From rhee at acoma.Stanford.EDU Mon Jan 15 18:58:47 2007 From: rhee at acoma.Stanford.EDU (Sue Rhee) Date: Mon, 15 Jan 2007 15:58:47 -0800 Subject: [Obo-cell-type] Annotations to cell types (using OBO-Cell) In-Reply-To: <75B96517-E540-443C-A684-2042678B9507@fruitfly.org> References: <75B96517-E540-443C-A684-2042678B9507@fruitfly.org> Message-ID: <45AC1537.7070001@acoma.stanford.edu> Chris, The Plant Ontology has a number of cell types under its Plant Structure branch and I think (though someone should confirm) that the Cell Type ontology's plant cell type terms have PO IDs as secondary IDs. Actually I think that this should be made bidirectional but am not sure if the PO terms have CT IDs as secondary IDs. In any case, there are 264 annotations to terms under plant cell, which are downloadable from the PO website (www.plantontology.org). Sue Chris Mungall wrote: > Is anyone aware of downloadable annotations to CL IDs? I know that > MGI provide cell type localisation info as qualifiers to their GO > annotations; this will be available through AmiGO sometime this year. > > There is also the FlyBase/ZFIN/NCBO phenotype annotations, many of > which are described as qualities borne by types of cell (eg > spermatocyte lacks asters) > > EVOC provides associations to dbEST libraries. > > Any others? > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Obo-cell-type mailing list > Obo-cell-type at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/obo-cell-type From cjm at fruitfly.org Tue Jan 16 10:31:55 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Tue, 16 Jan 2007 07:31:55 -0800 Subject: [Obo-cell-type] Annotations to cell types (using OBO-Cell) In-Reply-To: <45AC1537.7070001@acoma.stanford.edu> References: <75B96517-E540-443C-A684-2042678B9507@fruitfly.org> <45AC1537.7070001@acoma.stanford.edu> Message-ID: Why not add links to CL from PO as xrefs? This will help keep the two ontologies in sync, see http://www.bioontology.org/wiki/index.php/CL:Aligning_species- specific_anatomy_ontologies_with_CL See attached for a first pass at some automated mappings Hmm, according to OBO-Cell, zygote (CL:0000365) is both a plant and animal cell! I think the PO<->CL coordination effort could do with revisiting... On Jan 15, 2007, at 3:58 PM, Sue Rhee wrote: > Chris, > > The Plant Ontology has a number of cell types under its Plant > Structure branch and I think (though someone should confirm) that > the Cell Type ontology's plant cell type terms have PO IDs as > secondary IDs. Actually I think that this should be made > bidirectional but am not sure if the PO terms have CT IDs as > secondary IDs. In any case, there are 264 annotations to terms > under plant cell, which are downloadable from the PO website > (www.plantontology.org). > > Sue > > Chris Mungall wrote: >> Is anyone aware of downloadable annotations to CL IDs? I know >> that MGI provide cell type localisation info as qualifiers to >> their GO annotations; this will be available through AmiGO >> sometime this year. >> There is also the FlyBase/ZFIN/NCBO phenotype annotations, many >> of which are described as qualities borne by types of cell (eg >> spermatocyte lacks asters) >> EVOC provides associations to dbEST libraries. >> Any others? >> --------------------------------------------------------------------- >> ---- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys - and earn >> cash >> http://www.techsay.com/default.php? >> page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Obo-cell-type mailing list >> Obo-cell-type at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/obo-cell-type > From pj37 at cornell.edu Tue Jan 16 10:50:30 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 16 Jan 2007 10:50:30 -0500 Subject: Plant Ontology Asociations for January 2007 build Message-ID: <45ACF446.7050400@cornell.edu> Hi Everyone, Once again this is the monthly database build time for Plant Ontology. If your databases have new Plant Ontology associations that needs to be added/updated please let us know. Please use the default submission protocol by updating your association files using the POC cvs or contact Shuly Avraham for help. Previous versions of the association files can be accessed from http://brebiou.cshl.edu/viewcvs/Poc/associations/ Many thanks, Pankaj -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From pj37 at cornell.edu Tue Jan 16 11:20:17 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 16 Jan 2007 11:20:17 -0500 Subject: [Obo-cell-type] Annotations to cell types (using OBO-Cell) In-Reply-To: References: <75B96517-E540-443C-A684-2042678B9507@fruitfly.org> <45AC1537.7070001@acoma.stanford.edu> <45ACF17E.2020508@cornell.edu> Message-ID: <45ACFB41.4070205@cornell.edu> Chris Mungall wrote: > > On Jan 16, 2007, at 7:38 AM, Pankaj Jaiswal wrote: > >> Sue, its a good idea to establish Xrefs between CT and PO. > > yep! > >> Just a preliminary look at both the CT and PO for plant cell and its >> instances. > > You mean subtypes, not instances > > :-) Right. The subtypes. It's always confusing. > > Whilst I'm being picky, I recommend using either the unique ID-space > (CL) or root node (cell) as a way of identifying an ontology - CT is a > little confusing, it stands for too many other things > Got it. >> Seems to be that there are more cell types listed in PO (almost >> double). Also the free text definitions are not consistent with those >> from PO. So I am not sure what is the source of the plant cell types >> in CT. >> >> To avoid the inconsistencies, I suggest that the primary source of all >> the plant cell types in CT should be PO and not the other way round. >> If in case the CT needs new Plant cell types then a request be >> forwarded to PO. CT managers can later using an automated way >> collect/update it by pulling the plant cell type terms from PO. >> Alternatively we can also generate a mapping file PO2CT and use it for >> QC and consistency across both. Based on your suggestions I can ask >> Shuly to generate a mapping and add the related ontology DBXref to the >> PO terms. > > sounds reasonable. > I will work on it as soon as I get your mapping file (from previous mail) >> BTW one more suggestion, is it possible to add the 'subset: plant' or >> a namespace:plant to quickly identify which terms belong to the plant >> cell types. The same is suggested for cell types from other organisms >> as well. >> >> Any ideas? Is it a reasonable request? From pj37 at cornell.edu Tue Jan 16 11:18:03 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 16 Jan 2007 11:18:03 -0500 Subject: [Obo-cell-type] Annotations to cell types (using OBO-Cell) In-Reply-To: References: <75B96517-E540-443C-A684-2042678B9507@fruitfly.org> <45AC1537.7070001@acoma.stanford.edu> Message-ID: <45ACFABB.8080804@cornell.edu> Chris Mungall wrote: > > Why not add links to CL from PO as xrefs? This will help keep the two > ontologies in sync, see > http://www.bioontology.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL > I will add them to the PO. What about the CL will you add them too. > > See attached for a first pass at some automated mappings > Can you send the attachment again. I didn't get one. > Hmm, according to OBO-Cell, zygote (CL:0000365) is both a plant and > animal cell! > So what's the solution, create two subtypes of zygote (CL:0000365) one each for animal and plant. If I am not wrong the same may also apply to "zygospore" for many unicellular organisms. That's a different situation when we have this cell type developing by fusion of isogametes or nonisogametes. > I think the PO<->CL coordination effort could do with revisiting... > Sure. -Pankaj From cjm at fruitfly.org Tue Jan 16 11:00:53 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Tue, 16 Jan 2007 08:00:53 -0800 Subject: [Obo-cell-type] Annotations to cell types (using OBO-Cell) In-Reply-To: <45ACF17E.2020508@cornell.edu> References: <75B96517-E540-443C-A684-2042678B9507@fruitfly.org> <45AC1537.7070001@acoma.stanford.edu> <45ACF17E.2020508@cornell.edu> Message-ID: On Jan 16, 2007, at 7:38 AM, Pankaj Jaiswal wrote: > Sue, its a good idea to establish Xrefs between CT and PO. yep! > Just a preliminary look at both the CT and PO for plant cell and > its instances. You mean subtypes, not instances :-) Whilst I'm being picky, I recommend using either the unique ID-space (CL) or root node (cell) as a way of identifying an ontology - CT is a little confusing, it stands for too many other things > Seems to be that there are more cell types listed in PO (almost > double). Also the free text definitions are not consistent with > those from PO. So I am not sure what is the source of the plant > cell types in CT. > > To avoid the inconsistencies, I suggest that the primary source of > all the plant cell types in CT should be PO and not the other way > round. If in case the CT needs new Plant cell types then a request > be forwarded to PO. CT managers can later using an automated way > collect/update it by pulling the plant cell type terms from PO. > Alternatively we can also generate a mapping file PO2CT and use it > for QC and consistency across both. Based on your suggestions I can > ask Shuly to generate a mapping and add the related ontology DBXref > to the PO terms. sounds reasonable. > BTW one more suggestion, is it possible to add the 'subset: plant' > or a namespace:plant to quickly identify which terms belong to the > plant cell types. The same is suggested for cell types from other > organisms as well. > > Any ideas? > > Pankaj > > Sue Rhee wrote: >> Chris, >> The Plant Ontology has a number of cell types under its Plant >> Structure branch and I think (though someone should confirm) that >> the Cell Type ontology's plant cell type terms have PO IDs as >> secondary IDs. Actually I think that this should be made >> bidirectional but am not sure if the PO terms have CT IDs as >> secondary IDs. In any case, there are 264 annotations to terms >> under plant cell, which are downloadable from the PO website >> (www.plantontology.org). >> Sue >> Chris Mungall wrote: >>> Is anyone aware of downloadable annotations to CL IDs? I know >>> that MGI provide cell type localisation info as qualifiers to >>> their GO annotations; this will be available through AmiGO >>> sometime this year. >>> >>> There is also the FlyBase/ZFIN/NCBO phenotype annotations, many >>> of which are described as qualities borne by types of cell (eg >>> spermatocyte lacks asters) >>> >>> EVOC provides associations to dbEST libraries. >>> >>> Any others? >>> >>> -------------------------------------------------------------------- >>> ----- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to >>> share your >>> opinions on IT & business topics through brief surveys - and earn >>> cash >>> http://www.techsay.com/default.php? >>> page=join.php&p=sourceforge&CID=DEVDEV >>> _______________________________________________ >>> Obo-cell-type mailing list >>> Obo-cell-type at lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/obo-cell-type > > -- > Pankaj Jaiswal > G-15, Bradfield Hall > Dept. of Plant Breeding and Genetics > Cornell University > Ithaca, NY-14853, USA > > Ph. +1-607-255-3103 / 4199 > fax: +1-607-255-6683 > From pj37 at cornell.edu Tue Jan 16 10:38:38 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 16 Jan 2007 10:38:38 -0500 Subject: [Obo-cell-type] Annotations to cell types (using OBO-Cell) In-Reply-To: <45AC1537.7070001@acoma.stanford.edu> References: <75B96517-E540-443C-A684-2042678B9507@fruitfly.org> <45AC1537.7070001@acoma.stanford.edu> Message-ID: <45ACF17E.2020508@cornell.edu> Sue, its a good idea to establish Xrefs between CT and PO. Just a preliminary look at both the CT and PO for plant cell and its instances. Seems to be that there are more cell types listed in PO (almost double). Also the free text definitions are not consistent with those from PO. So I am not sure what is the source of the plant cell types in CT. To avoid the inconsistencies, I suggest that the primary source of all the plant cell types in CT should be PO and not the other way round. If in case the CT needs new Plant cell types then a request be forwarded to PO. CT managers can later using an automated way collect/update it by pulling the plant cell type terms from PO. Alternatively we can also generate a mapping file PO2CT and use it for QC and consistency across both. Based on your suggestions I can ask Shuly to generate a mapping and add the related ontology DBXref to the PO terms. BTW one more suggestion, is it possible to add the 'subset: plant' or a namespace:plant to quickly identify which terms belong to the plant cell types. The same is suggested for cell types from other organisms as well. Any ideas? Pankaj Sue Rhee wrote: > Chris, > > The Plant Ontology has a number of cell types under its Plant Structure > branch and I think (though someone should confirm) that the Cell Type > ontology's plant cell type terms have PO IDs as secondary IDs. Actually > I think that this should be made bidirectional but am not sure if the PO > terms have CT IDs as secondary IDs. In any case, there are 264 > annotations to terms under plant cell, which are downloadable from the > PO website (www.plantontology.org). > > Sue > > Chris Mungall wrote: >> Is anyone aware of downloadable annotations to CL IDs? I know that >> MGI provide cell type localisation info as qualifiers to their GO >> annotations; this will be available through AmiGO sometime this year. >> >> There is also the FlyBase/ZFIN/NCBO phenotype annotations, many of >> which are described as qualities borne by types of cell (eg >> spermatocyte lacks asters) >> >> EVOC provides associations to dbEST libraries. >> >> Any others? >> >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys - and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Obo-cell-type mailing list >> Obo-cell-type at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/obo-cell-type > > -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From cjm at fruitfly.org Tue Jan 16 11:03:25 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Tue, 16 Jan 2007 08:03:25 -0800 Subject: [Obo-cell-type] Annotations to cell types (using OBO-Cell) In-Reply-To: References: <75B96517-E540-443C-A684-2042678B9507@fruitfly.org> <45AC1537.7070001@acoma.stanford.edu> Message-ID: A non-text attachment was scrubbed... Name: cell-vs-poc.matches Type: application/octet-stream Size: 10560 bytes Desc: not available URL: -------------- next part -------------- again, with attachment On Jan 16, 2007, at 7:31 AM, Chris Mungall wrote: > > Why not add links to CL from PO as xrefs? This will help keep the two > ontologies in sync, see > http://www.bioontology.org/wiki/index.php/CL:Aligning_species- > specific_anatomy_ontologies_with_CL > > See attached for a first pass at some automated mappings > > Hmm, according to OBO-Cell, zygote (CL:0000365) is both a plant and > animal cell! > > I think the PO<->CL coordination effort could do with revisiting... > > On Jan 15, 2007, at 3:58 PM, Sue Rhee wrote: > >> Chris, >> >> The Plant Ontology has a number of cell types under its Plant >> Structure branch and I think (though someone should confirm) that >> the Cell Type ontology's plant cell type terms have PO IDs as >> secondary IDs. Actually I think that this should be made >> bidirectional but am not sure if the PO terms have CT IDs as >> secondary IDs. In any case, there are 264 annotations to terms >> under plant cell, which are downloadable from the PO website >> (www.plantontology.org). >> >> Sue >> >> Chris Mungall wrote: >>> Is anyone aware of downloadable annotations to CL IDs? I know >>> that MGI provide cell type localisation info as qualifiers to >>> their GO annotations; this will be available through AmiGO >>> sometime this year. >>> There is also the FlyBase/ZFIN/NCBO phenotype annotations, many >>> of which are described as qualities borne by types of cell (eg >>> spermatocyte lacks asters) >>> EVOC provides associations to dbEST libraries. >>> Any others? >>> -------------------------------------------------------------------- >>> - >>> ---- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to >>> share your >>> opinions on IT & business topics through brief surveys - and earn >>> cash >>> http://www.techsay.com/default.php? >>> page=join.php&p=sourceforge&CID=DEVDEV >>> _______________________________________________ >>> Obo-cell-type mailing list >>> Obo-cell-type at lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/obo-cell-type >> > > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Obo-cell-type mailing list > Obo-cell-type at lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/obo-cell-type > From pj37 at cornell.edu Tue Jan 16 14:37:41 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 16 Jan 2007 14:37:41 -0500 Subject: po_anatomy.obo file ver 1.33 and 1.34 Message-ID: <45AD2985.2000502@cornell.edu> Dear All, The new versions 1.33 and 1.34 of the po_anatomy.obo file were updated. The updates include the addition of following new terms from maize. It also includes many terms with new and/or updated term to term relationships. Many thanks to Leszek Vincent and Toby Kellogg for suggestions. id: PO:0009101 name: long lateral tassel branch id: PO:0009102 name: short tassel branch id: PO:0009103 name: short tassel branch meristem id: PO:0009104 name: long lateral tassel branch meristem id: PO:0009105 name: inflorescence lateral meristem id: PO:0009106 name: tassel meristem id: PO:0009107 name: tassel lateral meristem id: PO:0009108 name: inflorescence apical meristem id: PO:0009109 name: ear meristem id: PO:0009110 name: ear lateral meristem Sincerely Pankaj -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From pj37 at cornell.edu Tue Jan 16 15:57:10 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 16 Jan 2007 15:57:10 -0500 Subject: [Obo-cell-type] Annotations to cell types (using OBO-Cell) In-Reply-To: References: <75B96517-E540-443C-A684-2042678B9507@fruitfly.org> <45AC1537.7070001@acoma.stanford.edu> Message-ID: <45AD3C26.2050007@cornell.edu> Thanks. Got it. Pankaj Chris Mungall wrote: > again, with attachment > > On Jan 16, 2007, at 7:31 AM, Chris Mungall wrote: > >> >> Why not add links to CL from PO as xrefs? This will help keep the two >> ontologies in sync, see >> http://www.bioontology.org/wiki/index.php/CL:Aligning_species- >> specific_anatomy_ontologies_with_CL >> >> See attached for a first pass at some automated mappings >> >> Hmm, according to OBO-Cell, zygote (CL:0000365) is both a plant and >> animal cell! >> >> I think the PO<->CL coordination effort could do with revisiting... >> >> On Jan 15, 2007, at 3:58 PM, Sue Rhee wrote: >> >>> Chris, >>> >>> The Plant Ontology has a number of cell types under its Plant >>> Structure branch and I think (though someone should confirm) that >>> the Cell Type ontology's plant cell type terms have PO IDs as >>> secondary IDs. Actually I think that this should be made >>> bidirectional but am not sure if the PO terms have CT IDs as >>> secondary IDs. In any case, there are 264 annotations to terms >>> under plant cell, which are downloadable from the PO website >>> (www.plantontology.org). >>> >>> Sue >>> >>> Chris Mungall wrote: >>>> Is anyone aware of downloadable annotations to CL IDs? I know >>>> that MGI provide cell type localisation info as qualifiers to >>>> their GO annotations; this will be available through AmiGO >>>> sometime this year. >>>> There is also the FlyBase/ZFIN/NCBO phenotype annotations, many >>>> of which are described as qualities borne by types of cell (eg >>>> spermatocyte lacks asters) >>>> EVOC provides associations to dbEST libraries. >>>> Any others? >>>> --------------------------------------------------------------------- >>>> ---- >>>> Take Surveys. Earn Cash. Influence the Future of IT >>>> Join SourceForge.net's Techsay panel and you'll get the chance to >>>> share your >>>> opinions on IT & business topics through brief surveys - and earn >>>> cash >>>> http://www.techsay.com/default.php? >>>> page=join.php&p=sourceforge&CID=DEVDEV >>>> _______________________________________________ >>>> Obo-cell-type mailing list >>>> Obo-cell-type at lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/obo-cell-type >>> >> >> >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys - and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Obo-cell-type mailing list >> Obo-cell-type at lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/obo-cell-type >> > -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From cjm at fruitfly.org Wed Jan 17 11:02:55 2007 From: cjm at fruitfly.org (Chris Mungall) Date: Wed, 17 Jan 2007 08:02:55 -0800 Subject: [Obo-cell-type] Annotations to cell types (using OBO-Cell) In-Reply-To: <5C553736-5F90-496B-995F-4D70D3CBD217@sanbi.ac.za> References: <75B96517-E540-443C-A684-2042678B9507@fruitfly.org> <45AC1537.7070001@acoma.stanford.edu> <5C553736-5F90-496B-995F-4D70D3CBD217@sanbi.ac.za> Message-ID: On Jan 17, 2007, at 1:20 AM, Oliver Hofmann wrote: >> Why not add links to CL from PO as xrefs? > > Keeping a close eye on this, as is Minna. I was hoping to be able > to postpone some of the integration efforts until we have had a > chance to modify CL according to Lindsay's proposal, but that > timeframe might be unrealistic. I think it may actually be easier to figure out the correct placement of plant cell terms once the main framework has been revised... > Adding the preliminary mappings to the todo list. > > > Best wishes, > > Oliver > > > -- > Oliver Hofmann South African National Bioinformatics Institute > University of the Western Cape > > > From cwt6 at cornell.edu Tue Jan 23 15:36:03 2007 From: cwt6 at cornell.edu (Chih-Wei Tung) Date: Tue, 23 Jan 2007 15:36:03 -0500 Subject: Feedbacks from PAG 2007 Message-ID: Dear All, This is Chih-Wei, I just represented POC to present a poster in 2007 PAG meeting last week. During the time I was in San Diego, several people from Legume and Rosaceae research communities expressed their interests on applying PO to their projects. I browsed several public databases, such as http://www.bioinfo.wsu.edu/gdr/ and http://lin.ncgr.org/ui/index, currently, they don't have PO implemented in it. By browsing po-dev mail archives, I know Rex Nelson already worked with Katica on soybean ontology few years ago, I am wondering if the similar effort has been done in Medicago community, as well as in Rosaceae communities. If any of you have certain research groups in mind who may be interested in using PO, please let me know, I'd be happy to contact them as soon as possible. Chih-Wei From rhee at acoma.stanford.edu Tue Jan 23 16:03:16 2007 From: rhee at acoma.stanford.edu (Sue Rhee) Date: Tue, 23 Jan 2007 13:03:16 -0800 Subject: Feedbacks from PAG 2007 In-Reply-To: References: Message-ID: <45B67814.9070805@acoma.stanford.edu> For Medicago, you should contact Doug Cook and Nevin Young. For Rosaceae, you should contact Doreen Main. All three have been contacted by PO before so they should know what the project is about. Best, Sue Chih-Wei Tung wrote: > Dear All, > > This is Chih-Wei, I just represented POC to present a poster in 2007 PAG > meeting last week. > During the time I was in San Diego, several people from Legume and > Rosaceae research communities expressed their interests on applying PO > to their projects. I browsed several public databases, such as > http://www.bioinfo.wsu.edu/gdr/ and http://lin.ncgr.org/ui/index, > currently, they don't have PO implemented in it. By browsing po-dev > mail archives, I know Rex Nelson already worked with Katica on soybean > ontology few years ago, I am wondering if the similar effort has been > done in Medicago community, as well as in Rosaceae communities. If any > of you have certain research groups in mind who may be interested in > using PO, please let me know, I'd be happy to contact them as soon as > possible. > > Chih-Wei From pj37 at cornell.edu Tue Jan 23 20:45:39 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 23 Jan 2007 20:45:39 -0500 Subject: [Fwd: Re: Rosaceae db and PO collaboration] Message-ID: <45B6BA43.2000901@cornell.edu> Chih-wei, Another one with a Grape connection. -Pankaj -------- Original Message -------- Subject: Re: Rosaceae db and PO collaboration Date: Tue, 23 Jan 2007 20:32:07 -0500 From: angela baldo To: Pankaj Jaiswal CC: Chih-Wei Tung , Anne.Fennell at sdstate.edu References: <45B67B79.9020301 at cornell.edu> Hi Pankaj, Me again. Anne Fennell at SDSU was just asking about grape ontologies. She might be a good person to connect with in that community. GRIN has simple morphological characterization of some of the grape accessions in Geneva, summarized here: http://www.ars-grin.gov/npgs/descriptors/grape Regards, anja Pankaj Jaiswal wrote: > Hi Angela, > > Do you know someone who can work with us on this collaboration. We very > much appreciate the Rosaceae community to start using the PO in their > datasets and db. I am sure it will require us to add new terms > specifically required for Rosaceae community. > > Thanks > Pankaj > > PS: this mail is copied to our new coordinator Chih-wei Tung > > -------- Original Message -------- > Subject: Feedbacks from PAG 2007 > Date: Tue, 23 Jan 2007 15:36:03 -0500 > From: Chih-Wei Tung > Reply-To: po-dev at plantontology.org, Chih-Wei Tung > To: po-dev at plantontology.org > > > > Dear All, > > This is Chih-Wei, I just represented POC to present a poster in 2007 > PAG meeting last week. > During the time I was in San Diego, several people from Legume and > Rosaceae research communities expressed their interests on applying > PO to their projects. I browsed several public databases, such as > http://www.bioinfo.wsu.edu/gdr/ and http://lin.ncgr.org/ui/index, > currently, they don't have PO implemented in it. By browsing po-dev > mail archives, I know Rex Nelson already worked with Katica on > soybean ontology few years ago, I am wondering if the similar effort > has been done in Medicago community, as well as in Rosaceae > communities. If any of you have certain research groups in mind who > may be interested in using PO, please let me know, I'd be happy to > contact them as soon as possible. > > Chih-Wei > > > > > -- > Pankaj Jaiswal > G-15, Bradfield Hall > Dept. of Plant Breeding and Genetics > Cornell University > Ithaca, NY-14853, USA > > Ph. +1-607-255-3103 / 4199 > fax: +1-607-255-6683 > From pj37 at cornell.edu Tue Jan 23 20:44:19 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 23 Jan 2007 20:44:19 -0500 Subject: [Fwd: Re: Rosaceae db and PO collaboration] Message-ID: <45B6B9F3.4050602@cornell.edu> Hi Chih-wei, As Sue said in her mail and this one from Angela Baldo, looks like you need to contact Dorrie Main. I will forward another mail from Angela in a moment with a contact for grape project. In the meantime take a look at the link Angela has sent and see if there are new terms that we need in ontology. Though it is mainly on phenotypes, a quick look tells that we need some terms like calyx tube calyx lobe fruit flesh fruit lenticel There may be more terms but certainly the STL group would be able to tell us more on the proper terms for various parts. Pankaj PS: the mail is copied to Dorrie -------- Original Message -------- Subject: Re: Rosaceae db and PO collaboration Date: Tue, 23 Jan 2007 20:27:49 -0500 From: angela baldo To: Pankaj Jaiswal CC: dorrie at wsu.edu References: <45B67B79.9020301 at cornell.edu> Hi Pankaj, Good to hear from you! I'd recommend starting with Dorrie Main, who is the PI in charge of GDR. (I've cc'ed Dorrie on this message.) She would know who in the international community has made progress in this direction, and if there's already a committee charged with something like that. There has been a certain amount of simple morphological characterization of some of the USDA apple accessions in Geneva; you can see a report, here: http://www.ars-grin.gov/npgs/descriptors/apple Hope this helps, anja Pankaj Jaiswal wrote: > Hi Angela, > > Do you know someone who can work with us on this collaboration. We very > much appreciate the Rosaceae community to start using the PO in their > datasets and db. I am sure it will require us to add new terms > specifically required for Rosaceae community. > > Thanks > Pankaj > > PS: this mail is copied to our new coordinator Chih-wei Tung > > -------- Original Message -------- > Subject: Feedbacks from PAG 2007 > Date: Tue, 23 Jan 2007 15:36:03 -0500 > From: Chih-Wei Tung > Reply-To: po-dev at plantontology.org, Chih-Wei Tung > To: po-dev at plantontology.org > > > > Dear All, > > This is Chih-Wei, I just represented POC to present a poster in 2007 > PAG meeting last week. > During the time I was in San Diego, several people from Legume and > Rosaceae research communities expressed their interests on applying > PO to their projects. I browsed several public databases, such as > http://www.bioinfo.wsu.edu/gdr/ and http://lin.ncgr.org/ui/index, > currently, they don't have PO implemented in it. By browsing po-dev > mail archives, I know Rex Nelson already worked with Katica on > soybean ontology few years ago, I am wondering if the similar effort > has been done in Medicago community, as well as in Rosaceae > communities. If any of you have certain research groups in mind who > may be interested in using PO, please let me know, I'd be happy to > contact them as soon as possible. > > Chih-Wei > > > > > -- > Pankaj Jaiswal > G-15, Bradfield Hall > Dept. of Plant Breeding and Genetics > Cornell University > Ithaca, NY-14853, USA > > Ph. +1-607-255-3103 / 4199 > fax: +1-607-255-6683 > From peter.stevens at mobot.org Wed Jan 24 16:48:41 2007 From: peter.stevens at mobot.org (Peter Stevens) Date: Wed, 24 Jan 2007 17:48:41 -0400 Subject: [Fwd: Re: Rosaceae db and PO collaboration] In-Reply-To: <45B6B9F3.4050602@cornell.edu> References: <45B6B9F3.4050602@cornell.edu> Message-ID: Fruit flesh is decidedly vague - perhaps a synonym of mesocarp. But if strawberry, then it has no fruit flesh at all, ditto apple and pear. P. >Hi Chih-wei, > >As Sue said in her mail and this one from Angela Baldo, looks like >you need to contact Dorrie Main. I will forward another mail from >Angela in a moment with a contact for grape project. In the meantime >take a look at the link Angela has sent and see if there are new >terms that we need in ontology. Though it is mainly on phenotypes, a >quick look tells that we need some terms like >calyx tube >calyx lobe >fruit flesh >fruit lenticel > >There may be more terms but certainly the STL group would be able to >tell us more on the proper terms for various parts. > >Pankaj > >PS: the mail is copied to Dorrie > >-------- Original Message -------- >Subject: Re: Rosaceae db and PO collaboration >Date: Tue, 23 Jan 2007 20:27:49 -0500 >From: angela baldo >To: Pankaj Jaiswal >CC: dorrie at wsu.edu >References: <45B67B79.9020301 at cornell.edu> > >Hi Pankaj, > >Good to hear from you! > >I'd recommend starting with Dorrie Main, who is the PI in charge of GDR. > (I've cc'ed Dorrie on this message.) She would know who in the >international community has made progress in this direction, and if >there's already a committee charged with something like that. > >There has been a certain amount of simple morphological characterization >of some of the USDA apple accessions in Geneva; you can see a report, >here: http://www.ars-grin.gov/npgs/descriptors/apple > >Hope this helps, > >anja > >Pankaj Jaiswal wrote: >>Hi Angela, >> >>Do you know someone who can work with us on this collaboration. We >>very much appreciate the Rosaceae community to start using the PO >>in their datasets and db. I am sure it will require us to add new >>terms specifically required for Rosaceae community. >> >>Thanks >>Pankaj >> >>PS: this mail is copied to our new coordinator Chih-wei Tung >> >>-------- Original Message -------- >>Subject: Feedbacks from PAG 2007 >>Date: Tue, 23 Jan 2007 15:36:03 -0500 >>From: Chih-Wei Tung >>Reply-To: po-dev at plantontology.org, Chih-Wei Tung >>To: po-dev at plantontology.org >> >> >> >>Dear All, >> >>This is Chih-Wei, I just represented POC to present a poster in >>2007 PAG meeting last week. >>During the time I was in San Diego, several people from Legume and >>Rosaceae research communities expressed their interests on applying >>PO to their projects. I browsed several public databases, such as >>http://www.bioinfo.wsu.edu/gdr/ and http://lin.ncgr.org/ui/index, >>currently, they don't have PO implemented in it. By browsing >>po-dev mail archives, I know Rex Nelson already worked with Katica >>on soybean ontology few years ago, I am wondering if the similar >>effort has been done in Medicago community, as well as in Rosaceae >>communities. If any of you have certain research groups in mind who >>may be interested in using PO, please let me know, I'd be happy to >>contact them as soon as possible. >> >>Chih-Wei >> >> >> >>-- >>Pankaj Jaiswal >>G-15, Bradfield Hall >>Dept. of Plant Breeding and Genetics >>Cornell University >>Ithaca, NY-14853, USA >> >>Ph. +1-607-255-3103 / 4199 >>fax: +1-607-255-6683 From shuly at cshl.edu Thu Jan 25 09:12:44 2007 From: shuly at cshl.edu (Shuly Avraham) Date: Thu, 25 Jan 2007 09:12:44 -0500 Subject: Fwd: [Fwd: Re: Rosaceae db and PO collaboration] References: Message-ID: <9A64C88D-9725-49D2-8F23-31EEDE760D0B@cshl.edu> Begin forwarded message: > From: Peter Stevens > Date: January 24, 2007 4:48:41 PM EST > To: po-dev at plantontology.org, Pankaj Jaiswal > Subject: Re: [Fwd: Re: Rosaceae db and PO collaboration] > Reply-To: po-dev at plantontology.org, Peter Stevens > > > Fruit flesh is decidedly vague - perhaps a synonym of mesocarp. > But if strawberry, then it has no fruit flesh at all, ditto apple > and pear. > > P. > > >> Hi Chih-wei, >> >> As Sue said in her mail and this one from Angela Baldo, looks like >> you need to contact Dorrie Main. I will forward another mail from >> Angela in a moment with a contact for grape project. In the >> meantime take a look at the link Angela has sent and see if there >> are new terms that we need in ontology. Though it is mainly on >> phenotypes, a quick look tells that we need some terms like >> calyx tube >> calyx lobe >> fruit flesh >> fruit lenticel >> >> There may be more terms but certainly the STL group would be able >> to tell us more on the proper terms for various parts. >> >> Pankaj >> >> PS: the mail is copied to Dorrie >> >> -------- Original Message -------- >> Subject: Re: Rosaceae db and PO collaboration >> Date: Tue, 23 Jan 2007 20:27:49 -0500 >> From: angela baldo >> To: Pankaj Jaiswal >> CC: dorrie at wsu.edu >> References: <45B67B79.9020301 at cornell.edu> >> >> Hi Pankaj, >> >> Good to hear from you! >> >> I'd recommend starting with Dorrie Main, who is the PI in charge >> of GDR. >> (I've cc'ed Dorrie on this message.) She would know who in the >> international community has made progress in this direction, and if >> there's already a committee charged with something like that. >> >> There has been a certain amount of simple morphological >> characterization >> of some of the USDA apple accessions in Geneva; you can see a report, >> here: http://www.ars-grin.gov/npgs/descriptors/apple >> >> Hope this helps, >> >> anja >> >> Pankaj Jaiswal wrote: >>> Hi Angela, >>> >>> Do you know someone who can work with us on this collaboration. >>> We very much appreciate the Rosaceae community to start using the >>> PO in their datasets and db. I am sure it will require us to add >>> new terms specifically required for Rosaceae community. >>> >>> Thanks >>> Pankaj >>> >>> PS: this mail is copied to our new coordinator Chih-wei Tung >>> >>> -------- Original Message -------- >>> Subject: Feedbacks from PAG 2007 >>> Date: Tue, 23 Jan 2007 15:36:03 -0500 >>> From: Chih-Wei Tung >>> Reply-To: po-dev at plantontology.org, Chih-Wei Tung >>> To: po-dev at plantontology.org >>> >>> >>> >>> Dear All, >>> >>> This is Chih-Wei, I just represented POC to present a poster in >>> 2007 PAG meeting last week. >>> During the time I was in San Diego, several people from Legume >>> and Rosaceae research communities expressed their interests on >>> applying PO to their projects. I browsed several public >>> databases, such as http://www.bioinfo.wsu.edu/gdr/ and http:// >>> lin.ncgr.org/ui/index, currently, they don't have PO implemented >>> in it. By browsing po-dev mail archives, I know Rex Nelson >>> already worked with Katica on soybean ontology few years ago, I >>> am wondering if the similar effort has been done in Medicago >>> community, as well as in Rosaceae communities. If any of you have >>> certain research groups in mind who may be interested in using >>> PO, please let me know, I'd be happy to contact them as soon as >>> possible. >>> >>> Chih-Wei >>> >>> >>> >>> -- >>> Pankaj Jaiswal >>> G-15, Bradfield Hall >>> Dept. of Plant Breeding and Genetics >>> Cornell University >>> Ithaca, NY-14853, USA >>> >>> Ph. +1-607-255-3103 / 4199 >>> fax: +1-607-255-6683 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pj37 at cornell.edu Thu Jan 25 13:56:32 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Thu, 25 Jan 2007 13:56:32 -0500 Subject: NEW: tool for requesting for Plant Ontology (PO) new terms and/or modification Message-ID: <45B8FD60.4020807@cornell.edu> Dear Everyone, We have set up the PO-term request tracker at the sorceforge site http://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835555 From now on we will try to login all the requests that we get. This will help us to keeping track of the discussions and resolutions. It is open for the people and does not require registration to submit the requests or post comments. However, we will continue to take the requests sent by e-mails as well but either myself or Chih-wei the project coordinator will use the request tracker to open new items/update old ones. We hope the new request tracker will enhance our operations. If at some point we see that there is a misuse of this tracker (being open to anonymous users) resulting in Spams. We will remove the anonymous user option. Best regards Pankaj PS: The documentation for posting new requests using this tool will be provided soon on our website www.plantontology.org -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From pj37 at cornell.edu Tue Jan 9 14:57:40 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 09 Jan 2007 14:57:40 -0500 Subject: POC Presentation at Plant and Animal genome Meeting, San Diego, January 13-17, 2007 Message-ID: <45A3F3B4.6010209@cornell.edu> Dear All, At the next week's Plant and Animal Genome (PAG) Meeting, to be held at San Diego, January 13-17, 2007 the Plant Ontology project updates will be presented in a poster by Dr. Chih-wei Tung. If you are attending the PAG meeting, we encourage you to meet the project representative (Chih-wei Tung) and visit the poster # P841. The abstract can be found at http://intl-pag.org/15/abstracts/PAG15_P08a_841.html Many thanks Pankaj -- Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683 From pj37 at cornell.edu Tue Jan 9 14:49:31 2007 From: pj37 at cornell.edu (Pankaj Jaiswal) Date: Tue, 09 Jan 2007 14:49:31 -0500 Subject: [Dr. Chih-wei Tung] The new plant ontology editor and coordinator at Cornell Univ. Message-ID: <45A3F1CB.1080902@cornell.edu> Dear All, Our new plant ontology editor and coordinator, Dr. Chih-wei Tung has joined the POC project at Cornell University. Dr. Tung will coordinate the project activities so far being coordinated by Dr. Katica Ilic from Stanford Univ. and TAIR. She comes from the lab of Prof. June Nasrallah at Cornell Univ. who works on the self-incompatibility in Brassica. We had a very successful time with POC under the previous coordinator Dr. Katica Ilic and hope you all will help Dr. Chih-wei Tung in coming up to the speed, take on the project's responsibilities and share your previous experiences. Please continue to direct all your queries via e-mail to po-dev at plantontology.org or by visiting the project website http://www.plantontology.org Best regards Pankaj Pankaj Jaiswal G-15, Bradfield Hall Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY-14853, USA Ph. +1-607-255-3103 / 4199 fax: +1-607-255-6683