From jmtepp at uclink.berkeley.edu Mon Jan 3 13:34:40 2005 From: jmtepp at uclink.berkeley.edu (jmtepp at uclink.berkeley.edu) Date: Mon, 3 Jan 2005 10:34:40 -0800 Subject: batch queries? Message-ID: Dear Plant Ontology Folks I'd like to do a batch query for all the GO data for a subset of genes in Arabidopsis (~1500) using AGI locus designations. Is this possible on your website? Jim Tepperman -- James M. Tepperman Department of Plant and Microbial Biology University of California at Berkeley USDA/Plant Gene Expression Center 800 Buchanan St. Albany, CA 94710 Tel: 510-559-5935 Fax; 510-559-5678 email: jmtepp at berkeley.edu From jitterbug at plantontology.org Mon Jan 3 14:09:30 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Mon, 3 Jan 2005 14:09:30 -0500 Subject: PO users question - batch queries (fwd) (PR#51) Message-ID: <200501031909.j03J9UUq015325@brie4.cshl.org> Dear Jim, You can?t do this at the POC web site, simply because we don?t have GO associations uploaded to our PO AmiGO browser, but you can do it at TAIR web site (http://arabidopsis.org/): 1. On the main page, click on the Bulk Downloads (under Analysis Tools), 2. Click on GO Annotations, 3. Upload your AGI loci in the box, 4. Click on Get all Go Annotations... ...and you should get a table with all the GO annotations. If you have more than 1000 loci, only text output will be given. Good luck and let me know if you need any further help with bulk downloads for Arabidopsis. Best regards, Katica Ilic, POC Project Coordinator > Date: Mon, 3 Jan 2005 10:34:40 -0800 > From: jmtepp at uclink.berkeley.edu > Reply-To: po-dev at plantontology.org, jmtepp at uclink.berkeley.edu > To: po at plantontology.org > Subject: batch queries? > > Dear Plant Ontology Folks > > I'd like to do a batch query for all the GO data for a subset of > genes in Arabidopsis (~1500) using AGI locus designations. Is this > possible on your website? > > Jim Tepperman > -- > James M. Tepperman > Department of Plant and Microbial Biology > University of California at Berkeley > USDA/Plant Gene Expression Center > 800 Buchanan St. > Albany, CA 94710 > > Tel: 510-559-5935 > Fax; 510-559-5678 > email: jmtepp at berkeley.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 jitterbug at plantontology.org Mon Jan 3 14:26:09 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Mon, 3 Jan 2005 14:26:09 -0500 Subject: PO is listed at BRENDA enzyme database (fwd) (PR#52) Message-ID: <200501031926.j03JQ9Uq015483@brie4.cshl.org> Dear Christian, Thank you for downloading the Plant Ontology to your local browser at the BRENDA enzyme database (URL:www.brenda.uni-koeln.de). I have a minor comment for the web page where all the ontologies are listed, just as clarification: The ontology is Plant Ontology, and not the Plant Ontology Consortium (to be more specific, it is the Plant Structure Ontology), while the web source is Plant Ontology Consortium. If you could just swap these two around, I would appreciate it. Best Regards, Katica Ilic, POC Project Coordinator > Date: Wed, 22 Dec 2004 15:11:04 +0100 > From: Christian Ebeling > Reply-To: po-dev at plantontology.org, Christian Ebeling > To: go at geneontology.org, Henning.Hermjakob at ebi.ac.uk, po-dev at plantontology.org, > pheno at informatics.jax.org, maria at genome.stanford.edu, gramene at gramene.org, > curator at arabidopsis.org > Subject: Your ontology is listed at BRENDA enzyme database > > Dear curator of an ontology, > > we want inform you that we have integrated in our ontology browser and > "Fulltext Search" engine 9 new ontologies. I inform you because your email > address was listed on http://obo.sourceforge.net/cgi-bin/table.cgi as contact > to your ontology. > > We list your ontology with a link to your webpage and an email contact. > > Please don't hesitate to contact me if you have found any malfunctions or if > you have any suggestions. > > Yours sincerely > Christian > -- > Christian Ebeling > www.brenda.uni-koeln.de > Zuelpicher Str. 47 > 50674 Cologne > Germany > > 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 c.ebeling at uni-koeln.de Tue Jan 4 04:42:54 2005 From: c.ebeling at uni-koeln.de (Christian Ebeling) Date: Tue, 4 Jan 2005 10:42:54 +0100 Subject: PO is listed at BRENDA enzyme database (fwd) (PR#52) In-Reply-To: <200501031926.j03JQ9Uq015483@brie4.cshl.org> References: <200501031926.j03JQ9Uq015483@brie4.cshl.org> Message-ID: <200501041042.55140.c.ebeling@uni-koeln.de> Dear Katica Ilic, thanks for your hints. I changed the ontology name ( to "Plant structure" ) and the source/webpage link name ( to "Plant Ontology Consortium"). Yours sincerely Christian Ebeling Am Montag, 3. Januar 2005 20:26 schrieb Katica Ilic: > Dear Christian, > > Thank you for downloading the Plant Ontology to your local browser at the > BRENDA enzyme database (URL:www.brenda.uni-koeln.de). I have a minor > comment for the web page where all the ontologies are listed, just as > clarification: > > The ontology is Plant Ontology, and not the Plant Ontology Consortium (to > be more specific, it is the Plant Structure Ontology), while the web source > is Plant Ontology Consortium. If you could just swap these two around, I > would appreciate it. > > Best Regards, > > Katica Ilic, POC Project Coordinator > > > Date: Wed, 22 Dec 2004 15:11:04 +0100 > > From: Christian Ebeling > > Reply-To: po-dev at plantontology.org, Christian Ebeling > > > > > To: go at geneontology.org, Henning.Hermjakob at ebi.ac.uk, > > po-dev at plantontology.org, > > > pheno at informatics.jax.org, maria at genome.stanford.edu, > > gramene at gramene.org, > > > curator at arabidopsis.org > > Subject: Your ontology is listed at BRENDA enzyme database > > > > Dear curator of an ontology, > > > > we want inform you that we have integrated in our ontology browser and > > "Fulltext Search" engine 9 new ontologies. I inform you because your > > email address was listed on http://obo.sourceforge.net/cgi-bin/table.cgi > > as contact to your ontology. > > > > We list your ontology with a link to your webpage and an email contact. > > > > Please don't hesitate to contact me if you have found any malfunctions or > > if you have any suggestions. > > > > Yours sincerely > > Christian > > -- > > Christian Ebeling > > www.brenda.uni-koeln.de > > Zuelpicher Str. 47 > > 50674 Cologne > > Germany > > 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. -- Christian Ebeling www.brenda.uni-koeln.de Zuelpicher Str. 47 50674 Cologne Germany From denby at science.uct.ac.za Tue Jan 4 01:52:10 2005 From: denby at science.uct.ac.za (Dr Katherine J. Denby) Date: Tue, 04 Jan 2005 08:52:10 +0200 Subject: [Fwd: First release of gene annotations for Arabidopsis, rice and maize] Message-ID: <41DA3D1A.937115E2@science.uct.ac.za> Hello I am having trouble locating AMiGo - I went to the plant ontology web site and can see the news item about gene annotations and AmiGo but can't find a link to the AmiGo ontology browser. Please can you help? thanks alot Katherine Katica Ilic wrote: > > The Plant Ontology Consortium is pleased to announce the first release of > gene annotations for Arabidopsis, rice and maize associated to the Plant > Structure Ontology terms. Over 3,000 gene annotations from three > species-specific databases, TAIR, Gramene and MaizeGDB, can now be queried > and retrieved using our ontology browser, the Plant Ontology AmiGO. You > can perform searches using plant ontology terms and gene symbols; > filtering options allow you to retrieve annotations for all or a subset of > species (for details, please see the AmiGO Help document). > > We hope the plant research community will benefit from using this > resource. Please fell free to contact us with additional requests for > on-line help with browser and information about the plant ontologies and > annotations (po at plantontology.org). > > Best Regards, > > Plant Ontology Consortium > URL: www.plantontology.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. > -------------------------------------------------------------------------- > > --- -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr Katherine Denby Department of Molecular and Cell Biology University of Cape Town Private Bag Rondebosch 7701 South Africa tel: +27 21 650 2408 fax: +27 21 689 7573 email: denby at science.uct.ac.za web site: http://www.mcb.uct.ac.za//Staff/Denby.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From Leszek at missouri.edu Tue Jan 4 12:25:03 2005 From: Leszek at missouri.edu (Vincent, Leszek) Date: Tue, 4 Jan 2005 11:25:03 -0600 Subject: [Fwd: First release of gene annotations for Arabidopsis, rice and maize] Message-ID: Hi Katherine, Access the Plant Ontology Consortium website (www.plantontology.org) and then select the "Ontology Browser" 'button' near the top left of the page. This button will take you to the Plant Ontology AmiGO browser. Katica Ilic may follow up with further info. - but this will get you going. Thanks for exploring PO. Sincerely, Leszek Vincent *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* P. Leszek D. Vincent Ph.D., FLS Division of Plant Sciences Res. Prof. Dept. of Horticulture 215 Curtis Hall University of Missouri-Columbia Columbia MO 65211-7020 USA Ph: (573) 884-3716; Fax:(573) 884-7850; Email: Leszek at missouri.edu Associate Curator, Dunn-Palmer Herbarium (UMO); Research Associate, Missouri Botanical Garden (MO), USA; Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 (www.plantontology.org) *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=* -----Original Message----- From: owner-po-dev at brie4.cshl.org [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Dr Katherine J. Denby Sent: Tuesday, January 04, 2005 12:52 AM To: po at plantontology.org Subject: [Fwd: First release of gene annotations for Arabidopsis, rice and maize] Hello I am having trouble locating AMiGo - I went to the plant ontology web site and can see the news item about gene annotations and AmiGo but can't find a link to the AmiGo ontology browser. Please can you help? thanks alot Katherine Katica Ilic wrote: > > The Plant Ontology Consortium is pleased to announce the first release > of gene annotations for Arabidopsis, rice and maize associated to the > Plant Structure Ontology terms. Over 3,000 gene annotations from three > species-specific databases, TAIR, Gramene and MaizeGDB, can now be > queried and retrieved using our ontology browser, the Plant Ontology > AmiGO. You can perform searches using plant ontology terms and gene > symbols; filtering options allow you to retrieve annotations for all > or a subset of species (for details, please see the AmiGO Help document). > > We hope the plant research community will benefit from using this > resource. Please fell free to contact us with additional requests for > on-line help with browser and information about the plant ontologies > and annotations (po at plantontology.org). > > Best Regards, > > Plant Ontology Consortium > URL: www.plantontology.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. > ---------------------------------------------------------------------- > ---- > > --- -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr Katherine Denby Department of Molecular and Cell Biology University of Cape Town Private Bag Rondebosch 7701 South Africa tel: +27 21 650 2408 fax: +27 21 689 7573 email: denby at science.uct.ac.za web site: http://www.mcb.uct.ac.za//Staff/Denby.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~ From jitterbug at plantontology.org Tue Jan 4 12:26:39 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Tue, 4 Jan 2005 12:26:39 -0500 Subject: User's question - Link to PO AmiGO (fwd) (PR#53) Message-ID: <200501041726.j04HQdUq022566@brie4.cshl.org> Dear Katherine, Link to the Plant Ontology browser is located at the top navigation bar, second from the left (below the PO logo), in the upper left corner of the main POC web page. I'll also add the link to the last line of the Dec 16 News item. Best regards Katica Ilic, POC Project Coordinator > ---------- Forwarded message ---------- > Date: Tue, 04 Jan 2005 08:52:10 +0200 > From: Dr Katherine J. Denby > Reply-To: po-dev at plantontology.org, > Dr Katherine J. Denby > To: po at plantontology.org > Subject: [Fwd: First release of gene annotations for Arabidopsis, > rice and maize] > > Hello > > I am having trouble locating AMiGo - I went to the plant ontology web > site and can see the news item about gene annotations and AmiGo but > can't find a link to the AmiGo ontology browser. > Please can you help? > thanks alot > Katherine > > > Katica Ilic wrote: >> >> The Plant Ontology Consortium is pleased to announce the first release of >> gene annotations for Arabidopsis, rice and maize associated to the Plant >> Structure Ontology terms. Over 3,000 gene annotations from three >> species-specific databases, TAIR, Gramene and MaizeGDB, can now be queried >> and retrieved using our ontology browser, the Plant Ontology AmiGO. You >> can perform searches using plant ontology terms and gene symbols; >> filtering options allow you to retrieve annotations for all or a subset of >> species (for details, please see the AmiGO Help document). >> >> We hope the plant research community will benefit from using this >> resource. Please fell free to contact us with additional requests for >> on-line help with browser and information about the plant ontologies and >> annotations (po at plantontology.org). >> >> Best Regards, >> >> Plant Ontology Consortium >> URL: www.plantontology.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. >> -------------------------------------------------------------------------- >> >> --- > > -- > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Dr Katherine Denby > Department of Molecular and Cell Biology > University of Cape Town > Private Bag > Rondebosch 7701 > South Africa > > tel: +27 21 650 2408 > fax: +27 21 689 7573 > email: denby at science.uct.ac.za > web site: http://www.mcb.uct.ac.za//Staff/Denby.htm > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > 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 jitterbug at plantontology.org Tue Jan 4 12:27:35 2005 From: jitterbug at plantontology.org (Katica Ilic) Date: Tue, 4 Jan 2005 12:27:35 -0500 Subject: User's question - Link to PO AmiGO (fwd) (PR#53) Message-ID: <200501041727.j04HRZUq022578@brie4.cshl.org> Dear Katherine, Link to the Plant Ontology browser is located at the top navigation bar, second from the left (below the PO logo), in the upper left corner of the main POC web page. I'll also add the link to the last line of the Dec 16 News item. Best regards Katica Ilic, POC Project Coordinator > ---------- Forwarded message ---------- > Date: Tue, 04 Jan 2005 08:52:10 +0200 > From: Dr Katherine J. Denby > Reply-To: po-dev at plantontology.org, > Dr Katherine J. Denby > To: po at plantontology.org > Subject: [Fwd: First release of gene annotations for Arabidopsis, > rice and maize] > > Hello > > I am having trouble locating AMiGo - I went to the plant ontology web > site and can see the news item about gene annotations and AmiGo but > can't find a link to the AmiGo ontology browser. > Please can you help? > thanks alot > Katherine > > > Katica Ilic wrote: >> >> The Plant Ontology Consortium is pleased to announce the first release of >> gene annotations for Arabidopsis, rice and maize associated to the Plant >> Structure Ontology terms. Over 3,000 gene annotations from three >> species-specific databases, TAIR, Gramene and MaizeGDB, can now be queried >> and retrieved using our ontology browser, the Plant Ontology AmiGO. You >> can perform searches using plant ontology terms and gene symbols; >> filtering options allow you to retrieve annotations for all or a subset of >> species (for details, please see the AmiGO Help document). >> >> We hope the plant research community will benefit from using this >> resource. Please fell free to contact us with additional requests for >> on-line help with browser and information about the plant ontologies and >> annotations (po at plantontology.org). >> >> Best Regards, >> >> Plant Ontology Consortium >> URL: www.plantontology.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. >> -------------------------------------------------------------------------- >> >> --- > > -- > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Dr Katherine Denby > Department of Molecular and Cell Biology > University of Cape Town > Private Bag > Rondebosch 7701 > South Africa > > tel: +27 21 650 2408 > fax: +27 21 689 7573 > email: denby at science.uct.ac.za > web site: http://www.mcb.uct.ac.za//Staff/Denby.htm > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > 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 denby at science.uct.ac.za Wed Jan 5 01:37:41 2005 From: denby at science.uct.ac.za (Dr Katherine J. Denby) Date: Wed, 05 Jan 2005 08:37:41 +0200 Subject: User's question - Link to PO AmiGO (fwd) (PR#53) References: <200501041727.j04HRZUq022578@brie4.cshl.org> Message-ID: <41DB8B35.DB9505C9@science.uct.ac.za> thanks alot - obvious now! k Katica Ilic wrote: > > Dear Katherine, > > Link to the Plant Ontology browser is located at the top navigation bar, second > from the left (below the PO logo), in the upper left corner of the main POC web > page. > > I'll also add the link to the last line of the Dec 16 News item. > > Best regards > > Katica Ilic, POC Project Coordinator > > > ---------- Forwarded message ---------- > > Date: Tue, 04 Jan 2005 08:52:10 +0200 > > From: Dr Katherine J. Denby > > Reply-To: po-dev at plantontology.org, > > Dr Katherine J. Denby > > To: po at plantontology.org > > Subject: [Fwd: First release of gene annotations for Arabidopsis, > > rice and maize] > > > > Hello > > > > I am having trouble locating AMiGo - I went to the plant ontology web > > site and can see the news item about gene annotations and AmiGo but > > can't find a link to the AmiGo ontology browser. > > Please can you help? > > thanks alot > > Katherine > > > > > > Katica Ilic wrote: > >> > >> The Plant Ontology Consortium is pleased to announce the first release of > >> gene annotations for Arabidopsis, rice and maize associated to the Plant > >> Structure Ontology terms. Over 3,000 gene annotations from three > >> species-specific databases, TAIR, Gramene and MaizeGDB, can now be queried > >> and retrieved using our ontology browser, the Plant Ontology AmiGO. You > >> can perform searches using plant ontology terms and gene symbols; > >> filtering options allow you to retrieve annotations for all or a subset of > >> species (for details, please see the AmiGO Help document). > >> > >> We hope the plant research community will benefit from using this > >> resource. Please fell free to contact us with additional requests for > >> on-line help with browser and information about the plant ontologies and > >> annotations (po at plantontology.org). > >> > >> Best Regards, > >> > >> Plant Ontology Consortium > >> URL: www.plantontology.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. > >> -------------------------------------------------------------------------- > >> > >> --- > > > > -- > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > Dr Katherine Denby > > Department of Molecular and Cell Biology > > University of Cape Town > > Private Bag > > Rondebosch 7701 > > South Africa > > > > tel: +27 21 650 2408 > > fax: +27 21 689 7573 > > email: denby at science.uct.ac.za > > web site: http://www.mcb.uct.ac.za//Staff/Denby.htm > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > 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. -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr Katherine Denby Department of Molecular and Cell Biology University of Cape Town Private Bag Rondebosch 7701 South Africa tel: +27 21 650 2408 fax: +27 21 689 7573 email: denby at science.uct.ac.za web site: http://www.mcb.uct.ac.za//Staff/Denby.htm ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From feedback_submission at filetta.cshl.edu Sat Jan 15 20:20:42 2005 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Sat, 15 Jan 2005 20:20:42 -0500 Subject: Feedback on POC Message-ID: <200501160120.j0G1Kgq1021499@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: http://www.plantontology.org/index.html comments: in the nav bar, instaed of calling POC tutorials, can we call it "tutorials" only. name: pankaj email: pj37 at cornell.edu organization: CU send_feedback: Send your feedback From shuly at cshl.edu Sun Jan 16 14:31:53 2005 From: shuly at cshl.edu (Shuly Avraham) Date: Sun, 16 Jan 2005 14:31:53 -0500 Subject: Feedback on POC In-Reply-To: <200501160120.j0G1Kgq1021499@filetta.cshl.org> References: <200501160120.j0G1Kgq1021499@filetta.cshl.org> Message-ID: <41EAC129.9010209@cshl.edu> OK. I changed the option in nav bar to 'Tutorials'. Shuly. feedback_submission at filetta.cshl.edu wrote: > *** Feedback from Plant Ontology Live Site *** > >refer_to_url: http://www.plantontology.org/index.html > >comments: in the nav bar, instaed of calling POC tutorials, can we call it "tutorials" only. > > >name: pankaj > >email: pj37 at cornell.edu > >organization: CU > >send_feedback: Send your feedback > > > From shuly at cshl.edu Mon Jan 24 10:11:27 2005 From: shuly at cshl.edu (Shuly Avraham) Date: Mon, 24 Jan 2005 10:11:27 -0500 Subject: [Fwd: Important: Computer and network outage Tuesday, Jan 25th.] Message-ID: <41F5101F.4070006@cshl.edu> Hi All, Plant Ontology web site will not be available between 5:30 pm and 10:30 pm tomorrow. I put up a note on the web site index page. Shuly. -------------- next part -------------- An embedded message was scrubbed... From: Peter Van Buren Subject: Important: Computer and network outage Tuesday, Jan 25th. Date: Fri, 21 Jan 2005 01:53:53 -0500 (EST) Size: 1711 URL: From katica at acoma.Stanford.EDU Mon Jan 24 16:43:59 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 24 Jan 2005 13:43:59 -0800 (PST) Subject: New node in the Plant Structure Ontology Message-ID: Hi all, I finally put together In vitro (experimental) node for the Plant Structure Ontology. Additional terms can be introduced later, these are the terms needed for annotations in TAIR, Gramene and maizeGDB. I've had second thoughts about terms that have 'culture' in the name, but these are already existing terms, at least in TAIR and MaizeDGB. I would greatly appreciate your suggestions and comments, especially regarding the definitions. The top node term is 'In vitro cell, tissue and organ culture' and this term will go under the 'plant structure', as sibling to the four top nodes: PO:0009002 : cell PO:0009004 : gametophyte PO:0009003 : sporophyte PO:0009007 : tissue New term: In vitro cell, tissue and organ culture (i) protoplast culture (i) cell culture (i) leaf cell culture (i) root cell culture (i) callus (i) callus culture (i) embryo culture (i) somatic embryo Suggested definitions for the new terms: Term: in vitro cell, tissue and organ culture Definition: Experimentaly isolated and grown plant protoplast, cell, tissue and organ, that involves, as a common factor, growth of microbe-free plant material in an aseptic (sterile) environment, such as sterilized nutrient medium in a test tube or petri dish. Term: protoplast culture Def: In vitro isolation and maintenance of the cells from which the entire cell wall has been enzymatically removed. Term: cell culture Synonym: Cell suspension culture (cell suspension, carrot cell suspension, tobacco cell suspension, maize cell suspension) Def: In vitro grown isolated cells and small cell aggregates that proliferate while suspended in liquid sterile medium or spread on a solid agar medium. Comment: In cell cultures, the cells are no longer organized into tissues. Term: leaf cell culture Def: In vitro grown isolated cells and small cell aggregates that originated from isolated leaf protoplasts (after they re-established cell wall, or from callus that was induced from leaf tissue). Term: root cell culture Def: In vitro grown isolated cells and small cell aggregates that originated from isolated protoplasts after they re-established cell wall, or from callus that was induced from segment of root. Term: somatic embryo: Def: An embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote. Term: Callus: An unorganized, proliferative mass of large, thin-walled cells; a wound response. Term: Callus culture Def: In vitro grown cell aggregates that originated from isolated protoplasts, cell suspensions, or from callus that was induced in sterile medium the supplemented by plant growth regulators. Term: embryo culture: Def: In vitro development or maintenance of isolated mature or immature zygotic embryos, or somatic embryos. 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 Tue Jan 25 11:32:10 2005 From: PolaccoM at missouri.edu (Mary Polacco) Date: Tue, 25 Jan 2005 10:32:10 -0600 Subject: making it easier for databases to use the PO In-Reply-To: Message-ID: Hi all Is there any reason not to post a list of the PO accessions and the terms, alphabetically - ie no ontology structure? It makes it easier for database folks such as myself both to retrofit, and use the approved terms and their the accession IDs. Attached is a list - from last fall, the CVS dump of terms with accessions and ontology structure, that I used to help map to MaizeGDB. Missing terms, eg synonyms for husk, I mapped using the PO AmiGO browser. It should be trivial for a regular update of this sort to be dumped from the AmiGO database. mary -------------- next part -------------- A non-text attachment was scrubbed... Name: POID_2004.txt Type: application/octet-stream Size: 74208 bytes Desc: not available URL: From shuly at cshl.edu Tue Jan 25 11:38:43 2005 From: shuly at cshl.edu (Shuly Avraham) Date: Tue, 25 Jan 2005 11:38:43 -0500 Subject: making it easier for databases to use the PO In-Reply-To: References: Message-ID: <41F67613.8070502@cshl.edu> Hi Mary, This kind of list is very easy to generate. If all you need is a flat list of terms organized alphabetically, I can generate the list and place the file on our (soon to come) FTP site. If there are other kinds of requsets or database queries, I can generate those as well. In addition, in the near future we will have a mysql database dump on the ftp site, so you can create a local copy of the database, and query it as you need. Shuly. Mary Polacco wrote: >Hi all > >Is there any reason not to post a list of the PO accessions and the terms, >alphabetically - ie no ontology structure? > >It makes it easier for database folks such as myself both to retrofit, and >use the approved terms and their the accession IDs. > >Attached is a list - from last fall, the CVS dump of terms with accessions >and ontology structure, that I used to help map to MaizeGDB. Missing terms, >eg synonyms for husk, I mapped using the PO AmiGO browser. It should be >trivial for a regular update of this sort to be dumped from the AmiGO >database. > > mary > > From PolaccoM at missouri.edu Tue Jan 25 11:54:33 2005 From: PolaccoM at missouri.edu (Mary Polacco) Date: Tue, 25 Jan 2005 10:54:33 -0600 Subject: making it easier for databases to use the PO In-Reply-To: <41F67613.8070502@cshl.edu> Message-ID: Great. Let me know when you do that - I will point the micro-array dudes there - I have been in contact re the maize terms and have sent them my flat file, attached in last email, with instructions to use AmiGO PO browser if they couldn't find a term -- eg synonyms such as husk and kernel for a consensus PO term -- or simply new terms not in my flat file. Another issue about usage by databases - some folks (or at least when they are talking to me) think that they should be using the Zea ontology posting for maize. Leszek and I will post a README in the CVS for the Zea ontology indicating it is NOT the PO, but was used to develop the PO, and has maize oriented definitions, etc etc. m On 1/25/05 10:38 AM, "Shuly Avraham" wrote: > Hi Mary, > > This kind of list is very easy to generate. If all you need is a flat > list of terms organized alphabetically, I can generate the list and > place the file on our (soon to come) FTP site. > If there are other kinds of requsets or database queries, I can generate > those as well. > In addition, in the near future we will have a mysql database dump on > the ftp site, so you can create a local copy of the database, and query > it as you need. > > Shuly. > > Mary Polacco wrote: > >> Hi all >> >> Is there any reason not to post a list of the PO accessions and the terms, >> alphabetically - ie no ontology structure? >> >> It makes it easier for database folks such as myself both to retrofit, and >> use the approved terms and their the accession IDs. >> >> Attached is a list - from last fall, the CVS dump of terms with accessions >> and ontology structure, that I used to help map to MaizeGDB. Missing terms, >> eg synonyms for husk, I mapped using the PO AmiGO browser. It should be >> trivial for a regular update of this sort to be dumped from the AmiGO >> database. >> >> mary >> >> > From pj37 at cornell.edu Tue Jan 25 12:34:38 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 25 Jan 2005 12:34:38 -0500 Subject: making it easier for databases to use the PO In-Reply-To: <41F67613.8070502@cshl.edu> References: <41F67613.8070502@cshl.edu> Message-ID: <41F6832E.50200@cornell.edu> I think Mary wants something like they have for GO Tab-delimited GO.terms_and_ids file containing GO term IDs, names and ontologies in the following format GO:0000001 mitochondrion inheritance P GO:0000002 mitochondrial genome maintenance P http://www.geneontology.org/doc/GO.terms_and_ids However, I would suggest Mary to generate a file for MaizeGDB and POC's reference like a mapping file namely MaizeGDB2PO. MaizeGDB can decide on how often they would like to update this and can help her in automating the association dump. Here is a more precise suggestion on format of this file. Shuly you can put this into your SOPs for creating mappings to the external vocabularies. This was taken from Go documents and updated for PO purposes. reference: ftp://ftp.geneontology.org/pub/go/external2go -Pankaj ----------------------------- Indices of Other Classification Systems to PO PO is not the only attempt to build structured controlled vocabularies for plant anatomical and growth stage annotation. Nor is it the only such series of catalogs in current use. We have, in a series of files in the folder /external2go--->[SHULY : create this in CVS] attempted to make translation tables between these catalogs and PO. We caution that these mappings are neither complete nor exact; they are to be used as a guide and is the sole responsibility of the curator or the information resource that generates them. One reason for this is absence of definitions from many of the other catalogs and of a complete set of definitions in PO itself. The line: !Uses: e.g. !Uses:Source name and URL if possible gives the source of the external file. The line syntax is: database: > PO: ; PO: e.g.: MaizeGDB:123456 > PO:seed ; PO:0009010 MaizeGDB:123457 > PO:seed coat ; PO:0009088 _________________________________________ Shuly Avraham wrote: > Hi Mary, > > This kind of list is very easy to generate. If all you need is a flat > list of terms organized alphabetically, I can generate the list and > place the file on our (soon to come) FTP site. > If there are other kinds of requsets or database queries, I can generate > those as well. > In addition, in the near future we will have a mysql database dump on > the ftp site, so you can create a local copy of the database, and query > it as you need. > > Shuly. > > Mary Polacco wrote: > >> Hi all >> >> Is there any reason not to post a list of the PO accessions and the >> terms, >> alphabetically - ie no ontology structure? >> >> It makes it easier for database folks such as myself both to retrofit, >> and >> use the approved terms and their the accession IDs. >> >> Attached is a list - from last fall, the CVS dump of terms with >> accessions >> and ontology structure, that I used to help map to MaizeGDB. Missing >> terms, >> eg synonyms for husk, I mapped using the PO AmiGO browser. It should be >> trivial for a regular update of this sort to be dumped from the AmiGO >> database. >> >> mary >> >> > -- ************************ 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 Tue Jan 25 12:38:24 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Tue, 25 Jan 2005 09:38:24 -0800 (PST) Subject: making it easier for databases to use the PO In-Reply-To: Message-ID: Mary, I like the idea, we can just put it on the ftp site. Shuly and Doreen, here is another item to discuss for the upcoming conf call. Katica On Tue, 25 Jan 2005, Mary Polacco wrote: > Hi all > > Is there any reason not to post a list of the PO accessions and the terms, > alphabetically - ie no ontology structure? > > It makes it easier for database folks such as myself both to retrofit, and > use the approved terms and their the accession IDs. > > Attached is a list - from last fall, the CVS dump of terms with accessions > and ontology structure, that I used to help map to MaizeGDB. Missing terms, > eg synonyms for husk, I mapped using the PO AmiGO browser. It should be > trivial for a regular update of this sort to be dumped from the AmiGO > database. > > mary > > -------------------------------------------------------------------------- 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 Tue Jan 25 12:41:04 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Tue, 25 Jan 2005 09:41:04 -0800 (PST) Subject: making it easier for databases to use the PO In-Reply-To: <41F67613.8070502@cshl.edu> Message-ID: Sorry for the redundancy, didn't read Shuly's message. She and I have been thinking the same thing, ftp site. Other files of interest to the PO users could be placed there too. Katica On Tue, 25 Jan 2005, Shuly Avraham wrote: > Hi Mary, > > This kind of list is very easy to generate. If all you need is a flat > list of terms organized alphabetically, I can generate the list and > place the file on our (soon to come) FTP site. > If there are other kinds of requsets or database queries, I can generate > those as well. > In addition, in the near future we will have a mysql database dump on > the ftp site, so you can create a local copy of the database, and query > it as you need. > > Shuly. > > Mary Polacco wrote: > > >Hi all > > > >Is there any reason not to post a list of the PO accessions and the terms, > >alphabetically - ie no ontology structure? > > > >It makes it easier for database folks such as myself both to retrofit, and > >use the approved terms and their the accession IDs. > > > >Attached is a list - from last fall, the CVS dump of terms with accessions > >and ontology structure, that I used to help map to MaizeGDB. Missing terms, > >eg synonyms for husk, I mapped using the PO AmiGO browser. It should be > >trivial for a regular update of this sort to be dumped from the AmiGO > >database. > > > > mary > > > > > -------------------------------------------------------------------------- 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 Tue Jan 25 13:57:17 2005 From: PolaccoM at missouri.edu (Mary Polacco) Date: Tue, 25 Jan 2005 12:57:17 -0600 Subject: making it easier for databases to use the PO In-Reply-To: <41F67A44.7030905@cshl.edu> Message-ID: Shuly, Thanks much.!!!:))) Synonyms would be great - not sure that we are talking about a large quantity of terms - but I can send them on to Jack who is mapping the microarray library terms. RE second issue (below) I was just referring to the file on the CVS server for the Zea ontology. This is different than than the POC and has different PO accession space. I am encouraging users in the maize community to look to PO files (not the Zea files) for the accessions ID and to contact me, or Leszek, if they have a problem in the mapping. mary On 1/25/05 10:56 AM, "Shuly Avraham" wrote: > Mary, > > I can also generate a file with the synonyms for each term, and email it > to you if you need it now. > > About the second issue, I am not sure I understand correctly, but the > reason I am using Zea and not maize, is because that's the taxonomy > number in the association file you provided. But, again, I am not sure I > understood the problem right. > > Shuly. > > Mary Polacco wrote: > >> Great. >> Let me know when you do that - I will point the micro-array dudes there - I >> have been in contact re the maize terms and have sent them my flat file, >> attached in last email, with instructions to use AmiGO PO browser if they >> couldn't find a term -- eg synonyms such as husk and kernel for a consensus >> PO term -- or simply new terms not in my flat file. >> >> Another issue about usage by databases - some folks (or at least when they >> are talking to me) think that they should be using the Zea ontology posting >> for maize. Leszek and I will post a README in the CVS for the Zea ontology >> indicating it is NOT the PO, but was used to develop the PO, and has maize >> oriented definitions, etc etc. >> >> m >> >> On 1/25/05 10:38 AM, "Shuly Avraham" wrote: >> >> >> >>> Hi Mary, >>> >>> This kind of list is very easy to generate. If all you need is a flat >>> list of terms organized alphabetically, I can generate the list and >>> place the file on our (soon to come) FTP site. >>> If there are other kinds of requsets or database queries, I can generate >>> those as well. >>> In addition, in the near future we will have a mysql database dump on >>> the ftp site, so you can create a local copy of the database, and query >>> it as you need. >>> >>> Shuly. >>> >>> Mary Polacco wrote: >>> >>> >>> >>>> Hi all >>>> >>>> Is there any reason not to post a list of the PO accessions and the terms, >>>> alphabetically - ie no ontology structure? >>>> >>>> It makes it easier for database folks such as myself both to retrofit, and >>>> use the approved terms and their the accession IDs. >>>> >>>> Attached is a list - from last fall, the CVS dump of terms with accessions >>>> and ontology structure, that I used to help map to MaizeGDB. Missing terms, >>>> eg synonyms for husk, I mapped using the PO AmiGO browser. It should be >>>> trivial for a regular update of this sort to be dumped from the AmiGO >>>> database. >>>> >>>> mary >>>> >>>> >>>> >>>> >> >> >> > From pj37 at cornell.edu Tue Jan 25 13:58:20 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 25 Jan 2005 13:58:20 -0500 Subject: New node in the Plant Structure Ontology In-Reply-To: References: Message-ID: <41F696CC.70200@cornell.edu> I still do not think that we need to create a separate node "In vitro cell, tissue and organ culture". All the instances of this term can easily go under either cell/tissue/sprorophyte depending on the cultured plant structure. Also I would rephrase them as below, because one studies the expression of the genes or extracts enzymes/proteins/RNA from the actual cells or a tissue that were grown in an in-vitro culture, where the use of term "culture" is a recognition of method. The methodology can be described in the definition. leaf cell culture > cultured leaf cell root cell culture > cultured root cell protoplast culture > protoplast and appear in the tree as cell ..i..cultured leaf cell ..i..cultured root cell ..i..protoplast tissue ..i..callus-->I am sure it is an instance of meristem. embryo ..i..somatic embryo -Pankaj Katica Ilic wrote: > Hi all, > > I finally put together In vitro (experimental) node for the Plant > Structure Ontology. > > Additional terms can be introduced later, these are the terms needed for > annotations in TAIR, Gramene and maizeGDB. I've had second thoughts about > terms that have 'culture' in the name, but these are already existing > terms, at least in TAIR and MaizeDGB. > > I would greatly appreciate your suggestions and comments, especially > regarding the definitions. > > The top node term is 'In vitro cell, tissue and organ culture' and this > term will go under the 'plant structure', as sibling to the four top > nodes: > > PO:0009002 : cell > PO:0009004 : gametophyte > PO:0009003 : sporophyte > PO:0009007 : tissue > New term: In vitro cell, tissue and organ culture > (i) protoplast culture > (i) cell culture > (i) leaf cell culture > (i) root cell culture > (i) callus > (i) callus culture > (i) embryo culture > (i) somatic embryo > > > Suggested definitions for the new terms: > > Term: in vitro cell, tissue and organ culture > Definition: > Experimentaly isolated and grown plant protoplast, cell, tissue and > organ, that involves, as a common factor, growth of microbe-free > plant material in an aseptic (sterile) environment, such as > sterilized nutrient medium in a test tube or petri dish. > > Term: protoplast culture > Def: In vitro isolation and maintenance of the cells from which the entire > cell wall has been enzymatically removed. > > Term: cell culture > Synonym: Cell suspension culture (cell suspension, carrot cell suspension, > tobacco cell suspension, maize cell suspension) > Def: In vitro grown isolated cells and small cell aggregates that > proliferate while suspended in liquid sterile medium or spread on a solid > agar medium. > Comment: In cell cultures, the cells are no longer organized into > tissues. > > Term: leaf cell culture > Def: In vitro grown isolated cells and small cell aggregates that > originated from isolated leaf protoplasts (after they re-established cell > wall, or from callus that was induced from leaf tissue). > > Term: root cell culture > Def: In vitro grown isolated cells and small cell aggregates that > originated from isolated protoplasts after they re-established cell wall, > or from callus that was induced from segment of root. > > Term: somatic embryo: > Def: An embryo arising from previously differentiated somatic cells in > vitro, rather than from fused haploid gametes, i.e., zygote. > > Term: Callus: An unorganized, proliferative mass of large, thin-walled > cells; a wound response. > > Term: Callus culture > Def: In vitro grown cell aggregates that originated from isolated > protoplasts, cell suspensions, or from callus that was induced in sterile > medium the supplemented by plant growth regulators. > > Term: embryo culture: > Def: In vitro development or maintenance of isolated mature or > immature zygotic embryos, or somatic embryos. > > > 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. > -------------------------------------------------------------------------- > > > -- ************************ 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 lstein at cshl.edu Tue Jan 25 14:59:01 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Tue, 25 Jan 2005 14:59:01 -0500 Subject: New node in the Plant Structure Ontology In-Reply-To: <41F696CC.70200@cornell.edu> References: <41F696CC.70200@cornell.edu> Message-ID: <200501251459.01382.lstein@cshl.edu> Hi all, I think we hashed through this at the spring meeting and the issue that came up is that there are cultured lines that don't correspond directly to any normal tissue. The equivalent in human would be the HeLa cell line, which was derived (a long long time ago) from an ovarian cancer, but would hardly be described as "ovarian tissue" now. Certainly for primary cultures an annotator might want to describe the source of a microarray tissue as "derived from primary culture of leaf tissue", where "leaf tissue" uses the appropriate PO term. For established lines, though, I would be more comfortable descending from an "in vitro cell, tissue, organ culture" node. Lincoln On Tuesday 25 January 2005 01:58 pm, Pankaj Jaiswal wrote: > I still do not think that we need to create a separate node "In > vitro cell, tissue and organ culture". All the instances of this > term can easily go under either cell/tissue/sprorophyte depending > on the cultured plant structure. > > Also I would rephrase them as below, because one studies the > expression of the genes or extracts enzymes/proteins/RNA from the > actual cells or a tissue that were grown in an in-vitro culture, > where the use of term "culture" is a recognition of method. The > methodology can be described in the definition. > > leaf cell culture > cultured leaf cell > root cell culture > cultured root cell > protoplast culture > protoplast > > and appear in the tree as > > cell > .i..cultured leaf cell > .i..cultured root cell > .i..protoplast > > tissue > .i..callus-->I am sure it is an instance of meristem. > > embryo > .i..somatic embryo > > -Pankaj > > Katica Ilic wrote: > > Hi all, > > > > I finally put together In vitro (experimental) node for the Plant > > Structure Ontology. > > > > Additional terms can be introduced later, these are the terms > > needed for annotations in TAIR, Gramene and maizeGDB. I've had > > second thoughts about terms that have 'culture' in the name, but > > these are already existing terms, at least in TAIR and MaizeDGB. > > > > I would greatly appreciate your suggestions and comments, > > especially regarding the definitions. > > > > The top node term is 'In vitro cell, tissue and organ culture' > > and this term will go under the 'plant structure', as sibling to > > the four top nodes: > > > > PO:0009002 : cell > > PO:0009004 : gametophyte > > PO:0009003 : sporophyte > > PO:0009007 : tissue > > New term: In vitro cell, tissue and organ culture > > (i) protoplast culture > > (i) cell culture > > (i) leaf cell culture > > (i) root cell culture > > (i) callus > > (i) callus culture > > (i) embryo culture > > (i) somatic embryo > > > > > > Suggested definitions for the new terms: > > > > Term: in vitro cell, tissue and organ culture > > Definition: > > Experimentaly isolated and grown plant protoplast, cell, tissue > > and organ, that involves, as a common factor, growth of > > microbe-free plant material in an aseptic (sterile) environment, > > such as sterilized nutrient medium in a test tube or petri dish. > > > > Term: protoplast culture > > Def: In vitro isolation and maintenance of the cells from which > > the entire cell wall has been enzymatically removed. > > > > Term: cell culture > > Synonym: Cell suspension culture (cell suspension, carrot cell > > suspension, tobacco cell suspension, maize cell suspension) > > Def: In vitro grown isolated cells and small cell aggregates that > > proliferate while suspended in liquid sterile medium or spread on > > a solid agar medium. > > Comment: In cell cultures, the cells are no longer organized > > into tissues. > > > > Term: leaf cell culture > > Def: In vitro grown isolated cells and small cell aggregates that > > originated from isolated leaf protoplasts (after they > > re-established cell wall, or from callus that was induced from > > leaf tissue). > > > > Term: root cell culture > > Def: In vitro grown isolated cells and small cell aggregates that > > originated from isolated protoplasts after they re-established > > cell wall, or from callus that was induced from segment of root. > > > > Term: somatic embryo: > > Def: An embryo arising from previously differentiated somatic > > cells in vitro, rather than from fused haploid gametes, i.e., > > zygote. > > > > Term: Callus: An unorganized, proliferative mass of large, > > thin-walled cells; a wound response. > > > > Term: Callus culture > > Def: In vitro grown cell aggregates that originated from isolated > > protoplasts, cell suspensions, or from callus that was induced in > > sterile medium the supplemented by plant growth regulators. > > > > Term: embryo culture: > > Def: In vitro development or maintenance of isolated mature or > > immature zygotic embryos, or somatic embryos. > > > > > > 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. > > ----------------------------------------------------------------- > >--------- -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 NOTE: Please copy Sandra Michelsen on all emails regarding scheduling and other time-critical topics. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: not available URL: From pj37 at cornell.edu Tue Jan 25 15:13:11 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 25 Jan 2005 15:13:11 -0500 Subject: New node in the Plant Structure Ontology In-Reply-To: <200501251459.01382.lstein@cshl.edu> References: <41F696CC.70200@cornell.edu> <200501251459.01382.lstein@cshl.edu> Message-ID: <41F6A857.1080405@cornell.edu> Hi Lincoln, I forgot to mention in my suggestion that there will not be any instantiation of second relationship to the tissue or organ from where the cells/callus was extracted. Therefore the following terms for cultured cell for example will have only one parent "cell" with IS_A (i) relationship. cell .i..cultured leaf cell .i..cultured root cell .i..protoplast Similarly in your example of HeLa cells will remain as instances of cells only and there will not be any second relationship to the ovarian tissue. -Pankaj Lincoln Stein wrote: > Hi all, > > I think we hashed through this at the spring meeting and the issue > that came up is that there are cultured lines that don't correspond > directly to any normal tissue. The equivalent in human would be the > HeLa cell line, which was derived (a long long time ago) from an > ovarian cancer, but would hardly be described as "ovarian tissue" > now. > > Certainly for primary cultures an annotator might want to describe the > source of a microarray tissue as "derived from primary culture of > leaf tissue", where "leaf tissue" uses the appropriate PO term. For > established lines, though, I would be more comfortable descending > from an "in vitro cell, tissue, organ culture" node. > > Lincoln > > On Tuesday 25 January 2005 01:58 pm, Pankaj Jaiswal wrote: > >>I still do not think that we need to create a separate node "In >>vitro cell, tissue and organ culture". All the instances of this >>term can easily go under either cell/tissue/sprorophyte depending >>on the cultured plant structure. >> >>Also I would rephrase them as below, because one studies the >>expression of the genes or extracts enzymes/proteins/RNA from the >>actual cells or a tissue that were grown in an in-vitro culture, >>where the use of term "culture" is a recognition of method. The >>methodology can be described in the definition. >> >>leaf cell culture > cultured leaf cell >>root cell culture > cultured root cell >>protoplast culture > protoplast >> >>and appear in the tree as >> >>cell >>.i..cultured leaf cell >>.i..cultured root cell >>.i..protoplast >> >>tissue >>.i..callus-->I am sure it is an instance of meristem. >> >>embryo >>.i..somatic embryo >> >>-Pankaj >> >>Katica Ilic wrote: >> >>>Hi all, >>> >>>I finally put together In vitro (experimental) node for the Plant >>>Structure Ontology. >>> >>>Additional terms can be introduced later, these are the terms >>>needed for annotations in TAIR, Gramene and maizeGDB. I've had >>>second thoughts about terms that have 'culture' in the name, but >>>these are already existing terms, at least in TAIR and MaizeDGB. >>> >>>I would greatly appreciate your suggestions and comments, >>>especially regarding the definitions. >>> >>>The top node term is 'In vitro cell, tissue and organ culture' >>>and this term will go under the 'plant structure', as sibling to >>>the four top nodes: >>> >>>PO:0009002 : cell >>>PO:0009004 : gametophyte >>>PO:0009003 : sporophyte >>>PO:0009007 : tissue >>>New term: In vitro cell, tissue and organ culture >>> (i) protoplast culture >>> (i) cell culture >>> (i) leaf cell culture >>> (i) root cell culture >>> (i) callus >>> (i) callus culture >>> (i) embryo culture >>> (i) somatic embryo >>> >>> >>>Suggested definitions for the new terms: >>> >>>Term: in vitro cell, tissue and organ culture >>>Definition: >>>Experimentaly isolated and grown plant protoplast, cell, tissue >>>and organ, that involves, as a common factor, growth of >>>microbe-free plant material in an aseptic (sterile) environment, >>>such as sterilized nutrient medium in a test tube or petri dish. >>> >>>Term: protoplast culture >>>Def: In vitro isolation and maintenance of the cells from which >>>the entire cell wall has been enzymatically removed. >>> >>>Term: cell culture >>>Synonym: Cell suspension culture (cell suspension, carrot cell >>>suspension, tobacco cell suspension, maize cell suspension) >>>Def: In vitro grown isolated cells and small cell aggregates that >>>proliferate while suspended in liquid sterile medium or spread on >>>a solid agar medium. >>>Comment: In cell cultures, the cells are no longer organized >>>into tissues. >>> >>>Term: leaf cell culture >>>Def: In vitro grown isolated cells and small cell aggregates that >>>originated from isolated leaf protoplasts (after they >>>re-established cell wall, or from callus that was induced from >>>leaf tissue). >>> >>>Term: root cell culture >>>Def: In vitro grown isolated cells and small cell aggregates that >>>originated from isolated protoplasts after they re-established >>>cell wall, or from callus that was induced from segment of root. >>> >>>Term: somatic embryo: >>>Def: An embryo arising from previously differentiated somatic >>>cells in vitro, rather than from fused haploid gametes, i.e., >>>zygote. >>> >>>Term: Callus: An unorganized, proliferative mass of large, >>>thin-walled cells; a wound response. >>> >>>Term: Callus culture >>>Def: In vitro grown cell aggregates that originated from isolated >>>protoplasts, cell suspensions, or from callus that was induced in >>>sterile medium the supplemented by plant growth regulators. >>> >>>Term: embryo culture: >>>Def: In vitro development or maintenance of isolated mature or >>>immature zygotic embryos, or somatic embryos. >>> >>> >>>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. >>>----------------------------------------------------------------- >>>--------- > > -- ************************ 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 Tue Jan 25 16:42:40 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Tue, 25 Jan 2005 13:42:40 -0800 (PST) Subject: New node in the Plant Structure Ontology In-Reply-To: <200501251459.01382.lstein@cshl.edu> Message-ID: Pankaj, We came to the conclusion on having a separate node for in vitro term back last spring, and this idea of propagating annotations from 'cell culture' term all the way up to the cell node just does't make sense to me. However, I would consider renaming the terms like 'root cell culture' to 'cultured root cell', or 'protoplast culture' to cultured protoplast'. I wouldn't call it just 'protoplast', to avoid possible confusion (if this term is to stay in 'in vitro ' node). Def from K. Esau: Protoplast: The organized living unit of a single cell including protoplasmic and nonprotoplasmic contents of a cell but excluding the cell wall. (PO) suggested def: In vitro isolated cells from which the entire cell wall has been enzymatically removed. I am not sure about annotations to 'somatic embryos'; if we want those appearing under 'embryo', but we can certainly discuss this. Also, callus is NOT a meristem, even in tissue culture, researchers don't refer to it as meristem. K Esau described it as a tissue (see her definition), and in a broad sense it is tissue. Esau def: Callus: A tissue composed of large thin-walled cells developing as a result of injury, as in wound healing or grafting, and in tissue culture. I don't know what is the best solution for the term 'callus'; in a strict sense, it doesn't belong to the 'in vitro' node, but it dsoesn't belong to the rest of the structure ontology either. I've been thinking of defining this top node in a broad way that would acomodate terms like 'callus', which means it wouldn't be specifically called "in vitro cell, tissue, organ culture". Any ideas? Katica On Tue, 25 Jan 2005, Lincoln Stein wrote: > Hi all, > > I think we hashed through this at the spring meeting and the issue > that came up is that there are cultured lines that don't correspond > directly to any normal tissue. The equivalent in human would be the > HeLa cell line, which was derived (a long long time ago) from an > ovarian cancer, but would hardly be described as "ovarian tissue" > now. > > Certainly for primary cultures an annotator might want to describe the > source of a microarray tissue as "derived from primary culture of > leaf tissue", where "leaf tissue" uses the appropriate PO term. For > established lines, though, I would be more comfortable descending > from an "in vitro cell, tissue, organ culture" node. > > Lincoln > > On Tuesday 25 January 2005 01:58 pm, Pankaj Jaiswal wrote: > > I still do not think that we need to create a separate node "In > > vitro cell, tissue and organ culture". All the instances of this > > term can easily go under either cell/tissue/sprorophyte depending > > on the cultured plant structure. > > > > Also I would rephrase them as below, because one studies the > > expression of the genes or extracts enzymes/proteins/RNA from the > > actual cells or a tissue that were grown in an in-vitro culture, > > where the use of term "culture" is a recognition of method. The > > methodology can be described in the definition. > > > > leaf cell culture > cultured leaf cell > > root cell culture > cultured root cell > > protoplast culture > protoplast > > > > and appear in the tree as > > > > cell > > .i..cultured leaf cell > > .i..cultured root cell > > .i..protoplast > > > > tissue > > .i..callus-->I am sure it is an instance of meristem. > > > > embryo > > .i..somatic embryo > > > > -Pankaj > > > > Katica Ilic wrote: > > > Hi all, > > > > > > I finally put together In vitro (experimental) node for the Plant > > > Structure Ontology. > > > > > > Additional terms can be introduced later, these are the terms > > > needed for annotations in TAIR, Gramene and maizeGDB. I've had > > > second thoughts about terms that have 'culture' in the name, but > > > these are already existing terms, at least in TAIR and MaizeDGB. > > > > > > I would greatly appreciate your suggestions and comments, > > > especially regarding the definitions. > > > > > > The top node term is 'In vitro cell, tissue and organ culture' > > > and this term will go under the 'plant structure', as sibling to > > > the four top nodes: > > > > > > PO:0009002 : cell > > > PO:0009004 : gametophyte > > > PO:0009003 : sporophyte > > > PO:0009007 : tissue > > > New term: In vitro cell, tissue and organ culture > > > (i) protoplast culture > > > (i) cell culture > > > (i) leaf cell culture > > > (i) root cell culture > > > (i) callus > > > (i) callus culture > > > (i) embryo culture > > > (i) somatic embryo > > > > > > > > > Suggested definitions for the new terms: > > > > > > Term: in vitro cell, tissue and organ culture > > > Definition: > > > Experimentaly isolated and grown plant protoplast, cell, tissue > > > and organ, that involves, as a common factor, growth of > > > microbe-free plant material in an aseptic (sterile) environment, > > > such as sterilized nutrient medium in a test tube or petri dish. > > > > > > Term: protoplast culture > > > Def: In vitro isolation and maintenance of the cells from which > > > the entire cell wall has been enzymatically removed. > > > > > > Term: cell culture > > > Synonym: Cell suspension culture (cell suspension, carrot cell > > > suspension, tobacco cell suspension, maize cell suspension) > > > Def: In vitro grown isolated cells and small cell aggregates that > > > proliferate while suspended in liquid sterile medium or spread on > > > a solid agar medium. > > > Comment: In cell cultures, the cells are no longer organized > > > into tissues. > > > > > > Term: leaf cell culture > > > Def: In vitro grown isolated cells and small cell aggregates that > > > originated from isolated leaf protoplasts (after they > > > re-established cell wall, or from callus that was induced from > > > leaf tissue). > > > > > > Term: root cell culture > > > Def: In vitro grown isolated cells and small cell aggregates that > > > originated from isolated protoplasts after they re-established > > > cell wall, or from callus that was induced from segment of root. > > > > > > Term: somatic embryo: > > > Def: An embryo arising from previously differentiated somatic > > > cells in vitro, rather than from fused haploid gametes, i.e., > > > zygote. > > > > > > Term: Callus: An unorganized, proliferative mass of large, > > > thin-walled cells; a wound response. > > > > > > Term: Callus culture > > > Def: In vitro grown cell aggregates that originated from isolated > > > protoplasts, cell suspensions, or from callus that was induced in > > > sterile medium the supplemented by plant growth regulators. > > > > > > Term: embryo culture: > > > Def: In vitro development or maintenance of isolated mature or > > > immature zygotic embryos, or somatic embryos. > > > > > > > > > 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. > > > ----------------------------------------------------------------- > > >--------- > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > > NOTE: Please copy Sandra Michelsen on > all emails regarding scheduling and other time-critical topics. > -------------------------------------------------------------------------- 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 Tue Jan 25 17:36:22 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Tue, 25 Jan 2005 14:36:22 -0800 Subject: PAG2005_POtalk References: <41F67613.8070502@cshl.edu> Message-ID: <005f01c5032e$4bfb5a70$7d2042ab@poc> enjoy!!! there is a lot more in POC tutorials Katica -------------- next part -------------- A non-text attachment was scrubbed... Name: PAG workshop2005fnl.ppt Type: application/vnd.ms-powerpoint Size: 643584 bytes Desc: not available URL: From katica at acoma.Stanford.EDU Tue Jan 25 17:40:50 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Tue, 25 Jan 2005 14:40:50 -0800 (PST) Subject: PAG2005_POtalk In-Reply-To: <005f01c5032e$4bfb5a70$7d2042ab@poc> Message-ID: I am sorry, the previous message I sent to po-dev was meant for Shuly only. Please delete it. I apologize 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 katica at acoma.Stanford.EDU Wed Jan 26 15:01:20 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Wed, 26 Jan 2005 12:01:20 -0800 (PST) Subject: New terms in the Plant Structure Ontology In-Reply-To: <41F7F464.5050300@cornell.edu> Message-ID: Hi all, I am planning to commit changes in PO this afternoon. To avoid mistakes from the past, here is what I am going to do regarding new terms in PO (based on your comments and suggestions so far): Note: this is not the list that Simon Yupp suggested; these are the terms I brought up to your attention earlier this week. Also, I am adding the following unresolved) items on the agenda for next ontology group conf call: 1. Terms: callus, whole plant, somatic embryo -what is the most appropriate place in the PO? 2. Apical hook - does it refer to hypogeal seeds? 3. Propagating terms from 'in vitro' node, such as 'cultured cell' to the other nodes in the PO (see Pankaj's suggestion, Jan 25, po-dev thread). There are the new terms in PO (with short explanation for some terms): 1. I'll add the term 'whole plant' to the PO as a child of 'Plant structure', sibling of 'cell' gametophyte' 'sporophyte' and 'tissue' nodes. On the next conf call we shall discuss the appropriate place for this term. Term: Whole plant Def: The entire plant, including roots, shoots and leaves, at any stage of its life cycle. Comment: This term is so general that it should be avoided whenever possible. 2. New node in PO I am adding top node 'In vitro cell, tissue and organ culture' (under the 'plant structure'), and most of the terms in this node are needed for annotations. I am leaving out term 'callus' for now, till we decide where to put this term. Plant structure (i) In vitro cell, tissue and organ culture (i) cultured cell (i) cultured protoplast (i) cultured leaf cell (i) cultured root cell (i) cultured callus (i) cultured embryo (i) somatic embryo Term: in vitro cell, tissue and organ culture Definition: Isolated and grown plant protoplast, cell, tissue and organ, involving, as a common factor, growth of microbe-free plant material in sterile environment, such as sterilized nutrient medium in a test tube or petri dish. Term: cultured protoplast Def: In vitro isolated cells from which the entire cell wall has been enzymatically removed. Term: cultured cell Synonym: cell suspension Def: In vitro grown isolated cells and small cell aggregates that proliferate while suspended in liquid sterile medium or spread on a solid agar medium. Comment: In cell cultures, the cells are no longer organized into tissues. Term: cultured leaf cell Def: In vitro grown isolated cells and small cell aggregates that originated from isolated leaf protoplasts (after they re-established cell wall, or from callus that was induced from leaf tissue). Term: cultured root cell Def: In vitro grown isolated cells and small cell aggregates that originated from isolated protoplasts after they re-established cell wall, or from callus that was induced from segment of root. Term: somatic embryo: Def: An embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote. Term: cultured callus Def: In vitro grown cell aggregates that originated from isolated protoplasts, cell suspensions, or from callus that was induced in sterile medium the supplemented by plant growth regulators. Term: cultured embryo Def: In vitro development or maintenance of isolated mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte). 3. Old terms revisited: These two terms will go under 'leaf' node as an instance_of. Term: Cauline leaf Def: Leaf or pairs/whorls of leaves borne on the stem. Comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches. Term: Rosette leaf Def: One of multiple leaves borne in a rosette. Rosette - a group of leaves, generally borne at the base of the plant, that are separated by very short internodes. Comment: In Arabidopsis, vegetative development is characterized by the production of the rosette leaves. This term is part_of 'primary shoot'. Term: apical hook Synonym: hypocotyl hook Def: hook-like structure which develops at the apical part of the hypocotyl in dark-grown seedlings in dicots. 4. Primordial terms I am adding the following terms under respective organs as instance_of. For the time being, I am leaving out top node term 'organ primordium', since we voted not to have node 'organ', the 'organ primordium is not needed fro similar reasons. Term: organ primordium Def: An organized group of cells from which an organ develops. Term: cotyledon primordium Def: An organized group of cells that will differentiate into a cotyledon. Term: lateral root primordium Def: An organized group of cells derived from the root pericycle that will differentiate into a new root. Term: leaf primordium Def: An organized group of cells that will differentiate into leaf that are emerging as a outgrowth in the shoot apex (flanking the meristem). Term: ovule primordium Def: An organized group of cells that will differentiate into ovule. Term: gynoecium primordium Def: The very first appearance of gynoecium. Term: petal primordium Def: The very first appearance of a petal. Many thanks, 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 ap343 at cornell.edu Wed Jan 26 15:21:50 2005 From: ap343 at cornell.edu (Anuradha Pujar) Date: Wed, 26 Jan 2005 15:21:50 -0500 (EST) Subject: New terms in the Plant Structure Ontology In-Reply-To: References: <41F7F464.5050300@cornell.edu> Message-ID: <4546.128.253.246.53.1106770910.squirrel@128.253.246.53> Primordium terms needs further discussion, there are additional xx primordium terms that are required for cereals and i am working on it, to see, if it fits in with the relationship and definition that you are suggesting. anu > > Hi all, > > I am planning to commit changes in PO this afternoon. To avoid mistakes > from the past, here is what I am going to do regarding new terms in PO > (based on your comments and suggestions so far): > > Note: this is not the list that Simon Yupp suggested; these are the terms > I brought up to your attention earlier this week. > Also, I am adding the following unresolved) items on the agenda for next > ontology group conf call: > > 1. Terms: callus, whole plant, somatic embryo -what is the most > appropriate place in the PO? > 2. Apical hook - does it refer to hypogeal seeds? > 3. Propagating terms from 'in vitro' node, such as 'cultured cell' to > the other nodes in the PO (see Pankaj's suggestion, Jan 25, po-dev > thread). > > There are the new terms in PO (with short explanation for some terms): > > 1. I'll add the term 'whole plant' to the PO as a child of 'Plant > structure', sibling of 'cell' gametophyte' 'sporophyte' and 'tissue' > nodes. > On the next conf call we shall discuss the appropriate place for this > term. > > Term: Whole plant > Def: The entire plant, including roots, shoots and leaves, at any stage of > its life cycle. > Comment: This term is so general that it should be avoided whenever > possible. > > 2. New node in PO > I am adding top node 'In vitro cell, tissue and organ culture' (under the > 'plant structure'), and most of the terms in this node are needed for > annotations. I am leaving out term 'callus' for now, till we decide where > to put this term. > > Plant structure > (i) In vitro cell, tissue and organ culture > (i) cultured cell > (i) cultured protoplast > (i) cultured leaf cell > (i) cultured root cell > (i) cultured callus > (i) cultured embryo > (i) somatic embryo > > > Term: in vitro cell, tissue and organ culture > Definition: > Isolated and grown plant protoplast, cell, tissue and organ, involving, as > a common factor, growth of microbe-free plant material in sterile > environment, such as sterilized nutrient medium in a test tube or petri > dish. > > Term: cultured protoplast > Def: In vitro isolated cells from which the entire cell wall has been > enzymatically removed. > > Term: cultured cell > Synonym: cell suspension > Def: In vitro grown isolated cells and small cell aggregates that > proliferate while suspended in liquid sterile medium or spread on a solid > agar medium. > Comment: In cell cultures, the cells are no longer organized into > tissues. > > Term: cultured leaf cell > Def: In vitro grown isolated cells and small cell aggregates that > originated from isolated leaf protoplasts (after they re-established cell > wall, or from callus that was induced from leaf tissue). > > Term: cultured root cell > Def: In vitro grown isolated cells and small cell aggregates that > originated from isolated protoplasts after they re-established cell wall, > or from callus that was induced from segment of root. > > Term: somatic embryo: > Def: An embryo arising from previously differentiated somatic cells in > vitro, rather than from fused haploid gametes, i.e., zygote. > > Term: cultured callus > Def: In vitro grown cell aggregates that originated from isolated > protoplasts, cell suspensions, or from callus that was induced in sterile > medium the supplemented by plant growth regulators. > > Term: cultured embryo > Def: In vitro development or maintenance of isolated mature or immature > zygotic embryos, somatic embryos or haploid embryos (derived from male > gametophyte). > > 3. Old terms revisited: > These two terms will go under 'leaf' node as an instance_of. > > Term: Cauline leaf > Def: Leaf or pairs/whorls of leaves borne on the stem. > Comment: In Arabidopsis, refers to the leaves that are borne on the > elongated inflorescence branches. > > Term: Rosette leaf > Def: One of multiple leaves borne in a rosette. Rosette - a group of > leaves, generally borne at the base of the plant, that are separated by > very short internodes. > Comment: In Arabidopsis, vegetative development is characterized by the > production of the rosette leaves. > > This term is part_of 'primary shoot'. > Term: apical hook > > Synonym: hypocotyl hook > Def: hook-like structure which develops at the apical part of the > hypocotyl in dark-grown seedlings in dicots. > > 4. Primordial terms > > I am adding the following terms under respective organs as instance_of. > For the time being, I am leaving out top node term 'organ primordium', > since we voted not to have node 'organ', the 'organ primordium is not > needed fro similar reasons. > > Term: organ primordium > Def: An organized group of cells from which an organ develops. > > Term: cotyledon primordium > Def: An organized group of cells that will differentiate into a cotyledon. > > Term: lateral root primordium > Def: An organized group of cells derived from the root pericycle that will > differentiate into a new root. > > Term: leaf primordium > Def: An organized group of cells that will differentiate into leaf that > are emerging as a outgrowth in the shoot apex (flanking the meristem). > > > Term: ovule primordium > Def: An organized group of cells that will differentiate into ovule. > > > Term: gynoecium primordium > Def: The very first appearance of gynoecium. > > > Term: petal primordium > Def: The very first appearance of a petal. > > Many thanks, > > 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 pj37 at cornell.edu Wed Jan 26 15:30:42 2005 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Wed, 26 Jan 2005 15:30:42 -0500 Subject: New terms in the Plant Structure Ontology In-Reply-To: References: Message-ID: <41F7FDF2.5030800@cornell.edu> Katica Ilic wrote: > > Term: cultured callus > Def: In vitro grown cell aggregates that originated from isolated > protoplasts, cell suspensions, or from callus that was induced in sterile > medium the supplemented by plant growth regulators. > There are two instances of callus, one developing as a result of injury, and another instance is the same as you have. So you may like to add both. In the definition you may want to rephrase " cell aggregates" to undifferentiated mass of cells/tissue. > Term: cultured embryo > Def: In vitro development or maintenance of isolated mature or immature > zygotic embryos, somatic embryos or haploid embryos (derived from male > gametophyte). > > 3. Old terms revisited: > These two terms will go under 'leaf' node as an instance_of. > > Term: Cauline leaf > Def: Leaf or pairs/whorls of leaves borne on the stem. > Comment: In Arabidopsis , refers to the leaves that are borne on the > elongated inflorescence branches. > > Term: Rosette leaf > Def: One of multiple leaves borne in a rosette. Rosette - a group of > leaves, generally borne at the base of the plant, that are separated by > very short internodes. > Comment: In Arabidopsis, vegetative development is characterized by the > production of the rosette leaves. > Under the comments in place of Arabidopsis, can we say Brassicaceae? > This term is part_of 'primary shoot'. > Term: apical hook > > Synonym: hypocotyl hook > Def: hook-like structure which develops at the apical part of the > hypocotyl in dark-grown seedlings in dicots. > > 4. Primordial terms > > I am adding the following terms under respective organs as instance_of. > For the time being, I am leaving out top node term 'organ primordium', > since we voted not to have node 'organ', the 'organ primordium is not > needed fro similar reasons. > This still needs further discussion, wait until we have come to a conclusion. I am not sure if we can call XX-primordium as an instance of XX, where XX is a mature organ. -Pankaj From katica at acoma.Stanford.EDU Wed Jan 26 15:31:32 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Wed, 26 Jan 2005 12:31:32 -0800 (PST) Subject: New terms in the Plant Structure Ontology In-Reply-To: <4546.128.253.246.53.1106770910.squirrel@128.253.246.53> Message-ID: Anu, Just send me a list of the terms you need, if you need more time, we can add them in the next cvs round. I just don't want to postpone this any longer, we discussed primordia terms a couple of months ago, and I took some of the Pankaj suggestion at that time (I don't know exactly what terms he suggested). I can look into that. Easiest would be just to see what you have. I'll be commiting new terms all week (hopefuly). If you have comments or suggestions for the listed terms, proposed structure, or definition, please, send it to me asap. Again, additional terms can be added at later time (even this week). Katica P.S. Besides, Shuly is waiting for me to commit the new ontology files. On Wed, 26 Jan 2005, Anuradha Pujar wrote: > Primordium terms needs further discussion, there are additional xx > primordium terms that are required for cereals and i am working on it, to > see, if it fits in with the relationship and definition that you are > suggesting. > anu > > > > Hi all, > > > > I am planning to commit changes in PO this afternoon. To avoid mistakes > > from the past, here is what I am going to do regarding new terms in PO > > (based on your comments and suggestions so far): > > > > Note: this is not the list that Simon Yupp suggested; these are the terms > > I brought up to your attention earlier this week. > > Also, I am adding the following unresolved) items on the agenda for next > > ontology group conf call: > > > > 1. Terms: callus, whole plant, somatic embryo -what is the most > > appropriate place in the PO? > > 2. Apical hook - does it refer to hypogeal seeds? > > 3. Propagating terms from 'in vitro' node, such as 'cultured cell' to > > the other nodes in the PO (see Pankaj's suggestion, Jan 25, po-dev > > thread). > > > > There are the new terms in PO (with short explanation for some terms): > > > > 1. I'll add the term 'whole plant' to the PO as a child of 'Plant > > structure', sibling of 'cell' gametophyte' 'sporophyte' and 'tissue' > > nodes. > > On the next conf call we shall discuss the appropriate place for this > > term. > > > > Term: Whole plant > > Def: The entire plant, including roots, shoots and leaves, at any stage of > > its life cycle. > > Comment: This term is so general that it should be avoided whenever > > possible. > > > > 2. New node in PO > > I am adding top node 'In vitro cell, tissue and organ culture' (under the > > 'plant structure'), and most of the terms in this node are needed for > > annotations. I am leaving out term 'callus' for now, till we decide where > > to put this term. > > > > Plant structure > > (i) In vitro cell, tissue and organ culture > > (i) cultured cell > > (i) cultured protoplast > > (i) cultured leaf cell > > (i) cultured root cell > > (i) cultured callus > > (i) cultured embryo > > (i) somatic embryo > > > > > > Term: in vitro cell, tissue and organ culture > > Definition: > > Isolated and grown plant protoplast, cell, tissue and organ, involving, as > > a common factor, growth of microbe-free plant material in sterile > > environment, such as sterilized nutrient medium in a test tube or petri > > dish. > > > > Term: cultured protoplast > > Def: In vitro isolated cells from which the entire cell wall has been > > enzymatically removed. > > > > Term: cultured cell > > Synonym: cell suspension > > Def: In vitro grown isolated cells and small cell aggregates that > > proliferate while suspended in liquid sterile medium or spread on a solid > > agar medium. > > Comment: In cell cultures, the cells are no longer organized into > > tissues. > > > > Term: cultured leaf cell > > Def: In vitro grown isolated cells and small cell aggregates that > > originated from isolated leaf protoplasts (after they re-established cell > > wall, or from callus that was induced from leaf tissue). > > > > Term: cultured root cell > > Def: In vitro grown isolated cells and small cell aggregates that > > originated from isolated protoplasts after they re-established cell wall, > > or from callus that was induced from segment of root. > > > > Term: somatic embryo: > > Def: An embryo arising from previously differentiated somatic cells in > > vitro, rather than from fused haploid gametes, i.e., zygote. > > > > Term: cultured callus > > Def: In vitro grown cell aggregates that originated from isolated > > protoplasts, cell suspensions, or from callus that was induced in sterile > > medium the supplemented by plant growth regulators. > > > > Term: cultured embryo > > Def: In vitro development or maintenance of isolated mature or immature > > zygotic embryos, somatic embryos or haploid embryos (derived from male > > gametophyte). > > > > 3. Old terms revisited: > > These two terms will go under 'leaf' node as an instance_of. > > > > Term: Cauline leaf > > Def: Leaf or pairs/whorls of leaves borne on the stem. > > Comment: In Arabidopsis, refers to the leaves that are borne on the > > elongated inflorescence branches. > > > > Term: Rosette leaf > > Def: One of multiple leaves borne in a rosette. Rosette - a group of > > leaves, generally borne at the base of the plant, that are separated by > > very short internodes. > > Comment: In Arabidopsis, vegetative development is characterized by the > > production of the rosette leaves. > > > > This term is part_of 'primary shoot'. > > Term: apical hook > > > > Synonym: hypocotyl hook > > Def: hook-like structure which develops at the apical part of the > > hypocotyl in dark-grown seedlings in dicots. > > > > 4. Primordial terms > > > > I am adding the following terms under respective organs as instance_of. > > For the time being, I am leaving out top node term 'organ primordium', > > since we voted not to have node 'organ', the 'organ primordium is not > > needed fro similar reasons. > > > > Term: organ primordium > > Def: An organized group of cells from which an organ develops. > > > > Term: cotyledon primordium > > Def: An organized group of cells that will differentiate into a cotyledon. > > > > Term: lateral root primordium > > Def: An organized group of cells derived from the root pericycle that will > > differentiate into a new root. > > > > Term: leaf primordium > > Def: An organized group of cells that will differentiate into leaf that > > are emerging as a outgrowth in the shoot apex (flanking the meristem). > > > > > > Term: ovule primordium > > Def: An organized group of cells that will differentiate into ovule. > > > > > > Term: gynoecium primordium > > Def: The very first appearance of gynoecium. > > > > > > Term: petal primordium > > Def: The very first appearance of a petal. > > > > Many thanks, > > > > 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. > > -------------------------------------------------------------------------- > > > > > > > > -------------------------------------------------------------------------- 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 kellogge at msx.umsl.edu Wed Jan 26 15:40:06 2005 From: kellogge at msx.umsl.edu (kellogge) Date: Wed, 26 Jan 2005 14:40:06 -0600 Subject: New terms in the Plant Structure Ontology In-Reply-To: <41F7FDF2.5030800@cornell.edu> References: <41F7FDF2.5030800@cornell.edu> Message-ID: <76685B8F-6FDA-11D9-AE36-000D93B827BC@msx.umsl.edu> On Jan 26, 2005, at 2:30 PM, Pankaj Jaiswal wrote: > > > Katica Ilic wrote: > >> Term: cultured callus >> Def: In vitro grown cell aggregates that originated from isolated >> protoplasts, cell suspensions, or from callus that was induced in >> sterile >> medium the supplemented by plant growth regulators. > > There are two instances of callus, one developing as a result of > injury, and another instance is the same as you have. So you may like > to add both. > > In the definition you may want to rephrase " cell aggregates" to > undifferentiated mass of cells/tissue. > >> Term: cultured embryo >> Def: In vitro development or maintenance of isolated mature or >> immature >> zygotic embryos, somatic embryos or haploid embryos (derived from male >> gametophyte). >> 3. Old terms revisited: >> These two terms will go under 'leaf' node as an instance_of. >> Term: Cauline leaf >> Def: Leaf or pairs/whorls of leaves borne on the stem. >> Comment: In Arabidopsis , refers to the leaves that are borne on the >> elongated inflorescence branches. >> Term: Rosette leaf >> Def: One of multiple leaves borne in a rosette. Rosette - a group of >> leaves, generally borne at the base of the plant, that are separated >> by >> very short internodes. >> Comment: In Arabidopsis, vegetative development is characterized by >> the >> production of the rosette leaves. > > Under the comments in place of Arabidopsis, can we say Brassicaceae? No - they don't all go in for rosettes. And rosettes occur frequently in other families as well (even some Poaceae!), so either we have to leave the comment for the Arabidopsis people, or just delete it entirely. > >> This term is part_of 'primary shoot'. >> Term: apical hook >> Synonym: hypocotyl hook >> Def: hook-like structure which develops at the apical part of the >> hypocotyl in dark-grown seedlings in dicots. >> 4. Primordial terms >> I am adding the following terms under respective organs as >> instance_of. >> For the time being, I am leaving out top node term 'organ primordium', >> since we voted not to have node 'organ', the 'organ primordium is not >> needed fro similar reasons. > > This still needs further discussion, wait until we have come to a > conclusion. I am not sure if we can call XX-primordium as an instance > of XX, where XX is a mature organ. > > -Pankaj > > Elizabeth A. Kellogg E. Desmond Lee and Family Professor of Botanical Studies Department of Biology University of Missouri-St. Louis St. Louis, MO 63121 Tel: 314-516-6217 FAX: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ home.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 2626 bytes Desc: not available URL: From katica at acoma.Stanford.EDU Wed Jan 26 15:42:56 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Wed, 26 Jan 2005 12:42:56 -0800 (PST) Subject: New terms in the Plant Structure Ontology In-Reply-To: <41F7FDF2.5030800@cornell.edu> Message-ID: pankaj, please see below, On Wed, 26 Jan 2005, Pankaj Jaiswal wrote: > > > Katica Ilic wrote: > > > > > Term: cultured callus > > Def: In vitro grown cell aggregates that originated from isolated > > protoplasts, cell suspensions, or from callus that was induced in sterile > > medium the supplemented by plant growth regulators. > > > > There are two instances of callus, one developing as a result of injury, > and another instance is the same as you have. So you may like to add both. In my e-mail, I mentioned that we shall discuss this on the ontology conf call. > In the definition you may want to rephrase " cell aggregates" to > undifferentiated mass of cells/tissue. I think cell aggregates is OK, that more descriptive than undifferentiated mass of cells/tissue (at least for us who accually had a hands-on experience with cell suspensions). > > Term: cultured embryo > > Def: In vitro development or maintenance of isolated mature or immature > > zygotic embryos, somatic embryos or haploid embryos (derived from male > > gametophyte). > > > > 3. Old terms revisited: > > These two terms will go under 'leaf' node as an instance_of. > > > > Term: Cauline leaf > > Def: Leaf or pairs/whorls of leaves borne on the stem. > > Comment: In Arabidopsis , refers to the leaves that are borne on the > > elongated inflorescence branches. > > > > Term: Rosette leaf > > Def: One of multiple leaves borne in a rosette. Rosette - a group of > > leaves, generally borne at the base of the plant, that are separated by > > very short internodes. > > Comment: In Arabidopsis, vegetative development is characterized by the > > production of the rosette leaves. > > > > Under the comments in place of Arabidopsis, can we say Brassicaceae? I would leave it as it is for now, since I am not really sure if it is aplicable to all Brassicaceae. > > > This term is part_of 'primary shoot'. > > Term: apical hook > > > > Synonym: hypocotyl hook > > Def: hook-like structure which develops at the apical part of the > > hypocotyl in dark-grown seedlings in dicots. > > > > 4. Primordial terms > > > > I am adding the following terms under respective organs as instance_of. > > For the time being, I am leaving out top node term 'organ primordium', > > since we voted not to have node 'organ', the 'organ primordium is not > > needed fro similar reasons. > > > > This still needs further discussion, wait until we have come to a > conclusion. I am not sure if we can call XX-primordium as an instance of > XX, where XX is a mature organ. For the time being, there is no harm in having them as instances (we have them as instance_of in TAIR). Once they are in the PO, and we agreeed that we need these terms, right, we can discuss the relationships and adding additional terms. Katica > > -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 Wed Jan 26 15:48:19 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Wed, 26 Jan 2005 12:48:19 -0800 (PST) Subject: New terms in the Plant Structure Ontology In-Reply-To: <76685B8F-6FDA-11D9-AE36-000D93B827BC@msx.umsl.edu> Message-ID: On Wed, 26 Jan 2005, kellogge wrote: > > On Jan 26, 2005, at 2:30 PM, Pankaj Jaiswal wrote: > > Under the comments in place of Arabidopsis, can we say Brassicaceae? > No - they don't all go in for rosettes. And rosettes occur frequently > in other families as well (even some Poaceae!), so either we have to > leave the comment for the Arabidopsis people, or just delete it > entirely. Thank you Toby. I think Peter gave a similar comment in St Loius. Let's leave it for now as it is, since Arabidopsis people are mostly going to be using this term. However, I general, I agree, we should try avoiding species-specific references in the Comment section (to keep it simple). Katica > > > >> This term is part_of 'primary shoot'. > >> Term: apical hook > >> Synonym: hypocotyl hook > >> Def: hook-like structure which develops at the apical part of the > >> hypocotyl in dark-grown seedlings in dicots. > >> 4. Primordial terms > >> I am adding the following terms under respective organs as > >> instance_of. > >> For the time being, I am leaving out top node term 'organ primordium', > >> since we voted not to have node 'organ', the 'organ primordium is not > >> needed fro similar reasons. > > > > This still needs further discussion, wait until we have come to a > > conclusion. I am not sure if we can call XX-primordium as an instance > > of XX, where XX is a mature organ. > > > > -Pankaj > > > > > Elizabeth A. Kellogg > E. Desmond Lee and Family Professor of Botanical Studies > Department of Biology > University of Missouri-St. Louis > St. Louis, MO 63121 > Tel: 314-516-6217 > FAX: 314-516-6233 > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ > home.html > -------------------------------------------------------------------------- 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 peter.stevens at mobot.org Wed Jan 26 16:37:41 2005 From: peter.stevens at mobot.org (Peter Stevens) Date: Wed, 26 Jan 2005 17:37:41 -0400 Subject: New terms in the Plant Structure Ontology In-Reply-To: <41F7FDF2.5030800@cornell.edu> References: <41F7FDF2.5030800@cornell.edu> Message-ID: >At 3:30 PM -0500 1/26/05, Pankaj Jaiswal wrote: >Term: Rosette leaf >Def: One of multiple leaves borne in a rosette. Rosette - a group of >leaves, generally borne at the base of the plant, that are separated by >very short internodes. >Comment: In Arabidopsis, vegetative development is characterized by the >production of the rosette leaves. > >> Under the comments in place of Arabidopsis, can we say Brassicaceae? Not all Brassicaceae have rosettes, etc. From katica at acoma.Stanford.EDU Wed Jan 26 19:35:59 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Wed, 26 Jan 2005 16:35:59 -0800 (PST) Subject: New revision of Plant Ontology is in cvs In-Reply-To: Message-ID: Hi all, I just committed ontology files to cvs: anatomy.ontology, revision 1.31 anatomy.definition, revision 1.30 temporal.ontology (no changes), 1.2 New terms: whole plant in vitro cell, tissue and organ culture cultured protoplast cultured cell (Synonym: cell suspension) cultured leaf cell cultured root cell somatic embryo cultured callus cultured embryo cauline leaf apical hook (Synonym: hypocotyl hook) cotyledon primordium lateral root primordium leaf primordium ovule primordium gynoecium primordium petal primordium Definitions: Term: Whole plant Def: The entire plant, including roots, shoots and leaves, at any stage of its life cycle. Comment: This term is so general that it should be avoided whenever possible Term: in vitro cell, tissue and organ culture Definition: Isolated and grown plant protoplast, cell, tissue and organ, involving, as a common factor, growth of microbe-free plant material in sterile environment, such as sterilized nutrient medium in a test tube or petri dish. Term: cultured protoplast Def: In vitro isolated cells from which the entire cell wall has been enzymatically removed. Term: cultured cell Synonym: cell suspension Def: In vitro grown isolated cells and small cell aggregates that proliferate while suspended in liquid sterile medium or spread on a solid agar medium. Comment: In cell cultures, the cells are no longer organized into tissues. Term: cultured leaf cell Def: In vitro grown isolated cells and small cell aggregates that originated from isolated leaf protoplasts (after they re-established cell wall, or from callus that was induced from leaf tissue). Term: cultured root cell Def: In vitro grown isolated cells and small cell aggregates that originated from isolated protoplasts after they re-established cell wall, or from callus that was induced from segment of root. Term: somatic embryo Def: An embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote. Term: cultured callus Def: In vitro grown cell aggregates that originated from isolated protoplasts, cell suspensions, or from callus that was induced in sterile medium the supplemented by plant growth regulators. Term: cultured embryo Def: In vitro isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte). Term: Cauline leaf Def: Leaf or pairs/whorls of leaves borne on the stem. Comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches. Term: Rosette leaf Def: One of multiple leaves borne in a rosette. Rosette - a group of leaves, generally borne at the base of the plant, that are separated by very short internodes. Comment: In Arabidopsis, vegetative development is characterized by the production of the rosette leaves. Term: apical hook Synonym: hypocotyl hook Def: hook-like structure which develops at the apical part of the hypocotyl in dark-grown seedlings in dicots. Term: cotyledon primordium Def: An organized group of cells that will differentiate into a cotyledon. Term: lateral root primordium Def: An organized group of cells derived from the root pericycle that will differentiate into a new root. Term: leaf primordium Def: An organized group of cells that will differentiate into leaf that are emerging as an outgrowth in the shoot apex (flanking the meristem). Term: ovule primordium Def :The very first appearance of ovule. Term: gynoecium primordium Def: The very first appearance of gynoecium. Term: petal primordium Def: The very first appearance of a petal. Felipe's updated definitions: Stem: the axial system of plants that bears leaves and buds. Comment: it is usually above ground and more or less negatively geotropic, is exogenous in origin, often indeterminate in growth and with secondary thickening. Inflorescence: That part of the axial system of plants above the uppermost foliage leaf/pair of foliage leaves that bears flowers. Peduncle: The stalk of an inflorescence; that part of the inflorescence below the first flower or inflorescence branch and above the last foliage leaf/pair of foliage leaves. 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 katica at acoma.Stanford.EDU Thu Jan 27 17:15:56 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Thu, 27 Jan 2005 14:15:56 -0800 (PST) Subject: New terms for the Plant Ontology In-Reply-To: Message-ID: Hi all, Here is the latest set of terms that are either requested by users or needed for annotations. As you can see, there are subcellular structures listed below; these terms are not present in GO and are plant specific, so we need to consider them. I am not sure about filiform apparatus, does it go as a child of synergid cell or egg apparatus (or both). My recollection is that this structure is not just part of two synergid cells, but also exceed to the egg cell. Also, I am not sure about terms 'septum' and 'valve', where exactly to put these (see below). Your suggestions and comments are very appreciated. Many thanks, Katica Term: cuticle Def: A layer of fatty material, cutin, rather impervious to water, located on the outer walls of epidermal cells. Cell (i) epidermal cell (p) cuticle Term: casparian strip Def: A band-like wall formation within primary walls that contains suberin and lignin; typical of endodermal cells in roots, in which it occurs in radial and transverse anticlinal walls. root (p) root cortex (p) root endodermis (p) casparian strip Term: filiform apparatus Def: A complex of cell wall invaginations in a synergid cell similar to those in transfer cells. Synergid cell (p) filiform apparatus or egg apparatus (p) filiform apparatus Term: lateral root tip Def: The portion of the lateral root including the meristem and root cap. Term: root tip Def: Top portion of the root including meristem and root cap. This is the case were we need to instantiate 'root tip' (creating three terms, root tip, primary root tip, lateral root tip). root (p) root tip (i) lateral root (p) lateral root tip (i) primary root (p) primary root tip root tip (i) lateral root tip (i) primary root tip Term: pollen tube tip Tip portion of the pollen tube that is rapidly growing. male gametophyte (p) pollen tube (p) pollen tube tip Term: root hair tip Tip portion of an outgrowth of a root epidermal cell epidermis (p) epidermal cell (i) root hair (p) root hair tip I think we don't need to propagate 'root hair tip' everywhere where 'root hair' is present as 'develops_from' (it's optional). Term: septum - A thin partition or membrane that divides two cavities or soft masses of tissue of anther, ovary or fruit. Since we have three terms for each, carpel and anther, my suggestion is to add 'septum' as a child of generic term only, and not to instantiate under any 'sensu' term. carpel (p) septum and anther (p) septum and fruit (p) septum Term: lenticel Def: Loosely-packed mass of cork cells occurring especially in the young stem, bark or even leaf of a plant, visible on the surface as a raised, often powdery-appearing spot, through which gaseous exchange occurs. stem (p) lenticel also, leaf (p) lenticel Term: tetrad of microspores A group of four haploid cells that remained joined together shortly after meiosis. Each cell will give rise to the male gametophyte. androecium (p) stamen (p) anther (p) microsporangium (p) microsporocyte (d) tetrads of microspore (d) microspore In this case, we have 'tetrad of microspores' with only develops_from relationship. Term: valve Def: valve: a portion of an organ that is fragmented; in capsule, the portions into which the pericarp splits at maturity. fruit (p) fruit abscission zone (p) pericarp (p) seed (p) valve and flower (p) gynoecium (p) carpel (p) ovary -------------------------------------------------------------------------- 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 peter.stevens at mobot.org Thu Jan 27 17:41:48 2005 From: peter.stevens at mobot.org (Peter Stevens) Date: Thu, 27 Jan 2005 18:41:48 -0400 Subject: New terms for the Plant Ontology In-Reply-To: References: Message-ID: At 2:15 PM -0800 1/27/05, Katica Ilic wrote: > >Term: septum - A thin partition or membrane that divides two cavities or >soft masses of tissue of anther, ovary or fruit. > >Since we have three terms for each, carpel and anther, my suggestion is to >add 'septum' as a child of generic term only, and not to instantiate under >any 'sensu' term. Better: Term: septum - A thin partition or membrane that divides a cavity or mass of tissue, e.g. in anther, ovary or fruit. Septate pith is quite common. P. From katica at acoma.Stanford.EDU Fri Jan 28 11:03:40 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Fri, 28 Jan 2005 08:03:40 -0800 (PST) Subject: New terms in PO and ontology group conf call In-Reply-To: Message-ID: Hi ontology developers, Since I realized that Toby is leaving next week to South Africa for three weeks, I would like to ask you all if you think we need a group conf call to discuss issues on the new terms that I just introduced to PO and those currently pending. We can arrange the call sometimes next week while Toby is still available, if you think it's necessary (if there are issues that cannot be discussed through e-mail). Thank you, 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 feedback_submission at filetta.cshl.edu Sun Jan 30 13:43:32 2005 From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu) Date: Sun, 30 Jan 2005 13:43:32 -0500 Subject: Feedback on POC Message-ID: <200501301843.j0UIhWM3026838@filetta.cshl.org> *** Feedback from Plant Ontology Live Site *** refer_to_url: comments: http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0000256 Database group, I just happened to look at the terms trichoblast and root hair. They have the develops from relationships. At one of the STL meetings we agreed that whenever a develops from relationship is encountered in the tree, the asociations from child term should not propagate with the parent term. Considering the fact that a gene or phenotype that is expressed in the child body part term may not always express in the parent body part from which it develops. In the example URL the associations from root hair should not appear with trichome. Similarly epidermal initial should not accumulate any association from the trichoblast. name: Pankaj email: pj37 at cornell.edu organization: CU send_feedback: Send your feedback From shuly at cshl.edu Sun Jan 30 13:44:40 2005 From: shuly at cshl.edu (Shuly Avraham) Date: Sun, 30 Jan 2005 13:44:40 -0500 Subject: [Fwd: Feedback on POC] Message-ID: <41FD2B18.8020009@cshl.edu> -------------- next part -------------- An embedded message was scrubbed... From: feedback_submission at filetta.cshl.edu Subject: Feedback on POC Date: Sun, 30 Jan 2005 13:43:32 -0500 Size: 1942 URL: From lstein at cshl.edu Mon Jan 31 09:43:52 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Mon, 31 Jan 2005 09:43:52 -0500 Subject: Fwd: Re: Status of GO slots? Message-ID: <200501310943.52300.lstein@cshl.edu> Hello, Some information from Chris Mungall about the prospects for automatically expanding "slots" (by which he means modifier terms such as "dorsal") into instantiated terms. Lincoln ---------- Forwarded Message ---------- Subject: Re: Status of GO slots? Date: Friday 28 January 2005 07:21 pm From: Chris Mungall To: Lincoln Stein The tricky part of the code is automatically computing the relationships in the derived DAG - luckily that part is essentially done as part of Obol. It should only be a few days work, hopefully I can do it sometime in the next 3 weeks On Fri, 21 Jan 2005, Lincoln Stein wrote: > Hi Chris, > > Yes, I did pick up on the slot expander idea from your earlier > email and I suggested it at the POC meeting. People seemed a bit > puzzled by the idea, so I'll send out a longer description of it by > email. > > Any idea of when work on the expander will start and when we might > be able to start working with it? > > Lincoln > > On Friday 21 January 2005 04:47 pm, Chris Mungall wrote: > > OK. Sometime I hope I can convince you not to be disappointed at > > the alternatives. > > > > For example, how about this: a SlotExpander tool that maps a file > > of slot-based annotations to simple annotations, creating a new > > DAG with appropriate combinatorial terms (and naming them > > sensibly) on-the-fly. The simple annotations and extended DAG > > could be treated with all existing GO tools, including the > > DB/AmiGO. Granted it doesn't solve the DAG navigation problem (we > > are working on this) but it does solve most of the ontology > > curation and annotation crises. > > > > The tool isn't written yet, but it's easy to do using the current > > obol infrastructure. It could be written if it would be useful & > > if POC were to be willing to help test it. > > > > c. > > > > On Tue, 18 Jan 2005, Lincoln Stein wrote: > > > Hi Chris, > > > > > > Thanks for the update. I'm disappointed at your answer, but I > > > understand the tradeoff between costs and benefits that the GO > > > project is facing. > > > > > > Lincoln > > > > > > On Monday 17 January 2005 07:03 pm, you wrote: > > > > Hi Lincoln > > > > > > > > I was probably a little vague in my message here: > > > > http://www.geneontology.org/email-go/go-arc/go-2004/2438.html > > > > > > > > My analysis of GO is that the introduction of annotation > > > > slots would complicate things unnecessarily for the MODs > > > > implementing GO queries, and would introduce lots of other > > > > problems. It's better to manage the complexity centrally and > > > > in an automated fashion, using formal definitions of terms. > > > > This can go a long way to ameliorating the complexity of > > > > combinatorial terms. I can give more details on this approach > > > > if you like. > > > > > > > > This is partly due to the nature of GO, whereby the matrix of > > > > meaningful combinatorial terms is quite sparse; this may not > > > > hold for other ontologies such as POC - I don't know enough > > > > about plant anatomy to follow the examples in the document > > > > Katica sent. > > > > > > > > At the moment, the implementation of slot-based annotations > > > > in the GO database and AmiGO isn't a high priority. I believe > > > > that OBO-Edit does or will soon allow you to define slots (or > > > > annotation_properties and datatype_properties in OBO/OWL > > > > lingo) for classes. However, the database and query support > > > > for this isn't there. Implementing queries over annotations > > > > with recursive slot values is actually a fairly tricky > > > > problem, and not something that will work with direct SQL > > > > queries. > > > > > > > > One thing we have considered in the database is a vastly > > > > simplified formalism allowing annotation conjunctions (eg > > > > function F is exercised during process P in component CC in > > > > cell type CT in anatomical part A). This is simpler to query > > > > over, but has some severe limitations. The structure for this > > > > is there in the GO DB schema, but as yet there is no > > > > immediate plans to populate or query over it. > > > > > > > > There may be similar simplifications that can be made to the > > > > slot formalism to support the immediate needs of the POC - > > > > but this may not be generic enough to cover other more > > > > general cases. > > > > > > > > I'm interested in looking into this further; we will > > > > eventually need some kind of advanced description logic or > > > > slot-based querying system for phenotypic data, where the > > > > combinatorial explosion is enormous (and possibly infinite in > > > > the case of quantative values). At this stage I'm not sure > > > > whether the best solution is a home-grown relational one, a > > > > special purpose object/knowledge-based db, or a hybrid one > > > > (such as > > > > Manchester's InstanceStore). However, we're lacking the > > > > programmer resources for this at the moment... > > > > > > > > Sorry to be vague and handwavey. I can be more specific on > > > > any of the points above if you like.. but the short answer is > > > > there is no timetable > > > > > > > > Cheers > > > > Chris > > > > > > > > On Mon, 17 Jan 2005, Lincoln Stein wrote: > > > > > Hi Chris, > > > > > > > > > > There's a POC meeting tomorrow and I wanted to check in > > > > > about the progress towards software to handle ontology > > > > > slots. We need it here to handle the "multiplicative > > > > > crisis" introduced by multiple similar anatomic structures > > > > > that appear in different contexts. As I understand it, > > > > > DAG-Edit with OBO already handles slots, but the GO > > > > > database doesn't utilize the slots for associations. Is > > > > > this correct? Can you fill me in on the development plans > > > > > and timetable? > > > > > > > > > > Lincoln ------------------------------------------------------- -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 NOTE: Please copy Sandra Michelsen on all emails regarding scheduling and other time-critical topics. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: not available URL: From kellogge at msx.umsl.edu Mon Jan 31 15:11:54 2005 From: kellogge at msx.umsl.edu (kellogge) Date: Mon, 31 Jan 2005 14:11:54 -0600 Subject: Status of GO slots? In-Reply-To: <200501310943.52300.lstein@cshl.edu> References: <200501310943.52300.lstein@cshl.edu> Message-ID: <59C53FC8-73C4-11D9-9626-000D93B827BC@msx.umsl.edu> Thanks for forwarding this Lincoln. It seems as though it would be worth trying this software if Chris can write it. He seems to have hit the crux of the problem when he states that "This is partly due to the nature of GO, whereby the matrix of meaningful combinatorial terms is quite sparse; this may not hold for other ontologies such as POC...." The matrix of meaningful combinatorial terms in the Plant Ontology is indeed very large, and is also necessary; plant structure is not intrinsically hierarchical, it's modular and combinatorial. He also notes that "I'm interested in looking into this further; we will eventually need some kind of advanced description logic or slot-based querying system for phenotypic data, where the combinatorial explosion is enormous (and possibly infinite in the case of quantative values)." Yes - this is exactly the problem that the PO has run into repeatedly and continuously, starting with our first meeting. (From Chris) "At this stage I'm not sure whether the best solution is a home-grown relational one, a special purpose object/knowledge-based db, or a hybrid one (such as Manchester's InstanceStore)." I certainly don't have the expertise to answer this question - the only sort of db I'm familiar with is a relational one, and I suspect it will work, but maybe there are better things out there. It will be interesting to see how the "slot expander" works, and if it solves the immediate problem. Toby On Jan 31, 2005, at 8:43 AM, Lincoln Stein wrote: > Hello, > > Some information from Chris Mungall about the prospects for > automatically expanding "slots" (by which he means modifier terms > such as "dorsal") into instantiated terms. > > Lincoln > > ---------- Forwarded Message ---------- > > Subject: Re: Status of GO slots? > Date: Friday 28 January 2005 07:21 pm > From: Chris Mungall > To: Lincoln Stein > > The tricky part of the code is automatically computing the > relationships in the derived DAG - luckily that part is essentially > done as part of Obol. It should only be a few days work, hopefully I > can do it sometime in the next 3 weeks > > On Fri, 21 Jan 2005, Lincoln Stein wrote: >> Hi Chris, >> >> Yes, I did pick up on the slot expander idea from your earlier >> email and I suggested it at the POC meeting. People seemed a bit >> puzzled by the idea, so I'll send out a longer description of it by >> email. >> >> Any idea of when work on the expander will start and when we might >> be able to start working with it? >> >> Lincoln >> >> On Friday 21 January 2005 04:47 pm, Chris Mungall wrote: >>> OK. Sometime I hope I can convince you not to be disappointed at >>> the alternatives. >>> >>> For example, how about this: a SlotExpander tool that maps a file >>> of slot-based annotations to simple annotations, creating a new >>> DAG with appropriate combinatorial terms (and naming them >>> sensibly) on-the-fly. The simple annotations and extended DAG >>> could be treated with all existing GO tools, including the >>> DB/AmiGO. Granted it doesn't solve the DAG navigation problem (we >>> are working on this) but it does solve most of the ontology >>> curation and annotation crises. >>> >>> The tool isn't written yet, but it's easy to do using the current >>> obol infrastructure. It could be written if it would be useful & >>> if POC were to be willing to help test it. >>> >>> c. >>> >>> On Tue, 18 Jan 2005, Lincoln Stein wrote: >>>> Hi Chris, >>>> >>>> Thanks for the update. I'm disappointed at your answer, but I >>>> understand the tradeoff between costs and benefits that the GO >>>> project is facing. >>>> >>>> Lincoln >>>> >>>> On Monday 17 January 2005 07:03 pm, you wrote: >>>>> Hi Lincoln >>>>> >>>>> I was probably a little vague in my message here: >>>>> http://www.geneontology.org/email-go/go-arc/go-2004/2438.html >>>>> >>>>> My analysis of GO is that the introduction of annotation >>>>> slots would complicate things unnecessarily for the MODs >>>>> implementing GO queries, and would introduce lots of other >>>>> problems. It's better to manage the complexity centrally and >>>>> in an automated fashion, using formal definitions of terms. >>>>> This can go a long way to ameliorating the complexity of >>>>> combinatorial terms. I can give more details on this approach >>>>> if you like. >>>>> >>>>> This is partly due to the nature of GO, whereby the matrix of >>>>> meaningful combinatorial terms is quite sparse; this may not >>>>> hold for other ontologies such as POC - I don't know enough >>>>> about plant anatomy to follow the examples in the document >>>>> Katica sent. >>>>> >>>>> At the moment, the implementation of slot-based annotations >>>>> in the GO database and AmiGO isn't a high priority. I believe >>>>> that OBO-Edit does or will soon allow you to define slots (or >>>>> annotation_properties and datatype_properties in OBO/OWL >>>>> lingo) for classes. However, the database and query support >>>>> for this isn't there. Implementing queries over annotations >>>>> with recursive slot values is actually a fairly tricky >>>>> problem, and not something that will work with direct SQL >>>>> queries. >>>>> >>>>> One thing we have considered in the database is a vastly >>>>> simplified formalism allowing annotation conjunctions (eg >>>>> function F is exercised during process P in component CC in >>>>> cell type CT in anatomical part A). This is simpler to query >>>>> over, but has some severe limitations. The structure for this >>>>> is there in the GO DB schema, but as yet there is no >>>>> immediate plans to populate or query over it. >>>>> >>>>> There may be similar simplifications that can be made to the >>>>> slot formalism to support the immediate needs of the POC - >>>>> but this may not be generic enough to cover other more >>>>> general cases. >>>>> >>>>> I'm interested in looking into this further; we will >>>>> eventually need some kind of advanced description logic or >>>>> slot-based querying system for phenotypic data, where the >>>>> combinatorial explosion is enormous (and possibly infinite in >>>>> the case of quantative values). At this stage I'm not sure >>>>> whether the best solution is a home-grown relational one, a >>>>> special purpose object/knowledge-based db, or a hybrid one >>>>> (such as >>>>> Manchester's InstanceStore). However, we're lacking the >>>>> programmer resources for this at the moment... >>>>> >>>>> Sorry to be vague and handwavey. I can be more specific on >>>>> any of the points above if you like.. but the short answer is >>>>> there is no timetable >>>>> >>>>> Cheers >>>>> Chris >>>>> >>>>> On Mon, 17 Jan 2005, Lincoln Stein wrote: >>>>>> Hi Chris, >>>>>> >>>>>> There's a POC meeting tomorrow and I wanted to check in >>>>>> about the progress towards software to handle ontology >>>>>> slots. We need it here to handle the "multiplicative >>>>>> crisis" introduced by multiple similar anatomic structures >>>>>> that appear in different contexts. As I understand it, >>>>>> DAG-Edit with OBO already handles slots, but the GO >>>>>> database doesn't utilize the slots for associations. Is >>>>>> this correct? Can you fill me in on the development plans >>>>>> and timetable? >>>>>> >>>>>> Lincoln > > ------------------------------------------------------- > > -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > > NOTE: Please copy Sandra Michelsen on > all emails regarding scheduling and other time-critical topics. > Elizabeth A. Kellogg E. Desmond Lee and Family Professor of Botanical Studies Department of Biology University of Missouri-St. Louis St. Louis, MO 63121 Tel: 314-516-6217 FAX: 314-516-6233 http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ home.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 7460 bytes Desc: not available URL: From ap343 at cornell.edu Mon Jan 31 16:07:50 2005 From: ap343 at cornell.edu (Anuradha Pujar) Date: Mon, 31 Jan 2005 16:07:50 -0500 (EST) Subject: New terms in the Plant Structure Ontology In-Reply-To: <4546.128.253.246.53.1106770910.squirrel@128.253.246.53> References: <41F7F464.5050300@cornell.edu> <4546.128.253.246.53.1106770910.squirrel@128.253.246.53> Message-ID: <1415.128.253.246.53.1107205670.squirrel@128.253.246.53> Hello, In complete awareness that the primordium terms have been committed, I wish to draw attention to the fact that these terms will have an implicit link with the body part development stage ontology and having the develops_from relationship is significant. All plant body part develops from a primordium and the primordium itself is defined as a stage by Esau. Nevertheless, the larger scientific community uses this term as an anatomical entity. Strictly, by Esau?s definition, a primordium could be a cell, organ or an organized series of cells, in their earliest stage of differentiation. E.g. leaf primordium, sclerid primordium, vessel member primordium. Therefore our suggestion is 1.The term primordium is botanically defined and should be available on the PO per se. Though Pankaj suggested xx-primordium as a grouping term, we should consider making it more generic i.e. "primordium". Any instances of it suggesting cell/tissue/organ primordium should then be listed with IS_A relationship. 2. In defining, composite terms like ?leaf primordium? both ?leaf? and ?primordium? should be defined independently, as in the case of every other composite term in the PO such as ?leaf epidermis?. This will make it easier for the developers and the automation script to use SLOTS (today's e mail from Lincoln) and make cross products. 3.The temporal development stages of body part ontology, will have a number of anatomical structures as a part of their developmental history. BUT the exact definition of those terms (primordium included) will be retrieved from the structure ontology. Would, having the term ?primordium? at the same level of sporophyte be justified for the above reasons? With children terms that could be a cell, tissue or organs? I agree with Pankaj, that, develops_from relationship is more appropriate biologically, to say, that leaf develops from a leaf primordium, rather than the suggested relationship, of leaf primordium is_a instance of leaf. Plant structure i--cell i--tissue i--sporophyte i--gametophyte i--Primordium i-Phyllome primordium i-leaf primordium i- bract primordium i-sporophyll primordium i--carpel primordium i--stamen primordium The current state of structure, committed last week suggests that a gene that is expressed in a leaf primordium is also expressed in the leaf or any of its instances. Whereas the relationships suggested by Pankaj and here in this mail, suggests, that a given primordium is in its earliest stages of differentiation, which means, it has not yet fully differentiated into an actual organ. Thus if we go by, the develops from relationship, the annotations as well as the concept remains intact, validating the statement that a gene expressed in leaf primordium is not necessarily expressed in leaf or its instances. Individual definitions of gynoecium and petal primordium also requires changes. anu > > Primordium terms needs further discussion, there are additional xx > primordium terms that are required for cereals and i am working on it, to > see, if it fits in with the relationship and definition that you are > suggesting. > anu >> >> Hi all, >> >> I am planning to commit changes in PO this afternoon. To avoid mistakes >> from the past, here is what I am going to do regarding new terms in PO >> (based on your comments and suggestions so far): >> >> Note: this is not the list that Simon Yupp suggested; these are the >> terms >> I brought up to your attention earlier this week. >> Also, I am adding the following unresolved) items on the agenda for next >> ontology group conf call: >> >> 1. Terms: callus, whole plant, somatic embryo -what is the most >> appropriate place in the PO? >> 2. Apical hook - does it refer to hypogeal seeds? >> 3. Propagating terms from 'in vitro' node, such as 'cultured cell' to >> the other nodes in the PO (see Pankaj's suggestion, Jan 25, po-dev >> thread). >> >> There are the new terms in PO (with short explanation for some terms): >> >> 1. I'll add the term 'whole plant' to the PO as a child of 'Plant >> structure', sibling of 'cell' gametophyte' 'sporophyte' and 'tissue' >> nodes. >> On the next conf call we shall discuss the appropriate place for this >> term. >> >> Term: Whole plant >> Def: The entire plant, including roots, shoots and leaves, at any stage >> of >> its life cycle. >> Comment: This term is so general that it should be avoided whenever >> possible. >> >> 2. New node in PO >> I am adding top node 'In vitro cell, tissue and organ culture' (under >> the >> 'plant structure'), and most of the terms in this node are needed for >> annotations. I am leaving out term 'callus' for now, till we decide >> where >> to put this term. >> >> Plant structure >> (i) In vitro cell, tissue and organ culture >> (i) cultured cell >> (i) cultured protoplast >> (i) cultured leaf cell >> (i) cultured root cell >> (i) cultured callus >> (i) cultured embryo >> (i) somatic embryo >> >> >> Term: in vitro cell, tissue and organ culture >> Definition: >> Isolated and grown plant protoplast, cell, tissue and organ, involving, >> as >> a common factor, growth of microbe-free plant material in sterile >> environment, such as sterilized nutrient medium in a test tube or petri >> dish. >> >> Term: cultured protoplast >> Def: In vitro isolated cells from which the entire cell wall has been >> enzymatically removed. >> >> Term: cultured cell >> Synonym: cell suspension >> Def: In vitro grown isolated cells and small cell aggregates that >> proliferate while suspended in liquid sterile medium or spread on a >> solid >> agar medium. >> Comment: In cell cultures, the cells are no longer organized into >> tissues. >> >> Term: cultured leaf cell >> Def: In vitro grown isolated cells and small cell aggregates that >> originated from isolated leaf protoplasts (after they re-established >> cell >> wall, or from callus that was induced from leaf tissue). >> >> Term: cultured root cell >> Def: In vitro grown isolated cells and small cell aggregates that >> originated from isolated protoplasts after they re-established cell >> wall, >> or from callus that was induced from segment of root. >> >> Term: somatic embryo: >> Def: An embryo arising from previously differentiated somatic cells in >> vitro, rather than from fused haploid gametes, i.e., zygote. >> >> Term: cultured callus >> Def: In vitro grown cell aggregates that originated from isolated >> protoplasts, cell suspensions, or from callus that was induced in >> sterile >> medium the supplemented by plant growth regulators. >> >> Term: cultured embryo >> Def: In vitro development or maintenance of isolated mature or immature >> zygotic embryos, somatic embryos or haploid embryos (derived from male >> gametophyte). >> >> 3. Old terms revisited: >> These two terms will go under 'leaf' node as an instance_of. >> >> Term: Cauline leaf >> Def: Leaf or pairs/whorls of leaves borne on the stem. >> Comment: In Arabidopsis, refers to the leaves that are borne on the >> elongated inflorescence branches. >> >> Term: Rosette leaf >> Def: One of multiple leaves borne in a rosette. Rosette - a group of >> leaves, generally borne at the base of the plant, that are separated by >> very short internodes. >> Comment: In Arabidopsis, vegetative development is characterized by the >> production of the rosette leaves. >> >> This term is part_of 'primary shoot'. >> Term: apical hook >> >> Synonym: hypocotyl hook >> Def: hook-like structure which develops at the apical part of the >> hypocotyl in dark-grown seedlings in dicots. >> >> 4. Primordial terms >> >> I am adding the following terms under respective organs as instance_of. >> For the time being, I am leaving out top node term 'organ primordium', >> since we voted not to have node 'organ', the 'organ primordium is not >> needed fro similar reasons. >> >> Term: organ primordium >> Def: An organized group of cells from which an organ develops. >> >> Term: cotyledon primordium >> Def: An organized group of cells that will differentiate into a >> cotyledon. >> >> Term: lateral root primordium >> Def: An organized group of cells derived from the root pericycle that >> will >> differentiate into a new root. >> >> Term: leaf primordium >> Def: An organized group of cells that will differentiate into leaf that >> are emerging as a outgrowth in the shoot apex (flanking the meristem). >> >> >> Term: ovule primordium >> Def: An organized group of cells that will differentiate into ovule. >> >> >> Term: gynoecium primordium >> Def: The very first appearance of gynoecium. >> >> >> Term: petal primordium >> Def: The very first appearance of a petal. >> >> Many thanks, >> >> 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 katica at acoma.Stanford.EDU Mon Jan 31 16:30:38 2005 From: katica at acoma.Stanford.EDU (Katica Ilic) Date: Mon, 31 Jan 2005 13:30:38 -0800 (PST) Subject: New terms in the Plant Structure Ontology In-Reply-To: <1415.128.253.246.53.1107205670.squirrel@128.253.246.53> Message-ID: Hi Anu, Just brief comments, see below On Mon, 31 Jan 2005, Anuradha Pujar wrote: > Hello, > In complete awareness that the primordium terms have been committed, I > wish to draw attention to the fact that these terms will have an implicit > link with the body part development stage ontology and having the > develops_from relationship is significant. > > All plant body part develops from a primordium and the primordium itself > is defined as a stage by Esau. Nevertheless, the larger scientific > community uses this term as an anatomical entity. Strictly, by Esau?s > definition, a primordium could be a cell, organ or an organized series of > cells, in their earliest stage of differentiation. E.g. leaf primordium, > sclerid primordium, vessel member primordium. > > Therefore our suggestion is > > 1.The term primordium is botanically defined and should be available on > the PO per se. > Though Pankaj suggested xx-primordium as a grouping term, we should > consider making it more generic i.e. "primordium". Any instances of it > suggesting cell/tissue/organ primordium should then be listed with IS_A > relationship. Term primordium is more appropriate that organ primordium (in sync wiuth the decision to obsolete top node 'organ'), though we do not necessarilly need the groping term if all the primordia terms have instance_of relationships. > > 2. In defining, composite terms like ?leaf primordium? both ?leaf? and > ?primordium? should be defined independently, as in the case of every > other composite term in the PO such as ?leaf epidermis?. > This will make it easier for the developers and the automation script to > use SLOTS (today's e mail from Lincoln) and make cross products. > > > 3.The temporal development stages of body part ontology, will have a > number of anatomical structures as a part of their developmental history. > BUT the exact definition of those terms (primordium included) will be > retrieved from the structure ontology. > > Would, having the term ?primordium? at the same level of sporophyte be > justified for the above reasons? With children terms that could be a > cell, tissue or organs? > > I agree with Pankaj, that, develops_from relationship is more appropriate > biologically, to say, that leaf develops from a leaf primordium, rather > than the suggested relationship, of leaf primordium is_a instance of leaf. I don't agree to include develops_from with primordia terms in the structure thet you and Pankaj are suggesting, for two main reasons: 1. Develops_from relationship has a considerable limitations (see Documentation on the POC live site, True path rule), and should be used only when absolutely necessary, since annotations should not be propagated beyong the firs parental node. This proposition imply revoking develops_from relationships all over the ontology (if we are to be consistent), that would lead to potential violations of the true path rule, and creating cyclic structures, as oppose to hierarchy. After all, as we stated before, everything develops from zygote, and we decided not to follow this 'logics' when creating the top nodes. 2. Instance_of is not a wrong relationship, but a truly appropriate one ontologicaly and biologicaly as well, and we have several examples of similar situations, all with instance_of. Embryo (p) embryo proper (though this should be instance_of, considering remarks from Tereza Tykarska in my personal communications with her) sporophyte (i) seed leaf (i) embryonic leaf ...and perhaps others I cannot remeber now, since I am leaving for a meeting.. Katica > > > Plant structure > i--cell > i--tissue > i--sporophyte > i--gametophyte > i--Primordium > i-Phyllome primordium > i-leaf primordium > i- bract primordium > i-sporophyll primordium > i--carpel primordium > i--stamen primordium > > The current state of structure, committed last week suggests that a gene > that is expressed in a leaf primordium is also expressed in the leaf or > any of its > instances. Whereas the relationships suggested by Pankaj and here in this > mail, suggests, that a given primordium is in its earliest stages of > differentiation, which means, it has not yet fully differentiated into an > actual organ. Thus if we go by, the develops from relationship, the > annotations as well as the concept remains intact, validating the > statement that a gene expressed in leaf primordium is not necessarily > expressed in leaf or its instances. > > Individual definitions of gynoecium and petal primordium also requires > changes. > > anu > > > > > > Primordium terms needs further discussion, there are additional xx > > primordium terms that are required for cereals and i am working on it, to > > see, if it fits in with the relationship and definition that you are > > suggesting. > > anu > >> > >> Hi all, > >> > >> I am planning to commit changes in PO this afternoon. To avoid mistakes > >> from the past, here is what I am going to do regarding new terms in PO > >> (based on your comments and suggestions so far): > >> > >> Note: this is not the list that Simon Yupp suggested; these are the > >> terms > >> I brought up to your attention earlier this week. > >> Also, I am adding the following unresolved) items on the agenda for next > >> ontology group conf call: > >> > >> 1. Terms: callus, whole plant, somatic embryo -what is the most > >> appropriate place in the PO? > >> 2. Apical hook - does it refer to hypogeal seeds? > >> 3. Propagating terms from 'in vitro' node, such as 'cultured cell' to > >> the other nodes in the PO (see Pankaj's suggestion, Jan 25, po-dev > >> thread). > >> > >> There are the new terms in PO (with short explanation for some terms): > >> > >> 1. I'll add the term 'whole plant' to the PO as a child of 'Plant > >> structure', sibling of 'cell' gametophyte' 'sporophyte' and 'tissue' > >> nodes. > >> On the next conf call we shall discuss the appropriate place for this > >> term. > >> > >> Term: Whole plant > >> Def: The entire plant, including roots, shoots and leaves, at any stage > >> of > >> its life cycle. > >> Comment: This term is so general that it should be avoided whenever > >> possible. > >> > >> 2. New node in PO > >> I am adding top node 'In vitro cell, tissue and organ culture' (under > >> the > >> 'plant structure'), and most of the terms in this node are needed for > >> annotations. I am leaving out term 'callus' for now, till we decide > >> where > >> to put this term. > >> > >> Plant structure > >> (i) In vitro cell, tissue and organ culture > >> (i) cultured cell > >> (i) cultured protoplast > >> (i) cultured leaf cell > >> (i) cultured root cell > >> (i) cultured callus > >> (i) cultured embryo > >> (i) somatic embryo > >> > >> > >> Term: in vitro cell, tissue and organ culture > >> Definition: > >> Isolated and grown plant protoplast, cell, tissue and organ, involving, > >> as > >> a common factor, growth of microbe-free plant material in sterile > >> environment, such as sterilized nutrient medium in a test tube or petri > >> dish. > >> > >> Term: cultured protoplast > >> Def: In vitro isolated cells from which the entire cell wall has been > >> enzymatically removed. > >> > >> Term: cultured cell > >> Synonym: cell suspension > >> Def: In vitro grown isolated cells and small cell aggregates that > >> proliferate while suspended in liquid sterile medium or spread on a > >> solid > >> agar medium. > >> Comment: In cell cultures, the cells are no longer organized into > >> tissues. > >> > >> Term: cultured leaf cell > >> Def: In vitro grown isolated cells and small cell aggregates that > >> originated from isolated leaf protoplasts (after they re-established > >> cell > >> wall, or from callus that was induced from leaf tissue). > >> > >> Term: cultured root cell > >> Def: In vitro grown isolated cells and small cell aggregates that > >> originated from isolated protoplasts after they re-established cell > >> wall, > >> or from callus that was induced from segment of root. > >> > >> Term: somatic embryo: > >> Def: An embryo arising from previously differentiated somatic cells in > >> vitro, rather than from fused haploid gametes, i.e., zygote. > >> > >> Term: cultured callus > >> Def: In vitro grown cell aggregates that originated from isolated > >> protoplasts, cell suspensions, or from callus that was induced in > >> sterile > >> medium the supplemented by plant growth regulators. > >> > >> Term: cultured embryo > >> Def: In vitro development or maintenance of isolated mature or immature > >> zygotic embryos, somatic embryos or haploid embryos (derived from male > >> gametophyte). > >> > >> 3. Old terms revisited: > >> These two terms will go under 'leaf' node as an instance_of. > >> > >> Term: Cauline leaf > >> Def: Leaf or pairs/whorls of leaves borne on the stem. > >> Comment: In Arabidopsis, refers to the leaves that are borne on the > >> elongated inflorescence branches. > >> > >> Term: Rosette leaf > >> Def: One of multiple leaves borne in a rosette. Rosette - a group of > >> leaves, generally borne at the base of the plant, that are separated by > >> very short internodes. > >> Comment: In Arabidopsis, vegetative development is characterized by the > >> production of the rosette leaves. > >> > >> This term is part_of 'primary shoot'. > >> Term: apical hook > >> > >> Synonym: hypocotyl hook > >> Def: hook-like structure which develops at the apical part of the > >> hypocotyl in dark-grown seedlings in dicots. > >> > >> 4. Primordial terms > >> > >> I am adding the following terms under respective organs as instance_of. > >> For the time being, I am leaving out top node term 'organ primordium', > >> since we voted not to have node 'organ', the 'organ primordium is not > >> needed fro similar reasons. > >> > >> Term: organ primordium > >> Def: An organized group of cells from which an organ develops. > >> > >> Term: cotyledon primordium > >> Def: An organized group of cells that will differentiate into a > >> cotyledon. > >> > >> Term: lateral root primordium > >> Def: An organized group of cells derived from the root pericycle that > >> will > >> differentiate into a new root. > >> > >> Term: leaf primordium > >> Def: An organized group of cells that will differentiate into leaf that > >> are emerging as a outgrowth in the shoot apex (flanking the meristem). > >> > >> > >> Term: ovule primordium > >> Def: An organized group of cells that will differentiate into ovule. > >> > >> > >> Term: gynoecium primordium > >> Def: The very first appearance of gynoecium. > >> > >> > >> Term: petal primordium > >> Def: The very first appearance of a petal. > >> > >> Many thanks, > >> > >> 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. > >> -------------------------------------------------------------------------- > >> > >> > >> > > > > > > > > -------------------------------------------------------------------------- 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. --------------------------------------------------------------------------