From jclark at ebi.ac.uk Thu Aug 5 08:50:48 2004 From: jclark at ebi.ac.uk (Jennifer I Clark) Date: Thu, 05 Aug 2004 13:50:48 +0100 Subject: plants in GO Message-ID: <41122D28.7050609@ebi.ac.uk> Hi, There is a new plant related sourceforge item for terms in the GO biological process ontology. Any comments would be greatly appreciated. [ 1003916 ] female gametophyte development https://sourceforge.net/tracker/index.php?func=detail&aid=1003916&group_id=36855&atid=440764 Thanks, Jen From s.gregorio at cgiar.org Thu Aug 5 02:42:37 2004 From: s.gregorio at cgiar.org (Gregorio, Sergio (IRRI)) Date: Wed, 04 Aug 2004 23:42:37 -0700 Subject: Query on PO Message-ID: <2A491C94FFBC5843A212A69CBEA5CEC7328DB0@IRRIMAIL.irri.cgiar.org> To Whom it may concern: I'd like to follow up an earlier query. I recently downloaded copies of your Plant Ontologies. Upon examining your definition and ontology structure files, I noticed you have entries (terms) appearing in the structure file but not in the definition files. I would like to know how this came to be and what you would recommend that I do, if I wish to load your data into say, a MySQL database using the Chado schema. We would certainly appreciate any clarification on the matter. Thank you very much! Regards, Serge Gregorio -------------- next part -------------- An HTML attachment was scrubbed... URL: From katica at acoma.Stanford.EDU Mon Aug 9 14:14:13 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 9 Aug 2004 11:14:13 -0700 (PDT) Subject: Query on PO In-Reply-To: <2A491C94FFBC5843A212A69CBEA5CEC7328DB0@IRRIMAIL.irri.cgiar.org> Message-ID: Dear Serge, Thank you for your interest in Plant Ontology. In the most recent revision of Plant Ontology (anatomy.definition, revision 1.28, and anatomy.ontology, revision 1.27, buth publicly released on June 23, 2004), all 632 terms have definitions, so if you download these files, it shouldn't be any problem. Earlier revisions were lacking some definitions, as we were in the process of building the ontology. Please, let me know if you are still experiencing problems with the files. I don't know much about Chado schema right now, I would need to look it up, so, either I or my colleagues at CSHL (who are in charge of the POC database) will get back to you soon on this matter. Best regards, Katica On Wed, 4 Aug 2004, Gregorio, Sergio (IRRI) wrote: > To Whom it may concern: > > I'd like to follow up an earlier query. I recently downloaded copies of > your Plant Ontologies. Upon examining your definition and ontology > structure files, I noticed you have entries (terms) appearing in the > structure file but not in the definition files. I would like to know how > this came to be and what you would recommend that I do, if I wish to load > your data into say, a MySQL database using the Chado schema. > > We would certainly appreciate any clarification on the matter. Thank you > very much! > > Regards, > > Serge Gregorio > -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From katica at acoma.Stanford.EDU Mon Aug 9 14:38:00 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 9 Aug 2004 11:38:00 -0700 (PDT) Subject: POC In-Reply-To: <000801c34fe6$c646b1a0$dc1638d2@x6u2q3> Message-ID: Dear Dr, Wahid, I apologize for the delayed response to your e-mail. Thank you for your complements and for the encouraging words to POC. We all appreciate it. No, we haven't published definitions that are included the Plant Structure Ontology yet, but you can access the Angiosperm Phylogeny Web Glossary either through the University of Missouri at St Louis link (http://www.mobot.org/MOBOT/Research/APweb/top/glossaryA_H.html), or, you can also access it from our POC web site: http://www.plantontology.org/docs/otherdocs/resources.html. Our structured vocabulary (Plant Ontology) is meant to be a web-based tool, and you can download ontology and definition files from our web site. We are planning to publish our work on Plant Ontology very soon, and this will be announced on the POC web site (News section) later this year. I am very pleased to hear that our Plant Ontology is useful as a teaching tool. Now that ontology is out, its educational aspect is certainly something we will be paying more attention in near future. Best regards, Katica On Tue, 22 Jul 2003, Abdul Wahid wrote: > POC is a great effort and should be continued. This is highly useful to teachers as well as students. Have you published the plant vocabolary in the form of book. If yes, can you provide a copy of that. > > Best regards. > > Dr. A. Wahid. > -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From shuly at cshl.edu Wed Aug 11 01:16:28 2004 From: shuly at cshl.edu (Shuly) Date: Wed, 11 Aug 2004 01:16:28 -0400 Subject: Query on PO In-Reply-To: <2A491C94FFBC5843A212A69CBEA5CEC7328DB0@IRRIMAIL.irri.cgiar.org> References: <2A491C94FFBC5843A212A69CBEA5CEC7328DB0@IRRIMAIL.irri.cgiar.org> Message-ID: <4119ABAC.2050402@cshl.org> Hi Sergio, My name is Shuly, and I am responsible for the technical aspect of the PO database and data uploads. We are currently using the GO schema and the go-dev package to generate the schemas and upload PO data into the database.. You can find the go-dev package on the geneontology web site, download it from SourceForge, or get it in the monthly release of the GO. I am afraid we don't have the specific PO documentation on that particular aspect yet, but you can find suitable info on the geneontology web site: http://www.godatabase.org/dev/sql/doc/godb-sql-doc.html. Switching to the chado schema is one of the future directions of GO, but I am not sure where is stands at the moment. Shuly. Gregorio, Sergio (IRRI) wrote: > To Whom it may concern: > > I'd like to follow up an earlier query. I recently downloaded copies > of your Plant Ontologies. Upon examining your definition and ontology > structure files, I noticed you have entries (terms) appearing in the > structure file but not in the definition files. I would like to know > how this came to be and what you would recommend that I do, if I wish > to load your data into say, a MySQL database using the Chado schema. > > We would certainly appreciate any clarification on the matter. Thank > you very much! > > Regards, > > Serge Gregorio packa -------------- next part -------------- An HTML attachment was scrubbed... URL: From rhee at acoma.Stanford.EDU Wed Aug 11 13:25:39 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Wed, 11 Aug 2004 10:25:39 -0700 (PDT) Subject: Informatics meeting In-Reply-To: <4119ABAC.2050402@cshl.org> Message-ID: Hi, Shuly I was planning on going to the Genome informatics meeting but have decided not to go in the end. I am too burnt from traveling. Sue ----------------------------------------------------------------------------- Sue Rhee rhee at acoma.stanford.edu The Arabidopsis Information Resource URL: www.arabidopsis.org Carnegie Institution of Washington FAX: +1-650-325-6857 Department of Plant Biology Tel: +1-650-325-1521 ext. 251 260 Panama St. Stanford, CA 94305 U.S.A. ----------------------------------------------------------------------------- From katica at acoma.Stanford.EDU Mon Aug 16 13:26:52 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 16 Aug 2004 10:26:52 -0700 (PDT) Subject: Changes in tentative date for POC in-person meeting Message-ID: Hi all, It turned out that the early November date for our in-person meeting is not going to work, Pankaj will be away in November. The late October one is now only alternative date. So, let's see if Oct 27-30 would be OK with everyone (it's Wed to Sat). Please let me know asap, we are running out of available dates; it seems that most of us are going to have a busy schedule in fall. Katica From katica at acoma.Stanford.EDU Mon Aug 16 13:32:15 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 16 Aug 2004 10:32:15 -0700 (PDT) Subject: Please ignore the last messsage Message-ID: The last message I sent was addressed to po-dev by mistake. That was a POC internal message. I appologize for the inconvenience. Katica -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From PolaccoM at missouri.edu Mon Aug 16 14:20:05 2004 From: PolaccoM at missouri.edu (Mary Polacco) Date: Mon, 16 Aug 2004 13:20:05 -0500 Subject: Changes in tentative date for POC in-person meeting In-Reply-To: Message-ID: Katica, SO far this works for me, mary On 8/16/04 12:26 PM, "Katica Ilic" wrote: > So, let's see if Oct 27-30 would be OK From lstein at cshl.edu Mon Aug 16 17:10:47 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 16 Aug 2004 17:10:47 -0400 Subject: Changes in tentative date for POC in-person meeting In-Reply-To: References: Message-ID: <200408161710.47667.lstein@cshl.edu> Unfortunately I am completely unavailable from Oct 20 through the end of November due to teaching commitments, but please go ahead without me. Lincoln On Monday 16 August 2004 02:20 pm, Mary Polacco wrote: > Katica, > SO far this works for me, > mary > > On 8/16/04 12:26 PM, "Katica Ilic" wrote: > > So, let's see if Oct 27-30 would be OK -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 From r.bruskiewich at cgiar.org Tue Aug 17 19:52:37 2004 From: r.bruskiewich at cgiar.org (Bruskiewich, Richard (IRRI)) Date: Tue, 17 Aug 2004 16:52:37 -0700 Subject: Changes in tentative date for POC in-person meeting Message-ID: <2A491C94FFBC5843A212A69CBEA5CEC78DA1E3@IRRIMAIL.irri.cgiar.org> Hi Katica, Where is this meeting going to be held? Gloria is going to be in North America for the SOFG meeting FROM October 23 - 26, 2004 at the University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA. If the POC is 27-30, she might be able to participate as an observer/collaborator. Richard ============================================== Richard Bruskiewich, PhD Senior Bioinformatics Specialist International Rice Research Institute DAPO 7777, Metro Manila, Philippines r.bruskiewich at cgiar.org Web: www.irri.org Tel: +63-2-580-5600 Fax: +63-2-580-5699 ============================================ -----Original Message----- From: Katica Ilic [mailto:katica at acoma.Stanford.EDU] Sent: Tuesday, August 17, 2004 1:27 AM To: po-dev at plantontology.org Subject: Changes in tentative date for POC in-person meeting Hi all, It turned out that the early November date for our in-person meeting is not going to work, Pankaj will be away in November. The late October one is now only alternative date. So, let's see if Oct 27-30 would be OK with everyone (it's Wed to Sat). Please let me know asap, we are running out of available dates; it seems that most of us are going to have a busy schedule in fall. Katica From rhee at acoma.Stanford.EDU Mon Aug 23 18:43:26 2004 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 23 Aug 2004 15:43:26 -0700 (PDT) Subject: Changes in tentative date for POC in-person meeting In-Reply-To: Message-ID: Should be OK with me. Sue On Mon, 16 Aug 2004, Katica Ilic wrote: > > Hi all, > > It turned out that the early November date for our in-person meeting is > not going to work, Pankaj will be away in November. The late October > one is now only alternative date. So, let's see if Oct 27-30 would be OK > with everyone (it's Wed to Sat). Please let me know asap, we are running > out of available dates; it seems that most of us are going to have a busy > schedule in fall. > > Katica > ----------------------------------------------------------------------------- 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 feedback_submission at brie4.plantontology.org Wed Aug 25 12:15:09 2004 From: feedback_submission at brie4.plantontology.org (feedback_submission at brie4.plantontology.org) Date: Wed, 25 Aug 2004 12:15:09 -0400 Subject: Feedback Submission from Plant Ontology Live Site Message-ID: <200408251615.i7PGF9cn026865@brie4.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& comments: Is this the best URL to use to lookup a term when linking from an external database such as MaizeGDB? In particular when I wish to be able to access the PO associations for that term. What about 'sensu' generics, eg anther. name: Mary Polacco email: PolaccoM at missouri.edu organization: send_feedback: Send your feedback From pj37 at cornell.edu Wed Aug 25 12:34:11 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 25 Aug 2004 12:34:11 -0400 Subject: Feedback Submission from Plant Ontology Live Site In-Reply-To: <200408251615.i7PGF9cn026865@brie4.cshl.org> References: <200408251615.i7PGF9cn026865@brie4.cshl.org> Message-ID: <412CBF83.5040000@cornell.edu> I guess the best would be the following. These are taking the user to a query result page. http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=anther http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=anther (sensu Zea) http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0005360 These would allow a generic search for "anther" or to a specific one "anther (sensu Zea)" or by a term_accession (=term_id from flat files). The link provided by you is going directly to the term detail page where many of the options are not available. -Pankaj feedback_submission at brie4.plantontology.org wrote: > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& > > comments: Is this the best URL to use to lookup a term when linking from an external database such as MaizeGDB? > > In particular when I wish to be able to access the PO associations for that term. > > What about 'sensu' generics, eg anther. > > name: Mary Polacco > > email: PolaccoM at missouri.edu > > organization: > > send_feedback: Send your feedback > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From polaccom at missouri.edu Wed Aug 25 13:02:28 2004 From: polaccom at missouri.edu (Polacco, Mary L.) Date: Wed, 25 Aug 2004 12:02:28 -0500 Subject: Feedback Submission from Plant Ontology Live Site Message-ID: <26C435999318FC49A6AB243CC8ACA623091A39@UM-EMAIL07.um.umsystem.edu> Thanks Pankaj. Another question, are there any entries with associations from Gramene and TAIR - on public or dev sites? -mary -----Original Message----- From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal Sent: Wed 8/25/2004 11:34 AM To: po-dev at plantontology.org Subject: Re: Feedback Submission from Plant Ontology Live Site I guess the best would be the following. These are taking the user to a query result page. http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=anther http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=anther (sensu Zea) http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0005360 These would allow a generic search for "anther" or to a specific one "anther (sensu Zea)" or by a term_accession (=term_id from flat files). The link provided by you is going directly to the term detail page where many of the options are not available. -Pankaj feedback_submission at brie4.plantontology.org wrote: > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& > > comments: Is this the best URL to use to lookup a term when linking from an external database such as MaizeGDB? > > In particular when I wish to be able to access the PO associations for that term. > > What about 'sensu' generics, eg anther. > > name: Mary Polacco > > email: PolaccoM at missouri.edu > > organization: > > send_feedback: Send your feedback > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 3490 bytes Desc: not available URL: From pj37 at cornell.edu Wed Aug 25 13:25:55 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 25 Aug 2004 13:25:55 -0400 Subject: Feedback Submission from Plant Ontology Live Site In-Reply-To: <26C435999318FC49A6AB243CC8ACA623091A39@UM-EMAIL07.um.umsystem.edu> References: <26C435999318FC49A6AB243CC8ACA623091A39@UM-EMAIL07.um.umsystem.edu> Message-ID: <412CCBA3.6070505@cornell.edu> Not yet. Gramene is expected to do a transition in the September for its db build. Hopefully by the end of October we will be in a position to submit the associations for POC. Katica has similar plans for TAIR. Sometime back we tried with a small set of associations from TAIR and Gramene to test the db and AmiGo. It worked, however, those were discarded at the time of public release. I may be able to help you more if you can tell us more about your concerns. Thanks Pankaj Polacco, Mary L. wrote: > Thanks Pankaj. > Another question, are there any entries with associations from Gramene and TAIR - on public or dev sites? > -mary > > -----Original Message----- > From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal > Sent: Wed 8/25/2004 11:34 AM > To: po-dev at plantontology.org > Subject: Re: Feedback Submission from Plant Ontology Live Site > > I guess the best would be the following. These are taking the user to a > query result page. > > http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=anther > > http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=anther > (sensu Zea) > > http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0005360 > > These would allow a generic search for "anther" or to a specific one > "anther (sensu Zea)" or by a term_accession (=term_id from flat files). > The link provided by you is going directly to the term detail page where > many of the options are not available. > > -Pankaj > > > > feedback_submission at brie4.plantontology.org wrote: > > >> *** Feedback from Plant Ontology Live Site *** >> >>refer_to_url: http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& >> >>comments: Is this the best URL to use to lookup a term when linking from an external database such as MaizeGDB? >> >>In particular when I wish to be able to access the PO associations for that term. >> >>What about 'sensu' generics, eg anther. >> >>name: Mary Polacco >> >>email: PolaccoM at missouri.edu >> >>organization: >> >>send_feedback: Send your feedback >> >> > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From polaccom at missouri.edu Wed Aug 25 14:18:09 2004 From: polaccom at missouri.edu (Polacco, Mary L.) Date: Wed, 25 Aug 2004 13:18:09 -0500 Subject: Feedback Submission from Plant Ontology Live Site Message-ID: <26C435999318FC49A6AB243CC8ACA623091A3B@UM-EMAIL07.um.umsystem.edu> Pankaj, No concerns other than my perennial difficulty with generic sensu ;) On a related topic, I am working with MaizeGDB folks now on deliverying the associations files for Genes and Stocks. Are we doing any other categories? Is the format basically the same as for GO? -mary ----Original Message----- From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal Sent: Wed 8/25/2004 12:25 PM To: po-dev at plantontology.org Subject: Re: Feedback Submission from Plant Ontology Live Site Not yet. Gramene is expected to do a transition in the September for its db build. Hopefully by the end of October we will be in a position to submit the associations for POC. Katica has similar plans for TAIR. Sometime back we tried with a small set of associations from TAIR and Gramene to test the db and AmiGo. It worked, however, those were discarded at the time of public release. I may be able to help you more if you can tell us more about your concerns. Thanks Pankaj Polacco, Mary L. wrote: > Thanks Pankaj. > Another question, are there any entries with associations from Gramene and TAIR - on public or dev sites? > -mary > > -----Original Message----- > From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal > Sent: Wed 8/25/2004 11:34 AM > To: po-dev at plantontology.org > Subject: Re: Feedback Submission from Plant Ontology Live Site > > I guess the best would be the following. These are taking the user to a > query result page. > > http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=anther > > http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=anther > (sensu Zea) > > http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0005360 > > These would allow a generic search for "anther" or to a specific one > "anther (sensu Zea)" or by a term_accession (=term_id from flat files). > The link provided by you is going directly to the term detail page where > many of the options are not available. > > -Pankaj > > > > feedback_submission at brie4.plantontology.org wrote: > > >> *** Feedback from Plant Ontology Live Site *** >> >>refer_to_url: http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& >> >>comments: Is this the best URL to use to lookup a term when linking from an external database such as MaizeGDB? >> >>In particular when I wish to be able to access the PO associations for that term. >> >>What about 'sensu' generics, eg anther. >> >>name: Mary Polacco >> >>email: PolaccoM at missouri.edu >> >>organization: >> >>send_feedback: Send your feedback >> >> > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 4086 bytes Desc: not available URL: From ap343 at cornell.edu Thu Aug 26 16:04:22 2004 From: ap343 at cornell.edu (Anuradha Pujar) Date: Thu, 26 Aug 2004 16:04:22 -0400 (EDT) Subject: Gramene mapping Message-ID: <4298.128.253.246.53.1093550662.squirrel@128.253.246.53> Hello, After mapping gramene anatomy, a list of unmapped terms has been made (find attached) a second list containing some terms to which synonyms can be assigned in POC is also attached. Please give your feedback as to whether these unmapped terms have to be created as new term, raised toa generic term or be excluded. Thanks anu -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: def for GR_POC1.txt URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: list of terms with POC synonym.txt URL: From ap343 at cornell.edu Thu Aug 26 16:25:16 2004 From: ap343 at cornell.edu (Anuradha Pujar) Date: Thu, 26 Aug 2004 16:25:16 -0400 (EDT) Subject: Vascular bundle Message-ID: <4371.128.253.246.53.1093551916.squirrel@128.253.246.53> Hello I may be picking on an old debate, but i would like to know the response for the introduction of the term 'vascular bundle' into POC. anu From katica at acoma.Stanford.EDU Thu Aug 26 17:04:50 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 26 Aug 2004 14:04:50 -0700 (PDT) Subject: Vascular bundle In-Reply-To: <4371.128.253.246.53.1093551916.squirrel@128.253.246.53> Message-ID: Anu, We had this term in PO and obsoleted it back in May, but somehow, it didn't make it to the obsolete node. The reason for obsoleting it was that it was a vaguely defined term (if I remmber correctly). Katica On Thu, 26 Aug 2004, Anuradha Pujar wrote: > Hello > > > I may be picking on an old debate, but i would like to know the response > for the introduction of the term 'vascular bundle' into POC. > > anu > > -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From pj37 at cornell.edu Thu Aug 26 17:18:10 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 26 Aug 2004 17:18:10 -0400 Subject: Vascular bundle In-Reply-To: References: Message-ID: <412E5392.7090301@cornell.edu> Hi, Now we need this term for the annotation of glutamate synthase from rice. reference: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11373307 as well as some of the phenotypes are there too http://www.gramene.org/db/qtl/qtl_display?query=*vascular+bundle*&search_field=trait_name&species=&submit=Submit -Pankaj Katica Ilic wrote: > Anu, > > We had this term in PO and obsoleted it back in May, but somehow, it > didn't make it to the obsolete node. The reason for obsoleting it was > that it was a vaguely defined term (if I remmber correctly). > > Katica > > > On Thu, 26 Aug 2004, Anuradha Pujar wrote: > > >>Hello >> >> >>I may be picking on an old debate, but i would like to know the response >>for the introduction of the term 'vascular bundle' into POC. >> >>anu >> >> > > > -------------------------------------------------------------------------- > Katica Ilic katica at acoma.stanford.edu > The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 > Carnegie Institution of Washington FAX: (650) 325-6857 > Department of Plant Biology URL: http://arabidopsis.org/ > 260 Panama St. > Stanford, CA 94305 > U.S.A. > -------------------------------------------------------------------------- > > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From katica at acoma.Stanford.EDU Thu Aug 26 19:13:22 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 26 Aug 2004 16:13:22 -0700 (PDT) Subject: Vascular bundle In-Reply-To: <412E5392.7090301@cornell.edu> Message-ID: Pankaj, In the first publication (J Exp Bot, Tobin and Yamaya, 2001), they are indeed reffering to vascular bundle, but once you see the micrographs, (though it's not very clear), you can perhaps annotate it to a more granular term (see fig 6 in the paper). If you can't use more granular term, the appropriate PO term that can be used here is PO:0020138 : leaf vein Definition: A strand of vascular tissue in the leaf blade. This definition nicely describes what they are showing it the manuscript. As for the second link, I didn't understand why you need to use 'vascular bundle' specificaly. Can't you just use coresponding PO term (leaf vein or similar)? I thought we agreed to look into PO first and see what is already there, before we started considering adding new terms. In this particular case, it seems to me we are going in circles (since we already got rid of term 'vascular bundle'). Katica On Thu, 26 Aug 2004, Pankaj Jaiswal wrote: > Hi, > > Now we need this term for the annotation of glutamate synthase from rice. > reference: > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11373307 > > as well as some of the phenotypes are there too > http://www.gramene.org/db/qtl/qtl_display?query=*vascular+bundle*&search_field=trait_name&species=&submit=Submit > > -Pankaj > > Katica Ilic wrote: > > > Anu, > > > > We had this term in PO and obsoleted it back in May, but somehow, it > > didn't make it to the obsolete node. The reason for obsoleting it was > > that it was a vaguely defined term (if I remmber correctly). > > > > Katica > > > > > > On Thu, 26 Aug 2004, Anuradha Pujar wrote: > > > > > >>Hello > >> > >> > >>I may be picking on an old debate, but i would like to know the response > >>for the introduction of the term 'vascular bundle' into POC. > >> > >>anu > >> > >> > > > > > > -------------------------------------------------------------------------- > > Katica Ilic katica at acoma.stanford.edu > > The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 > > Carnegie Institution of Washington FAX: (650) 325-6857 > > Department of Plant Biology URL: http://arabidopsis.org/ > > 260 Panama St. > > Stanford, CA 94305 > > U.S.A. > > -------------------------------------------------------------------------- > > > > > > > > -- > ************************ > Pankaj Jaiswal, PhD > G15-Bradfield Hall > Dept. of Plant Breeding > Cornell University > Ithaca, NY-14853, USA > > Tel: +1-607-255-3103 > +1-607-255-4109 > Fax: +1-607-255-6683 > http://www.gramene.org > ************************ > -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From matthews at greengenes.cit.cornell.edu Thu Aug 26 20:49:27 2004 From: matthews at greengenes.cit.cornell.edu (Dave Matthews) Date: Thu, 26 Aug 2004 20:49:27 -0400 (EDT) Subject: Vascular bundle Message-ID: <200408270049.i7R0nRM9026642@greengenes.cit.cornell.edu> Hi Katica, I'm out of my league here, I'm no anatomist. But I think a vascular bundle is quite different from a vein. Refers to a feature that's specific for C4 plants. Containing a cell type called bundle sheath cells that also are found only in C4 plants. Searching PubMed for "vascular bundle C4" found some abstracts that might be worth peeking at. E.g. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11432917 - Dave > Date: Thu, 26 Aug 2004 16:13:22 -0700 (PDT) > From: Katica Ilic > > Pankaj, > > In the first publication (J Exp Bot, Tobin and Yamaya, 2001), they are > indeed reffering to vascular bundle, but once you see the micrographs, > (though it's not very clear), you can perhaps annotate it to a more > granular term (see fig 6 in the paper). If you can't use more granular term, > the appropriate PO term that can be used here is > > PO:0020138 : leaf vein > Definition: A strand of vascular tissue in the leaf blade. > > This definition nicely describes what they are showing it the manuscript. > > As for the second link, I didn't understand why you need to use > 'vascular bundle' specificaly. Can't you just use coresponding PO term > (leaf vein or similar)? > > I thought we agreed to look into PO first and see what is already there, > before we started considering adding new terms. In this particular case, > it seems to me we are going in circles (since we already got rid of term > 'vascular bundle'). > > Katica ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ David E. Matthews, Ph.D. USDA-ARS Plant Genome Database Curator Cornell University Email: matthews at greengenes.cit.cornell.edu Department of Plant Breeding 409 Bradfield Hall Phone: 607-255-9951 (Voice) Ithaca, New York 14853, USA 607-255-6683 (Fax) From katica at acoma.Stanford.EDU Thu Aug 26 21:29:19 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 26 Aug 2004 18:29:19 -0700 (PDT) Subject: Gramene mapping In-Reply-To: <4298.128.253.246.53.1093550662.squirrel@128.253.246.53> Message-ID: Hi Anu and Pankaj, Attached is my response to the list of Gramene terms that are unmapped to PO. There are very few terms that need to be introduced to PO, others are either subcellular structures, developmental stages terms, obsoleted terms that could be mapped to the existing PO terms, or terms that already have corresponding term in PO (though under different term name). Bottom line here is that we do not want to loose any annotation in Gramene, TAIR or Maize GDB. So, that's why I asked you earlier today for a list of Gramene terms that already have annotations associated to them. We don't have to introduce every term from Gramene and TAIR to PO. I think we all agreed back in January in San Diego and said " We do need to go down to granularity to allow species-specific annotation" (quoted from the minutes). However, we also said that not all species-specific terms would need to be introduced to the PO. Could you send me the list of Gramene terms 'with current annotations'? We can start from there and go up to include terms that are needed in near future for annotation purposes. Attached is your list of terms with my comments in red italic font. Underlined are 'problematic terms'(in my humble opinion). I may have omitted comments to some terms, since I commented only the most obvious. Once you guys 'weed the list out', it will be easier to talk about terms that need to be introduced in PO. Greetings, Katica On Thu, 26 Aug 2004, Anuradha Pujar wrote: > Hello, > > After mapping gramene anatomy, a list of unmapped terms has been made > (find attached) a second list containing some terms to which synonyms can > be assigned in POC is also attached. Please give your feedback as to > whether these unmapped terms have to be created as new term, raised toa > generic term or be excluded. > > Thanks > anu -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- -------------- next part -------------- {\rtf1\ansi\ansicpg1252\uc1 \deff0\deflang1033\deflangfe1033{\fonttbl{\f0\froman\fcharset0\fprq2{\*\panose 02020603050405020304}Times New Roman;}{\f1\fswiss\fcharset0\fprq2{\*\panose 020b0604020202020204}Arial;} {\f66\froman\fcharset238\fprq2 Times New Roman CE;}{\f67\froman\fcharset204\fprq2 Times New Roman Cyr;}{\f69\froman\fcharset161\fprq2 Times New Roman Greek;}{\f70\froman\fcharset162\fprq2 Times New Roman Tur;} {\f71\froman\fcharset177\fprq2 Times New Roman (Hebrew);}{\f72\froman\fcharset178\fprq2 Times New Roman (Arabic);}{\f73\froman\fcharset186\fprq2 Times New Roman Baltic;}{\f74\fswiss\fcharset238\fprq2 Arial CE;}{\f75\fswiss\fcharset204\fprq2 Arial Cyr;} {\f77\fswiss\fcharset161\fprq2 Arial Greek;}{\f78\fswiss\fcharset162\fprq2 Arial Tur;}{\f79\fswiss\fcharset177\fprq2 Arial (Hebrew);}{\f80\fswiss\fcharset178\fprq2 Arial (Arabic);}{\f81\fswiss\fcharset186\fprq2 Arial Baltic;}} {\colortbl;\red0\green0\blue0;\red0\green0\blue255;\red0\green255\blue255;\red0\green255\blue0;\red255\green0\blue255;\red255\green0\blue0;\red255\green255\blue0;\red255\green255\blue255;\red0\green0\blue128;\red0\green128\blue128;\red0\green128\blue0; 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the pollen grain emerges through the aperture. }{\i\f1\cf17 (PO has mapping term)}{\f1 \par }\pard\plain \s1\ql \li0\ri0\sl360\slmult1\keepn\widctlpar\aspalpha\aspnum\faauto\outlinelevel0\adjustright\rin0\lin0\itap0 \b\f1\fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {PO:0020018 : germination pore \par }\pard\plain \ql \li0\ri0\sl360\slmult1\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\f1\ul Atactostele:}{\f1 A stele consisting of vascular bundles scattered throughout the ground tissue as in the Monocots}{ \par }{\f1\ul Bran:}{\f1 The pericarp, testa and usually the aleurone layer of cereal seeds which are removed in milling. }{\i\f1\cf17 (This is not a botanical term, and I doubted that any gene would need to be annotated to this term \endash KI) \par }{\f1\ul Casparian strip: }{\f1 A band like wall formation within primary walls that contains suberin and lignin; typical of endodermal cells, in which it occurs in radial and transverse anticlinal walls. }{\i\f1\cf17 (this is a subcellular structure \endash KI)}{\f1 \par }{\f1\ul Cotyledon primordium:}{\f1 The earliest differentiated state of a cotyledon. }{\f1\cf17 (}{\i\f1\cf17 this is really a dev stage term \endash KI)}{\i\f1 \par }{\f1 Crown: Located between the coleoptile and the mesocotyl, the crown contains the growing point where the rest of the plant will begin to form and the nodes where the nodal or permanent roots will form. \par }{\f1\ul Cuticle:}{\f1 It is a continuous layer of cutin secreted by the epidermis, it prevents plant desiccation by being impervious to water and gas exchange and covers the aerial parts of the plant body, broken only by stomata and lenticels}{ \i\f1\cf17 . (this is perhaps GO term, though I didn\rquote t find it in GO - KI)}{\f1 \par Embryonic ground tissue: Ground tissue (parenchymatous) layers found in the embryo. \par }{\f1\ul Fibrous root:}{\f1 Roots characterized by many similar branching roots of common length and thickness. Generally not highly adapted for food storage. \endash plant anatomy glossary. \par }{\f1\ul Gametophytic cell:}{\f1 A haploid (1n) cell developing into a male or female gametophyte in heterosporous plants. Synonym for gametophyte. \par }{\i\f1\cf17 (Which one, megaspore or microspore? WE have both in PO! \endash KI)}{\i\f1 \par }{\f1\ul First embryonic leaf:}{\f1 The first leaf of the plant, often found developing with the embryo (}{\i\f1\cf17 this is a dev stage term \endash KI)}{\f1 \par }{\f1\ul First leaf:}{\f1 The first mature leaf present just below the flag leaf in a cereal crop plant.}{\i\f1\cf17 (this is a dev stage term \endash KI)}{\f1 \par }{\f1\ul Floral primordium:}{\f1 Primordial tissue giving rise to the floral whorls.}{\i\f1\cf17 (this is a dev stage term \endash KI)}{\f1 \par }{\b\f1\ul Laticiferous vessel:}{\f1 An articulated laticifer in which the cell walls between cells are partially or wholly lacking. Plant anatomy glossary}{\i\f1\cf17 (PO has mapping term)}{\f1 \par }\pard\plain \s2\ql \li0\ri0\sl360\slmult1\keepn\widctlpar\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0 \b\i\f1\fs24\cf17\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {PO:0006221 : articulated laticifer cell}{\i0 \par }\pard\plain \ql \li0\ri0\sl360\slmult1\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\f1\ul Leaflet midvein:}{\f1 The central conducting and supporting structure of the blade of a leaflet of a compound leaf. \par }{\f1\ul Leaflet veinlet:}{\f1 Branched secondary veinlets conducting and supporting structure of the blade of a leaflet. \par }{\f1\ul Medine:}{\f1 Layer between the exine and intine. \par }{\f1\ul Nucellar cells:}{\f1 Crushed nucellar cells present in multiple layers. }{\i\f1\cf17 (Sorry, I have no idea what this is. We do have term nucellus in PO:0020020 , def: Subepidermal tissue in the ovule surrounding the megasporocyte. - KI)}{\f1 \par }{\f1\ul Organ primordium:}{\f1 An organ or a part in its most rudimentary form or stage of development. \par }{\f1\ul Ovary inner epidermis:}{\f1 Inner epidermal layer of the ovary wall.}{\i\f1\cf17 (Obsoleted, I suppose this can be annotated to PO:0006063 : ovary epidermis, but I would need to see the original paper first\endash KI)}{\f1 \par Ovary locule : An opening or cavity within ovary. Plant anatomy glossary. \par }{\f1\ul Ovary outer epidermis:}{\f1 Outer epidermal layer of the ovary wall.}{\i\f1\cf17 (Obsoleted, same as for inner epidermis \endash KI)}{\f1 \par Ovary parenchyma: Parenchyma layer of the ovary wall. \par Ovary vascular system: vascular system of the ovary. \par }{\f1\ul Perforation plate:}{\f1 That region of a cell wall which is perforated, and found in a vessel member. Plant anatomy glossary.}{\i\f1\cf17 (this is a subcellular structure \endash KI)}{\f1 \par }{\f1\ul Phloem fiber:}{\f1 Fiber found in phloem parenchyma. }{\i\f1\cf17 (Sorry, I don\rquote t know what phloem fiber is \endash KI)}{\f1 \par Phloem Parenchyma: Parenchyma found in phloem. \par }{\f1\ul Plant organ:}{\f1 Represents the organs and its sub-types in a plant. }{\i\f1\cf17 ( ??? \endash why do you need this term for annotation? We obsoleted it)}{\f1 \par Primary endosperm nucleus: Nucleus resulting from the fusion of the male gamete and two polar nuclei in the central cell of the embryo sac.}{\i\f1\cf17 \par }{\f1 Prop root: Aerial adventitious roots which usually provide support \par Proximal root meristem: Lies next to the quiescent centre of the root tip and participates in the formation of root epidermis, stele and cortex. -Annals of Botany, 79,375-389,1997. \par Replum: Persistent septum after dehiscence of fruits, as in the Brassicaceae \par }{\f1\ul Rhexigenous aerenchyma:}{\f1 Applied to an aerenchyma originating by rupture of cells (}{\i\f1\cf17 We obsoleted it)}{\f1 \par Root primordium: The primordial tissue of the root. \par Sclerenchyma perivascular: Sclerenchyma located along the outer periphery of the vascular cylinder and not originating in the phloem. \par }{\f1\ul Sclerenchyma sclereid cell:}{\f1 Type of sclerenchyma cell that differs from the fiber cell by not being greatly elongated \par }{\f1\ul Sieve plate:}{\f1 Wall of a sieve element with sieve areas.}{\i\f1\cf17 (this is a subcellular structure \endash KI}{\f1 \par Septum: A partition. Plant anatomy glossary. \par Staminal disc: A fleshy, elevated cushion formed from coalesced staminodia or nectaries. \par Stamonodium: Sterile stamen, may be modified as a nectary or petaloid structure. \par Stem vascular system: The vascular system of the stem. \par }{\b\i\f1\ul Stomatal pore:}{\f1 The pore in the epidermis, surrounded by two guard cells. Meant for gaseous exchange.}{\i\f1\cf17 (PO has mapping term)}{\f1 \par }\pard\plain \s2\ql \li0\ri0\sl360\slmult1\keepn\widctlpar\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0 \b\i\f1\fs24\cf17\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {PO:0002000 : stomatal complex \par }\pard\plain \ql \li0\ri0\sl360\slmult1\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\f1\ul Third leaf:}{\f1 The thi rd meture leaf present below the flag leaf in a cereal crop plant.}{\i\f1\cf17 (this is a dev stage term \endash KI)}{\f1 \par }{\f1\ul Vascular bundle:}{\f1 A strand of conducting tissue comprising of phloem, xylem, and cambium.}{\i\f1\cf17 (We obsoleted it)}{\f1 \par }{\f1\ul Xylem cell radial:}{\f1 The secondary xylem cell aligned, forming radial files of cells that are produced from a single cambium initial cell. http://koning.ecsu.ctstateu.edu/plant_biology/secondary.html \par }{\b\f1\ul Xylem fiber libriform:}{\b\f1 }{\f1 A very long xylem fiber with thick walls and simple pits. Plant anatomy glossary. \par }\pard\plain \s2\ql \li0\ri0\sl360\slmult1\keepn\widctlpar\aspalpha\aspnum\faauto\outlinelevel1\adjustright\rin0\lin0\itap0 \b\i\f1\fs24\cf17\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {PO:0000274 : xylem fiber cell \par }\pard\plain \ql \li0\ri0\sl360\slmult1\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 {\f1\ul Xylem parenchyma axial:}{\f1 Parenchyma cells running axially, derived from elongated fusiform cambial cells. \par }{\f1\ul Xylem parenchyma radial:}{\f1 Parenchyma cells extending radially between the secondary xylem and phloem. \par }{\f1\ul Xylem parenchyma radial procumbent:}{\f1 The ray cell with longest diameter arranged radially. \par }{\f1\ul Xylem parenchyma radial upright:}{\f1 The axially elongated cell in radial xylem parenchyma. Appear generally at the upper and lower margins of the ray. \par }{\f1\ul Xylem parenchyma radial homocellular:}{\f1 Xylem ray composed of one type of cell. \par }{\f1\ul Xylem parenchyma radial heterocellular:}{\f1 Xylem ray containing procumbent and upright cells. \par }{\f1\ul Xylem tracheary element wall: \par }{\f1 http://www.mhhe.com/biosci/pae/botany/crang/gloss_top.html \par \par }} From katica at acoma.Stanford.EDU Thu Aug 26 22:05:25 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 26 Aug 2004 19:05:25 -0700 (PDT) Subject: Vascular bundle In-Reply-To: <200408270049.i7R0nRM9026642@greengenes.cit.cornell.edu> Message-ID: Hi Dave, Thanks for your reply. I am so glad to see some action on po-dev. I've always thought that: 1) veins are vascular bundles in the leaves, and 2) vascular bundle is a very broad term applicable to all vascular plants. I have an excellent book chapter writen by my dear former colleague, Nancy Dangler (actually she was my boss when I taught a few lectures in one of her classes) from U of Toronto, entitled: "Developmental aspects of C4 photosyntesis". I will look into this and get back to you. Katica On Thu, 26 Aug 2004, Dave Matthews wrote: > Hi Katica, > > I'm out of my league here, I'm no anatomist. But I think a vascular bundle > is quite different from a vein. Refers to a feature that's specific for > C4 plants. Containing a cell type called bundle sheath cells that also > are found only in C4 plants. Searching PubMed for "vascular bundle C4" > found some abstracts that might be worth peeking at. E.g. > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11432917 > > - Dave > > > Date: Thu, 26 Aug 2004 16:13:22 -0700 (PDT) > > From: Katica Ilic > > > > Pankaj, > > > > In the first publication (J Exp Bot, Tobin and Yamaya, 2001), they are > > indeed reffering to vascular bundle, but once you see the micrographs, > > (though it's not very clear), you can perhaps annotate it to a more > > granular term (see fig 6 in the paper). If you can't use more granular term, > > the appropriate PO term that can be used here is > > > > PO:0020138 : leaf vein > > Definition: A strand of vascular tissue in the leaf blade. > > > > This definition nicely describes what they are showing it the manuscript. > > > > As for the second link, I didn't understand why you need to use > > 'vascular bundle' specificaly. Can't you just use coresponding PO term > > (leaf vein or similar)? > > > > I thought we agreed to look into PO first and see what is already there, > > before we started considering adding new terms. In this particular case, > > it seems to me we are going in circles (since we already got rid of term > > 'vascular bundle'). > > > > Katica > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > David E. Matthews, Ph.D. USDA-ARS Plant Genome Database Curator > Cornell University Email: matthews at greengenes.cit.cornell.edu > Department of Plant Breeding > 409 Bradfield Hall Phone: 607-255-9951 (Voice) > Ithaca, New York 14853, USA 607-255-6683 (Fax) > -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From ap343 at cornell.edu Fri Aug 27 09:42:09 2004 From: ap343 at cornell.edu (Anuradha Pujar) Date: Fri, 27 Aug 2004 09:42:09 -0400 (EDT) Subject: Mapping Message-ID: <3121.128.253.246.53.1093614129.squirrel@128.253.246.53> Hello katica, Thanks for looking into the terms and the response, like i said this is just a list of unmapped terms from gramene, i am working on the annotated terms and will send it when it is ready. bye anu From ap343 at cornell.edu Fri Aug 27 10:15:12 2004 From: ap343 at cornell.edu (Anuradha Pujar) Date: Fri, 27 Aug 2004 10:15:12 -0400 (EDT) Subject: vascular bundle Message-ID: <3202.128.253.246.53.1093616112.squirrel@128.253.246.53> Hello, These are just a couple of references, please have a look. http://www.plantphysiol.org/cgi/content/full/129/3/1019 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14630956 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15258165 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14614507 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12615934 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2102372 anu From pj37 at cornell.edu Fri Aug 27 10:55:50 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Fri, 27 Aug 2004 10:55:50 -0400 Subject: vascular bundle In-Reply-To: <3202.128.253.246.53.1093616112.squirrel@128.253.246.53> References: <3202.128.253.246.53.1093616112.squirrel@128.253.246.53> Message-ID: <412F4B76.3000001@cornell.edu> The purpose for asking this term was, that they are present in all kinds of organs and not just limited to the leaves. In leaves mid veins are representing the vasculature and the leaf VB is a part of that network of vasculature and as Dave pointed out there are many other parts as well. My suggestion is to include this term. If agreed, the other question would be, where should we place it, it's not just a tissue, but contains a lot of tissue types. Thus it is an organized structure or a region in an organ. The proposed structure is i = instance of p = part of Sporophyte --p--vascular bundle -----i--leaf VB -----i--stem VB -----i--root VB -----i--stamen VB -----p--xylem -----p--phloem -----p--cambium --p--shoot -----p--stem --------p--stem VB -----p--leaf --------p--root VB --p--root -----p--root VB I am not sure.... #1 Its true that that the three terms xylem, phloem and cambium are not always part of VB. But as we know the PART of relationship we have suggests that, a child is a partof but not always a partof parent term. Thus this lineage seems correct. #2 Do gametophytes also have VB? Suggested definitions for VB are by Fahn: A strand of conducting tissue By Essau: A strand like part of the vascular system composed of xylem and phloem. occurs in stem, leaf and flower. By Dickison: A strand like association of primary xylem and phloem that extends throughout the plant body. http://www.cogsci.princeton.edu/cgi-bin/webwn?stage=1&word=vascular+bundle a unit strand of the vascular system in stems and leaves of higher plants consisting essentially of xylem and phloem If that is an accepted structure then we may need a further instantiation of the terms xylem, phloem and cambium, because as of now these are the generic terms. But that is a topic for another request to be sent on the mailing list. Thanks Pankaj Anuradha Pujar wrote: > > Hello, > > These are just a couple of references, please have a look. > > > http://www.plantphysiol.org/cgi/content/full/129/3/1019 > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14630956 > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15258165 > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14614507 > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12615934 > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2102372 > > anu > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From ap343 at cornell.edu Fri Aug 27 12:01:54 2004 From: ap343 at cornell.edu (Anuradha Pujar) Date: Fri, 27 Aug 2004 12:01:54 -0400 (EDT) Subject: vascular bundle In-Reply-To: <3202.128.253.246.53.1093616112.squirrel@128.253.246.53> References: <3202.128.253.246.53.1093616112.squirrel@128.253.246.53> Message-ID: <3469.128.253.246.53.1093622514.squirrel@128.253.246.53> > Hello, I should have explained the need for these references in the first mail itself, sorry about that and thanks katica for pointing it out to me. The term vascular bundle seems to be coming up quite often in gene expression studies and the following are just a few papers that i came across. anu > Hello, > > These are just a couple of references, please have a look. > > > http://www.plantphysiol.org/cgi/content/full/129/3/1019 > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14630956 > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15258165 > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14614507 > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12615934 > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2102372 > > anu > > From feedback_submission at brie4.plantontology.org Fri Aug 27 15:33:10 2004 From: feedback_submission at brie4.plantontology.org (feedback_submission at brie4.plantontology.org) Date: Fri, 27 Aug 2004 15:33:10 -0400 Subject: Feedback Submission from Plant Ontology Live Site Message-ID: <200408271933.i7RJXAql018176@brie4.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/download/download.html comments: Iam interested in starting work on a legume developmental and anatomy ontology project. Who do I contact? name: Rex Nelson email: nelsonrt at iastate.edu organization: USDA-ARS CICGR Soybase send_feedback: Send your feedback From peter.stevens at mobot.org Fri Aug 27 17:06:34 2004 From: peter.stevens at mobot.org (Peter Stevens) Date: Fri, 27 Aug 2004 17:06:34 -0400 Subject: vascular bundle In-Reply-To: <412F4B76.3000001@cornell.edu> References: <3202.128.253.246.53.1093616112.squirrel@128.253.246.53> <412F4B76.3000001@cornell.edu> Message-ID: >It is an open question whether gametophytes have vascular tissue - >probably not, but... Vascular bundles in levaes usually do not have cambium, they are closed (no cambium develops); when vascular bundles develop in the stem of broad-leaved angiosperms, they often/usually have cambium (such vascular bundles are called "open"), but not all broad-leaved angiosperms have separate and recognisable vascular bundles; in monocots and things like Ranunculaceae the cauline vasular bundles are also closed. P. >The purpose for asking this term was, that they are present in all >kinds of organs and not just limited to the leaves. > >In leaves mid veins are representing the vasculature and the leaf VB >is a part of that network of vasculature and as Dave pointed out >there are many other parts as well. > >My suggestion is to include this term. If agreed, the other question >would be, where should we place it, it's not just a tissue, but >contains a lot of tissue types. Thus it is an organized structure or >a region in an organ. > >The proposed structure is >i = instance of >p = part of > > >Sporophyte >--p--vascular bundle >-----i--leaf VB >-----i--stem VB >-----i--root VB >-----i--stamen VB >-----p--xylem >-----p--phloem >-----p--cambium >--p--shoot >-----p--stem >--------p--stem VB >-----p--leaf >--------p--root VB >--p--root >-----p--root VB > >I am not sure.... > >#1 >Its true that that the three terms xylem, phloem and cambium are not >always part of VB. > >But as we know the PART of relationship we have suggests that, a >child is a partof but not always a partof parent term. Thus this >lineage seems correct. > >#2 >Do gametophytes also have VB? > > > >Suggested definitions for VB are > >by Fahn: A strand of conducting tissue > >By Essau: A strand like part of the vascular system composed of >xylem and phloem. occurs in stem, leaf and flower. > >By Dickison: A strand like association of primary xylem and phloem >that extends throughout the plant body. > >http://www.cogsci.princeton.edu/cgi-bin/webwn?stage=1&word=vascular+bundle >a unit strand of the vascular system in stems and leaves of higher >plants consisting essentially of xylem and phloem > > > >If that is an accepted structure then we may need a further >instantiation of the terms xylem, phloem and cambium, because as of >now these are the generic terms. But that is a topic for another >request to be sent on the mailing list. > > >Thanks >Pankaj > > > > >Anuradha Pujar wrote: > >> >>Hello, >> >>These are just a couple of references, please have a look. >> >> >>http://www.plantphysiol.org/cgi/content/full/129/3/1019 >> >>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14630956 >> >>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15258165 >>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14614507 >>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12615934 >>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2102372 >> >>anu >> > >-- >************************ >Pankaj Jaiswal, PhD >G15-Bradfield Hall >Dept. of Plant Breeding >Cornell University >Ithaca, NY-14853, USA > >Tel: +1-607-255-3103 > +1-607-255-4109 >Fax: +1-607-255-6683 >http://www.gramene.org >************************ From jitterbug at plantontology.org Fri Aug 27 18:40:29 2004 From: jitterbug at plantontology.org (Katica Ilic) Date: Fri, 27 Aug 2004 18:40:29 -0400 Subject: Soybean ontology (Feedback Submission from Plant Ontology Live Site) (PR#23) Message-ID: <200408272240.i7RMeTYb019293@brie4.cshl.org> Hi Rex, The short answer to your question would be: us at Plant Ontology Consortium. You have definitively contacted the right people. I am happy to hear that you are interested in working on the ontology for soybean. At present time, I am not aware of any ongoing effort in the public sector with respect to developing anatomy and developmental stages ontologies for soybean. However, there is a growing interestin the plant research community and we have often had people asking us about such project. It would help (to give you more specific suggestions and tips) if you could tell me a bit more about the ontology project you have in mind, for instance, a scope of the project. Is it going to be a tool to facilitate ?in-house? projects (for instance, large-scale gene expression profiling), or do you have in mind a comprehensive species-specific ontology that would be freely available for a large number of researches working with soybean (and others as well). In either case, I can offer you help, and since we at POC are open to collaboration and welcome everyone who is genuinely interested in collaborating, we can certainly initiate a dialog by discussing our mutual interests in soybean ontology project. Since the first version of the Plant Structure Ontology was released last month, the current task of the POC is work on the growth and developmental stages ontology, primarily having in mind an integration of Arabidopsis and cereal ontologies for the first release. Starting at the beginning of 2005, we hope to make our two plant ontologies applicable to most of the flowering plants by including other plant species, among others, tomato and legumes (such as Medicago and soybean). Furthermore, over the next two years, POC project will expand its plant-ontology-development effort to include other angiosperms (tomato, barley, cotton and others). At the end, the controlled vocabularies developed by the POC will be generic enough to encompass/cover all the plant model systems; this includes cereals/brassicas/solanaceae/gossypium/legumes. Since I don?t know if you need any specific information about ontology editing tools or ontology structure at this point, I decided to leave it out for now. If you need suggestions and help with the software for editing your ontology, please let me know and don't hesitate to contact us for any other ontology related issues. I would be happy to provide you with information and perhaps give you some suggestions how to build your ontology. If you are interested in collaboration with POC, I would like to discuss such a possibility with you. Best regards, Katica Ilic Katica Ilic, TAIR Curator, E-mail: katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington Fax: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305, U.S.A. From tkellogg at umsl.edu Sat Aug 28 10:10:32 2004 From: tkellogg at umsl.edu (Kellogg, Elizabeth A.) Date: Sat, 28 Aug 2004 09:10:32 -0500 Subject: vascular bundle Message-ID: <7953D8E2E57BF94393CA6B8D2599ADDFFA5927@STL-MAIL2.umsl.edu> Isn't "vascular bundle" simply the term applied to a vein when viewed in cross section? I agree with Katica's earlier message that the term vascular bundle should remain obsolete. The gene in question can be annotated to vein or vascular tissue if it can't be annotated to one of the parts of the vein. I haven't checked the publication myself, but I'd be pretty surpirsed if it were actually expressed in every cell of the vein. If the group decides to un-obsolete (great verb!) the term, then the ontology would have to be considerably more complex than Pankaj outlined earlier. I think it would be more like: Sporophyte --p--vascular bundle -----i--leaf VB -----i--stem VB -----i--root VB -----i--stamen VB -----i--petal VB -----i--sepal VB -----i---etc., one each for every organ -----p--xylem -----p--phloem -----p--cambium -----p--bundle sheath ---------i--mestome sheath ---------i--parenchyma sheath -----p--parenchyma -----p--schlerenchyma --p--shoot -----p--stem --------p--stem VB -----p--leaf --------p--root VB --p--root -----p--root VB Finally, to respond to an earlier message in this thread - veins (vascular bundles) are present in all plants, not just C4s. Toby -----Original Message----- From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal Sent: Fri 8/27/2004 9:55 AM To: po-dev at plantontology.org Cc: Subject: Re: vascular bundle The purpose for asking this term was, that they are present in all kinds of organs and not just limited to the leaves. In leaves mid veins are representing the vasculature and the leaf VB is a part of that network of vasculature and as Dave pointed out there are many other parts as well. My suggestion is to include this term. If agreed, the other question would be, where should we place it, it's not just a tissue, but contains a lot of tissue types. Thus it is an organized structure or a region in an organ. The proposed structure is i = instance of p = part of Sporophyte --p--vascular bundle -----i--leaf VB -----i--stem VB -----i--root VB -----i--stamen VB -----p--xylem -----p--phloem -----p--cambium --p--shoot -----p--stem --------p--stem VB -----p--leaf --------p--root VB --p--root -----p--root VB I am not sure.... #1 Its true that that the three terms xylem, phloem and cambium are not always part of VB. But as we know the PART of relationship we have suggests that, a child is a partof but not always a partof parent term. Thus this lineage seems correct. #2 Do gametophytes also have VB? Suggested definitions for VB are by Fahn: A strand of conducting tissue By Essau: A strand like part of the vascular system composed of xylem and phloem. occurs in stem, leaf and flower. By Dickison: A strand like association of primary xylem and phloem that extends throughout the plant body. http://www.cogsci.princeton.edu/cgi-bin/webwn?stage=1&word=vascular+bundle a unit strand of the vascular system in stems and leaves of higher plants consisting essentially of xylem and phloem If that is an accepted structure then we may need a further instantiation of the terms xylem, phloem and cambium, because as of now these are the generic terms. But that is a topic for another request to be sent on the mailing list. Thanks Pankaj Anuradha Pujar wrote: > > Hello, > > These are just a couple of references, please have a look. > > > http://www.plantphysiol.org/cgi/content/full/129/3/1019 > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14630956 > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15258165 > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14614507 > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12615934 > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2102372 > > anu > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 4456 bytes Desc: not available URL: From msachs at uiuc.edu Sat Aug 28 17:07:08 2004 From: msachs at uiuc.edu (Marty Sachs) Date: Sat, 28 Aug 2004 16:07:08 -0500 Subject: aleurone (was :RE: Feedback Submission from Plant Ontology Live Site) In-Reply-To: <26C435999318FC49A6AB243CC8ACA623091A39@UM-EMAIL07.um.umsystem.edu> References: <26C435999318FC49A6AB243CC8ACA623091A39@UM-EMAIL07.um.umsystem.edu> Message-ID: Where did the definition for aleurone.... The outermost endosperm tissue of the seeds, its cells being characterized by presence of protein bodies containing seed storage proteins. ....contained in... http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0005360 ...and... http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& ....come from? My understanding is more in line with: From: http://www.wheatbp.net/glossary.htm aleurone (Aleurone layer). The outermost cell layer of the endosperm, usually only one cell thick in wheat and the only endosperm tissue alive at maturity. The cells of this layer are responsible for the de-novo synthesis of enzymes needed at germination. At least in maize, 'protein bodies containing seed storage proteins' are in the endosperm proper. -Marty >From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal >Sent: Wed 8/25/2004 11:34 AM >To: po-dev at plantontology.org >Subject: Re: Feedback Submission from Plant Ontology Live Site > > >http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0005360 > >These would allow a generic search for "anther" or to a specific one >"anther (sensu Zea)" or by a term_accession (=term_id from flat files). >The link provided by you is going directly to the term detail page where >many of the options are not available. > >-Pankaj > > > >feedback_submission at brie4.plantontology.org wrote: > >> *** Feedback from Plant Ontology Live Site *** >> > > refer_to_url: >http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& > > >> comments: Is this the best URL to use to lookup a term when >>linking from an external database such as MaizeGDB? >> >> In particular when I wish to be able to access the PO associations >>for that term. >> >> What about 'sensu' generics, eg anther. >> >> name: Mary Polacco >> >> email: PolaccoM at missouri.edu >> >> organization: >> >> send_feedback: Send your feedback >> >> > >-- >************************ >Pankaj Jaiswal, PhD >G15-Bradfield Hall >Dept. of Plant Breeding >Cornell University >Ithaca, NY-14853, USA > >Tel: +1-607-255-3103 > +1-607-255-4109 >Fax: +1-607-255-6683 >http://www.gramene.org >************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Mon Aug 30 09:32:39 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 30 Aug 2004 09:32:39 -0400 Subject: vascular bundle In-Reply-To: <7953D8E2E57BF94393CA6B8D2599ADDFFA5927@STL-MAIL2.umsl.edu> References: <7953D8E2E57BF94393CA6B8D2599ADDFFA5927@STL-MAIL2.umsl.edu> Message-ID: <41332C77.6080709@cornell.edu> Kellogg, Elizabeth A. wrote: > Isn't "vascular bundle" simply the term applied to a vein when viewed in cross section? > I agree with Katica's earlier message that the term vascular bundle should remain obsolete. > The gene in question can be annotated to vein or vascular tissue if it can't be > annotated to one of the parts of the vein. I haven't checked the publication myself, but I'd be pretty > surpirsed if it were actually expressed in every cell of the vein. > I don't think so. As a curator I would be very cautious on making such a statement and extrapolating the information provided by the author. In the first instance, I would go by the authors suggestions. This is also a sort of leverage given to the curator since he/she may not be an expert in plant anatomy and by having a term like this the curator still has an option of doing the correct annotation as well as the user finding the right query term. Another argument is that from the top, (intact tissue) and not the section, it is hard to tell whether the location of the expressed gene as we are suggesting to annotate to vein (only for leaf) is actually expressed in bundle sheath/surrounding bundle sheath extensions or anywhere inside the leaf VB. This was just a case of leaf VB/vein, but in other parts, I doubt if people call it veins. Its either Vascular bundle/tissue/strand. > If the group decides to un-obsolete (great verb!) the term, then the ontology would > have to be considerably more complex than Pankaj outlined earlier. I think it would be more like: > > Sporophyte > --p--vascular bundle > -----i--leaf VB > -----i--stem VB > -----i--root VB > -----i--stamen VB > -----i--petal VB > -----i--sepal VB > -----i---etc., one each for every organ I agree on this, the example I gave was just a simple representation. > -----p--xylem > -----p--phloem > -----p--cambium > -----p--bundle sheath > ---------i--mestome sheath > ---------i--parenchyma sheath > -----p--parenchyma > -----p--schlerenchyma > --p--shoot > -----p--stem > --------p--stem VB > -----p--leaf > --------p--root VB > --p--root > -----p--root VB > > Finally, to respond to an earlier message in this thread - veins (vascular bundles) are present in all plants, not just C4s. > Toby > > > -----Original Message----- > From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal > Sent: Fri 8/27/2004 9:55 AM > To: po-dev at plantontology.org > Cc: > Subject: Re: vascular bundle > > The purpose for asking this term was, that they are present in all kinds > of organs and not just limited to the leaves. > > In leaves mid veins are representing the vasculature and the leaf VB is > a part of that network of vasculature and as Dave pointed out there are > many other parts as well. > > My suggestion is to include this term. If agreed, the other question > would be, where should we place it, it's not just a tissue, but contains > a lot of tissue types. Thus it is an organized structure or a region in > an organ. > > The proposed structure is > i = instance of > p = part of > > > Sporophyte > --p--vascular bundle > -----i--leaf VB > -----i--stem VB > -----i--root VB > -----i--stamen VB > -----p--xylem > -----p--phloem > -----p--cambium > --p--shoot > -----p--stem > --------p--stem VB > -----p--leaf > --------p--root VB > --p--root > -----p--root VB > > I am not sure.... > > #1 > Its true that that the three terms xylem, phloem and cambium are not > always part of VB. > > But as we know the PART of relationship we have suggests that, a child > is a partof but not always a partof parent term. Thus this lineage seems > correct. > > #2 > Do gametophytes also have VB? > > > > Suggested definitions for VB are > > by Fahn: A strand of conducting tissue > > By Essau: A strand like part of the vascular system composed of xylem > and phloem. occurs in stem, leaf and flower. > > By Dickison: A strand like association of primary xylem and phloem that > extends throughout the plant body. > > http://www.cogsci.princeton.edu/cgi-bin/webwn?stage=1&word=vascular+bundle > a unit strand of the vascular system in stems and leaves of higher > plants consisting essentially of xylem and phloem > > > > If that is an accepted structure then we may need a further > instantiation of the terms xylem, phloem and cambium, because as of now > these are the generic terms. But that is a topic for another request to > be sent on the mailing list. > > > Thanks > Pankaj > > > > > Anuradha Pujar wrote: > > >>Hello, >> >>These are just a couple of references, please have a look. >> >> >>http://www.plantphysiol.org/cgi/content/full/129/3/1019 >> >>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14630956 >> >>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15258165 >>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14614507 >>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12615934 >>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2102372 >> >>anu >> >> > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From pj37 at cornell.edu Mon Aug 30 10:12:50 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 30 Aug 2004 10:12:50 -0400 Subject: vascular bundle In-Reply-To: <41332C77.6080709@cornell.edu> References: <7953D8E2E57BF94393CA6B8D2599ADDFFA5927@STL-MAIL2.umsl.edu> <41332C77.6080709@cornell.edu> Message-ID: <413335E2.6050706@cornell.edu> BTW, the term "vascular bundle" was never introduced to the POC anatomy files, despite Gramene having it. So no question of obsolete or un-obsolete. This is a new term request based on our mapping and new annotation requirements. I was the one who was doing tissue node and did not introduce the term at that time because, VB is not a tissue type. One another note, we have a term called bundle sheath which is suggesting there is a plant structure called VB. bundle sheath * Accession: PO:0006023 * Aspect: plant structure * Synonyms: None * Definition: A layer or layers of cells surrounding the vascular bundles of leaves. It may consist of parenchyma or sclerenchyma. -Pankaj Pankaj Jaiswal wrote: > > > Kellogg, Elizabeth A. wrote: > >> Isn't "vascular bundle" simply the term applied to a vein when viewed >> in cross section? > > > > I agree with Katica's earlier message that the term vascular bundle > should remain obsolete. > >> The gene in question can be annotated to vein or vascular tissue if it >> can't be > > > annotated to one of the parts of the vein. I haven't checked the > publication myself, but I'd be pretty > > surpirsed if it were actually expressed in every cell of the vein. > >> > I don't think so. As a curator I would be very cautious on making such a > statement and extrapolating the information provided by the author. In > the first instance, I would go by the authors suggestions. This is also > a sort of leverage given to the curator since he/she may not be an > expert in plant anatomy and by having a term like this the curator still > has an option of doing the correct annotation as well as the user > finding the right query term. Another argument is that from the top, > (intact tissue) and not the section, it is hard to tell whether the > location of the expressed gene as we are suggesting to annotate to vein > (only for leaf) is actually expressed in bundle sheath/surrounding > bundle sheath extensions or anywhere inside the leaf VB. > > This was just a case of leaf VB/vein, but in other parts, I doubt if > people call it veins. Its either Vascular bundle/tissue/strand. > > >> If the group decides to un-obsolete (great verb!) the term, then the >> ontology would > > > have to be considerably more complex than Pankaj outlined earlier. I > think it would be more like: > >> >> Sporophyte >> --p--vascular bundle >> -----i--leaf VB >> -----i--stem VB >> -----i--root VB >> -----i--stamen VB >> -----i--petal VB >> -----i--sepal VB >> -----i---etc., one each for every organ > > > I agree on this, the example I gave was just a simple representation. > >> -----p--xylem >> -----p--phloem >> -----p--cambium >> -----p--bundle sheath >> ---------i--mestome sheath >> ---------i--parenchyma sheath >> -----p--parenchyma >> -----p--schlerenchyma >> --p--shoot >> -----p--stem >> --------p--stem VB >> -----p--leaf >> --------p--root VB >> --p--root >> -----p--root VB >> >> Finally, to respond to an earlier message in this thread - veins >> (vascular bundles) are present in all plants, not just C4s. Toby >> >> >> -----Original Message----- >> From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal >> Sent: Fri 8/27/2004 9:55 AM >> To: po-dev at plantontology.org >> Cc: >> Subject: Re: vascular bundle >> >> The purpose for asking this term was, that they are present in all >> kinds of organs and not just limited to the leaves. >> >> In leaves mid veins are representing the vasculature and the leaf VB >> is a part of that network of vasculature and as Dave pointed out there >> are many other parts as well. >> >> My suggestion is to include this term. If agreed, the other question >> would be, where should we place it, it's not just a tissue, but >> contains a lot of tissue types. Thus it is an organized structure or a >> region in an organ. >> >> The proposed structure is >> i = instance of >> p = part of >> >> >> Sporophyte >> --p--vascular bundle >> -----i--leaf VB >> -----i--stem VB >> -----i--root VB >> -----i--stamen VB >> -----p--xylem >> -----p--phloem >> -----p--cambium >> --p--shoot >> -----p--stem >> --------p--stem VB >> -----p--leaf >> --------p--root VB >> --p--root >> -----p--root VB >> >> I am not sure.... >> >> #1 >> Its true that that the three terms xylem, phloem and cambium are not >> always part of VB. >> >> But as we know the PART of relationship we have suggests that, a child >> is a partof but not always a partof parent term. Thus this lineage >> seems correct. >> >> #2 >> Do gametophytes also have VB? >> >> >> >> Suggested definitions for VB are >> >> by Fahn: A strand of conducting tissue >> >> By Essau: A strand like part of the vascular system composed of xylem >> and phloem. occurs in stem, leaf and flower. >> >> By Dickison: A strand like association of primary xylem and phloem >> that extends throughout the plant body. >> >> http://www.cogsci.princeton.edu/cgi-bin/webwn?stage=1&word=vascular+bundle >> >> a unit strand of the vascular system in stems and leaves of higher >> plants consisting essentially of xylem and phloem >> >> >> >> If that is an accepted structure then we may need a further >> instantiation of the terms xylem, phloem and cambium, because as of >> now these are the generic terms. But that is a topic for another >> request to be sent on the mailing list. >> >> >> Thanks >> Pankaj From pj37 at cornell.edu Mon Aug 30 10:26:55 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Mon, 30 Aug 2004 10:26:55 -0400 Subject: aleurone (was :RE: Feedback Submission from Plant Ontology Live Site) In-Reply-To: References: <26C435999318FC49A6AB243CC8ACA623091A39@UM-EMAIL07.um.umsystem.edu> Message-ID: <4133392F.7000701@cornell.edu> Hi Marty, I was the one. The definition was picked up from the glossary given in Plant Anatomy by Fahn. However the definition was modified because the glossary term was for "aleurone" and not "aleurone layer". By Fahn: Aleurone grain: a characteristic structure of reserve protein present in the seeds of numerous plants. In the endosperm of certain plants such grains are found in the outermost cell layer which is then termed the aleurone layer. By Essau: Aleuron/aleurone: Granules of proteins present in the seeds of numerous plants. Usually restricted to the external part, the aleurone layer of endosperm as in wheat or other cereals. If no one objects, I can modify the definition to The outermost cell layer of the endosperm, usually only one cell thick and the only endosperm tissue alive at maturity. The cells of this layer are responsible for the de-novo synthesis of enzymes needed at germination. A good reference is Physiology of the aleurone layer and starchy endosperm during grain development and early seedling growth: new insights from cell and molecular biology Ritchie S.; Swanson S.J.; Gilroy S. Seed Science Research, September 2000, vol. 10, no. 3, pp. 193-212(20) http://www.ingenta.com/isis/searching/Expand/ingenta?pub=infobike://cabi/ssr/2000/00000010/00000003/art00001 Marty Sachs wrote: > Where did the definition for aleurone.... > > The outermost endosperm tissue of the seeds, its cells being > characterized by presence of protein bodies containing seed storage > proteins. > > ....contained in... > > http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0005360 > > ...and... > > http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& > > ....come from? > > My understanding is more in line with: > > From: http://www.wheatbp.net/glossary.htm > > aleurone (Aleurone layer). The outermost cell layer of the endosperm, > usually only one cell thick in wheat and the only endosperm tissue alive > at maturity. The cells of this layer are responsible for the de-novo > synthesis of enzymes needed at germination. > > At least in maize, 'protein bodies containing seed storage proteins' are > in the endosperm proper. > > -Marty > >> From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal >> Sent: Wed 8/25/2004 11:34 AM >> To: po-dev at plantontology.org > >> Subject: Re: Feedback Submission from Plant Ontology Live Site >> > >> >> http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0005360 > >> >> These would allow a generic search for "anther" or to a specific one >> "anther (sensu Zea)" or by a term_accession (=term_id from flat files). >> The link provided by you is going directly to the term detail page where >> many of the options are not available. >> >> -Pankaj >> >> >> >> feedback_submission at brie4.plantontology.org wrote: >> >> > *** Feedback from Plant Ontology Live Site *** >> > > >> > refer_to_url: >> http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& > >> > >> > comments: Is this the best URL to use to lookup a term when linking >> from an external database such as MaizeGDB? >> > >> > In particular when I wish to be able to access the PO associations >> for that term. >> > >> > What about 'sensu' generics, eg anther. >> > >> > name: Mary Polacco >> > >> > email: PolaccoM at missouri.edu >> > >> > organization: >> > >> > send_feedback: Send your feedback >> > >> > >> >> -- >> ************************ >> Pankaj Jaiswal, PhD >> G15-Bradfield Hall >> Dept. of Plant Breeding >> Cornell University >> Ithaca, NY-14853, USA >> >> Tel: +1-607-255-3103 >> +1-607-255-4109 >> Fax: +1-607-255-6683 >> http://www.gramene.org >> ************************ > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From msachs at uiuc.edu Mon Aug 30 10:46:40 2004 From: msachs at uiuc.edu (Marty Sachs) Date: Mon, 30 Aug 2004 09:46:40 -0500 Subject: aleurone (was :RE: Feedback Submission from Plant Ontology Live Site) In-Reply-To: <4133392F.7000701@cornell.edu> References: <26C435999318FC49A6AB243CC8ACA623091A39@UM-EMAIL07.um.umsystem.edu> <4133392F.7000701@cornell.edu> Message-ID: Pankaj, Thanks. A couple of references that show the sub-aleurone location of protein bodies containing seed storage proteins: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=159838&rendertype=abstract http://ejournal.sinica.edu.tw/bbas/content/2004/1/bot451-08.html -Marty At 10:26 AM -0400 8/30/04, Pankaj Jaiswal wrote: >Hi Marty, > >I was the one. The definition was picked up from the glossary given >in Plant Anatomy by Fahn. However the definition was modified >because the glossary term was for "aleurone" and not "aleurone >layer". > >By Fahn: >Aleurone grain: a characteristic structure of reserve protein >present in the seeds of numerous plants. In the endosperm of certain >plants such grains are found in the outermost cell layer which is >then termed the aleurone layer. > >By Essau: >Aleuron/aleurone: Granules of proteins present in the seeds of >numerous plants. Usually restricted to the external part, the >aleurone layer of endosperm as in wheat or other cereals. > >If no one objects, I can modify the definition to > >The outermost cell layer of the endosperm, usually only one cell >thick and the only endosperm tissue alive at maturity. The cells of >this layer are responsible for the de-novo synthesis of enzymes >needed at germination. > >A good reference is >Physiology of the aleurone layer and starchy endosperm during grain >development and early seedling growth: new insights from cell and >molecular biology >Ritchie S.; Swanson S.J.; Gilroy S. >Seed Science Research, September 2000, vol. 10, no. 3, pp. 193-212(20) >http://www.ingenta.com/isis/searching/Expand/ingenta?pub=infobike://cabi/ssr/2000/00000010/00000003/art00001 > > >Marty Sachs wrote: > >>Where did the definition for aleurone.... >> >>The outermost endosperm tissue of the seeds, its cells being >>characterized by presence of protein bodies containing seed storage >>proteins. >> >>....contained in... >> >>http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0005360 >> >>...and... >> >>http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& >> >>....come from? >> >>My understanding is more in line with: >> >>From: http://www.wheatbp.net/glossary.htm >> >>aleurone (Aleurone layer). The outermost cell layer of the >>endosperm, usually only one cell thick in wheat and the only >>endosperm tissue alive at maturity. The cells of this layer are >>responsible for the de-novo synthesis of enzymes needed at >>germination. >> >>At least in maize, 'protein bodies containing seed storage >>proteins' are in the endosperm proper. >> >> -Marty >> >>>From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal >>>Sent: Wed 8/25/2004 11:34 AM >>>To: po-dev at plantontology.org >> >>>Subject: Re: Feedback Submission from Plant Ontology Live Site >>> >> >>> >>>http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0005360 >> >>> >>>These would allow a generic search for "anther" or to a specific one >>>"anther (sensu Zea)" or by a term_accession (=term_id from flat files). >>>The link provided by you is going directly to the term detail page where >>>many of the options are not available. >>> >>>-Pankaj >>> >>> >>> >>>feedback_submission at brie4.plantontology.org wrote: >>> >>>> *** Feedback from Plant Ontology Live Site *** >>>> >> >>> > refer_to_url: >>>http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& >> >>> > >>>> comments: Is this the best URL to use to lookup a term when >>>>linking from an external database such as MaizeGDB? >>>> >>>> In particular when I wish to be able to access the PO >>>>associations for that term. >>>> >>>> What about 'sensu' generics, eg anther. >>>> >>>> name: Mary Polacco >>>> >>>> email: PolaccoM at missouri.edu >>>> >>>> organization: >>>> >>>> send_feedback: Send your feedback >>>> >>>> >>> >>>-- >>>************************ >>>Pankaj Jaiswal, PhD >>>G15-Bradfield Hall >>>Dept. of Plant Breeding >>>Cornell University >>>Ithaca, NY-14853, USA >>> >>>Tel: +1-607-255-3103 >>> +1-607-255-4109 >>>Fax: +1-607-255-6683 >>>http://www.gramene.org >>>************************ >> >> > >-- >************************ >Pankaj Jaiswal, PhD >G15-Bradfield Hall >Dept. of Plant Breeding >Cornell University >Ithaca, NY-14853, USA > >Tel: +1-607-255-3103 > +1-607-255-4109 >Fax: +1-607-255-6683 >http://www.gramene.org >************************ From ap343 at cornell.edu Mon Aug 30 13:17:14 2004 From: ap343 at cornell.edu (Anuradha Pujar) Date: Mon, 30 Aug 2004 13:17:14 -0400 (EDT) Subject: vascular bundle In-Reply-To: <7953D8E2E57BF94393CA6B8D2599ADDFFA5927@STL-MAIL2.umsl.edu> References: <7953D8E2E57BF94393CA6B8D2599ADDFFA5927@STL-MAIL2.umsl.edu> Message-ID: <3741.128.253.246.53.1093886234.squirrel@128.253.246.53> A few genes whose expression is related to vascular tissue/pattern/development/differentiation are listed below. Due to the use of the term ?vascular bundle? by these authors it would be difficult to clearly annotate them to a particular vascular cell type. CVP1 genes: involved in vascular tissue pattern, the author has shown whole leaf pictures and refers to vasculature/vein as the vascular bundle Fig 1, and also with reference to the cross section it is referred to as the anatomy of ?cotyledon vascular bundle? Fig 6. http://www.plantcell.org/cgi/content/full/11/11/2123 AtPIN1 gene: involved in the regulation of polar auxin transport, in Fig 4 the authors mention that the anti AtPIN1 formed continuous vertical cell strands in vascular bundle. http://www.sciencemag.org/cgi/content/full/282/5397/2226 ATHB 8 gene: the gene involved in regulation of vascular development, the authors refer to vascular bundle in the cross-section Fig 5 http://www.plantphysiol.org/cgi/content/full/126/2/643 COV1 gene: this gene is involved with the regulation of vascular pattern refer to Fig 1. http://dev.biologists.org/cgi/content/full/130/10/2139 These genes are from Arabidopsis, my concern is with genes/gene products related to cereal plants wherein the localization within vascular tissue is not clear such as the Glutamine synthase in rice and barley. And auxin related genes. GS1: Glutamate synthase is specific to vascular bundle according this paper. http://jxb.oupjournals.org/cgi/reprint/52/356/591 anu > Isn't "vascular bundle" simply the term applied to a vein when viewed in > cross section? I agree with Katica's earlier message that the term > vascular bundle should remain obsolete. The gene in question can be > annotated to vein or vascular tissue if it can't be annotated to one of > the parts of the vein. I haven't checked the publication myself, but I'd > be pretty surpirsed if it were actually expressed in every cell of the > vein. > > If the group decides to un-obsolete (great verb!) the term, then the > ontology would have to be considerably more complex than Pankaj outlined > earlier. I think it would be more like: > > Sporophyte > --p--vascular bundle > -----i--leaf VB > -----i--stem VB > -----i--root VB > -----i--stamen VB > -----i--petal VB > -----i--sepal VB > -----i---etc., one each for every organ > -----p--xylem > -----p--phloem > -----p--cambium > -----p--bundle sheath > ---------i--mestome sheath > ---------i--parenchyma sheath > -----p--parenchyma > -----p--schlerenchyma > --p--shoot > -----p--stem > --------p--stem VB > -----p--leaf > --------p--root VB > --p--root > -----p--root VB > > Finally, to respond to an earlier message in this thread - veins (vascular > bundles) are present in all plants, not just C4s. > Toby > > > -----Original Message----- > From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal > Sent: Fri 8/27/2004 9:55 AM > To: po-dev at plantontology.org > Cc: > Subject: Re: vascular bundle > > The purpose for asking this term was, that they are present in all kinds > of organs and not just limited to the leaves. > > In leaves mid veins are representing the vasculature and the leaf VB is > a part of that network of vasculature and as Dave pointed out there are > many other parts as well. > > My suggestion is to include this term. If agreed, the other question > would be, where should we place it, it's not just a tissue, but contains > a lot of tissue types. Thus it is an organized structure or a region in > an organ. > > The proposed structure is > i = instance of > p = part of > > > Sporophyte > --p--vascular bundle > -----i--leaf VB > -----i--stem VB > -----i--root VB > -----i--stamen VB > -----p--xylem > -----p--phloem > -----p--cambium > --p--shoot > -----p--stem > --------p--stem VB > -----p--leaf > --------p--root VB > --p--root > -----p--root VB > > I am not sure.... > > #1 > Its true that that the three terms xylem, phloem and cambium are not > always part of VB. > > But as we know the PART of relationship we have suggests that, a child > is a partof but not always a partof parent term. Thus this lineage seems > correct. > > #2 > Do gametophytes also have VB? > > > > Suggested definitions for VB are > > by Fahn: A strand of conducting tissue > > By Essau: A strand like part of the vascular system composed of xylem > and phloem. occurs in stem, leaf and flower. > > By Dickison: A strand like association of primary xylem and phloem that > extends throughout the plant body. > > http://www.cogsci.princeton.edu/cgi-bin/webwn?stage=1&word=vascular+bundle > a unit strand of the vascular system in stems and leaves of higher > plants consisting essentially of xylem and phloem > > > > If that is an accepted structure then we may need a further > instantiation of the terms xylem, phloem and cambium, because as of now > these are the generic terms. But that is a topic for another request to > be sent on the mailing list. > > > Thanks > Pankaj > > > > > Anuradha Pujar wrote: > >> >> Hello, >> >> These are just a couple of references, please have a look. >> >> >> http://www.plantphysiol.org/cgi/content/full/129/3/1019 >> >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14630956 >> >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15258165 >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14614507 >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12615934 >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2102372 >> >> anu >> >> > > -- > ************************ > Pankaj Jaiswal, PhD > G15-Bradfield Hall > Dept. of Plant Breeding > Cornell University > Ithaca, NY-14853, USA > > Tel: +1-607-255-3103 > +1-607-255-4109 > Fax: +1-607-255-6683 > http://www.gramene.org > ************************ > > > > From katica at acoma.Stanford.EDU Mon Aug 30 14:57:01 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 30 Aug 2004 11:57:01 -0700 (PDT) Subject: vascular bundle In-Reply-To: <413335E2.6050706@cornell.edu> Message-ID: Hi all, Mea culpa! I admit, it was my mistake saying that vascular bundle was obsoleted. Reason for that was that we obsoleted some other 'vascular terms' and not all obsoleted terms are in the 'obsoleted' node (some terms were just deleted). As a result, we have fewer terms in the obsolete node. I looked into all the older revisions in cvs and didn't find this term, so Pankaj rightly stated, VB was never in the PO. We did discuss it and opted not to have term vascular bundle in PO, since it is not a tissue type, but a kind of 'grouping term' and we already had several terms in PO that seemed sufficient at the time (back in the May). However, it really doesn't change much my point (and Toby's elaboration of problems that we are going to face if we introduce VB the way Pankaj suggested). To summarize, 1) we can use terms that are already in the PO, and/or 2) annotation can be made to a more granular term, 3) having vascular bundle everywhere under sporophyte node will cause large-scale term proliferation, resulting in a dozens of terms like 'xylem of the vascular bundle of the stamen'. This is the case of 'full instantiation' or structure 3 in the POC Documentation. Now, we had discussion about the full instantiation and problems associated with it, and decided to go with this option ONLY when absolutely needed for annotation purposes. I have hard time believing that we need VB everywhere under sporophyte for annotation purposes (and I would like to believe that question about gametophyte was a joke). I want to remind you of a similar situation with sensu terms (I can't let go), where we ended up with 74 sensu terms only to find out later that less than 50% of those were indeed required for maize annotation in near future (if I recall correctly Mary's information). And we also said for sensu terms 'only when absolutely required'. So my suggestion is to look in the Gramene and TAIR and see how many gene annotations are currently associated to term 'vascular bundle'. Term 'vascular bundle' is also present in TAIR: Term: vascular bundle (TAIR:0000362) Def: A strandline part of the vascular system composed of xylem and phloem. However, I have not finished my list of unmapped terms for TAIR, so this one is still not on my list. Mapping on one-to-one basis (meaning term-to-term) is just a first round. There are terms that have different names but they refer to the same structure, and this is determined by a curator on case-to-case basis. We need to look into definitions, synonyms and other info provided for each term, in some cases even looking into annotations and original papers (if required). This is the most time consuming part of the mapping process, and the most important one too. In most cases, (I am still going through details) annotations in TAIR are referring to the leaf vascular bundle, although the term definition itself is very general. At the end, just to remind you that we have following PO terms: vascular cambium, vascular tissue, root stele, leaf vein, midvein, secondary vein, lateral vein. As I said earlier, we are going in circles with this issue of instantiation and term proliferation, and it is one of the issues that will come up over and over again. In nature, it is similar to problem with sensu terms. Toby described it nicely in the documentation she sent to Lincoln, and I hope we can discuss this next week. GO folks are aware of this problem and are currently thinking of solutions as well. One of the possible solutions is to change the way the annotations are done. Again, I hope we can discuss it soon. Katica On Mon, 30 Aug 2004, Pankaj Jaiswal wrote: > BTW, the term "vascular bundle" was never introduced to the POC anatomy > files, despite Gramene having it. So no question of obsolete or > un-obsolete. This is a new term request based on our mapping and new > annotation requirements. I was the one who was doing tissue node and did > not introduce the term at that time because, VB is not a tissue type. > > > One another note, we have a term called bundle sheath which is > suggesting there is a plant structure called VB. > > bundle sheath > > * Accession: PO:0006023 > * Aspect: plant structure > * Synonyms: None > * Definition: > A layer or layers of cells surrounding the vascular bundles > of leaves. It may consist of parenchyma or sclerenchyma. > > -Pankaj > > > Pankaj Jaiswal wrote: > > > > > > Kellogg, Elizabeth A. wrote: > > > >> Isn't "vascular bundle" simply the term applied to a vein when viewed > >> in cross section? > > > > > > > I agree with Katica's earlier message that the term vascular bundle > > should remain obsolete. > > > >> The gene in question can be annotated to vein or vascular tissue if it > >> can't be > > > > > annotated to one of the parts of the vein. I haven't checked the > > publication myself, but I'd be pretty > > > surpirsed if it were actually expressed in every cell of the vein. > > > >> > > I don't think so. As a curator I would be very cautious on making such a > > statement and extrapolating the information provided by the author. In > > the first instance, I would go by the authors suggestions. This is also > > a sort of leverage given to the curator since he/she may not be an > > expert in plant anatomy and by having a term like this the curator still > > has an option of doing the correct annotation as well as the user > > finding the right query term. Another argument is that from the top, > > (intact tissue) and not the section, it is hard to tell whether the > > location of the expressed gene as we are suggesting to annotate to vein > > (only for leaf) is actually expressed in bundle sheath/surrounding > > bundle sheath extensions or anywhere inside the leaf VB. > > > > This was just a case of leaf VB/vein, but in other parts, I doubt if > > people call it veins. Its either Vascular bundle/tissue/strand. > > > > > >> If the group decides to un-obsolete (great verb!) the term, then the > >> ontology would > > > > > have to be considerably more complex than Pankaj outlined earlier. I > > think it would be more like: > > > >> > >> Sporophyte > >> --p--vascular bundle > >> -----i--leaf VB > >> -----i--stem VB > >> -----i--root VB > >> -----i--stamen VB > >> -----i--petal VB > >> -----i--sepal VB > >> -----i---etc., one each for every organ > > > > > > I agree on this, the example I gave was just a simple representation. > > > >> -----p--xylem > >> -----p--phloem > >> -----p--cambium > >> -----p--bundle sheath > >> ---------i--mestome sheath > >> ---------i--parenchyma sheath > >> -----p--parenchyma > >> -----p--schlerenchyma > >> --p--shoot > >> -----p--stem > >> --------p--stem VB > >> -----p--leaf > >> --------p--root VB > >> --p--root > >> -----p--root VB > >> > >> Finally, to respond to an earlier message in this thread - veins > >> (vascular bundles) are present in all plants, not just C4s. Toby > >> > >> > >> -----Original Message----- > >> From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal > >> Sent: Fri 8/27/2004 9:55 AM > >> To: po-dev at plantontology.org > >> Cc: > >> Subject: Re: vascular bundle > >> > >> The purpose for asking this term was, that they are present in all > >> kinds of organs and not just limited to the leaves. > >> > >> In leaves mid veins are representing the vasculature and the leaf VB > >> is a part of that network of vasculature and as Dave pointed out there > >> are many other parts as well. > >> > >> My suggestion is to include this term. If agreed, the other question > >> would be, where should we place it, it's not just a tissue, but > >> contains a lot of tissue types. Thus it is an organized structure or a > >> region in an organ. > >> > >> The proposed structure is > >> i = instance of > >> p = part of > >> > >> > >> Sporophyte > >> --p--vascular bundle > >> -----i--leaf VB > >> -----i--stem VB > >> -----i--root VB > >> -----i--stamen VB > >> -----p--xylem > >> -----p--phloem > >> -----p--cambium > >> --p--shoot > >> -----p--stem > >> --------p--stem VB > >> -----p--leaf > >> --------p--root VB > >> --p--root > >> -----p--root VB > >> > >> I am not sure.... > >> > >> #1 > >> Its true that that the three terms xylem, phloem and cambium are not > >> always part of VB. > >> > >> But as we know the PART of relationship we have suggests that, a child > >> is a partof but not always a partof parent term. Thus this lineage > >> seems correct. > >> > >> #2 > >> Do gametophytes also have VB? > >> > >> > >> > >> Suggested definitions for VB are > >> > >> by Fahn: A strand of conducting tissue > >> > >> By Essau: A strand like part of the vascular system composed of xylem > >> and phloem. occurs in stem, leaf and flower. > >> > >> By Dickison: A strand like association of primary xylem and phloem > >> that extends throughout the plant body. > >> > >> http://www.cogsci.princeton.edu/cgi-bin/webwn?stage=1&word=vascular+bundle > >> > >> a unit strand of the vascular system in stems and leaves of higher > >> plants consisting essentially of xylem and phloem > >> > >> > >> > >> If that is an accepted structure then we may need a further > >> instantiation of the terms xylem, phloem and cambium, because as of > >> now these are the generic terms. But that is a topic for another > >> request to be sent on the mailing list. > >> > >> > >> Thanks > >> Pankaj > -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From katica at acoma.Stanford.EDU Mon Aug 30 17:19:08 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 30 Aug 2004 14:19:08 -0700 (PDT) Subject: vascular bundle In-Reply-To: <3741.128.253.246.53.1093886234.squirrel@128.253.246.53> Message-ID: Anu, I am curently looking at the annotations for Arabidopsis associated with term 'vascular bundle, and will come up with details soon. Can you tell me exactly how many annotations (how many genes are annotated to it and how many annotations) do you have in the Gramene that are associated to the term 'vascular bundle'? Let's start from the bottom up, find out if we need to add this term, and if so, how many different terms for vascular bundle we need to have in PO, in order not to lose any annotations. Please look thoroughly in the literature for details. The term 'vascular bundle' will not be needed for microarray expressions studies (for obvious reasons). It's mainly is situ hybridization studies and gene expressions involving GUS, and often, authors (although using term vascular bundles) are more specific in their descriptions and they refer to the particular tissue withing vascular bundle (xylem, phloem or transfussion tissue) whenever possible. Otherwords, this is not the most granular term that will be often used for the annotations. In a couple of references I looked, whenever they just say vascular bundle, they mean in the leaf, which in my opinion, is a leaf vein. Also, I will talk to some experts in the field and see what they think. Katica On Mon, 30 Aug 2004, Anuradha Pujar wrote: > > A few genes whose expression is related to vascular > tissue/pattern/development/differentiation are listed below. > > Due to the use of the term ?vascular bundle? by these authors it would be > difficult to clearly annotate them to a particular vascular cell type. > > CVP1 genes: involved in vascular tissue pattern, the author has shown > whole leaf pictures and refers to vasculature/vein as the vascular bundle > Fig 1, and also with reference to the cross section it is referred to as > the anatomy of ?cotyledon vascular bundle? Fig 6. > > http://www.plantcell.org/cgi/content/full/11/11/2123 > > AtPIN1 gene: involved in the regulation of polar auxin transport, in Fig > 4 the authors mention that the anti AtPIN1 formed continuous vertical cell > strands in vascular bundle. > http://www.sciencemag.org/cgi/content/full/282/5397/2226 > > ATHB 8 gene: the gene involved in regulation of vascular development, the > authors refer to vascular bundle in the cross-section Fig 5 > http://www.plantphysiol.org/cgi/content/full/126/2/643 > > COV1 gene: this gene is involved with the regulation of vascular pattern > refer to Fig 1. > http://dev.biologists.org/cgi/content/full/130/10/2139 > > These genes are from Arabidopsis, my concern is with genes/gene products > related to cereal plants wherein the localization within vascular tissue > is not clear such as the Glutamine synthase in rice and barley. And auxin > related genes. > > GS1: Glutamate synthase is specific to vascular bundle according this paper. > http://jxb.oupjournals.org/cgi/reprint/52/356/591 > > anu > > > Isn't "vascular bundle" simply the term applied to a vein when viewed in > > cross section? I agree with Katica's earlier message that the term > > vascular bundle should remain obsolete. The gene in question can be > > annotated to vein or vascular tissue if it can't be annotated to one of > > the parts of the vein. I haven't checked the publication myself, but I'd > > be pretty surpirsed if it were actually expressed in every cell of the > > vein. > > > > If the group decides to un-obsolete (great verb!) the term, then the > > ontology would have to be considerably more complex than Pankaj outlined > > earlier. I think it would be more like: > > > > Sporophyte > > --p--vascular bundle > > -----i--leaf VB > > -----i--stem VB > > -----i--root VB > > -----i--stamen VB > > -----i--petal VB > > -----i--sepal VB > > -----i---etc., one each for every organ > > -----p--xylem > > -----p--phloem > > -----p--cambium > > -----p--bundle sheath > > ---------i--mestome sheath > > ---------i--parenchyma sheath > > -----p--parenchyma > > -----p--schlerenchyma > > --p--shoot > > -----p--stem > > --------p--stem VB > > -----p--leaf > > --------p--root VB > > --p--root > > -----p--root VB > > > > Finally, to respond to an earlier message in this thread - veins (vascular > > bundles) are present in all plants, not just C4s. > > Toby > > > > > > -----Original Message----- > > From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal > > Sent: Fri 8/27/2004 9:55 AM > > To: po-dev at plantontology.org > > Cc: > > Subject: Re: vascular bundle > > > > The purpose for asking this term was, that they are present in all kinds > > of organs and not just limited to the leaves. > > > > In leaves mid veins are representing the vasculature and the leaf VB is > > a part of that network of vasculature and as Dave pointed out there are > > many other parts as well. > > > > My suggestion is to include this term. If agreed, the other question > > would be, where should we place it, it's not just a tissue, but contains > > a lot of tissue types. Thus it is an organized structure or a region in > > an organ. > > > > The proposed structure is > > i = instance of > > p = part of > > > > > > Sporophyte > > --p--vascular bundle > > -----i--leaf VB > > -----i--stem VB > > -----i--root VB > > -----i--stamen VB > > -----p--xylem > > -----p--phloem > > -----p--cambium > > --p--shoot > > -----p--stem > > --------p--stem VB > > -----p--leaf > > --------p--root VB > > --p--root > > -----p--root VB > > > > I am not sure.... > > > > #1 > > Its true that that the three terms xylem, phloem and cambium are not > > always part of VB. > > > > But as we know the PART of relationship we have suggests that, a child > > is a partof but not always a partof parent term. Thus this lineage seems > > correct. > > > > #2 > > Do gametophytes also have VB? > > > > > > > > Suggested definitions for VB are > > > > by Fahn: A strand of conducting tissue > > > > By Essau: A strand like part of the vascular system composed of xylem > > and phloem. occurs in stem, leaf and flower. > > > > By Dickison: A strand like association of primary xylem and phloem that > > extends throughout the plant body. > > > > http://www.cogsci.princeton.edu/cgi-bin/webwn?stage=1&word=vascular+bundle > > a unit strand of the vascular system in stems and leaves of higher > > plants consisting essentially of xylem and phloem > > > > > > > > If that is an accepted structure then we may need a further > > instantiation of the terms xylem, phloem and cambium, because as of now > > these are the generic terms. But that is a topic for another request to > > be sent on the mailing list. > > > > > > Thanks > > Pankaj > > > > > > > > > > Anuradha Pujar wrote: > > > >> > >> Hello, > >> > >> These are just a couple of references, please have a look. > >> > >> > >> http://www.plantphysiol.org/cgi/content/full/129/3/1019 > >> > >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14630956 > >> > >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15258165 > >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14614507 > >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12615934 > >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2102372 > >> > >> anu > >> > >> > > > > -- > > ************************ > > Pankaj Jaiswal, PhD > > G15-Bradfield Hall > > Dept. of Plant Breeding > > Cornell University > > Ithaca, NY-14853, USA > > > > Tel: +1-607-255-3103 > > +1-607-255-4109 > > Fax: +1-607-255-6683 > > http://www.gramene.org > > ************************ > > > > > > > > > > -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From katica at acoma.Stanford.EDU Mon Aug 30 22:00:29 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 30 Aug 2004 19:00:29 -0700 (PDT) Subject: aleurone (was :RE: Feedback Submission from Plant Ontology Live Site) In-Reply-To: <4133392F.7000701@cornell.edu> Message-ID: Pankaj, Dicots have aleurone layer too (for instance, Arabidopsis, see Debeaujon et al, Plant Physiol, 122:403-413), and I am not sure if the new definition you suggested is broad enough to include both dicots and monocots (Peter or Leonore would know this better). You included reference talking about grain development (Seed Science Research) and Marty was mainly talking about maize and wheat, so I just want to make sure that the definition is appropriate and apply to the most of the flowering plants, and not just monocots. In fact, it looks like you took the definition from http://www.wheatbp.net/glossary.htm, and just removed 'in wheat'. Here is Peter's APWeb definition (since we agreed on using this glossary whenever is appropriate): aleurone: the outermost layer(s) of the endosperm, living cells containing proteins, the other cells being more or less dead and with much thickened walls, the lumen being more or less occluded e.g. by galactomannans (a hemicellulose). We can modify the part that refers to proteins, to make it more appropriate for grain crops. Peter and Felipe, do you have any suggestion here? Katica On Mon, 30 Aug 2004, Pankaj Jaiswal wrote: > Hi Marty, > > I was the one. The definition was picked up from the glossary given in > Plant Anatomy by Fahn. However the definition was modified because the > glossary term was for "aleurone" and not "aleurone layer". > > By Fahn: > Aleurone grain: a characteristic structure of reserve protein present in > the seeds of numerous plants. In the endosperm of certain plants such > grains are found in the outermost cell layer which is then termed the > aleurone layer. > > By Essau: > Aleuron/aleurone: Granules of proteins present in the seeds of numerous > plants. Usually restricted to the external part, the aleurone layer of > endosperm as in wheat or other cereals. > > If no one objects, I can modify the definition to > > The outermost cell layer of the endosperm, usually only one cell thick > and the only endosperm tissue alive at maturity. The cells of this layer > are responsible for the de-novo synthesis of enzymes needed at germination. > > A good reference is > Physiology of the aleurone layer and starchy endosperm during grain > development and early seedling growth: new insights from cell and > molecular biology > Ritchie S.; Swanson S.J.; Gilroy S. > Seed Science Research, September 2000, vol. 10, no. 3, pp. 193-212(20) > http://www.ingenta.com/isis/searching/Expand/ingenta?pub=infobike://cabi/ssr/2000/00000010/00000003/art00001 > > > Marty Sachs wrote: > > > Where did the definition for aleurone.... > > > > The outermost endosperm tissue of the seeds, its cells being > > characterized by presence of protein bodies containing seed storage > > proteins. > > > > ....contained in... > > > > http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0005360 > > > > ...and... > > > > http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& > > > > ....come from? > > > > My understanding is more in line with: > > > > From: http://www.wheatbp.net/glossary.htm > > > > aleurone (Aleurone layer). The outermost cell layer of the endosperm, > > usually only one cell thick in wheat and the only endosperm tissue alive > > at maturity. The cells of this layer are responsible for the de-novo > > synthesis of enzymes needed at germination. > > > > At least in maize, 'protein bodies containing seed storage proteins' are > > in the endosperm proper. > > > > -Marty > > > >> From: owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal > >> Sent: Wed 8/25/2004 11:34 AM > >> To: po-dev at plantontology.org > > > >> Subject: Re: Feedback Submission from Plant Ontology Live Site > >> > > > >> > >> http://amigo.plantontology.org/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0005360 > > > >> > >> These would allow a generic search for "anther" or to a specific one > >> "anther (sensu Zea)" or by a term_accession (=term_id from flat files). > >> The link provided by you is going directly to the term detail page where > >> many of the options are not available. > >> > >> -Pankaj > >> > >> > >> > >> feedback_submission at brie4.plantontology.org wrote: > >> > >> > *** Feedback from Plant Ontology Live Site *** > >> > > > > >> > refer_to_url: > >> http://amigo.plantontology.org/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0005360& > > > >> > > >> > comments: Is this the best URL to use to lookup a term when linking > >> from an external database such as MaizeGDB? > >> > > >> > In particular when I wish to be able to access the PO associations > >> for that term. > >> > > >> > What about 'sensu' generics, eg anther. > >> > > >> > name: Mary Polacco > >> > > >> > email: PolaccoM at missouri.edu > >> > > >> > organization: > >> > > >> > send_feedback: Send your feedback > >> > > >> > > >> > >> -- > >> ************************ > >> Pankaj Jaiswal, PhD > >> G15-Bradfield Hall > >> Dept. of Plant Breeding > >> Cornell University > >> Ithaca, NY-14853, USA > >> > >> Tel: +1-607-255-3103 > >> +1-607-255-4109 > >> Fax: +1-607-255-6683 > >> http://www.gramene.org > >> ************************ > > > > > > -- > ************************ > Pankaj Jaiswal, PhD > G15-Bradfield Hall > Dept. of Plant Breeding > Cornell University > Ithaca, NY-14853, USA > > Tel: +1-607-255-3103 > +1-607-255-4109 > Fax: +1-607-255-6683 > http://www.gramene.org > ************************ > -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From feedback_submission at brie4.plantontology.org Tue Aug 31 12:10:49 2004 From: feedback_submission at brie4.plantontology.org (feedback_submission at brie4.plantontology.org) Date: Tue, 31 Aug 2004 12:10:49 -0400 Subject: Feedback Submission from Plant Ontology Live Site Message-ID: <200408311610.i7VGAnSr012557@brie4.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: I teach a plant anatomy course at the University of Rhode Island and I have struggled with presenting antomical terms heirarachically for many years. I believe PO will be an excellent resource and I plan on having my students use it extensively. Over the last few week I have been working to make the terminology I use in class consistent with PO and have encountered a few difficulties. 1. The term "pericycle" (PO:0006203) is defined as "part of the tissue of the stele", yet it is listed as a child of the stem cortex. But, the cortex EXCLUDES the stele, being defined as occuring BETWEEN the vascular system (i.e. the stele) and epidermis. 2. The "cortex" (PO:0005708) includes the tissues "endodermis" and "hypodermis", but not "parenchyma", "collenchyma", "sclerenchyma", which are listed as separate tissue. This is related to the next point. 3. In most texts, the cortex (and also the pith) are not considered "TISSUES", but are described as "regions". Although the terms "cortex" and "pith" are useful and widely used, they do not fit well into a classification. Perhaps these terms should become obsolete as has "ground tissue". If "cortical parenchyma" and "pith parenchyma" are added as types of parenchyma, then all tissues of pith and cortex (both stem and root) will be accounted for. Thank you for your efforts, Alison Roberts name: Alison Roberts email: aroberts at uri.edu organization: University of Rhode Island send_feedback: Send your feedback From peter.stevens at mobot.org Tue Aug 31 13:05:53 2004 From: peter.stevens at mobot.org (Peter Stevens) Date: Tue, 31 Aug 2004 13:05:53 -0400 Subject: Feedback Submission from Plant Ontology Live Site In-Reply-To: <200408311610.i7VGAnSr012557@brie4.cshl.org> References: <200408311610.i7VGAnSr012557@brie4.cshl.org> Message-ID: >Pericycle should indeed be part of the stele. The pith is also part >of the stele as defined here, and anyway would have to include >sclerenchyma... P. > *** Feedback from Plant Ontology Live Site *** > >refer_to_url: http://www.plantontology.org/index.html > >comments: I teach a plant anatomy course at the University of Rhode >Island and I have struggled with presenting antomical terms >heirarachically for many years. I believe PO will be an excellent >resource and I plan on having my students use it extensively. > >Over the last few week I have been working to make the terminology I >use in class consistent with PO and have encountered a few >difficulties. > >1. The term "pericycle" (PO:0006203) is defined as "part of the >tissue of the stele", yet it is listed as a child of the stem >cortex. But, the cortex EXCLUDES the stele, being defined as >occuring BETWEEN the vascular system (i.e. the stele) and epidermis. > >2. The "cortex" (PO:0005708) includes the tissues "endodermis" and >"hypodermis", but not "parenchyma", "collenchyma", "sclerenchyma", >which are listed as separate tissue. This is related to the next >point. > >3. In most texts, the cortex (and also the pith) are not considered >"TISSUES", but are described as "regions". Although the terms >"cortex" and "pith" are useful and widely used, they do not fit well >into a classification. Perhaps these terms should become obsolete as >has "ground tissue". If "cortical parenchyma" and "pith parenchyma" >are added as types of parenchyma, then all tissues of pith and >cortex (both stem and root) will be accounted for. > >Thank you for your efforts, >Alison Roberts > >name: Alison Roberts > >email: aroberts at uri.edu > >organization: University of Rhode Island > >send_feedback: Send your feedback From pj37 at cornell.edu Tue Aug 31 14:43:32 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 31 Aug 2004 14:43:32 -0400 Subject: Feedback Submission from Plant Ontology Live Site In-Reply-To: <200408311610.i7VGAnSr012557@brie4.cshl.org> References: <200408311610.i7VGAnSr012557@brie4.cshl.org> Message-ID: <4134C6D4.7010004@cornell.edu> Dear Dr. Alison, Thank you for your suggestion. We really appreciate your feedback and hope to provide the best possible vocabulary of plant anatomy. Please look for my comments next to your suggestions. Best regards Pankaj feedback_submission at brie4.plantontology.org wrote: > *** Feedback from Plant Ontology Live Site *** > > refer_to_url: http://www.plantontology.org/index.html > > comments: I teach a plant anatomy course at the University of Rhode Island and I have struggled with presenting antomical terms heirarachically for many years. I believe PO will be an excellent resource and I plan on having my students use it extensively. > > Over the last few week I have been working to make the terminology I use in class consistent with PO and have encountered a few difficulties. > > 1. The term "pericycle" (PO:0006203) is defined as "part of the tissue of the stele", yet it is listed as a child of the stem cortex. But, the cortex EXCLUDES the stele, being defined as occuring BETWEEN the vascular system (i.e. the stele) and epidermis. > I agree with you and propose to organize this as follows by -deleting the relationship pericycle is part_of root cortex relationship -creating a new relationship pericycle is part_of root stele ---PO:0009075 : plant ontology ----i PO:0009011 : plant structure -------i PO:0009003 : sporophyte -----------p PO:0009005 : root --------------p PO:0000258 : root cortex --------------p PO:0020124 : root stele -------------------p PO:0006203 : pericycle -------i PO:0009007 : tissue -----------i PO:0005708 : cortex --------------i PO:0000258 : root cortex --------------i PO:0006203 : pericycle > 2. The "cortex" (PO:0005708) includes the tissues "endodermis" and "hypodermis", but not "parenchyma", "collenchyma", "sclerenchyma", which are listed as separate tissue. This is related to the next point. > It is so because the terms like parenchyma, collenchyma and sclerenchyma are generic tissue terms and there are many such instances, of these tissue types that are not always present in cortex. Whereas endodermis and hypodermis if found are always part of cortex. I just looked at the tree and propose for making following generic terms as part_of generic term for PO:0005708 : cortex. PO:0000252 : endodermis PO:0005051 : hypodermis > 3. In most texts, the cortex (and also the pith) are not considered "TISSUES", but are described as "regions". Although the terms "cortex" and "pith" are useful and widely used, they do not fit well into a classification. Perhaps these terms should become obsolete as has "ground tissue". If "cortical parenchyma" and "pith parenchyma" are added as types of parenchyma, then all tissues of pith and cortex (both stem and root) will be accounted for. > We are looking into your suggestions and will get back to you soon. > Thank you for your efforts, > Alison Roberts > > name: Alison Roberts > > email: aroberts at uri.edu > > organization: University of Rhode Island > > send_feedback: Send your feedback > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From pj37 at cornell.edu Tue Aug 31 14:51:40 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 31 Aug 2004 14:51:40 -0400 Subject: pericycle Message-ID: <4134C8BC.7070200@cornell.edu> Hi, Here is what I proposed in response to Alison's mail for pericycle ---PO:0009075 : plant ontology ----i PO:0009011 : plant structure -------i PO:0009003 : sporophyte -----------p PO:0009005 : root --------------p PO:0000258 : root cortex --------------p PO:0020124 : root stele -------------------p PO:0006203 : pericycle -------i PO:0009007 : tissue -----------i PO:0005708 : cortex --------------i PO:0000258 : root cortex --------------i PO:0006203 : pericycle But this is again leading us into a black hole, which we are trying to avoid. The term pericycle is a generic term and we need to create its instances such as -root pericycle -stem pericycle -leaf pericycle In order to make correct lineage the instantiation is required. Current definition and comments sauugest it so.. # Definition: * Part of the tissue of the stele located between the phloem and endodermis. # Comment: * In seed plants it is regularly present in roots and absent in most stems and leaves. -Pankaj From katica at acoma.Stanford.EDU Tue Aug 31 16:09:20 2004 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Tue, 31 Aug 2004 13:09:20 -0700 (PDT) Subject: pericycle In-Reply-To: <4134C8BC.7070200@cornell.edu> Message-ID: Pankaj, (Related to the sec part of your message), luckily, as we know it, pericycle is present only in the root, so we don't need to worry about having the term pericycle getting instantiated all over the place. Katica On Tue, 31 Aug 2004, Pankaj Jaiswal wrote: > Hi, > Here is what I proposed in response to Alison's mail for pericycle > > ---PO:0009075 : plant ontology > ----i PO:0009011 : plant structure > -------i PO:0009003 : sporophyte > -----------p PO:0009005 : root > --------------p PO:0000258 : root cortex > --------------p PO:0020124 : root stele > -------------------p PO:0006203 : pericycle > -------i PO:0009007 : tissue > -----------i PO:0005708 : cortex > --------------i PO:0000258 : root cortex > --------------i PO:0006203 : pericycle > > But this is again leading us into a black hole, which we are trying to > avoid. The term pericycle is a generic term and we need to create its > instances such as > -root pericycle > -stem pericycle > -leaf pericycle > > In order to make correct lineage the instantiation is required. > > Current definition and comments sauugest it so.. > > # Definition: > > * Part of the tissue of the stele located between the phloem and > endodermis. > > # Comment: > > * In seed plants it is regularly present in roots and absent in > most stems and leaves. > > > > -Pankaj > > -------------------------------------------------------------------------- Katica Ilic katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington FAX: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305 U.S.A. -------------------------------------------------------------------------- From pj37 at cornell.edu Tue Aug 31 17:30:03 2004 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 31 Aug 2004 17:30:03 -0400 Subject: pericycle In-Reply-To: References: Message-ID: <4134EDDB.7000608@cornell.edu> Katica Ilic wrote: > Pankaj, > > (Related to the sec part of your message), luckily, as we know it, > pericycle is present only in the root, so we don't > need to worry about having the term pericycle getting instantiated all > over the place. > > Katica That is fine, but then we need to delete the comment saying "in seed plants it is regularly present in roots and absent in most stems and leaves". It doesn't say it is absent altogether. Also while looking in the Essau, it says.. In the stems of higher vascular plants usually no separate layer is found between the phloem and the cortex and the term pericycle is then applied in the literature to the outermost part of the phloem in which the sieve elements are no longer functional. -Pankaj > On Tue, 31 Aug 2004, Pankaj Jaiswal wrote: > > >>Hi, >>Here is what I proposed in response to Alison's mail for pericycle >> >>---PO:0009075 : plant ontology >>----i PO:0009011 : plant structure >>-------i PO:0009003 : sporophyte >>-----------p PO:0009005 : root >>--------------p PO:0000258 : root cortex >>--------------p PO:0020124 : root stele >>-------------------p PO:0006203 : pericycle >>-------i PO:0009007 : tissue >>-----------i PO:0005708 : cortex >>--------------i PO:0000258 : root cortex >>--------------i PO:0006203 : pericycle >> >>But this is again leading us into a black hole, which we are trying to >>avoid. The term pericycle is a generic term and we need to create its >>instances such as >>-root pericycle >>-stem pericycle >>-leaf pericycle >> >>In order to make correct lineage the instantiation is required. >> >>Current definition and comments sauugest it so.. >> >># Definition: >> >> * Part of the tissue of the stele located between the phloem and >>endodermis. >> >># Comment: >> >> * In seed plants it is regularly present in roots and absent in >>most stems and leaves. >> >> >> >>-Pankaj >> >> > > > -------------------------------------------------------------------------- > Katica Ilic katica at acoma.stanford.edu > The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 > Carnegie Institution of Washington FAX: (650) 325-6857 > Department of Plant Biology URL: http://arabidopsis.org/ > 260 Panama St. > Stanford, CA 94305 > U.S.A. > -------------------------------------------------------------------------- > > > -- ************************ Pankaj Jaiswal, PhD G15-Bradfield Hall Dept. of Plant Breeding Cornell University Ithaca, NY-14853, USA Tel: +1-607-255-3103 +1-607-255-4109 Fax: +1-607-255-6683 http://www.gramene.org ************************ From jitterbug at plantontology.org Tue Aug 31 18:23:07 2004 From: jitterbug at plantontology.org (Katica Ilic) Date: Tue, 31 Aug 2004 18:23:07 -0400 Subject: Soybean ontology (PR#24) Message-ID: <200408312223.i7VMN7Uq015162@brie4.cshl.org> Hi Rex, Thanks again for your interest in plant ontologies. It's great that you have plans to create a comprehensive ontology for soybean and other legumes that will be freely available to the public. I am sure that both, developmental stages and anatomy/morphology ontologies for soybean will be used by a large number of researchers. Regarding a help with DAG-edit, I agree with you, it's not very intuitive tool, but after solving few initial problems, it's relatively easy to edit ontology using this tool. Of course, I'll be happy to help you with tips and suggestions (I had generous help from my colleagues at TAIR). Please feel free to contact me any time. To report bugs that you may sometimes discover, especially with new released versions of Dag-edit, please contact John Day-Richter (john.richter at aya.yale.edu). I look forward to hearing from you and Dr. Randy Schoemaker about possibility for collaboration and joining our efforts at POC. Best Regards, Katica On Tuesday, Aug 31, Rex Nelson wrote: > >Hi Rex, >> >>The short answer to your question would be: us >>at Plant Ontology Consortium. You >>have definitively contacted the right people. > > Yes, I knew it was the right place :> > >>At present time, I am not >>aware of any ongoing effort in the public sector with respect to developing >>anatomy and developmental stages ontologies for soybean. > > Good, I did not think that there was an organized > effort yet. That is why I wanted to contact you > (PO). > >>However, there is a >>growing interestin the plant research community and we have often had people >>asking us about such project. It would help (to give you more specific >>suggestions and tips) if you could tell me a bit >>more about the ontology project >>you have in mind, for instance, a scope of the >>project. Is it going to be a tool >>to facilitate ?in-house? projects (for instance, large-scale gene expression >>profiling), or do you have in mind a comprehensive species-specific ontology >>that would be freely available for a large number of researches working with >>soybean (and others as well). > > I work with Dr. Randy Shoemaker (Research > Geneticist USDA-ARS CICGR Ames, IA) we are > interested in starting an effort to put together > a comprehensive ontology for soybean and then > perhaps extend it to other legumes. As you may > know there are microarray chips currently > available for soybean and an Affy array will be > released soon, thus we are very interested in > getting a controlled vocabulary set to ensure > meaningful annotations to future microarray > experiments can be made. There are also Tilling > mutants for soybean and thus there will be a need > for a vocabulary to describe phenotypic variants. > Any efforts in this direction will of course be > in the public domain. > >>In either case, I can offer you help, and since we >>at POC are open to collaboration and welcome everyone who is genuinely >>interested in collaborating, we can certainly initiate a dialog by discussing >>our mutual interests in soybean ontology project. >> >>Since the first version of the Plant Structure >>Ontology was released last month, >>the current task of the POC is work on the growth and developmental stages >>ontology, primarily having in mind an integration of Arabidopsis and cereal >>ontologies for the first release. Starting at >>the beginning of 2005, we hope to >>make our two plant ontologies applicable to most of the flowering plants by >>including other plant species, among others, tomato and legumes (such as >>Medicago and soybean). > > The first part of our effort would be aimed at > getting a growth and developmental stage ontology > for soybean established. I think that this > should be the place to start because it will be > needed for the microarray experiments to come. > At the same time we will look at the published > anatomical vocabularies and make a list of terms > specific to soybean/legumes that may be needed. > >>Furthermore, over the next two years, POC project will >>expand its plant-ontology-development effort to include other angiosperms >>(tomato, barley, cotton and others). At the end, the controlled vocabularies >>developed by the POC will be generic enough to encompass/cover all the plant >>model systems; this includes cereals/brassicas/solanaceae/gossypium/legumes. >> >>Since I don?t know if you need any specific information about ontology editing >>tools or ontology structure at this point, I decided to leave it out for now. > > I have DAG-Edit and will use that for the > project. DAG-Edit does not seem intuitive to me > so I may have to ask for help from time to time. > It seems that I will also need at some point a > block of PO numbers for soybean/legumes. I also > have some questions regarding style and correct > procedures for the nomenclature. > >> If >>you need suggestions and help with the software for editing your ontology, >>please let me know and don't hesitate to contact us for any other ontology >>related issues. I would be happy to provide you with information and perhaps >>give you some suggestions how to build your ontology. If you are interested in >>collaboration with POC, I would like to discuss such a possibility with you. > > I will pass this note on to Randy for his > consideration and get back in touch with you. > > Regards, > > Rex Nelson > > -- > Rex Nelson Ph. D. > Postdoctoral Fellow > nelsonrt at iastate.edu Katica Ilic, TAIR Curator, E-mail: katica at acoma.stanford.edu The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253 Carnegie Institution of Washington Fax: (650) 325-6857 Department of Plant Biology URL: http://arabidopsis.org/ 260 Panama St. Stanford, CA 94305, U.S.A. From fzqhd at umsl.edu Tue Aug 24 10:38:11 2004 From: fzqhd at umsl.edu (Felipe Zapata) Date: Tue, 24 Aug 2004 09:38:11 -0500 Subject: Changes in tentative date for POC in-person meeting In-Reply-To: References: Message-ID: <39147D3A-F5DB-11D8-BF31-000A95AF2466@umsl.edu> I cannot on Thursday Oct 28. Felipe On Aug 23, 2004, at 5:43 PM, Sue Rhee wrote: > Should be OK with me. > > Sue > > On Mon, 16 Aug 2004, Katica Ilic wrote: > >> >> Hi all, >> >> It turned out that the early November date for our in-person meeting >> is >> not going to work, Pankaj will be away in November. The late October >> one is now only alternative date. So, let's see if Oct 27-30 would be >> OK >> with everyone (it's Wed to Sat). Please let me know asap, we are >> running >> out of available dates; it seems that most of us are going to have a >> busy >> schedule in fall. >> >> Katica >> > > ----------------------------------------------------------------------- > ------ > 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. > ----------------------------------------------------------------------- > ------ >