From jaiswalp at science.oregonstate.edu Fri Jun 19 17:41:03 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Fri, 19 Jun 2009 14:41:03 -0700 Subject: [Po-dev] job posting: Plant Ontology Project Coordinator Message-ID: <4A3C05EF.60509@science.oregonstate.edu> Position Title: Research Associate (Senior Postdoc) / Research Associate (Postdoc) Working Title: Plant Ontology Project Coordinator The Plant Ontology Consortium (www.plantontology.org) is seeking applicants for a full-time position of scientific curator who will coordinate the Consortium?s efforts. The Plant Ontology Consortium is a collaboration among researchers at Oregon State University, Cornell University and New York Botanical Garden. The project is funded by the National Science Foundation. The Consortium also collaborates with the curators of many model organism databases including rice, Arabidopsis, maize, grasses, legumes, Solanaceae, Bryophytes and plant phylogenomics. The project aims to develop shared vocabularies on plant anatomy and growth and developmental stages, to describe patterns of phenotype(s) and gene expression. How to Apply: To review the position description and apply, go to posting #0004322 at http://oregonstate.edu/jobs. When applying, you will be required to electronically submit your application, a cover letter citing your interest in the position and your experience, and a CV/resume including 3 references. Closing date 7/15/09. Duties / Responsibilities: Develop and refine the ontologies with the PO curators in participating databases and core labs, annotate gene products and stocks with the vocabularies in the ontologies, participate in the development and application of methods to streamline and enhance the quality of annotations, manage website content, set project milestones, organize and moderate project meetings, and work with the project members to deliver the database releases and project reports on strict timelines. Required qualifications: Ph.D. in an aspect of plant biology (e.g. Development, Physiology, Biochemistry, Genetics, Plant Pathology, Systematics) and/or genomics, Phylogenomics, Systematics, Plant Biology and Plant Anatomy. Available immediately to start working on the project. Demonstrated ability for independent, critical thinking and excellent communication, networking and teamwork skills. Previous work in any one or more areas of Plant Development, Plant Physiology, Plant Biochemistry, Plant Genetics and/or genomics, Plant Pathology, Museum specimen curation, Phylogenomics, Systematics, Plant Biology and Plant Anatomy. Excellent communication skills in English is a must. Experience in teaching and outreach. Familiarity with Plant Development and Anatomy. Able to travel and attend 3-4 meetings/year of the PO consortium. In order to be considered for the Research Associate (senior Postdoc) position, the candidate must have 3 or more years of postdoctoral/scientist research experience and supporting publications in peer reviewed international journals. The selection committee will judge the candidate based on the qualifications below; in addition, to showing the ability to lead on a scientific project as an independent researcher. Preferred qualifications: Past experience in project coordination, large scale gene expression and phenotype evaluation, familiarity with basic UNIX commands, spreadsheets, and commonly used biological research tools such as BLAST and Literature Database search is desired. A working knowledge of PERL and/or SQL will be considered an asset but not required. -- Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Ph.: +1-541-737-8471 Fax: +1-541-737-3573 Web: www.gramene.org www.plantontology.org From nm249 at cornell.edu Thu Jun 25 10:29:17 2009 From: nm249 at cornell.edu (Naama Menda) Date: Thu, 25 Jun 2009 10:29:17 -0400 Subject: [Po-dev] tuber developmental stages Message-ID: hi Chih-Wei, I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only http://www.ncbi.nlm.nih.gov/pubmed/16088399). These terms are not in PO. how's: -sprout development -tuber initiation -tuber growth -tuber maturation http://74.125.47.132/search?q=cache:wR_-xdH4-ykJ:www.ag.uidaho.edu/potato/PotatoProductionSystems/Topics/Growth%26Development.pdf+potato+tuber+growth+stages&cd=7&hl=en&ct=clnk&gl=us&client=firefox-a thanks! -Naama Naama Menda Boyce Thompson Institute for Plant Research Tower Rd Ithaca NY 14853 USA (607) 254 3569 Sol Genomics Network http://www.sgn.cornell.edu nm249 at cornell.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From dws at nybg.org Thu Jun 25 21:54:11 2009 From: dws at nybg.org (Dws) Date: Thu, 25 Jun 2009 21:54:11 -0400 Subject: [Po-dev] tuber developmental stages References: Message-ID: <40F38EDDE25B7B49B995267E735A9AEB2B3FDC@xmail.nybg.org> I need to think about these as synonyms. Particularly sprout development which is no more then and axillary bud released from dormancy. Dennis Dennis Wm. Stevenson Vice President for Botanical Science Editor, Botanical Review Associate Editor, FLORA Editor-in-Chief, Cladistics New York Botanical Garden 2900 Southern Blvd. Bronx, NY 10458 Telephone: 718-817-8632 email: dws at nybg.org http://www.plantsystematics.org/ http://plantnet.rbgsyd.gov.au/PlantNet/cycad/ http://www.nybg.org/science/scientist_profile.php?id_scientist=21 ________________________________ From: po-dev-bounces at plantontology.org on behalf of Naama Menda Sent: Thu 6/25/2009 10:29 AM To: Chih-Wei Tung Cc: Anuradha Pujar; po-dev at plantontology.org Subject: [Po-dev] tuber developmental stages hi Chih-Wei, I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only http://www.ncbi.nlm.nih.gov/pubmed/16088399). These terms are not in PO. how's: -sprout development -tuber initiation -tuber growth -tuber maturation http://74.125.47.132/search?q=cache:wR_-xdH4-ykJ:www.ag.uidaho.edu/potato/PotatoProductionSystems/Topics/Growth%26Development.pdf+potato+tuber+growth+stages&cd=7&hl=en&ct=clnk&gl=us&client=firefox-a thanks! -Naama Naama Menda Boyce Thompson Institute for Plant Research Tower Rd Ithaca NY 14853 USA (607) 254 3569 Sol Genomics Network http://www.sgn.cornell.edu nm249 at cornell.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From ap343 at cornell.edu Fri Jun 26 05:33:43 2009 From: ap343 at cornell.edu (Anuradha Pujar) Date: Fri, 26 Jun 2009 05:33:43 -0400 (EDT) Subject: [Po-dev] tuber developmental stages In-Reply-To: <40F38EDDE25B7B49B995267E735A9AEB2B3FDC@xmail.nybg.org> References: <40F38EDDE25B7B49B995267E735A9AEB2B3FDC@xmail.nybg.org> Message-ID: <60397.67.244.63.39.1246008823.squirrel@webmail.cornell.edu> Hi Dennis, Were thinking you of a specific term to which we could add this as synonym? We did have a discussion about growth stages in vegetative reproduction, but now I don't recall if the decision was to introduce the parent term or not. Chih wei? Best anu > I need to think about these as synonyms. Particularly sprout development > which is no more then and axillary bud released from dormancy. > > Dennis > Dennis Wm. Stevenson > Vice President for Botanical Science > > Editor, Botanical Review > Associate Editor, FLORA > Editor-in-Chief, Cladistics > > New York Botanical Garden > 2900 Southern Blvd. Bronx, NY 10458 > Telephone: 718-817-8632 email: dws at nybg.org > http://www.plantsystematics.org/ > http://plantnet.rbgsyd.gov.au/PlantNet/cycad/ > http://www.nybg.org/science/scientist_profile.php?id_scientist=21 > > ________________________________ > > From: po-dev-bounces at plantontology.org on behalf of Naama Menda > Sent: Thu 6/25/2009 10:29 AM > To: Chih-Wei Tung > Cc: Anuradha Pujar; po-dev at plantontology.org > Subject: [Po-dev] tuber developmental stages > > > hi Chih-Wei, > > I have a bunch of potato genes which are expressed in different tuber > developmental stages (e.g. the potato pmt gene is expressed in small > sprouts only http://www.ncbi.nlm.nih.gov/pubmed/16088399). > These terms are not in PO. > > how's: > -sprout development > -tuber initiation > -tuber growth > -tuber maturation > > > http://74.125.47.132/search?q=cache:wR_-xdH4-ykJ:www.ag.uidaho.edu/potato/PotatoProductionSystems/Topics/Growth%26Development.pdf+potato+tuber+growth+stages&cd=7&hl=en&ct=clnk&gl=us&client=firefox-a > > thanks! > -Naama > > > Naama Menda > Boyce Thompson Institute for Plant Research > Tower Rd > Ithaca NY 14853 > USA > > (607) 254 3569 > Sol Genomics Network > http://www.sgn.cornell.edu > nm249 at cornell.edu > > From jaiswalp at science.oregonstate.edu Fri Jun 26 13:40:34 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Fri, 26 Jun 2009 10:40:34 -0700 Subject: [Po-dev] tuber developmental stages In-Reply-To: <60397.67.244.63.39.1246008823.squirrel@webmail.cornell.edu> References: <40F38EDDE25B7B49B995267E735A9AEB2B3FDC@xmail.nybg.org> <60397.67.244.63.39.1246008823.squirrel@webmail.cornell.edu> Message-ID: <4A450812.8090408@science.oregonstate.edu> Following are my suggestions. Pankaj Looks like sprout development is a case of either adding synonyms or adding the new term under PO:0007073 : 2 formation of axillary shoot http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0007073 As a suggestion, we can have two siblings of this term. PO:0007073 : 2 formation of axillary shoot -is_a- formation of axillary shoot from non-dormant shoot (PO:new_A) -is_a- formation of axillary shoot from dormant shoot (PO:new_B) # Thus any axillary shoot developments from tuber would be annotated to PO:new_B # All the existing children of PO:0007073 : 2 formation of axillary shoot would become children of PO: new_A For the following three we need to come up with new terms may be for 'food storage structure development' under PO:0007021 : plant structure development stages e.g. PO:0007021 : plant structure development stages -is_a- food storage structure development (PO:new) ----is_a- tuber development (PO:new) -------is_a- tuber initiation (PO:new) -------is_a- tuber growth (PO:new) -------is_a- tuber maturation (PO:new) Anuradha Pujar wrote: > Hi Dennis, > > Were thinking you of a specific term to which we could add this as > synonym? We did have a discussion about growth stages in vegetative > reproduction, but now I don't recall if the decision was to introduce the > parent term or not. Chih wei? > > Best > anu > >> I need to think about these as synonyms. Particularly sprout development >> which is no more then and axillary bud released from dormancy. >> >> Dennis >> Dennis Wm. Stevenson >> Vice President for Botanical Science >> >> Editor, Botanical Review >> Associate Editor, FLORA >> Editor-in-Chief, Cladistics >> >> New York Botanical Garden >> 2900 Southern Blvd. Bronx, NY 10458 >> Telephone: 718-817-8632 email: dws at nybg.org >> http://www.plantsystematics.org/ >> http://plantnet.rbgsyd.gov.au/PlantNet/cycad/ >> http://www.nybg.org/science/scientist_profile.php?id_scientist=21 >> >> ________________________________ >> >> From: po-dev-bounces at plantontology.org on behalf of Naama Menda >> Sent: Thu 6/25/2009 10:29 AM >> To: Chih-Wei Tung >> Cc: Anuradha Pujar; po-dev at plantontology.org >> Subject: [Po-dev] tuber developmental stages >> >> >> hi Chih-Wei, >> >> I have a bunch of potato genes which are expressed in different tuber >> developmental stages (e.g. the potato pmt gene is expressed in small >> sprouts only http://www.ncbi.nlm.nih.gov/pubmed/16088399). >> These terms are not in PO. >> >> how's: >> -sprout development >> -tuber initiation >> -tuber growth >> -tuber maturation >> >> >> http://74.125.47.132/search?q=cache:wR_-xdH4-ykJ:www.ag.uidaho.edu/potato/PotatoProductionSystems/Topics/Growth%26Development.pdf+potato+tuber+growth+stages&cd=7&hl=en&ct=clnk&gl=us&client=firefox-a >> >> thanks! >> -Naama >> >> >> Naama Menda >> Boyce Thompson Institute for Plant Research >> Tower Rd >> Ithaca NY 14853 >> USA >> >> (607) 254 3569 >> Sol Genomics Network >> http://www.sgn.cornell.edu >> nm249 at cornell.edu >> >> > > > _______________________________________________ > Po-dev mailing list > Po-dev at plantontology.org > http://mail.plantontology.org/mailman/listinfo/po-dev -- Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Ph.: +1-541-737-8471 Fax: +1-541-737-3573 Web: www.gramene.org www.plantontology.org From jaiswalp at science.oregonstate.edu Fri Jun 26 17:42:37 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Fri, 26 Jun 2009 14:42:37 -0700 Subject: [Po-dev] tuber developmental stages In-Reply-To: <4A450812.8090408@science.oregonstate.edu> References: <40F38EDDE25B7B49B995267E735A9AEB2B3FDC@xmail.nybg.org> <60397.67.244.63.39.1246008823.squirrel@webmail.cornell.edu> <4A450812.8090408@science.oregonstate.edu> Message-ID: <4A4540CD.70009@science.oregonstate.edu> Peter Stevens wrote: > spuds are stem tubers; other taxa have root tubers... > > P. Pankaj Jaiswal (OSU) wrote: > Following are my suggestions. > > Pankaj > > Looks like sprout development is a case of either adding synonyms or > adding the new term under > PO:0007073 : 2 formation of axillary shoot > http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0007073 > > > As a suggestion, we can have two siblings of this term. > > PO:0007073 : 2 formation of axillary shoot > -is_a- formation of axillary shoot from non-dormant shoot (PO:new_A) > -is_a- formation of axillary shoot from dormant shoot (PO:new_B) > > # Thus any axillary shoot developments from tuber would be annotated to > PO:new_B > # All the existing children of PO:0007073 : 2 formation of axillary > shoot would become children of PO: new_A > > For the following three we need to come up with new terms may be for > 'food storage structure development' under > PO:0007021 : plant structure development stages > > e.g. > PO:0007021 : plant structure development stages > -is_a- food storage structure development (PO:new) > ----is_a- tuber development (PO:new) > -------is_a- tuber initiation (PO:new) > -------is_a- tuber growth (PO:new) > -------is_a- tuber maturation (PO:new) > > > Anuradha Pujar wrote: >> Hi Dennis, >> >> Were thinking you of a specific term to which we could add this as >> synonym? We did have a discussion about growth stages in vegetative >> reproduction, but now I don't recall if the decision was to introduce the >> parent term or not. Chih wei? >> >> Best >> anu >> >>> I need to think about these as synonyms. Particularly sprout >>> development >>> which is no more then and axillary bud released from dormancy. >>> >>> Dennis >>> Dennis Wm. Stevenson >>> Vice President for Botanical Science >>> >>> Editor, Botanical Review >>> Associate Editor, FLORA >>> Editor-in-Chief, Cladistics >>> >>> New York Botanical Garden >>> 2900 Southern Blvd. Bronx, NY 10458 >>> Telephone: 718-817-8632 email: dws at nybg.org >>> http://www.plantsystematics.org/ >>> http://plantnet.rbgsyd.gov.au/PlantNet/cycad/ >>> http://www.nybg.org/science/scientist_profile.php?id_scientist=21 >>> >>> ________________________________ >>> >>> From: po-dev-bounces at plantontology.org on behalf of Naama Menda >>> Sent: Thu 6/25/2009 10:29 AM >>> To: Chih-Wei Tung >>> Cc: Anuradha Pujar; po-dev at plantontology.org >>> Subject: [Po-dev] tuber developmental stages >>> >>> >>> hi Chih-Wei, >>> >>> I have a bunch of potato genes which are expressed in different tuber >>> developmental stages (e.g. the potato pmt gene is expressed in small >>> sprouts only http://www.ncbi.nlm.nih.gov/pubmed/16088399). >>> These terms are not in PO. >>> >>> how's: >>> -sprout development >>> -tuber initiation >>> -tuber growth >>> -tuber maturation >>> >>> >>> http://74.125.47.132/search?q=cache:wR_-xdH4-ykJ:www.ag.uidaho.edu/potato/PotatoProductionSystems/Topics/Growth%26Development.pdf+potato+tuber+growth+stages&cd=7&hl=en&ct=clnk&gl=us&client=firefox-a >>> >>> >>> thanks! >>> -Naama >>> >>> >>> Naama Menda >>> Boyce Thompson Institute for Plant Research >>> Tower Rd >>> Ithaca NY 14853 >>> USA >>> >>> (607) 254 3569 >>> Sol Genomics Network >>> http://www.sgn.cornell.edu >>> nm249 at cornell.edu >>> >>> >> >> >> _______________________________________________ >> Po-dev mailing list >> Po-dev at plantontology.org >> http://mail.plantontology.org/mailman/listinfo/po-dev > -- Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Ph.: +1-541-737-8471 Fax: +1-541-737-3573 Web: www.gramene.org www.plantontology.org From jaiswalp at science.oregonstate.edu Fri Jun 26 17:44:05 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Fri, 26 Jun 2009 14:44:05 -0700 Subject: [Po-dev] tuber developmental stages In-Reply-To: <4A4540CD.70009@science.oregonstate.edu> References: <40F38EDDE25B7B49B995267E735A9AEB2B3FDC@xmail.nybg.org> <60397.67.244.63.39.1246008823.squirrel@webmail.cornell.edu> <4A450812.8090408@science.oregonstate.edu> <4A4540CD.70009@science.oregonstate.edu> Message-ID: <4A454125.2000203@science.oregonstate.edu> I see. Then we need to define two terms clearly under 'plant structure' for 'tubers' http://www.plantontology.org/amigo/go.cgi?xpand=PO:0004543&search_constraint=terms&query=PO:0004543&view=details&show_associations=list they should be root tuber and stem/shoot tuber. The current term PO:0004543 : tuber is suggesting only a shoot/stem tuber only. Chih-Wei pl. add a new SF item for 'tuber'. Pankaj Pankaj Jaiswal (OSU) wrote: > > > Peter Stevens wrote: > > spuds are stem tubers; other taxa have root tubers... > > > > P. >