful! > > What does it take to post this on the downloads section so that other folks > who wish to import the terms into databases could have this without having > to figure out DAG EDIT? > -mary > > On 11/5/03 10:29 AM, "Pankaj Jaiswal" wrote: > > >>Hi Mary, >> >>I am copying this message to Liya. I guess this can be pulled out from the >>Ontology DB tables. I am not so sure about the hierarchy, but here is what I >>did. By using the Dag-EDIT ver 1.407, I saved the gramene ontology+definition >>file by using the OBO adapter and I can get a complete record of terms as >>following. I hope this will work. Earlier versions of Dag-EDIT used to have an >>adapter for generating an RDF format, but this one seems better. >> >> >>[Typedef] >>id: part_of >>name: Part of >> >>[Typedef] >>id: develops_from >>name: develops from >> >>[Term] >>id: GRO:0005050 >>name: phelloderm >>is_a: GRO:0005047 >>is_a: GRO:0005048 >> >>[Term] >>id: GRO:0005279 >>name: floral primordium >>is_a: GRO:0000136 >> >>[Term] >>id: GRO:0005598 >>name: vascular cambium >>is_a: GRO:0005597 >> >>[Term] >>id: GRO:0005580 >>name: floral nectary >>is_a: GRO:0005659 >> >>[Term] >>id: GRO:0006107 >>name: microspore mother cell >>is_a: GRO:0005825 >> >>[Term] >>id: GRO:0005352 >>name: xylem >>relationship: part_of GRO:0005369 >> >> >> >> >>Pankaj >> >>Mary Polacco wrote: >> >> >>>Pankaj, >>>Is there an easy way to get a table of the terms and their POC identifiers >>>other than writing a parser for the flat file that shows also the heirarchy? >>> >>>-mary >>> >>>On 11/4/03 6:15 PM, "Pankaj Jaiswal" wrote: >>> >>> >>> >>>>Unique identifiers assigned to Plant Ontology developer groups >>>> >>>>Every term in the anatomy or developmental stage ontology is identified by a >>>>unique identifier. Under the conventions that we have already established, >>>>the >>>>syntax of a PO identifier is PO:nnnnnnn, where nnnnnnn is a zero-padded >>>>unique >>>>integer of seven digits. >>>> >>>>In order to ensure database integrity, identifiers are never removed. Terms >>>>that >>>>are retired(deleted) from the ontology are moved into the obsolete category. >>>>To >>>>ensure that the same identifier is not used twice, each participating group >>>>will >>>>be assigned non-overlapping ID ranges and listed on this page for >>>>documentation >>>>purposes. These ranges will automatically act as (internal) identifiers for >>>>the >>>>group that submitted the term. If you want the identifiers assigned to your >>>>group, please send and e mail to po-dev at plantontology.org >>>> >>>>Group identifier range (from-to) >>>>TAIR 0000001-0005000 >>>>Gramene 0005001-0010000 >>>>IRRI 0010001-0015000 >>>>MaizeDB 0015001-0020000-->Change group name to MaizeGDB >>>> >>>>For the above 4 groups, the range was assigned prior to the award of this >>>>project http://www.plantontology.org/doc/poc_project.html >>>> >>>>Toby Kellogg 0020001-0025000 >>>>Open 0025001-0030000 >>>>Open 0030001-0035000 >>>>Open 0035001-0040000 >>>>Open 0040001-0045000 >>>>Open 0045001-0050000 >>>>Open 0050001-0055000 >>>> >>>>Setting your range of numbers within DAG-Edit. >>>> >>>>Once you have claimed a set of numbers from the ontology numbers file, you >>>>must >>>>also set these numbers within the configuration file of DAG-Edit. To do this >>>>you >>>>should open DAG-Edit, and chose from the 'plugins' menu the 'DAG-Edit >>>>Configuration Manager'. Within this window you can now fill in your range of >>>>numbers, starting in the 'start of id range' line and finishing in the 'End >>>>of >>>>id range' line. Press 'Save Configuration' to save your changes. >>>> >>>>In order to avoid conflicts, any new term contributed by the group should >>>>carry >>>>the Ontology term identifier from the assigned range. >>>> >>>> >>>> >>>>It is also an easy way to track the contribution. >>>> >>>> >>>>Pankaj >>>> >>>> >>> >>> >>> > > -- ****************************************** Pankaj Jaiswal, Ph.D. Research Associate Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel:+1-607-255-3103 / Fax:+1-607-255-6683 E mail: pj37 at cornell.edu http://www.gramene.org ****************************************** From PolaccoM at missouri.edu Wed Nov 12 14:56:10 2003 From: PolaccoM at missouri.edu (Mary Polacco) Date: Wed, 12 Nov 2003 13:56:10 -0600 Subject: Unique identifiers assigned to Plant Ontology developer groups In-Reply-To: <3FB288AD.1080208@cornell.edu> Message-ID: Pankaj, That would be great! -mary On 11/12/03 1:23 PM, "Pankaj Jaiswal" wrote: > Perhaps, this can be scheduled only with the DB release and > not every time we modify the flat files in the CVS. From pj37 at cornell.edu Thu Nov 13 11:18:54 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 13 Nov 2003 11:18:54 -0500 Subject: Bug tracking system- Follow up Message-ID: <3FB3AEEE.4000201@cornell.edu> Hi Everyone, I think we need to set up our own bug tracking system for PO. The sourceforge rejected our request. Doreen and Shuly, can you have a look at setting up something similar. In the last conf call on Nov-5 Lincoln mentioned that we can set up the whole SF site locally. Thanks Pankaj From ware at cshl.edu Thu Nov 13 11:26:01 2003 From: ware at cshl.edu (Ware, Doreen) Date: Thu, 13 Nov 2003 11:26:01 -0500 Subject: Bug tracking system- Follow up Message-ID: <39FDE54A4920D411AE0C0090274602F202D0A20B@exch01> Hi Pankaj, That is too bad. I am not surprised though. I would like Shuly to focus on the database for the next few weeks. As time allows she can identify a bug tracking system and work on implementation. Doreen -----Original Message----- From: Pankaj Jaiswal [mailto:pj37 at cornell.edu] Sent: Thursday, November 13, 2003 11:19 AM To: POC-dev Subject: Bug tracking system- Follow up Hi Everyone, I think we need to set up our own bug tracking system for PO. The sourceforge rejected our request. Doreen and Shuly, can you have a look at setting up something similar. In the last conf call on Nov-5 Lincoln mentioned that we can set up the whole SF site locally. Thanks Pankaj From lstein at cshl.edu Thu Nov 13 12:35:58 2003 From: lstein at cshl.edu (Lincoln Stein) Date: Thu, 13 Nov 2003 12:35:58 -0500 Subject: Bug tracking system- Follow up In-Reply-To: <3FB3AEEE.4000201@cornell.edu> References: <3FB3AEEE.4000201@cornell.edu> Message-ID: <200311131235.58190.lstein@cshl.edu> OK. We'll set up a bug tracking system locally. Lincoln On Thursday 13 November 2003 11:18 am, Pankaj Jaiswal wrote: > Hi Everyone, > > I think we need to set up our own bug tracking system for PO. The > sourceforge rejected our request. > > Doreen and Shuly, can you have a look at setting up something similar. In > the last conf call on Nov-5 Lincoln mentioned that we can set up the whole > SF site locally. > > Thanks > Pankaj -- Lincoln Stein lstein at cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From lreiser at acoma.Stanford.EDU Mon Nov 17 15:56:54 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Mon, 17 Nov 2003 12:56:54 -0800 (PST) Subject: Request for Symposium Support from BSA Systematics Section (fwd) Message-ID: FYI Seems like everyone is willing to support in name- though not in $ amounts. I'd like to respond to both Botany 2004 and ASPB regarding our plans for next year. Should we plan a main workshop at ASPB and a smaller introduction at Botany 2004 (since Toby will be attending anyway?). Id save it for an agenda item -but it would be good to respond sooner than that. 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: Mon, 17 Nov 2003 14:52:16 -0600 From: Wayne J. Elisens To: Leonore Reiser , Andi Wolfe , Jeff Osborn Subject: Request for Symposium Support from BSA Systematics Section Dear Dr. Reiser, I am sorry to inform you that the BSA Systematics Section will not be able to provide funds to offset expenses for your proposed symposium entitled "Biological Ontologies for Plant Biology: Development and Applications." The section is willing to 'sponsor' your proposed symposium for inclusion in the scientific program, but we are unable to provide funds. BSA Systematics had a limited amount of funds and an unprecedented number of funding requests from proposed symposia and colloquia for the Botany 2004 conference in Snow Bird Resort, Utah. On behalf of the BSA Systematics Section, we thank you for your proposal and we wish you good luck in the organization and presentation of your symposium. Best wishes, Wayne Elisens Chair, BSA Systematics Section -- Wayne J. Elisens Associate Professor and Curator of the Bebb Herbarium Department of Botany & Microbiology 770 Van Vleet Oval University of Oklahoma Norman, OK 73019-6131 Ph (405) 325 -5923 Fax (405) 325-7619 E-mail elisens at ou.edu THE BEBB IS ON THE WEB From peter.stevens at mobot.org Mon Nov 17 14:32:44 2003 From: peter.stevens at mobot.org (Peter Stevens) Date: Mon, 17 Nov 2003 15:32:44 -0400 Subject: Request for Symposium Support from BSA Systematics Section (fwd) In-Reply-To: References: Message-ID: >I will be at botany 2004, too, quite possibly Felipe, too - maybe >the three of us should think whether we need a symposium, or a >couple of back-to-back talks, or a talk and a poster, or something >else. Peter S. >FYI >Seems like everyone is willing to support in name- though not in $ >amounts. I'd like to respond to both Botany 2004 and ASPB regarding our >plans for next year. Should we plan a main workshop at ASPB and a smaller >introduction at Botany 2004 (since Toby will be attending anyway?). Id >save it for an agenda item -but it would be good to respond sooner than >that. >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: Mon, 17 Nov 2003 14:52:16 -0600 >From: Wayne J. Elisens >To: Leonore Reiser , Andi Wolfe >, > Jeff Osborn >Subject: Request for Symposium Support from BSA Systematics Section > >Dear Dr. Reiser, > > I am sorry to inform you that the BSA Systematics Section >will not be able to provide funds to offset expenses for your proposed >symposium entitled "Biological Ontologies for Plant Biology: >Development and Applications." The section is willing to 'sponsor' >your proposed symposium for inclusion in the scientific program, but we >are unable to provide funds. BSA Systematics had a limited amount of >funds and an unprecedented number of funding requests from proposed >symposia and colloquia for the Botany 2004 conference in Snow Bird >Resort, Utah. > > On behalf of the BSA Systematics Section, we thank you for your >proposal and we wish you good luck in the organization and presentation >of your symposium. > > Best wishes, > Wayne Elisens > Chair, BSA Systematics Section > >-- >Wayne J. Elisens >Associate Professor and Curator of the Bebb Herbarium > >Department of Botany & Microbiology >770 Van Vleet Oval >University of Oklahoma >Norman, OK 73019-6131 >Ph (405) 325 -5923 >Fax (405) 325-7619 >E-mail elisens at ou.edu > >THE BEBB IS ON THE WEB > From rhee at acoma.Stanford.EDU Mon Nov 17 16:51:30 2003 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 17 Nov 2003 13:51:30 -0800 (PST) Subject: Request for Symposium Support from BSA Systematics Section (fwd) In-Reply-To: Message-ID: sounds great to me Leonore. Sue On Mon, 17 Nov 2003, Leonore Reiser wrote: > > FYI > Seems like everyone is willing to support in name- though not in $ > amounts. I'd like to respond to both Botany 2004 and ASPB regarding our > plans for next year. Should we plan a main workshop at ASPB and a smaller > introduction at Botany 2004 (since Toby will be attending anyway?). Id > save it for an agenda item -but it would be good to respond sooner than > that. > 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: Mon, 17 Nov 2003 14:52:16 -0600 > From: Wayne J. Elisens > To: Leonore Reiser , Andi Wolfe , > Jeff Osborn > Subject: Request for Symposium Support from BSA Systematics Section > > Dear Dr. Reiser, > > I am sorry to inform you that the BSA Systematics Section > will not be able to provide funds to offset expenses for your proposed > symposium entitled "Biological Ontologies for Plant Biology: > Development and Applications." The section is willing to 'sponsor' > your proposed symposium for inclusion in the scientific program, but we > are unable to provide funds. BSA Systematics had a limited amount of > funds and an unprecedented number of funding requests from proposed > symposia and colloquia for the Botany 2004 conference in Snow Bird > Resort, Utah. > > On behalf of the BSA Systematics Section, we thank you for your > proposal and we wish you good luck in the organization and presentation > of your symposium. > > Best wishes, > Wayne Elisens > Chair, BSA Systematics Section > > -- > Wayne J. Elisens > Associate Professor and Curator of the Bebb Herbarium > > Department of Botany & Microbiology > 770 Van Vleet Oval > University of Oklahoma > Norman, OK 73019-6131 > Ph (405) 325 -5923 > Fax (405) 325-7619 > E-mail elisens at ou.edu > > THE BEBB IS ON THE WEB > > > > > > ----------------------------------------------------------------------------- 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 kellogge at msx.umsl.edu Mon Nov 17 17:33:16 2003 From: kellogge at msx.umsl.edu (Toby Kellogg) Date: Mon, 17 Nov 2003 17:33:16 -0500 Subject: Request for Symposium Support from BSA Systematics Section (fwd) In-Reply-To: References: Message-ID: I was thinking the same thing - how about if the St. Louis crew gives a set of talks at BSA, and so we won't worry about a formal workshop this year? Toby >>I will be at botany 2004, too, quite possibly Felipe, too - maybe >>the three of us should think whether we need a symposium, or a >>couple of back-to-back talks, or a talk and a poster, or something >>else. > > >Peter S. > >>FYI >>Seems like everyone is willing to support in name- though not in $ >>amounts. I'd like to respond to both Botany 2004 and ASPB regarding our >>plans for next year. Should we plan a main workshop at ASPB and a smaller >>introduction at Botany 2004 (since Toby will be attending anyway?). Id >>save it for an agenda item -but it would be good to respond sooner than >>that. >>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: Mon, 17 Nov 2003 14:52:16 -0600 >>From: Wayne J. Elisens >>To: Leonore Reiser , Andi Wolfe >>, >> Jeff Osborn >>Subject: Request for Symposium Support from BSA Systematics Section >> >>Dear Dr. Reiser, >> >> I am sorry to inform you that the BSA Systematics Section >>will not be able to provide funds to offset expenses for your proposed >>symposium entitled "Biological Ontologies for Plant Biology: >>Development and Applications." The section is willing to 'sponsor' >>your proposed symposium for inclusion in the scientific program, but we >>are unable to provide funds. BSA Systematics had a limited amount of >>funds and an unprecedented number of funding requests from proposed >>symposia and colloquia for the Botany 2004 conference in Snow Bird >>Resort, Utah. >> >> On behalf of the BSA Systematics Section, we thank you for your >>proposal and we wish you good luck in the organization and presentation >>of your symposium. >> >> Best wishes, >> Wayne Elisens >> Chair, BSA Systematics Section >> >>-- >>Wayne J. Elisens >>Associate Professor and Curator of the Bebb Herbarium >> >>Department of Botany & Microbiology >>770 Van Vleet Oval >>University of Oklahoma >>Norman, OK 73019-6131 >>Ph (405) 325 -5923 >>Fax (405) 325-7619 >>E-mail elisens at ou.edu >> >>THE BEBB IS ON THE WEB >> Elizabeth A. Kellogg Department of Biology University of Missouri-St. Louis 8001 Natural Bridge Road St. Louis, MO 63121 phone: 314-516-6217 fax: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ From lreiser at acoma.Stanford.EDU Mon Nov 17 17:30:43 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Mon, 17 Nov 2003 14:30:43 -0800 (PST) Subject: Request for Symposium Support from BSA Systematics Section (fwd) In-Reply-To: Message-ID: So how long would this be 1.5 hours?? I need to rephrase the request to Botany2004. On Mon, 17 Nov 2003, Toby Kellogg wrote: > I was thinking the same thing - how about if the St. Louis crew gives a set > of talks at BSA, and so we won't worry about a formal workshop this year? > Toby > > >>I will be at botany 2004, too, quite possibly Felipe, too - maybe > >>the three of us should think whether we need a symposium, or a > >>couple of back-to-back talks, or a talk and a poster, or something > >>else. > > > > > >Peter S. > > > >>FYI > >>Seems like everyone is willing to support in name- though not in $ > >>amounts. I'd like to respond to both Botany 2004 and ASPB regarding our > >>plans for next year. Should we plan a main workshop at ASPB and a smaller > >>introduction at Botany 2004 (since Toby will be attending anyway?). Id > >>save it for an agenda item -but it would be good to respond sooner than > >>that. > >>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: Mon, 17 Nov 2003 14:52:16 -0600 > >>From: Wayne J. Elisens > >>To: Leonore Reiser , Andi Wolfe > >>, > >> Jeff Osborn > >>Subject: Request for Symposium Support from BSA Systematics Section > >> > >>Dear Dr. Reiser, > >> > >> I am sorry to inform you that the BSA Systematics Section > >>will not be able to provide funds to offset expenses for your proposed > >>symposium entitled "Biological Ontologies for Plant Biology: > >>Development and Applications." The section is willing to 'sponsor' > >>your proposed symposium for inclusion in the scientific program, but we > >>are unable to provide funds. BSA Systematics had a limited amount of > >>funds and an unprecedented number of funding requests from proposed > >>symposia and colloquia for the Botany 2004 conference in Snow Bird > >>Resort, Utah. > >> > >> On behalf of the BSA Systematics Section, we thank you for your > >>proposal and we wish you good luck in the organization and presentation > >>of your symposium. > >> > >> Best wishes, > >> Wayne Elisens > >> Chair, BSA Systematics Section > >> > >>-- > >>Wayne J. Elisens > >>Associate Professor and Curator of the Bebb Herbarium > >> > >>Department of Botany & Microbiology > >>770 Van Vleet Oval > >>University of Oklahoma > >>Norman, OK 73019-6131 > >>Ph (405) 325 -5923 > >>Fax (405) 325-7619 > >>E-mail elisens at ou.edu > >> > >>THE BEBB IS ON THE WEB > >> > > > Elizabeth A. Kellogg > Department of Biology > University of Missouri-St. Louis > 8001 Natural Bridge Road > St. Louis, MO 63121 > phone: 314-516-6217 > fax: 314-516-6233 > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > > > ------------------------------------------------------------------------------- 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 pj37 at cornell.edu Mon Nov 17 17:36:03 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 17 Nov 2003 17:36:03 -0500 Subject: Request for Symposium Support from BSA Systematics Section (fwd) In-Reply-To: References: Message-ID: <3FB94D53.3040601@cornell.edu> I believe that is more than sufficient. Pankaj Leonore Reiser wrote: > So how long would this be 1.5 hours?? I need to rephrase the request to > Botany2004. > > On Mon, 17 Nov 2003, Toby Kellogg wrote: > > >>I was thinking the same thing - how about if the St. Louis crew gives a set >>of talks at BSA, and so we won't worry about a formal workshop this year? >>Toby >> >> >>>>I will be at botany 2004, too, quite possibly Felipe, too - maybe >>>>the three of us should think whether we need a symposium, or a >>>>couple of back-to-back talks, or a talk and a poster, or something >>>>else. >>> >>> >>>Peter S. >>> >>> >>>>FYI >>>>Seems like everyone is willing to support in name- though not in $ >>>>amounts. I'd like to respond to both Botany 2004 and ASPB regarding our >>>>plans for next year. Should we plan a main workshop at ASPB and a smaller >>>>introduction at Botany 2004 (since Toby will be attending anyway?). Id >>>>save it for an agenda item -but it would be good to respond sooner than >>>>that. >>>>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: Mon, 17 Nov 2003 14:52:16 -0600 >>>>From: Wayne J. Elisens >>>>To: Leonore Reiser , Andi Wolfe >>>>, >>>> Jeff Osborn >>>>Subject: Request for Symposium Support from BSA Systematics Section >>>> >>>>Dear Dr. Reiser, >>>> >>>> I am sorry to inform you that the BSA Systematics Section >>>>will not be able to provide funds to offset expenses for your proposed >>>>symposium entitled "Biological Ontologies for Plant Biology: >>>>Development and Applications." The section is willing to 'sponsor' >>>>your proposed symposium for inclusion in the scientific program, but we >>>>are unable to provide funds. BSA Systematics had a limited amount of >>>>funds and an unprecedented number of funding requests from proposed >>>>symposia and colloquia for the Botany 2004 conference in Snow Bird >>>>Resort, Utah. >>>> >>>> On behalf of the BSA Systematics Section, we thank you for your >>>>proposal and we wish you good luck in the organization and presentation >>>>of your symposium. >>>> >>>> Best wishes, >>>> Wayne Elisens >>>> Chair, BSA Systematics Section >>>> >>>>-- >>>>Wayne J. Elisens >>>>Associate Professor and Curator of the Bebb Herbarium >>>> >>>>Department of Botany & Microbiology >>>>770 Van Vleet Oval >>>>University of Oklahoma >>>>Norman, OK 73019-6131 >>>>Ph (405) 325 -5923 >>>>Fax (405) 325-7619 >>>>E-mail elisens at ou.edu >>>> >>>>THE BEBB IS ON THE WEB >>>> >> >> >>Elizabeth A. Kellogg >>Department of Biology >>University of Missouri-St. Louis >>8001 Natural Bridge Road >>St. Louis, MO 63121 >>phone: 314-516-6217 >>fax: 314-516-6233 >>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ >> >> >> > > > ------------------------------------------------------------------------------- > 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 > ------------------------------------------------------------------------------- > > -- ****************************************** Pankaj Jaiswal, Ph.D. Research Associate Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel:+1-607-255-3103 / Fax:+1-607-255-6683 E mail: pj37 at cornell.edu http://www.gramene.org ****************************************** From kellogge at msx.umsl.edu Mon Nov 17 18:00:58 2003 From: kellogge at msx.umsl.edu (Toby Kellogg) Date: Mon, 17 Nov 2003 18:00:58 -0500 Subject: Request for Symposium Support from BSA Systematics Section (fwd) In-Reply-To: References: Message-ID: BSA talks are typically 15 mins, so I guess we'd be looking at 45 minutes at most. Or 30 mins plus a poster. You could just tell them that we'll go through the regular submission process - I think they'll need abstracts by March 1 and we ought to have something to say by then. Toby >So how long would this be 1.5 hours?? I need to rephrase the request to >Botany2004. > >On Mon, 17 Nov 2003, Toby Kellogg wrote: > >> I was thinking the same thing - how about if the St. Louis crew gives a set >> of talks at BSA, and so we won't worry about a formal workshop this year? >> Toby >> >> >>I will be at botany 2004, too, quite possibly Felipe, too - maybe >> >>the three of us should think whether we need a symposium, or a >> >>couple of back-to-back talks, or a talk and a poster, or something >> >>else. >> > >> > >> >Peter S. >> > >> >>FYI >> >>Seems like everyone is willing to support in name- though not in $ >> >>amounts. I'd like to respond to both Botany 2004 and ASPB regarding our >> >>plans for next year. Should we plan a main workshop at ASPB and a smaller >> >>introduction at Botany 2004 (since Toby will be attending anyway?). Id >> >>save it for an agenda item -but it would be good to respond sooner than >> >>that. >> >>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: Mon, 17 Nov 2003 14:52:16 -0600 >> >>From: Wayne J. Elisens >> >>To: Leonore Reiser , Andi Wolfe >> >>, >> >> Jeff Osborn >> >>Subject: Request for Symposium Support from BSA Systematics Section >> >> >> >>Dear Dr. Reiser, >> >> >> >> I am sorry to inform you that the BSA Systematics Section >> >>will not be able to provide funds to offset expenses for your proposed >> >>symposium entitled "Biological Ontologies for Plant Biology: >> >>Development and Applications." The section is willing to 'sponsor' >> >>your proposed symposium for inclusion in the scientific program, but we >> >>are unable to provide funds. BSA Systematics had a limited amount of >> >>funds and an unprecedented number of funding requests from proposed >> >>symposia and colloquia for the Botany 2004 conference in Snow Bird >> >>Resort, Utah. >> >> >> >> On behalf of the BSA Systematics Section, we thank you for your >> >>proposal and we wish you good luck in the organization and presentation >> >>of your symposium. >> >> >> >> Best wishes, >> >> Wayne Elisens >> >> Chair, BSA Systematics Section >> >> >> >>-- >> >>Wayne J. Elisens >> >>Associate Professor and Curator of the Bebb Herbarium >> >> >> >>Department of Botany & Microbiology >> >>770 Van Vleet Oval >> >>University of Oklahoma >> >>Norman, OK 73019-6131 >> >>Ph (405) 325 -5923 >> >>Fax (405) 325-7619 >> >>E-mail elisens at ou.edu >> >> >> >>THE BEBB IS ON THE WEB >> >> >> >> >> Elizabeth A. Kellogg >> Department of Biology >> University of Missouri-St. Louis >> 8001 Natural Bridge Road >> St. Louis, MO 63121 >> phone: 314-516-6217 >> fax: 314-516-6233 >> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ >> >> >> > >------------------------------------------------------------------------------- >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 >------------------------------------------------------------------------------- Elizabeth A. Kellogg Department of Biology University of Missouri-St. Louis 8001 Natural Bridge Road St. Louis, MO 63121 phone: 314-516-6217 fax: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ From lreiser at acoma.Stanford.EDU Mon Nov 17 18:02:08 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Mon, 17 Nov 2003 15:02:08 -0800 (PST) Subject: Request for Symposium Support from BSA Systematics Section (fwd) In-Reply-To: Message-ID: Sounds fine- Ill just withdraw the proposal for the symposium (maybe put it forward for consideration another year) and let them know there will be ca. 3 talks. Leonore On Mon, 17 Nov 2003, Toby Kellogg wrote: > BSA talks are typically 15 mins, so I guess we'd be looking at 45 minutes > at most. Or 30 mins plus a poster. You could just tell them that we'll go > through the regular submission process - I think they'll need abstracts by > March 1 and we ought to have something to say by then. > Toby > > >So how long would this be 1.5 hours?? I need to rephrase the request to > >Botany2004. > > > >On Mon, 17 Nov 2003, Toby Kellogg wrote: > > > >> I was thinking the same thing - how about if the St. Louis crew gives a set > >> of talks at BSA, and so we won't worry about a formal workshop this year? > >> Toby > >> > >> >>I will be at botany 2004, too, quite possibly Felipe, too - maybe > >> >>the three of us should think whether we need a symposium, or a > >> >>couple of back-to-back talks, or a talk and a poster, or something > >> >>else. > >> > > >> > > >> >Peter S. > >> > > >> >>FYI > >> >>Seems like everyone is willing to support in name- though not in $ > >> >>amounts. I'd like to respond to both Botany 2004 and ASPB regarding our > >> >>plans for next year. Should we plan a main workshop at ASPB and a smaller > >> >>introduction at Botany 2004 (since Toby will be attending anyway?). Id > >> >>save it for an agenda item -but it would be good to respond sooner than > >> >>that. > >> >>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: Mon, 17 Nov 2003 14:52:16 -0600 > >> >>From: Wayne J. Elisens > >> >>To: Leonore Reiser , Andi Wolfe > >> >>, > >> >> Jeff Osborn > >> >>Subject: Request for Symposium Support from BSA Systematics Section > >> >> > >> >>Dear Dr. Reiser, > >> >> > >> >> I am sorry to inform you that the BSA Systematics Section > >> >>will not be able to provide funds to offset expenses for your proposed > >> >>symposium entitled "Biological Ontologies for Plant Biology: > >> >>Development and Applications." The section is willing to 'sponsor' > >> >>your proposed symposium for inclusion in the scientific program, but we > >> >>are unable to provide funds. BSA Systematics had a limited amount of > >> >>funds and an unprecedented number of funding requests from proposed > >> >>symposia and colloquia for the Botany 2004 conference in Snow Bird > >> >>Resort, Utah. > >> >> > >> >> On behalf of the BSA Systematics Section, we thank you for your > >> >>proposal and we wish you good luck in the organization and presentation > >> >>of your symposium. > >> >> > >> >> Best wishes, > >> >> Wayne Elisens > >> >> Chair, BSA Systematics Section > >> >> > >> >>-- > >> >>Wayne J. Elisens > >> >>Associate Professor and Curator of the Bebb Herbarium > >> >> > >> >>Department of Botany & Microbiology > >> >>770 Van Vleet Oval > >> >>University of Oklahoma > >> >>Norman, OK 73019-6131 > >> >>Ph (405) 325 -5923 > >> >>Fax (405) 325-7619 > >> >>E-mail elisens at ou.edu > >> >> > >> >>THE BEBB IS ON THE WEB > >> >> > >> > >> > >> Elizabeth A. Kellogg > >> Department of Biology > >> University of Missouri-St. Louis > >> 8001 Natural Bridge Road > >> St. Louis, MO 63121 > >> phone: 314-516-6217 > >> fax: 314-516-6233 > >> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > >> > >> > >> > > > >------------------------------------------------------------------------------- > >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 > >------------------------------------------------------------------------------- > > > Elizabeth A. Kellogg > Department of Biology > University of Missouri-St. Louis > 8001 Natural Bridge Road > St. Louis, MO 63121 > phone: 314-516-6217 > fax: 314-516-6233 > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > > > ------------------------------------------------------------------------------- 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 kellogge at msx.umsl.edu Mon Nov 17 18:22:03 2003 From: kellogge at msx.umsl.edu (Toby Kellogg) Date: Mon, 17 Nov 2003 18:22:03 -0500 Subject: Request for Symposium Support from BSA Systematics Section (fwd) In-Reply-To: References: Message-ID: Good idea. The symposia proposals are usually voted on pretty early - voting often at one meeting for the following year. I'll try to remember to react when they send out the call for symposia for 2005 and maybe we can put something together for that meeting. Toby >Sounds fine- Ill just withdraw the proposal for the symposium (maybe put >it forward for consideration another year) and let them know there will be >ca. 3 talks. >Leonore > >On Mon, 17 Nov 2003, Toby Kellogg wrote: > >> BSA talks are typically 15 mins, so I guess we'd be looking at 45 minutes >> at most. Or 30 mins plus a poster. You could just tell them that we'll go >> through the regular submission process - I think they'll need abstracts by >> March 1 and we ought to have something to say by then. >> Toby >> >> >So how long would this be 1.5 hours?? I need to rephrase the request to >> >Botany2004. >> > >> >On Mon, 17 Nov 2003, Toby Kellogg wrote: >> > >> >> I was thinking the same thing - how about if the St. Louis crew gives >>a set >> >> of talks at BSA, and so we won't worry about a formal workshop this year? >> >> Toby >> >> >> >> >>I will be at botany 2004, too, quite possibly Felipe, too - maybe >> >> >>the three of us should think whether we need a symposium, or a >> >> >>couple of back-to-back talks, or a talk and a poster, or something >> >> >>else. >> >> > >> >> > >> >> >Peter S. >> >> > >> >> >>FYI >> >> >>Seems like everyone is willing to support in name- though not in $ >> >> >>amounts. I'd like to respond to both Botany 2004 and ASPB regarding our >> >> >>plans for next year. Should we plan a main workshop at ASPB and a >>smaller >> >> >>introduction at Botany 2004 (since Toby will be attending anyway?). Id >> >> >>save it for an agenda item -but it would be good to respond sooner than >> >> >>that. >> >> >>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: Mon, 17 Nov 2003 14:52:16 -0600 >> >> >>From: Wayne J. Elisens >> >> >>To: Leonore Reiser , Andi Wolfe >> >> >>, >> >> >> Jeff Osborn >> >> >>Subject: Request for Symposium Support from BSA Systematics Section >> >> >> >> >> >>Dear Dr. Reiser, >> >> >> >> >> >> I am sorry to inform you that the BSA Systematics Section >> >> >>will not be able to provide funds to offset expenses for your proposed >> >> >>symposium entitled "Biological Ontologies for Plant Biology: >> >> >>Development and Applications." The section is willing to 'sponsor' >> >> >>your proposed symposium for inclusion in the scientific program, but we >> >> >>are unable to provide funds. BSA Systematics had a limited amount of >> >> >>funds and an unprecedented number of funding requests from proposed >> >> >>symposia and colloquia for the Botany 2004 conference in Snow Bird >> >> >>Resort, Utah. >> >> >> >> >> >> On behalf of the BSA Systematics Section, we thank you for >>your >> >> >>proposal and we wish you good luck in the organization and presentation >> >> >>of your symposium. >> >> >> >> >> >> Best wishes, >> >> >> Wayne Elisens >> >> >> Chair, BSA Systematics Section >> >> >> >> >> >>-- >> >> >>Wayne J. Elisens >> >> >>Associate Professor and Curator of the Bebb Herbarium >> >> >> >> >> >>Department of Botany & Microbiology >> >> >>770 Van Vleet Oval >> >> >>University of Oklahoma >> >> >>Norman, OK 73019-6131 >> >> >>Ph (405) 325 -5923 >> >> >>Fax (405) 325-7619 >> >> >>E-mail elisens at ou.edu >> >> >> >> >> >>THE BEBB IS ON THE WEB >> >> >> >> >> >> >> >> >> Elizabeth A. Kellogg >> >> Department of Biology >> >> University of Missouri-St. Louis >> >> 8001 Natural Bridge Road >> >> St. Louis, MO 63121 >> >> phone: 314-516-6217 >> >> fax: 314-516-6233 >> >> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ >> >> >> >> >> >> >> > >> >>>------------------------------------------------------------------------------- >> >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 >> >>>------------------------------------------------------------------------------- >> >> >> Elizabeth A. Kellogg >> Department of Biology >> University of Missouri-St. Louis >> 8001 Natural Bridge Road >> St. Louis, MO 63121 >> phone: 314-516-6217 >> fax: 314-516-6233 >> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ >> >> >> > >------------------------------------------------------------------------------- >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 >------------------------------------------------------------------------------- Elizabeth A. Kellogg Department of Biology University of Missouri-St. Louis 8001 Natural Bridge Road St. Louis, MO 63121 phone: 314-516-6217 fax: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ From lreiser at acoma.Stanford.EDU Mon Nov 17 18:19:16 2003 From: lreiser at acoma.Stanford.EDU (Leonore Reiser) Date: Mon, 17 Nov 2003 15:19:16 -0800 (PST) Subject: Request for Symposium Support from BSA Systematics Section (fwd) In-Reply-To: Message-ID: Yes- and it seems that if we want anything other than sponsorship in name- we should contact them much earlier- at least now they have a heads up (and heard of the project). Leonore On Mon, 17 Nov 2003, Toby Kellogg wrote: > Good idea. The symposia proposals are usually voted on pretty early - > voting often at one meeting for the following year. I'll try to remember > to react when they send out the call for symposia for 2005 and maybe we can > put something together for that meeting. > Toby > > >Sounds fine- Ill just withdraw the proposal for the symposium (maybe put > >it forward for consideration another year) and let them know there will be > >ca. 3 talks. > >Leonore > > > >On Mon, 17 Nov 2003, Toby Kellogg wrote: > > > >> BSA talks are typically 15 mins, so I guess we'd be looking at 45 minutes > >> at most. Or 30 mins plus a poster. You could just tell them that we'll go > >> through the regular submission process - I think they'll need abstracts by > >> March 1 and we ought to have something to say by then. > >> Toby > >> > >> >So how long would this be 1.5 hours?? I need to rephrase the request to > >> >Botany2004. > >> > > >> >On Mon, 17 Nov 2003, Toby Kellogg wrote: > >> > > >> >> I was thinking the same thing - how about if the St. Louis crew gives > >>a set > >> >> of talks at BSA, and so we won't worry about a formal workshop this year? > >> >> Toby > >> >> > >> >> >>I will be at botany 2004, too, quite possibly Felipe, too - maybe > >> >> >>the three of us should think whether we need a symposium, or a > >> >> >>couple of back-to-back talks, or a talk and a poster, or something > >> >> >>else. > >> >> > > >> >> > > >> >> >Peter S. > >> >> > > >> >> >>FYI > >> >> >>Seems like everyone is willing to support in name- though not in $ > >> >> >>amounts. I'd like to respond to both Botany 2004 and ASPB regarding our > >> >> >>plans for next year. Should we plan a main workshop at ASPB and a > >>smaller > >> >> >>introduction at Botany 2004 (since Toby will be attending anyway?). Id > >> >> >>save it for an agenda item -but it would be good to respond sooner than > >> >> >>that. > >> >> >>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: Mon, 17 Nov 2003 14:52:16 -0600 > >> >> >>From: Wayne J. Elisens > >> >> >>To: Leonore Reiser , Andi Wolfe > >> >> >>, > >> >> >> Jeff Osborn > >> >> >>Subject: Request for Symposium Support from BSA Systematics Section > >> >> >> > >> >> >>Dear Dr. Reiser, > >> >> >> > >> >> >> I am sorry to inform you that the BSA Systematics Section > >> >> >>will not be able to provide funds to offset expenses for your proposed > >> >> >>symposium entitled "Biological Ontologies for Plant Biology: > >> >> >>Development and Applications." The section is willing to 'sponsor' > >> >> >>your proposed symposium for inclusion in the scientific program, but we > >> >> >>are unable to provide funds. BSA Systematics had a limited amount of > >> >> >>funds and an unprecedented number of funding requests from proposed > >> >> >>symposia and colloquia for the Botany 2004 conference in Snow Bird > >> >> >>Resort, Utah. > >> >> >> > >> >> >> On behalf of the BSA Systematics Section, we thank you for > >>your > >> >> >>proposal and we wish you good luck in the organization and presentation > >> >> >>of your symposium. > >> >> >> > >> >> >> Best wishes, > >> >> >> Wayne Elisens > >> >> >> Chair, BSA Systematics Section > >> >> >> > >> >> >>-- > >> >> >>Wayne J. Elisens > >> >> >>Associate Professor and Curator of the Bebb Herbarium > >> >> >> > >> >> >>Department of Botany & Microbiology > >> >> >>770 Van Vleet Oval > >> >> >>University of Oklahoma > >> >> >>Norman, OK 73019-6131 > >> >> >>Ph (405) 325 -5923 > >> >> >>Fax (405) 325-7619 > >> >> >>E-mail elisens at ou.edu > >> >> >> > >> >> >>THE BEBB IS ON THE WEB > >> >> >> > >> >> > >> >> > >> >> Elizabeth A. Kellogg > >> >> Department of Biology > >> >> University of Missouri-St. Louis > >> >> 8001 Natural Bridge Road > >> >> St. Louis, MO 63121 > >> >> phone: 314-516-6217 > >> >> fax: 314-516-6233 > >> >> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > >> >> > >> >> > >> >> > >> > > >> > >>>------------------------------------------------------------------------------- > >> >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 > >> > >>>------------------------------------------------------------------------------- > >> > >> > >> Elizabeth A. Kellogg > >> Department of Biology > >> University of Missouri-St. Louis > >> 8001 Natural Bridge Road > >> St. Louis, MO 63121 > >> phone: 314-516-6217 > >> fax: 314-516-6233 > >> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > >> > >> > >> > > > >------------------------------------------------------------------------------- > >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 > >------------------------------------------------------------------------------- > > > Elizabeth A. Kellogg > Department of Biology > University of Missouri-St. Louis > 8001 Natural Bridge Road > St. Louis, MO 63121 > phone: 314-516-6217 > fax: 314-516-6233 > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > > > ------------------------------------------------------------------------------- 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 ware at cshl.edu Tue Nov 18 07:00:08 2003 From: ware at cshl.edu (Ware, Doreen) Date: Tue, 18 Nov 2003 07:00:08 -0500 Subject: Request for Symposium Support from BSA Systematics Section (f wd) Message-ID: <39FDE54A4920D411AE0C0090274602F202D0A237@exch01> Hi Leonore, Will be any problem for us to withdraw the program POC have already submitted for Botany? If not then I agree it is a better strategy to allow smaller talks at Botany and have the main workshop at ASPB. Doreen -----Original Message----- From: Leonore Reiser [mailto:lreiser at acoma.Stanford.EDU] Sent: Monday, November 17, 2003 3:57 PM To: po-dev at plantontology.org Subject: Request for Symposium Support from BSA Systematics Section (fwd) FYI Seems like everyone is willing to support in name- though not in $ amounts. I'd like to respond to both Botany 2004 and ASPB regarding our plans for next year. Should we plan a main workshop at ASPB and a smaller introduction at Botany 2004 (since Toby will be attending anyway?). Id save it for an agenda item -but it would be good to respond sooner than that. 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: Mon, 17 Nov 2003 14:52:16 -0600 From: Wayne J. Elisens To: Leonore Reiser , Andi Wolfe , Jeff Osborn Subject: Request for Symposium Support from BSA Systematics Section Dear Dr. Reiser, I am sorry to inform you that the BSA Systematics Section will not be able to provide funds to offset expenses for your proposed symposium entitled "Biological Ontologies for Plant Biology: Development and Applications." The section is willing to 'sponsor' your proposed symposium for inclusion in the scientific program, but we are unable to provide funds. BSA Systematics had a limited amount of funds and an unprecedented number of funding requests from proposed symposia and colloquia for the Botany 2004 conference in Snow Bird Resort, Utah. On behalf of the BSA Systematics Section, we thank you for your proposal and we wish you good luck in the organization and presentation of your symposium. Best wishes, Wayne Elisens Chair, BSA Systematics Section -- Wayne J. Elisens Associate Professor and Curator of the Bebb Herbarium Department of Botany & Microbiology 770 Van Vleet Oval University of Oklahoma Norman, OK 73019-6131 Ph (405) 325 -5923 Fax (405) 325-7619 E-mail elisens at ou.edu THE BEBB IS ON THE WEB From pj37 at cornell.edu Mon Nov 24 15:37:49 2003 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 24 Nov 2003 15:37:49 -0500 Subject: [Fwd: new ontology editing and mapping tool: COBrA] Message-ID: <3FC26C1D.4010507@cornell.edu> Just FYI. This might be an interesting tool to try out, since we are dealing with multiple anatomy ontologies. Pankaj -------- Original Message -------- From: stuart at inf.ed.ac.uk Subject: new ontology editing and mapping tool: COBrA To: gofriends at genome.stanford.edu CC: stuart at inf.ed.ac.uk, j.bard at ed.ac.uk, bonnie at inf.ed.ac.uk, Albert Burger , Roman.Korf at ed.ac.uk Our ontology editing and mapping tool COBrA is now available at: http://www.xspan.org/applications/cobra/ COBrA offers drag-and-drop editing of the ontology, plus import and export into GO RDF, plus RDFS and OWL for extensions of GO RDF we have developed. The novel feature of COBrA is the display of two ontologies simultaneously for the purpose of mapping terms. Mappings between ontologies are made manually, and stored in a separate file (also as a RDF ontology). For example, an OBO anatomy ontology can be mapped to the OBO cell-type ontology - where the mappings denote the cell types found in the tissues. Mappings to, and between, the Gene Ontologies are also possible. COBrA supports GO flat file, DAGEdit flat file, GO RDF, RDFS and OWL formats. See the user guide for details. We have also provided access to the inference and validation methods of the Jena toolkit in order to compare, merge, and extend ontologies by applying inference rules. COBrA is not a generic RDF editor, GO formats for term names are assumed (with the condition that they are valid XML Qnames). COBrA is being developed under the XSPAN project, http://www.xspan.org/ by Roman Korf and myself, comments and suggestions welcome, Stuart Aitken Dr Stuart Aitken Artificial Intelligence Applications Institute The University of Edinburgh Appleton Tower, Room 4.10 Crichton St Edinburgh EH8 9LE United Kingdom -- This message is from the GOFriends moderated mailing list. A list of public announcements and discussion of the Gene Ontology (GO) project. Problems with the list? E-mail: owner-gofriends at geneontology.org Subscribing send "subscribe" to gofriends-request at geneontology.org Unsubscribing send "unsubscribe" to gofriends-request at geneontology.org Web: http://www.geneontology.org/