https://wiki.planteome.org/api.php?action=feedcontributions&feedformat=atom&user=Cooperl 2026-04-04T22:41:18Z User contributions MediaWiki 1.41.1 https://wiki.planteome.org/index.php?title=Oct._30th,_2018_Web_Site_Refresh_Meeting&diff=3624 2018-10-31T23:08:00Z

<p>Cooperl: </p> <hr /> <div>* Date: Tuesday Oct 30th, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings:<br /> ** [[File:Planteome Ontology Meeting-Website refresh 10-30-2018 audio.m4a|thumb|Planteome Ontology Meeting-Website refresh 10-30-2018 audio]]<br /> ** [[File:Planteome Ontology Meeting-Website refresh 10-30-2018.mp4|thumb|Planteome Ontology Meeting-Website refresh 10-30-2018]]<br /> <br /> <br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=May_1st,_2018_Sanmita_Demo&diff=3623 2018-10-31T23:06:55Z

<p>Cooperl: </p> <hr /> <div>* Date: Tuesday May 1st, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings: <br /> ** [[File:Sanmita Demo 5-01-2018 audio only.m4a|thumb|Sanmita Demo 5-01-2018 audio only]]<br /> ** [[File:Sanmita Demo video 5-01-2018.mp4|thumb|Sanmita Demo video 5-01-2018]]<br /> <br /> <br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]<br /> <br /> Sanmita_Demo_5-01-2018</div>

Cooperl https://wiki.planteome.org/index.php?title=April_13th,_2018_Plant_Phenoscape_Group_Meeting&diff=3622 2018-10-31T23:05:46Z

<p>Cooperl: </p> <hr /> <div>Date: Tuesday April 13th, 2018<br /> <br /> * Meeting recordings: <br /> ** [[File:Planteome Ontology Plant Phenoscape Zoom Meeting 4-13-2018 audio only.m4a|thumb|Planteome Ontology Plant Phenoscape Zoom Meeting 4-13-2018 audio only]]<br /> ** [[File:Planteome Ontology Plant Phenoscape Zoom Meeting video 4-13-2018.mp4|thumb|Planteome Ontology Plant Phenoscape Zoom Meeting video 4-13-2018]]<br /> <br /> * Link to notes: [https://docs.google.com/document/d/1FVGWsqo6_AVWQ53Y05cULnprN1kLcbcGtpBdJnhUowk/edit?usp=sharing Plant Phensoscape Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=April_10th,_2018_Ontology_Working_Group_Meeting&diff=3621 2018-10-31T23:04:07Z

<p>Cooperl: </p> <hr /> <div>* Date: Tuesday April 10th, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings: <br /> ** [[File:Planteome Ontology Meeting 4-10-2018 audio only.m4a|thumb|Planteome Ontology Meeting 4-10-2018 audio only]]<br /> ** [[File:Planteome Ontology Meeting video 4-10-2018.mp4|thumb|Planteome Ontology Meeting video 4-10-2018]]<br /> <br /> <br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=March_16th,_2018_Ontology_Meeting-Avocado_%2B_Cherimoya&diff=3620 2018-10-31T23:02:48Z

<p>Cooperl: </p> <hr /> <div>* Date: Tuesday Mar 16th, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings: <br /> ** [[File:Planteome Ontology Meeting- Avocado + Cherimoya 3-16-2018 audio.m4a|thumb|Planteome Ontology Meeting- Avocado + Cherimoya 3-16-2018 audio]]<br /> ** [[File:Planteome Ontology Meeting- Avocado + Cherimoya 3-16-2018.mp4|thumb|Planteome Ontology Meeting- Avocado + Cherimoya 3-16-2018]]<br /> <br /> <br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=Feb_27th,_2018_Ontology_Working_Group_Meeting&diff=3619 2018-10-31T23:01:32Z

<p>Cooperl: </p> <hr /> <div>* Date: Tuesday Feb 27th, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Connection details: <br /> Join from PC, Mac, Linux, iOS or Android: TBA<br /> <br /> Meeting recordings: <br /> * [[File:Planteome Ontology Meeting audio 2-27-2018.m4a|thumb|Planteome Ontology Meeting audio 2-27-2018]]<br /> * [[File:Planteome Ontology Meeting video 2-27-2018.mp4|thumb|Planteome Ontology Meeting video 2-27-2018]]<br /> <br /> <br /> Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=File:Planteome_Ontology_Meeting_video_4-10-2018.mp4&diff=3618 2018-10-31T23:00:16Z

<p>Cooperl: User created page with UploadWizard</p> <hr /> <div>=={{int:filedesc}}==<br /> {{Information<br /> |description={{en|1=Planteome Ontology Meeting video 4-10-2018}}<br /> |date=2018-10-31 15:31:43<br /> |source={{own}}<br /> |author=[[User:Cooperl|Cooperl]]<br /> |permission=<br /> |other versions=<br /> }}<br /> <br /> =={{int:license-header}}==<br /> {{self|cc-by-sa-4.0}}<br /> <br /> <br /> [[Category:Uploaded with UploadWizard]]</div>

Cooperl https://wiki.planteome.org/index.php?title=File:Planteome_Ontology_Meeting-Website_refresh_10-30-2018.mp4&diff=3617 2018-10-31T23:00:13Z

<p>Cooperl: User created page with UploadWizard</p> <hr /> <div>=={{int:filedesc}}==<br /> {{Information<br /> |description={{en|1=Planteome Ontology Meeting-Website refresh 10-30-2018}}<br /> |date=2018-10-31 15:33:55<br /> |source={{own}}<br /> |author=[[User:Cooperl|Cooperl]]<br /> |permission=<br /> |other versions=<br /> }}<br /> <br /> =={{int:license-header}}==<br /> {{self|cc-by-sa-4.0}}<br /> <br /> <br /> [[Category:Uploaded with UploadWizard]]</div>

Cooperl https://wiki.planteome.org/index.php?title=File:Planteome_Ontology_Meeting-Website_refresh_10-30-2018_audio.m4a&diff=3616 2018-10-31T23:00:06Z

<p>Cooperl: User created page with UploadWizard</p> <hr /> <div>=={{int:filedesc}}==<br /> {{Information<br /> |description={{en|1=Planteome Ontology Meeting-Website refresh 10-30-2018 audio}}<br /> |date=2018-10-31 15:32:29<br /> |source={{own}}<br /> |author=[[User:Cooperl|Cooperl]]<br /> |permission=<br /> |other versions=<br /> }}<br /> <br /> =={{int:license-header}}==<br /> {{self|cc-by-sa-4.0}}<br /> <br /> <br /> [[Category:Uploaded with UploadWizard]]</div>

Cooperl https://wiki.planteome.org/index.php?title=File:Sanmita_Demo_video_5-01-2018.mp4&diff=3615 2018-10-31T23:00:05Z

<p>Cooperl: User created page with UploadWizard</p> <hr /> <div>=={{int:filedesc}}==<br /> {{Information<br /> |description={{en|1=Sanmita Demo video 5-01-2018}}<br /> |date=2018-10-31 15:33:16<br /> |source={{own}}<br /> |author=[[User:Cooperl|Cooperl]]<br /> |permission=<br /> |other versions=<br /> }}<br /> <br /> =={{int:license-header}}==<br /> {{self|cc-by-sa-4.0}}<br /> <br /> <br /> [[Category:Uploaded with UploadWizard]]</div>

Cooperl https://wiki.planteome.org/index.php?title=File:Sanmita_Demo_5-01-2018_audio_only.m4a&diff=3614 2018-10-31T23:00:01Z

<p>Cooperl: User created page with UploadWizard</p> <hr /> <div>=={{int:filedesc}}==<br /> {{Information<br /> |description={{en|1=Sanmita Demo 5-01-2018 audio only}}<br /> |date=2018-10-31 15:32:12<br /> |source={{own}}<br /> |author=[[User:Cooperl|Cooperl]]<br /> |permission=<br /> |other versions=<br /> }}<br /> <br /> =={{int:license-header}}==<br /> {{self|cc-by-sa-4.0}}<br /> <br /> <br /> [[Category:Uploaded with UploadWizard]]</div>

Cooperl https://wiki.planteome.org/index.php?title=File:Planteome_Ontology_Plant_Phenoscape_Zoom_Meeting_video_4-13-2018.mp4&diff=3613 2018-10-31T23:00:00Z

<p>Cooperl: User created page with UploadWizard</p> <hr /> <div>=={{int:filedesc}}==<br /> {{Information<br /> |description={{en|1=Planteome Ontology Plant Phenoscape Zoom Meeting video 4-13-2018}}<br /> |date=2018-10-31 15:32:47<br /> |source={{own}}<br /> |author=[[User:Cooperl|Cooperl]]<br /> |permission=<br /> |other versions=<br /> }}<br /> <br /> =={{int:license-header}}==<br /> {{self|cc-by-sa-4.0}}<br /> <br /> <br /> [[Category:Uploaded with UploadWizard]]</div>

Cooperl https://wiki.planteome.org/index.php?title=File:Planteome_Ontology_Plant_Phenoscape_Zoom_Meeting_4-13-2018_audio_only.m4a&diff=3612 2018-10-31T22:59:53Z

<p>Cooperl: User created page with UploadWizard</p> <hr /> <div>=={{int:filedesc}}==<br /> {{Information<br /> |description={{en|1=Planteome Ontology Plant Phenoscape Zoom Meeting 4-13-2018 audio only}}<br /> |date=2018-10-31 15:31:38<br /> |source={{own}}<br /> |author=[[User:Cooperl|Cooperl]]<br /> |permission=<br /> |other versions=<br /> }}<br /> <br /> =={{int:license-header}}==<br /> {{self|cc-by-sa-4.0}}<br /> <br /> <br /> [[Category:Uploaded with UploadWizard]]</div>

Cooperl https://wiki.planteome.org/index.php?title=File:Planteome_Ontology_Meeting_4-10-2018_audio_only.m4a&diff=3611 2018-10-31T22:59:53Z

<p>Cooperl: User created page with UploadWizard</p> <hr /> <div>=={{int:filedesc}}==<br /> {{Information<br /> |description={{en|1=Planteome Ontology Meeting 4-10-2018 audio only}}<br /> |date=2018-10-31 15:31:13<br /> |source={{own}}<br /> |author=[[User:Cooperl|Cooperl]]<br /> |permission=<br /> |other versions=<br /> }}<br /> <br /> =={{int:license-header}}==<br /> {{self|cc-by-sa-4.0}}<br /> <br /> <br /> [[Category:Uploaded with UploadWizard]]</div>

Cooperl https://wiki.planteome.org/index.php?title=File:Planteome_Ontology_Meeting-_Avocado_%2B_Cherimoya_3-16-2018.mp4&diff=3610 2018-10-31T22:59:52Z

<p>Cooperl: User created page with UploadWizard</p> <hr /> <div>=={{int:filedesc}}==<br /> {{Information<br /> |description={{en|1=Planteome Ontology Meeting- Avocado + Cherimoya 3-16-2018}}<br /> |date=2018-10-31 15:31:21<br /> |source={{own}}<br /> |author=[[User:Cooperl|Cooperl]]<br /> |permission=<br /> |other versions=<br /> }}<br /> <br /> =={{int:license-header}}==<br /> {{self|cc-by-sa-4.0}}<br /> <br /> <br /> [[Category:Uploaded with UploadWizard]]</div>

Cooperl https://wiki.planteome.org/index.php?title=File:Planteome_Ontology_Meeting-_Avocado_%2B_Cherimoya_3-16-2018_audio.m4a&diff=3609 2018-10-31T22:59:50Z

<p>Cooperl: User created page with UploadWizard</p> <hr /> <div>=={{int:filedesc}}==<br /> {{Information<br /> |description={{en|1=Planteome Ontology Meeting- Avocado + Cherimoya 3-16-2018 audio}}<br /> |date=2018-10-31 15:30:56<br /> |source={{own}}<br /> |author=[[User:Cooperl|Cooperl]]<br /> |permission=<br /> |other versions=<br /> }}<br /> <br /> =={{int:license-header}}==<br /> {{self|cc-by-sa-4.0}}<br /> <br /> <br /> [[Category:Uploaded with UploadWizard]]</div>

Cooperl https://wiki.planteome.org/index.php?title=File:Planteome_Ontology_Meeting_video_2-27-2018.mp4&diff=3608 2018-10-31T22:59:49Z

<p>Cooperl: User created page with UploadWizard</p> <hr /> <div>=={{int:filedesc}}==<br /> {{Information<br /> |description={{en|1=Planteome Ontology Meeting video 2-27-2018}}<br /> |date=2018-10-31 15:30:55<br /> |source={{own}}<br /> |author=[[User:Cooperl|Cooperl]]<br /> |permission=<br /> |other versions=<br /> }}<br /> <br /> =={{int:license-header}}==<br /> {{self|cc-by-sa-4.0}}<br /> <br /> <br /> [[Category:Uploaded with UploadWizard]]</div>

Cooperl https://wiki.planteome.org/index.php?title=File:Planteome_Ontology_Meeting_audio_2-27-2018.m4a&diff=3607 2018-10-31T22:59:46Z

<p>Cooperl: User created page with UploadWizard</p> <hr /> <div>=={{int:filedesc}}==<br /> {{Information<br /> |description={{en|1=Planteome Ontology Meeting audio 2-27-2018}}<br /> |date=2018-10-31 15:30:31<br /> |source={{own}}<br /> |author=[[User:Cooperl|Cooperl]]<br /> |permission=<br /> |other versions=<br /> }}<br /> <br /> =={{int:license-header}}==<br /> {{self|cc-by-sa-4.0}}<br /> <br /> <br /> [[Category:Uploaded with UploadWizard]]</div>

Cooperl https://wiki.planteome.org/index.php?title=Planteome_Ontology_Development_and_Coordination_Working_Group&diff=3606 2018-10-31T22:19:08Z

<p>Cooperl: /* Ontology Working Group Meetings: */</p> <hr /> <div>=Participants=<br /> * Jaiswal Lab (Oregon, OSU): Laurel Cooper (Project coordinator, Curator), Pankaj Jaiswal (PI), Justin Elser (System Admin), Austin Meier (Curator)<br /> * Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI, AmiGO2, Gene Ontology)<br /> * CGIAR Consortium (Montpellier, France and CG centers around the world): Elizabeth Arnaud (Co-PI, Crop Ontology), Marie Angelique Laporte (Ontology Engineer), Léo Valette* (former Curator, IBP + CO)<br /> ** Rosemary Shrestha (Wheat Traits, CIMMYT, Mexico, Curator), Kate Dreher (Maize Traits, CIMMYT, Mexico, Curator),<br /> * New York Botanic Garden (Bronx, NY): Dennis W. Stevenson (Co-PI), new curator to be added<br /> * Barry Smith, University at Buffalo (Ontology Consultant)<br /> * Georgios Gkoutos, University of Aberystwyth, UK (Senior Personnel, PATO), new curator to be added<br /> <br /> - Has left the project*<br /> <br /> =Ontology Working Group Meetings:=<br /> * Goal is to hold these meetings on a bi-weekly basis on Tuesday 8:15 am PST (GMT -8)/ PDT (GMT -7)<br /> * Please check for your specific local time, if you are not sure here is a handy site: http://www.timeanddate.com/worldclock/meeting.html. <br /> [[Ontology Working Group_Meetings- 2015]]<br /> <br /> [[Ontology Working Group_Meetings- 2016]]<br /> <br /> [[Ontology Working Group_Meetings- 2017]]<br /> <br /> [[Jan 23rd, 2018 Ontology Working Group Meeting]]<br /> <br /> [[Feb 27th, 2018 Ontology Working Group Meeting]]<br /> <br /> [[March 16th, 2018 Ontology Meeting-Avocado + Cherimoya]]<br /> <br /> [[April 10th, 2018 Ontology Working Group Meeting]]<br /> <br /> [[April 13th, 2018 Plant Phenoscape Group Meeting]]<br /> <br /> [[May 1st, 2018 Sanmita Demo]]<br /> <br /> [[Oct. 30th, 2018 Web Site Refresh Meeting]]<br /> <br /> =Goals and Objectives:=<br /> ==1. Develop a set of common reference ontologies to describe major knowledge domains of plant biology, comprising plant phenotype and traits, environments, and biotic and abiotic stresses, including plant diseases.==<br /> The project will provide a suite of reference and interoperable ontologies (Figure-1) relevant to the knowledge domain of plant biology required for annotating and describing the experiments, data sets, tagging published papers, and images. <br /> <br /> These ontologies include the Plant Ontology (PO); Trait Ontology (TO), Environment Ontology (EO) and Plant Stress Ontology (PSO) to be developed by the cROP project and will associate them to the existing reference ontologies for relevant knowledge domains (Figure-1 Table-1) being developed and funded by other resources. <br /> <br /> The Planteome project will also contribute to and enhance the existing reference ontologies, developed and maintained by the proposal partners. A network of national and international collaborators, representing major plant genomics resources, large-scale phenotype and genome annotation projects (Appendix-A3), will apply the set of reference ontologies to empower researchers to build their hypotheses, query, discover and analyze the plant genomics and genetics data sets.<br /> <br /> * Plant Trait Ontology (TO)<br /> * Plant Environment Ontology (EO)<br /> * Plant Ontology (PO) <br /> * Plant Stress Ontology (PSO) <br /> * Coordination with the Phenotypic Qualities Ontology (PATO)<br /> * Building references with the Crop Ontology (CO) as a resource of concepts for cROP<br /> <br /> ==2. Develop standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm.==<br /> ===2.1 Collaborative approaches on ontology development and annotation:=== <br /> * Transition to OWL Format<br /> * Introduction of Elk reasoner and Continuous Integration (CI) system<br /> * Development of TermGenie tool for TO and PO<br /> * Use of Inferred graph completion<br /> <br /> ===2.2 Improving ontology-based annotations for plant genomes and develop quality assessment matrix:===<br /> GOstruct method<br /> <br /> ===2.3 Annotating orphan plant genomes and maintaining reference genome annotations.===<br /> Details TBA<br /> <br /> ----<br /> =Ontology Development Workshops=<br /> [[Planteome Curator workshop Fall 2015]]<br /> ----<br /> <br /> =Links to current versions of the Ontologies:=<br /> [http://dev.planteome.org/amigo Planteome Development Browser] Updates nightly<br /> <br /> ==Plant Trait Ontology (TO)==<br /> Link to most recent changes on GitHub: <br /> [https://github.com/Planteome/plant-trait-ontology Plant Trait Ontology repository]<br /> ----<br /> <br /> ==Plant Ontology (PO)==<br /> <br /> ==Crop Ontology (TO)==<br /> * [[Crop Ontology Pages]] on wiki<br /> * Link to home page: [http://www.cropontology.org/ Crop Ontology Curation Tool]</div>

Cooperl https://wiki.planteome.org/index.php?title=May_1st,_2018_Ontology_Working_Group_Meeting&diff=3605 2018-10-31T22:18:35Z

<p>Cooperl: Cooperl moved page May 1st, 2018 Ontology Working Group Meeting to May 1st, 2018 Sanmita Demo</p> <hr /> <div>#REDIRECT [[May 1st, 2018 Sanmita Demo]]</div>

Cooperl https://wiki.planteome.org/index.php?title=May_1st,_2018_Sanmita_Demo&diff=3604 2018-10-31T22:18:35Z

<p>Cooperl: Cooperl moved page May 1st, 2018 Ontology Working Group Meeting to May 1st, 2018 Sanmita Demo</p> <hr /> <div>* Date: Tuesday May 1st, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings: TBA<br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]<br /> <br /> Sanmita_Demo_5-01-2018</div>

Cooperl https://wiki.planteome.org/index.php?title=May_1st,_2018_Sanmita_Demo&diff=3603 2018-10-31T22:17:48Z

<p>Cooperl: </p> <hr /> <div>* Date: Tuesday May 1st, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings: TBA<br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]<br /> <br /> Sanmita_Demo_5-01-2018</div>

Cooperl https://wiki.planteome.org/index.php?title=March_16th,_2018_Planteome_Ontology_Meeting-_Avocado_%2B_Cherimoya&diff=3602 2018-10-31T22:04:06Z

<p>Cooperl: Cooperl moved page March 16th, 2018 Planteome Ontology Meeting- Avocado + Cherimoya to March 16th, 2018 Ontology Meeting-Avocado + Cherimoya</p> <hr /> <div>#REDIRECT [[March 16th, 2018 Ontology Meeting-Avocado + Cherimoya]]</div>

Cooperl https://wiki.planteome.org/index.php?title=March_16th,_2018_Ontology_Meeting-Avocado_%2B_Cherimoya&diff=3601 2018-10-31T22:04:06Z

<p>Cooperl: Cooperl moved page March 16th, 2018 Planteome Ontology Meeting- Avocado + Cherimoya to March 16th, 2018 Ontology Meeting-Avocado + Cherimoya</p> <hr /> <div>* Date: Tuesday Mar 16th, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings: TBA<br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=Planteome_Ontology_Development_and_Coordination_Working_Group&diff=3600 2018-10-31T22:02:45Z

<p>Cooperl: /* Ontology Working Group Meetings: */</p> <hr /> <div>=Participants=<br /> * Jaiswal Lab (Oregon, OSU): Laurel Cooper (Project coordinator, Curator), Pankaj Jaiswal (PI), Justin Elser (System Admin), Austin Meier (Curator)<br /> * Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI, AmiGO2, Gene Ontology)<br /> * CGIAR Consortium (Montpellier, France and CG centers around the world): Elizabeth Arnaud (Co-PI, Crop Ontology), Marie Angelique Laporte (Ontology Engineer), Léo Valette* (former Curator, IBP + CO)<br /> ** Rosemary Shrestha (Wheat Traits, CIMMYT, Mexico, Curator), Kate Dreher (Maize Traits, CIMMYT, Mexico, Curator),<br /> * New York Botanic Garden (Bronx, NY): Dennis W. Stevenson (Co-PI), new curator to be added<br /> * Barry Smith, University at Buffalo (Ontology Consultant)<br /> * Georgios Gkoutos, University of Aberystwyth, UK (Senior Personnel, PATO), new curator to be added<br /> <br /> - Has left the project*<br /> <br /> =Ontology Working Group Meetings:=<br /> * Goal is to hold these meetings on a bi-weekly basis on Tuesday 8:15 am PST (GMT -8)/ PDT (GMT -7)<br /> * Please check for your specific local time, if you are not sure here is a handy site: http://www.timeanddate.com/worldclock/meeting.html. <br /> [[Ontology Working Group_Meetings- 2015]]<br /> <br /> [[Ontology Working Group_Meetings- 2016]]<br /> <br /> [[Ontology Working Group_Meetings- 2017]]<br /> <br /> [[Jan 23rd, 2018 Ontology Working Group Meeting]]<br /> <br /> [[Feb 27th, 2018 Ontology Working Group Meeting]]<br /> <br /> [[March 16th, 2018 Ontology Meeting-Avocado + Cherimoya]]<br /> <br /> [[April 10th, 2018 Ontology Working Group Meeting]]<br /> <br /> [[April 13th, 2018 Plant Phenoscape Group Meeting]]<br /> <br /> [[May 1st, 2018 Ontology Working Group Meeting]]<br /> <br /> [[Oct. 30th, 2018 Web Site Refresh Meeting]]<br /> <br /> =Goals and Objectives:=<br /> ==1. Develop a set of common reference ontologies to describe major knowledge domains of plant biology, comprising plant phenotype and traits, environments, and biotic and abiotic stresses, including plant diseases.==<br /> The project will provide a suite of reference and interoperable ontologies (Figure-1) relevant to the knowledge domain of plant biology required for annotating and describing the experiments, data sets, tagging published papers, and images. <br /> <br /> These ontologies include the Plant Ontology (PO); Trait Ontology (TO), Environment Ontology (EO) and Plant Stress Ontology (PSO) to be developed by the cROP project and will associate them to the existing reference ontologies for relevant knowledge domains (Figure-1 Table-1) being developed and funded by other resources. <br /> <br /> The Planteome project will also contribute to and enhance the existing reference ontologies, developed and maintained by the proposal partners. A network of national and international collaborators, representing major plant genomics resources, large-scale phenotype and genome annotation projects (Appendix-A3), will apply the set of reference ontologies to empower researchers to build their hypotheses, query, discover and analyze the plant genomics and genetics data sets.<br /> <br /> * Plant Trait Ontology (TO)<br /> * Plant Environment Ontology (EO)<br /> * Plant Ontology (PO) <br /> * Plant Stress Ontology (PSO) <br /> * Coordination with the Phenotypic Qualities Ontology (PATO)<br /> * Building references with the Crop Ontology (CO) as a resource of concepts for cROP<br /> <br /> ==2. Develop standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm.==<br /> ===2.1 Collaborative approaches on ontology development and annotation:=== <br /> * Transition to OWL Format<br /> * Introduction of Elk reasoner and Continuous Integration (CI) system<br /> * Development of TermGenie tool for TO and PO<br /> * Use of Inferred graph completion<br /> <br /> ===2.2 Improving ontology-based annotations for plant genomes and develop quality assessment matrix:===<br /> GOstruct method<br /> <br /> ===2.3 Annotating orphan plant genomes and maintaining reference genome annotations.===<br /> Details TBA<br /> <br /> ----<br /> =Ontology Development Workshops=<br /> [[Planteome Curator workshop Fall 2015]]<br /> ----<br /> <br /> =Links to current versions of the Ontologies:=<br /> [http://dev.planteome.org/amigo Planteome Development Browser] Updates nightly<br /> <br /> ==Plant Trait Ontology (TO)==<br /> Link to most recent changes on GitHub: <br /> [https://github.com/Planteome/plant-trait-ontology Plant Trait Ontology repository]<br /> ----<br /> <br /> ==Plant Ontology (PO)==<br /> <br /> ==Crop Ontology (TO)==<br /> * [[Crop Ontology Pages]] on wiki<br /> * Link to home page: [http://www.cropontology.org/ Crop Ontology Curation Tool]</div>

Cooperl https://wiki.planteome.org/index.php?title=Planteome_Ontology_Development_and_Coordination_Working_Group&diff=3599 2018-10-31T22:02:21Z

<p>Cooperl: /* Ontology Working Group Meetings: */</p> <hr /> <div>=Participants=<br /> * Jaiswal Lab (Oregon, OSU): Laurel Cooper (Project coordinator, Curator), Pankaj Jaiswal (PI), Justin Elser (System Admin), Austin Meier (Curator)<br /> * Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI, AmiGO2, Gene Ontology)<br /> * CGIAR Consortium (Montpellier, France and CG centers around the world): Elizabeth Arnaud (Co-PI, Crop Ontology), Marie Angelique Laporte (Ontology Engineer), Léo Valette* (former Curator, IBP + CO)<br /> ** Rosemary Shrestha (Wheat Traits, CIMMYT, Mexico, Curator), Kate Dreher (Maize Traits, CIMMYT, Mexico, Curator),<br /> * New York Botanic Garden (Bronx, NY): Dennis W. Stevenson (Co-PI), new curator to be added<br /> * Barry Smith, University at Buffalo (Ontology Consultant)<br /> * Georgios Gkoutos, University of Aberystwyth, UK (Senior Personnel, PATO), new curator to be added<br /> <br /> - Has left the project*<br /> <br /> =Ontology Working Group Meetings:=<br /> * Goal is to hold these meetings on a bi-weekly basis on Tuesday 8:15 am PST (GMT -8)/ PDT (GMT -7)<br /> * Please check for your specific local time, if you are not sure here is a handy site: http://www.timeanddate.com/worldclock/meeting.html. <br /> [[Ontology Working Group_Meetings- 2015]]<br /> <br /> [[Ontology Working Group_Meetings- 2016]]<br /> <br /> [[Ontology Working Group_Meetings- 2017]]<br /> <br /> [[Jan 23rd, 2018 Ontology Working Group Meeting]]<br /> <br /> [[Feb 27th, 2018 Ontology Working Group Meeting]]<br /> <br /> [[March 16th,2018 Ontology Meeting-Avocado + Cherimoya]]<br /> <br /> [[April 10th, 2018 Ontology Working Group Meeting]]<br /> <br /> [[April 13th, 2018 Plant Phenoscape Group Meeting]]<br /> <br /> [[May 1st, 2018 Ontology Working Group Meeting]]<br /> <br /> [[Oct. 30th, 2018 Web Site Refresh Meeting]]<br /> <br /> =Goals and Objectives:=<br /> ==1. Develop a set of common reference ontologies to describe major knowledge domains of plant biology, comprising plant phenotype and traits, environments, and biotic and abiotic stresses, including plant diseases.==<br /> The project will provide a suite of reference and interoperable ontologies (Figure-1) relevant to the knowledge domain of plant biology required for annotating and describing the experiments, data sets, tagging published papers, and images. <br /> <br /> These ontologies include the Plant Ontology (PO); Trait Ontology (TO), Environment Ontology (EO) and Plant Stress Ontology (PSO) to be developed by the cROP project and will associate them to the existing reference ontologies for relevant knowledge domains (Figure-1 Table-1) being developed and funded by other resources. <br /> <br /> The Planteome project will also contribute to and enhance the existing reference ontologies, developed and maintained by the proposal partners. A network of national and international collaborators, representing major plant genomics resources, large-scale phenotype and genome annotation projects (Appendix-A3), will apply the set of reference ontologies to empower researchers to build their hypotheses, query, discover and analyze the plant genomics and genetics data sets.<br /> <br /> * Plant Trait Ontology (TO)<br /> * Plant Environment Ontology (EO)<br /> * Plant Ontology (PO) <br /> * Plant Stress Ontology (PSO) <br /> * Coordination with the Phenotypic Qualities Ontology (PATO)<br /> * Building references with the Crop Ontology (CO) as a resource of concepts for cROP<br /> <br /> ==2. Develop standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm.==<br /> ===2.1 Collaborative approaches on ontology development and annotation:=== <br /> * Transition to OWL Format<br /> * Introduction of Elk reasoner and Continuous Integration (CI) system<br /> * Development of TermGenie tool for TO and PO<br /> * Use of Inferred graph completion<br /> <br /> ===2.2 Improving ontology-based annotations for plant genomes and develop quality assessment matrix:===<br /> GOstruct method<br /> <br /> ===2.3 Annotating orphan plant genomes and maintaining reference genome annotations.===<br /> Details TBA<br /> <br /> ----<br /> =Ontology Development Workshops=<br /> [[Planteome Curator workshop Fall 2015]]<br /> ----<br /> <br /> =Links to current versions of the Ontologies:=<br /> [http://dev.planteome.org/amigo Planteome Development Browser] Updates nightly<br /> <br /> ==Plant Trait Ontology (TO)==<br /> Link to most recent changes on GitHub: <br /> [https://github.com/Planteome/plant-trait-ontology Plant Trait Ontology repository]<br /> ----<br /> <br /> ==Plant Ontology (PO)==<br /> <br /> ==Crop Ontology (TO)==<br /> * [[Crop Ontology Pages]] on wiki<br /> * Link to home page: [http://www.cropontology.org/ Crop Ontology Curation Tool]</div>

Cooperl https://wiki.planteome.org/index.php?title=Mar_16th,_2018_Ontology_Working_Group_Meeting&diff=3598 2018-10-31T22:00:39Z

<p>Cooperl: Cooperl moved page Mar 16th, 2018 Ontology Working Group Meeting to March 16th, 2018 Planteome Ontology Meeting- Avocado + Cherimoya</p> <hr /> <div>#REDIRECT [[March 16th, 2018 Planteome Ontology Meeting- Avocado + Cherimoya]]</div>

Cooperl https://wiki.planteome.org/index.php?title=March_16th,_2018_Ontology_Meeting-Avocado_%2B_Cherimoya&diff=3597 2018-10-31T22:00:39Z

<p>Cooperl: Cooperl moved page Mar 16th, 2018 Ontology Working Group Meeting to March 16th, 2018 Planteome Ontology Meeting- Avocado + Cherimoya</p> <hr /> <div>* Date: Tuesday Mar 16th, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings: TBA<br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=Oct._30th,_2018_Web_Site_Refresh_Meeting&diff=3596 2018-10-31T20:53:28Z

<p>Cooperl: Created page with &quot;* Date: Tuesday Oct 30th, 2018 * Time: 8:15am PST (GMT-8) * Meeting recordings: TBA * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3o...&quot;</p> <hr /> <div>* Date: Tuesday Oct 30th, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings: TBA<br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=May_1st,_2018_Sanmita_Demo&diff=3595 2018-10-31T20:53:02Z

<p>Cooperl: Created page with &quot;* Date: Tuesday May 1st, 2018 * Time: 8:15am PST (GMT-8) * Meeting recordings: TBA * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oK...&quot;</p> <hr /> <div>* Date: Tuesday May 1st, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings: TBA<br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=Planteome_Ontology_Development_and_Coordination_Working_Group&diff=3594 2018-10-31T20:52:17Z

<p>Cooperl: /* Ontology Working Group Meetings: */</p> <hr /> <div>=Participants=<br /> * Jaiswal Lab (Oregon, OSU): Laurel Cooper (Project coordinator, Curator), Pankaj Jaiswal (PI), Justin Elser (System Admin), Austin Meier (Curator)<br /> * Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI, AmiGO2, Gene Ontology)<br /> * CGIAR Consortium (Montpellier, France and CG centers around the world): Elizabeth Arnaud (Co-PI, Crop Ontology), Marie Angelique Laporte (Ontology Engineer), Léo Valette* (former Curator, IBP + CO)<br /> ** Rosemary Shrestha (Wheat Traits, CIMMYT, Mexico, Curator), Kate Dreher (Maize Traits, CIMMYT, Mexico, Curator),<br /> * New York Botanic Garden (Bronx, NY): Dennis W. Stevenson (Co-PI), new curator to be added<br /> * Barry Smith, University at Buffalo (Ontology Consultant)<br /> * Georgios Gkoutos, University of Aberystwyth, UK (Senior Personnel, PATO), new curator to be added<br /> <br /> - Has left the project*<br /> <br /> =Ontology Working Group Meetings:=<br /> * Goal is to hold these meetings on a bi-weekly basis on Tuesday 8:15 am PST (GMT -8)/ PDT (GMT -7)<br /> * Please check for your specific local time, if you are not sure here is a handy site: http://www.timeanddate.com/worldclock/meeting.html. <br /> [[Ontology Working Group_Meetings- 2015]]<br /> <br /> [[Ontology Working Group_Meetings- 2016]]<br /> <br /> [[Ontology Working Group_Meetings- 2017]]<br /> <br /> [[Jan 23rd, 2018 Ontology Working Group Meeting]]<br /> <br /> [[Feb 27th, 2018 Ontology Working Group Meeting]]<br /> <br /> [[Mar 16th, 2018 Ontology Working Group Meeting]]<br /> <br /> [[April 10th, 2018 Ontology Working Group Meeting]]<br /> <br /> [[April 13th, 2018 Plant Phenoscape Group Meeting]]<br /> <br /> [[May 1st, 2018 Ontology Working Group Meeting]]<br /> <br /> [[Oct. 30th, 2018 Web Site Refresh Meeting]]<br /> <br /> =Goals and Objectives:=<br /> ==1. Develop a set of common reference ontologies to describe major knowledge domains of plant biology, comprising plant phenotype and traits, environments, and biotic and abiotic stresses, including plant diseases.==<br /> The project will provide a suite of reference and interoperable ontologies (Figure-1) relevant to the knowledge domain of plant biology required for annotating and describing the experiments, data sets, tagging published papers, and images. <br /> <br /> These ontologies include the Plant Ontology (PO); Trait Ontology (TO), Environment Ontology (EO) and Plant Stress Ontology (PSO) to be developed by the cROP project and will associate them to the existing reference ontologies for relevant knowledge domains (Figure-1 Table-1) being developed and funded by other resources. <br /> <br /> The Planteome project will also contribute to and enhance the existing reference ontologies, developed and maintained by the proposal partners. A network of national and international collaborators, representing major plant genomics resources, large-scale phenotype and genome annotation projects (Appendix-A3), will apply the set of reference ontologies to empower researchers to build their hypotheses, query, discover and analyze the plant genomics and genetics data sets.<br /> <br /> * Plant Trait Ontology (TO)<br /> * Plant Environment Ontology (EO)<br /> * Plant Ontology (PO) <br /> * Plant Stress Ontology (PSO) <br /> * Coordination with the Phenotypic Qualities Ontology (PATO)<br /> * Building references with the Crop Ontology (CO) as a resource of concepts for cROP<br /> <br /> ==2. Develop standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm.==<br /> ===2.1 Collaborative approaches on ontology development and annotation:=== <br /> * Transition to OWL Format<br /> * Introduction of Elk reasoner and Continuous Integration (CI) system<br /> * Development of TermGenie tool for TO and PO<br /> * Use of Inferred graph completion<br /> <br /> ===2.2 Improving ontology-based annotations for plant genomes and develop quality assessment matrix:===<br /> GOstruct method<br /> <br /> ===2.3 Annotating orphan plant genomes and maintaining reference genome annotations.===<br /> Details TBA<br /> <br /> ----<br /> =Ontology Development Workshops=<br /> [[Planteome Curator workshop Fall 2015]]<br /> ----<br /> <br /> =Links to current versions of the Ontologies:=<br /> [http://dev.planteome.org/amigo Planteome Development Browser] Updates nightly<br /> <br /> ==Plant Trait Ontology (TO)==<br /> Link to most recent changes on GitHub: <br /> [https://github.com/Planteome/plant-trait-ontology Plant Trait Ontology repository]<br /> ----<br /> <br /> ==Plant Ontology (PO)==<br /> <br /> ==Crop Ontology (TO)==<br /> * [[Crop Ontology Pages]] on wiki<br /> * Link to home page: [http://www.cropontology.org/ Crop Ontology Curation Tool]</div>

Cooperl https://wiki.planteome.org/index.php?title=April_13th,_2018_Plant_Phenoscape_Group_Meeting&diff=3593 2018-10-31T20:43:35Z

<p>Cooperl: </p> <hr /> <div>Date: Tuesday April 13th, 2018<br /> <br /> * Meeting recordings: TBA<br /> * Link to notes: [https://docs.google.com/document/d/1FVGWsqo6_AVWQ53Y05cULnprN1kLcbcGtpBdJnhUowk/edit?usp=sharing Plant Phensoscape Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=April_13th,_2018_Plant_Phenoscape_Group_Meeting&diff=3592 2018-10-31T20:42:19Z

<p>Cooperl: Created page with &quot;Date: Tuesday April 13th, 2018 * Meeting recordings: TBA * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing On...&quot;</p> <hr /> <div>Date: Tuesday April 13th, 2018<br /> <br /> * Meeting recordings: TBA<br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]-</div>

Cooperl https://wiki.planteome.org/index.php?title=April_10th,_2018_Ontology_Working_Group_Meeting&diff=3591 2018-10-31T20:39:21Z

<p>Cooperl: Created page with &quot;* Date: Tuesday April 10th, 2018 * Time: 8:15am PST (GMT-8) * Meeting recordings: TBA * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex...&quot;</p> <hr /> <div>* Date: Tuesday April 10th, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings: TBA<br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=March_16th,_2018_Ontology_Meeting-Avocado_%2B_Cherimoya&diff=3590 2018-10-31T20:37:31Z

<p>Cooperl: </p> <hr /> <div>* Date: Tuesday Mar 16th, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings: TBA<br /> * Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=March_16th,_2018_Ontology_Meeting-Avocado_%2B_Cherimoya&diff=3589 2018-10-31T20:35:09Z

<p>Cooperl: </p> <hr /> <div>* Date: Tuesday Mar 16th, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Meeting recordings: TBA<br /> * Link to notes: Ontology Meeting Notes</div>

Cooperl https://wiki.planteome.org/index.php?title=March_16th,_2018_Ontology_Meeting-Avocado_%2B_Cherimoya&diff=3588 2018-10-31T20:17:04Z

<p>Cooperl: Created page with &quot;* Date: Tuesday Mar 16th, 2018 * Time: 8:15am PST (GMT-8) Connection details: Join from PC, Mac, Linux, iOS or Android: TBA Meeting recordings: TBA Link to notes: Ontolog...&quot;</p> <hr /> <div>* Date: Tuesday Mar 16th, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> Connection details: <br /> <br /> Join from PC, Mac, Linux, iOS or Android: TBA<br /> <br /> Meeting recordings: TBA<br /> <br /> Link to notes: Ontology Meeting Notes</div>

Cooperl https://wiki.planteome.org/index.php?title=Planteome_Ontology_Development_and_Coordination_Working_Group&diff=3587 2018-10-31T20:14:22Z

<p>Cooperl: /* Ontology Working Group Meetings: */</p> <hr /> <div>=Participants=<br /> * Jaiswal Lab (Oregon, OSU): Laurel Cooper (Project coordinator, Curator), Pankaj Jaiswal (PI), Justin Elser (System Admin), Austin Meier (Curator)<br /> * Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI, AmiGO2, Gene Ontology)<br /> * CGIAR Consortium (Montpellier, France and CG centers around the world): Elizabeth Arnaud (Co-PI, Crop Ontology), Marie Angelique Laporte (Ontology Engineer), Léo Valette* (former Curator, IBP + CO)<br /> ** Rosemary Shrestha (Wheat Traits, CIMMYT, Mexico, Curator), Kate Dreher (Maize Traits, CIMMYT, Mexico, Curator),<br /> * New York Botanic Garden (Bronx, NY): Dennis W. Stevenson (Co-PI), new curator to be added<br /> * Barry Smith, University at Buffalo (Ontology Consultant)<br /> * Georgios Gkoutos, University of Aberystwyth, UK (Senior Personnel, PATO), new curator to be added<br /> <br /> - Has left the project*<br /> <br /> =Ontology Working Group Meetings:=<br /> * Goal is to hold these meetings on a bi-weekly basis on Tuesday 8:15 am PST (GMT -8)/ PDT (GMT -7)<br /> * Please check for your specific local time, if you are not sure here is a handy site: http://www.timeanddate.com/worldclock/meeting.html. <br /> [[Ontology Working Group_Meetings- 2015]]<br /> <br /> [[Ontology Working Group_Meetings- 2016]]<br /> <br /> [[Ontology Working Group_Meetings- 2017]]<br /> <br /> [[Jan 23rd, 2018 Ontology Working Group Meeting]]<br /> <br /> [[Feb 27th, 2018 Ontology Working Group Meeting]]<br /> <br /> [[Mar 16th, 2018 Ontology Working Group Meeting]]<br /> <br /> [[April 10th, 2018 Ontology Working Group Meeting]]<br /> <br /> [[April 13th, 2018 Plant Phenoscape Group Meeting]]<br /> <br /> [[May 1st, 2018 Plant Phenoscape Group Meeting]]<br /> <br /> [[Oct. 30th, 2018 Plant Phenoscape Group Meeting]]<br /> <br /> =Goals and Objectives:=<br /> ==1. Develop a set of common reference ontologies to describe major knowledge domains of plant biology, comprising plant phenotype and traits, environments, and biotic and abiotic stresses, including plant diseases.==<br /> The project will provide a suite of reference and interoperable ontologies (Figure-1) relevant to the knowledge domain of plant biology required for annotating and describing the experiments, data sets, tagging published papers, and images. <br /> <br /> These ontologies include the Plant Ontology (PO); Trait Ontology (TO), Environment Ontology (EO) and Plant Stress Ontology (PSO) to be developed by the cROP project and will associate them to the existing reference ontologies for relevant knowledge domains (Figure-1 Table-1) being developed and funded by other resources. <br /> <br /> The Planteome project will also contribute to and enhance the existing reference ontologies, developed and maintained by the proposal partners. A network of national and international collaborators, representing major plant genomics resources, large-scale phenotype and genome annotation projects (Appendix-A3), will apply the set of reference ontologies to empower researchers to build their hypotheses, query, discover and analyze the plant genomics and genetics data sets.<br /> <br /> * Plant Trait Ontology (TO)<br /> * Plant Environment Ontology (EO)<br /> * Plant Ontology (PO) <br /> * Plant Stress Ontology (PSO) <br /> * Coordination with the Phenotypic Qualities Ontology (PATO)<br /> * Building references with the Crop Ontology (CO) as a resource of concepts for cROP<br /> <br /> ==2. Develop standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm.==<br /> ===2.1 Collaborative approaches on ontology development and annotation:=== <br /> * Transition to OWL Format<br /> * Introduction of Elk reasoner and Continuous Integration (CI) system<br /> * Development of TermGenie tool for TO and PO<br /> * Use of Inferred graph completion<br /> <br /> ===2.2 Improving ontology-based annotations for plant genomes and develop quality assessment matrix:===<br /> GOstruct method<br /> <br /> ===2.3 Annotating orphan plant genomes and maintaining reference genome annotations.===<br /> Details TBA<br /> <br /> ----<br /> =Ontology Development Workshops=<br /> [[Planteome Curator workshop Fall 2015]]<br /> ----<br /> <br /> =Links to current versions of the Ontologies:=<br /> [http://dev.planteome.org/amigo Planteome Development Browser] Updates nightly<br /> <br /> ==Plant Trait Ontology (TO)==<br /> Link to most recent changes on GitHub: <br /> [https://github.com/Planteome/plant-trait-ontology Plant Trait Ontology repository]<br /> ----<br /> <br /> ==Plant Ontology (PO)==<br /> <br /> ==Crop Ontology (TO)==<br /> * [[Crop Ontology Pages]] on wiki<br /> * Link to home page: [http://www.cropontology.org/ Crop Ontology Curation Tool]</div>

Cooperl https://wiki.planteome.org/index.php?title=Ontology_Working_Group_Meetings-_2017&diff=3586 2018-10-31T20:09:38Z

<p>Cooperl: Created page with &quot;Jan 31st, 2017 Ontology Working Group Meeting Feb 21st, 2017 Ontology Working Group Meeting Mar 14th, 2017 Ontology Working Group Meeting Mar 21st, 2017 Ontol...&quot;</p> <hr /> <div>[[Jan 31st, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Feb 21st, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Mar 14th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Mar 21st, 2017 Ontology Working Group Meeting]]<br /> <br /> [[April 6th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[April 11th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[May 2nd, 2017 Ontology Working Group Meeting]]<br /> <br /> [[May 9th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Oct 5th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Oct 17th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Oct 31st, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Nov 14th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Dec 5th, 2017 Ontology Working Group Meeting]]</div>

Cooperl https://wiki.planteome.org/index.php?title=Planteome_Ontology_Development_and_Coordination_Working_Group&diff=3585 2018-10-31T20:09:29Z

<p>Cooperl: /* Ontology Working Group Meetings: */</p> <hr /> <div>=Participants=<br /> * Jaiswal Lab (Oregon, OSU): Laurel Cooper (Project coordinator, Curator), Pankaj Jaiswal (PI), Justin Elser (System Admin), Austin Meier (Curator)<br /> * Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI, AmiGO2, Gene Ontology)<br /> * CGIAR Consortium (Montpellier, France and CG centers around the world): Elizabeth Arnaud (Co-PI, Crop Ontology), Marie Angelique Laporte (Ontology Engineer), Léo Valette* (former Curator, IBP + CO)<br /> ** Rosemary Shrestha (Wheat Traits, CIMMYT, Mexico, Curator), Kate Dreher (Maize Traits, CIMMYT, Mexico, Curator),<br /> * New York Botanic Garden (Bronx, NY): Dennis W. Stevenson (Co-PI), new curator to be added<br /> * Barry Smith, University at Buffalo (Ontology Consultant)<br /> * Georgios Gkoutos, University of Aberystwyth, UK (Senior Personnel, PATO), new curator to be added<br /> <br /> - Has left the project*<br /> <br /> =Ontology Working Group Meetings:=<br /> * Goal is to hold these meetings on a bi-weekly basis on Tuesday 8:15 am PST (GMT -8)/ PDT (GMT -7)<br /> * Please check for your specific local time, if you are not sure here is a handy site: http://www.timeanddate.com/worldclock/meeting.html. <br /> [[Ontology Working Group_Meetings- 2015]]<br /> <br /> [[Ontology Working Group_Meetings- 2016]]<br /> <br /> [[Ontology Working Group_Meetings- 2017]]<br /> <br /> <br /> <br /> [[Jan 23rd, 2018 Ontology Working Group Meeting]]<br /> <br /> [[Feb 27th, 2018 Ontology Working Group Meeting]]<br /> <br /> =Goals and Objectives:=<br /> ==1. Develop a set of common reference ontologies to describe major knowledge domains of plant biology, comprising plant phenotype and traits, environments, and biotic and abiotic stresses, including plant diseases.==<br /> The project will provide a suite of reference and interoperable ontologies (Figure-1) relevant to the knowledge domain of plant biology required for annotating and describing the experiments, data sets, tagging published papers, and images. <br /> <br /> These ontologies include the Plant Ontology (PO); Trait Ontology (TO), Environment Ontology (EO) and Plant Stress Ontology (PSO) to be developed by the cROP project and will associate them to the existing reference ontologies for relevant knowledge domains (Figure-1 Table-1) being developed and funded by other resources. <br /> <br /> The Planteome project will also contribute to and enhance the existing reference ontologies, developed and maintained by the proposal partners. A network of national and international collaborators, representing major plant genomics resources, large-scale phenotype and genome annotation projects (Appendix-A3), will apply the set of reference ontologies to empower researchers to build their hypotheses, query, discover and analyze the plant genomics and genetics data sets.<br /> <br /> * Plant Trait Ontology (TO)<br /> * Plant Environment Ontology (EO)<br /> * Plant Ontology (PO) <br /> * Plant Stress Ontology (PSO) <br /> * Coordination with the Phenotypic Qualities Ontology (PATO)<br /> * Building references with the Crop Ontology (CO) as a resource of concepts for cROP<br /> <br /> ==2. Develop standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm.==<br /> ===2.1 Collaborative approaches on ontology development and annotation:=== <br /> * Transition to OWL Format<br /> * Introduction of Elk reasoner and Continuous Integration (CI) system<br /> * Development of TermGenie tool for TO and PO<br /> * Use of Inferred graph completion<br /> <br /> ===2.2 Improving ontology-based annotations for plant genomes and develop quality assessment matrix:===<br /> GOstruct method<br /> <br /> ===2.3 Annotating orphan plant genomes and maintaining reference genome annotations.===<br /> Details TBA<br /> <br /> ----<br /> =Ontology Development Workshops=<br /> [[Planteome Curator workshop Fall 2015]]<br /> ----<br /> <br /> =Links to current versions of the Ontologies:=<br /> [http://dev.planteome.org/amigo Planteome Development Browser] Updates nightly<br /> <br /> ==Plant Trait Ontology (TO)==<br /> Link to most recent changes on GitHub: <br /> [https://github.com/Planteome/plant-trait-ontology Plant Trait Ontology repository]<br /> ----<br /> <br /> ==Plant Ontology (PO)==<br /> <br /> ==Crop Ontology (TO)==<br /> * [[Crop Ontology Pages]] on wiki<br /> * Link to home page: [http://www.cropontology.org/ Crop Ontology Curation Tool]</div>

Cooperl https://wiki.planteome.org/index.php?title=Jan_23rd,_2018_Ontology_Working_Group_Meeting&diff=3584 2018-02-27T00:42:32Z

<p>Cooperl: /* Information systems: */</p> <hr /> <div>* Date: Tuesday Jan 23rd, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Connection details: <br /> Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/831712725<br /> <br /> Meeting recordings: <br /> * [[File:Ontology Working Group Meeting-video- 1-23-18.mp4|thumb|Ontology Working Group Meeting-video- 1-23-18]]<br /> * [[File:Ontology Working Group Meeting audio-1-23-18.m4a|thumb|Ontology Working Group Meeting audio-1-23-18]]<br /> <br /> =Agenda and Notes=<br /> Special presentation on [https://www6.montpellier.inra.fr/lepse_eng/M3P/PHENOARCH-platform PhenoArch] Data Management at INRA by Pascal Neveu, INRA SupAgro- (data &amp; databases) and [http://jobs.inra.fr/en/Career-opportunities/Portraits/Francois-tardieu François Tardieu] (platform leader). <br /> <br /> * PhenoArch is a phenotyping platform aimed at analysing the genetic determinisms of plant responses to environmental conditions in particular drought, temperature and light. It is hosted in the LEPSE group (INRA), with users belonging to several groups in INRA and CIRAD.<br /> <br /> ==Characterization of genotypes==<br /> * Ecophysiology<br /> * GWAS-GS<br /> <br /> ==Phenotyping platforms: --&gt; Omics==<br /> * roots for 200 plants<br /> * stomatal conductance- from transpiration and environmental conditions<br /> * Penman Monteith Equation- reversed<br /> * Field platforms- large mobile, rainout shelters<br /> * large scale offsite platforms- evaluate...<br /> * Network of field experiments- 16 fields X 2 years x 2 w. treatments -- QTL analyses<br /> * Three National, methodological ??<br /> * Images to traits- e.g. light interception<br /> * Phenomobiles, drones, RGB camera, field...?<br /> <br /> ==Information systems:==<br /> * Organize and share data<br /> * Cyril Pommier- ontologies<br /> *Pascal- different scales, levels, interactions<br /> <br /> ==PHIS- Big data Management System==<br /> * Different instances<br /> * FAIR data management, sparql queries based on: <br /> ** object class- instances identified by URI<br /> ** events- semantics relate object classes and events<br /> <br /> == Platform Ontology== <br /> * links to reference ontologies- SKOS<br /> * measurements associated<br /> * QR codes<br /> * Structuring the data- metadata, ontologies<br /> <br /> ==PHIS Architecture==<br /> * based on web services<br /> * R Interfaces <br /> * galaxy, Cline ??<br /> <br /> ==Phenoharmonis - from Images to traits==<br /> * EA: linking data back to germplasm<br /> * PHIS- links to other info systems<br /> * GWAS analysis done outside PHIS<br /> * network or pipeline<br /> <br /> ==Needs for ontology development:==<br /> * Need transversal links - e.g. links between plants and plots<br /> * Ontology of events...?<br /> * Environmental ontology<br /> * definition of objects-<br /> * description in MIAPPE - EMPHASIS project<br /> * Sensor data<br /> * core metadata of MIAPPE<br /> <br /> * Comment: Ann Sylvester NSF - familiar with EMPHASIS project<br /> *US Network on phenotyping interaction- new project in USA<br /> <br /> ==Notes from AM:==<br /> * Some traits measured:<br /> ** TO:0000522 - stomatal conductance<br /> ** TO:0012001 - leaf area index<br /> ** TO:0000207 - plant height<br /> ** root traits: branching angle, depth, amount of branching/hairs<br /> <br /> * all software is in-house??<br /> * KOS ontology? says reference ontology<br /> * raw data to clean data -- this is your most difficult challenge. They are responsible for doing some of this, and providing an overview for what was done.<br /> <br /> * Don't actually do experiments, they just maintain the facilities - and the DATA<br /> * knime - some sort of workflow software.<br /> <br /> * linking to the source germplasm = QR code<br /> <br /> * no standards. They deliver data, and the users decide how to interpret it. This is frustrating, because it does the opposite of standardizing. However, the metadata is standardized. What cameras, what environmental conditions.<br /> <br /> * They would like to have some terms for groupings of plants (plot) because they measure data on plots, or stands, not always individual plants.<br /> * they would also like standardizing of the &quot;elements&quot; plot, field, plant, etc<br /> <br /> ==Upcoming Events==<br /> * [http://phenome2018.org/ Phenome 2018], Tucson, AZ, Feb 14th-17th, 2018<br /> * Phenoharmonis May 14th-18th, 2018<br /> * ICBO 2018- Corvallis, OR, August 6-10th<br /> <br /> ==Next meeting: TBA==</div>

Cooperl https://wiki.planteome.org/index.php?title=Jan_23rd,_2018_Ontology_Working_Group_Meeting&diff=3583 2018-02-27T00:22:52Z

<p>Cooperl: /* Agenda and Notes */</p> <hr /> <div>* Date: Tuesday Jan 23rd, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Connection details: <br /> Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/831712725<br /> <br /> Meeting recordings: <br /> * [[File:Ontology Working Group Meeting-video- 1-23-18.mp4|thumb|Ontology Working Group Meeting-video- 1-23-18]]<br /> * [[File:Ontology Working Group Meeting audio-1-23-18.m4a|thumb|Ontology Working Group Meeting audio-1-23-18]]<br /> <br /> =Agenda and Notes=<br /> Special presentation on [https://www6.montpellier.inra.fr/lepse_eng/M3P/PHENOARCH-platform PhenoArch] Data Management at INRA by Pascal Neveu, INRA SupAgro- (data &amp; databases) and [http://jobs.inra.fr/en/Career-opportunities/Portraits/Francois-tardieu François Tardieu] (platform leader). <br /> <br /> * PhenoArch is a phenotyping platform aimed at analysing the genetic determinisms of plant responses to environmental conditions in particular drought, temperature and light. It is hosted in the LEPSE group (INRA), with users belonging to several groups in INRA and CIRAD.<br /> <br /> ==Characterization of genotypes==<br /> * Ecophysiology<br /> * GWAS-GS<br /> <br /> ==Phenotyping platforms: --&gt; Omics==<br /> * roots for 200 plants<br /> * stomatal conductance- from transpiration and environmental conditions<br /> * Penman Monteith Equation- reversed<br /> * Field platforms- large mobile, rainout shelters<br /> * large scale offsite platforms- evaluate...<br /> * Network of field experiments- 16 fields X 2 years x 2 w. treatments -- QTL analyses<br /> * Three National, methodological ??<br /> * Images to traits- e.g. light interception<br /> * Phenomobiles, drones, RGB camera, field...?<br /> <br /> ==Information systems:==<br /> <br /> <br /> <br /> Notes from AM:<br /> * Some traits measured:<br /> ** TO:0000522 - stomatal conductance<br /> ** TO:0012001 - leaf area index<br /> ** TO:0000207 - plant height<br /> ** root traits: branching angle, depth, amount of branching/hairs<br /> <br /> * all software is in-house??<br /> * KOS ontology? says reference ontology<br /> * raw data to clean data -- this is your most difficult challenge. They are responsible for doing some of this, and providing an overview for what was done.<br /> <br /> * Don't actually do experiments, they just maintain the facilities - and the DATA<br /> * knime - some sort of workflow software.<br /> <br /> * linking to the source germplasm = QR code<br /> <br /> * no standards. They deliver data, and the users decide how to interpret it. This is frustrating, because it does the opposite of standardizing. However, the metadata is standardized. What cameras, what environmental conditions.<br /> <br /> * They would like to have some terms for groupings of plants (plot) because they measure data on plots, or stands, not always individual plants.<br /> * they would also like standardizing of the &quot;elements&quot; plot, field, plant, etc<br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Upcoming Events==<br /> * [http://phenome2018.org/ Phenome 2018], Tucson, AZ, Feb 14th-17th, 2018<br /> * Phenoharmonis May 14th-18th, 2018<br /> * ICBO 2018- Corvallis, OR, August 6-10th<br /> <br /> ==Next meeting: TBA==</div>

Cooperl https://wiki.planteome.org/index.php?title=Jan_23rd,_2018_Ontology_Working_Group_Meeting&diff=3582 2018-02-27T00:22:15Z

<p>Cooperl: /* Agenda and Notes */</p> <hr /> <div>* Date: Tuesday Jan 23rd, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Connection details: <br /> Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/831712725<br /> <br /> Meeting recordings: <br /> * [[File:Ontology Working Group Meeting-video- 1-23-18.mp4|thumb|Ontology Working Group Meeting-video- 1-23-18]]<br /> * [[File:Ontology Working Group Meeting audio-1-23-18.m4a|thumb|Ontology Working Group Meeting audio-1-23-18]]<br /> <br /> =Agenda and Notes=<br /> Special presentation on [https://www6.montpellier.inra.fr/lepse_eng/M3P/PHENOARCH-platform PhenoArch] Data Management at INRA by Pascal Neveu, INRA SupAgro- (data &amp; databases) and [http://jobs.inra.fr/en/Career-opportunities/Portraits/Francois-tardieu François Tardieu] (platform leader). <br /> <br /> * PhenoArch is a phenotyping platform aimed at analysing the genetic determinisms of plant responses to environmental conditions in particular drought, temperature and light. It is hosted in the LEPSE group (INRA), with users belonging to several groups in INRA and CIRAD.<br /> <br /> * Characterization of genotypes<br /> * Ecophysiology<br /> * GWAS-GS<br /> <br /> Phenotyping platforms: --&gt; Omics<br /> * roots for 200 plants<br /> * stomatal conductance- from transpiration and environmental conditions<br /> * Penman Monteith Equation- reversed<br /> * Field platforms- large mobile, rainout shelters<br /> * large scale offsite platforms- evaluate...<br /> * Network of field experiments- 16 fields X 2 years x 2 w. treatments -- QTL analyses<br /> * Three National, methodological ??<br /> * Images to traits- e.g. light interception<br /> * Phenomobiles, drones, RGB camera, field...?<br /> <br /> Information systems:<br /> <br /> <br /> <br /> Notes from AM:<br /> * Some traits measured:<br /> ** TO:0000522 - stomatal conductance<br /> ** TO:0012001 - leaf area index<br /> ** TO:0000207 - plant height<br /> ** root traits: branching angle, depth, amount of branching/hairs<br /> <br /> * all software is in-house??<br /> * KOS ontology? says reference ontology<br /> * raw data to clean data -- this is your most difficult challenge. They are responsible for doing some of this, and providing an overview for what was done.<br /> <br /> * Don't actually do experiments, they just maintain the facilities - and the DATA<br /> * knime - some sort of workflow software.<br /> <br /> * linking to the source germplasm = QR code<br /> <br /> * no standards. They deliver data, and the users decide how to interpret it. This is frustrating, because it does the opposite of standardizing. However, the metadata is standardized. What cameras, what environmental conditions.<br /> <br /> * They would like to have some terms for groupings of plants (plot) because they measure data on plots, or stands, not always individual plants.<br /> * they would also like standardizing of the &quot;elements&quot; plot, field, plant, etc<br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Upcoming Events==<br /> * [http://phenome2018.org/ Phenome 2018], Tucson, AZ, Feb 14th-17th, 2018<br /> * Phenoharmonis May 14th-18th, 2018<br /> * ICBO 2018- Corvallis, OR, August 6-10th<br /> <br /> ==Next meeting: TBA==</div>

Cooperl https://wiki.planteome.org/index.php?title=Jan_23rd,_2018_Ontology_Working_Group_Meeting&diff=3581 2018-02-27T00:20:05Z

<p>Cooperl: /* Agenda and Notes */</p> <hr /> <div>* Date: Tuesday Jan 23rd, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Connection details: <br /> Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/831712725<br /> <br /> Meeting recordings: <br /> * [[File:Ontology Working Group Meeting-video- 1-23-18.mp4|thumb|Ontology Working Group Meeting-video- 1-23-18]]<br /> * [[File:Ontology Working Group Meeting audio-1-23-18.m4a|thumb|Ontology Working Group Meeting audio-1-23-18]]<br /> <br /> =Agenda and Notes=<br /> Special presentation on [https://www6.montpellier.inra.fr/lepse_eng/M3P/PHENOARCH-platform PhenoArch] Data Management at INRA by Pascal Neveu, INRA SupAgro- (data &amp; databases) and [http://jobs.inra.fr/en/Career-opportunities/Portraits/Francois-tardieu François Tardieu] (platform leader). <br /> <br /> * PhenoArch is a phenotyping platform aimed at analysing the genetic determinisms of plant responses to environmental conditions in particular drought, temperature and light. It is hosted in the LEPSE group (INRA), with users belonging to several groups in INRA and CIRAD.<br /> <br /> * Characterization of genotypes<br /> * Ecophysiology<br /> * GWAS-GS<br /> <br /> Phenotyping platforms: --&gt; Omics<br /> * roots for 200 plants<br /> * stomatal conductance- from transpiration and environmental conditions<br /> * Penman Monteith Equation- reversed<br /> * Field platforms- large mobile, rainout shelters<br /> * large scale offsite platforms- evaluate...<br /> * Network of field experiments- 16 fields X 2 years x 2 w. treatments -- QTL analyses<br /> <br /> * Some traits measured:<br /> ** TO:0000522 - stomatal conductance<br /> ** TO:0012001 - leaf area index<br /> ** TO:0000207 - plant height<br /> ** root traits: branching angle, depth, amount of branching/hairs<br /> <br /> * all software is in-house??<br /> * KOS ontology? says reference ontology<br /> * raw data to clean data -- this is your most difficult challenge. They are responsible for doing some of this, and providing an overview for what was done.<br /> <br /> * Don't actually do experiments, they just maintain the facilities - and the DATA<br /> * knime - some sort of workflow software.<br /> <br /> * linking to the source germplasm = QR code<br /> <br /> * no standards. They deliver data, and the users decide how to interpret it. This is frustrating, because it does the opposite of standardizing. However, the metadata is standardized. What cameras, what environmental conditions.<br /> <br /> * They would like to have some terms for groupings of plants (plot) because they measure data on plots, or stands, not always individual plants.<br /> * they would also like standardizing of the &quot;elements&quot; plot, field, plant, etc<br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Upcoming Events==<br /> * [http://phenome2018.org/ Phenome 2018], Tucson, AZ, Feb 14th-17th, 2018<br /> * Phenoharmonis May 14th-18th, 2018<br /> * ICBO 2018- Corvallis, OR, August 6-10th<br /> <br /> ==Next meeting: TBA==</div>

Cooperl https://wiki.planteome.org/index.php?title=Jan_23rd,_2018_Ontology_Working_Group_Meeting&diff=3580 2018-02-27T00:15:08Z

<p>Cooperl: /* Agenda */</p> <hr /> <div>* Date: Tuesday Jan 23rd, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Connection details: <br /> Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/831712725<br /> <br /> Meeting recordings: <br /> * [[File:Ontology Working Group Meeting-video- 1-23-18.mp4|thumb|Ontology Working Group Meeting-video- 1-23-18]]<br /> * [[File:Ontology Working Group Meeting audio-1-23-18.m4a|thumb|Ontology Working Group Meeting audio-1-23-18]]<br /> <br /> =Agenda and Notes=<br /> Special presentation on [https://www6.montpellier.inra.fr/lepse_eng/M3P/PHENOARCH-platform PhenoArch] Data Management at INRA by Pascal Neveu, INRA SupAgro- (data &amp; databases) and [http://jobs.inra.fr/en/Career-opportunities/Portraits/Francois-tardieu François Tardieu] (platform leader). <br /> <br /> * PhenoArch is a phenotyping platform aimed at analysing the genetic determinisms of plant responses to environmental conditions in particular drought, temperature and light. It is hosted in the LEPSE group (INRA), with users belonging to several groups in INRA and CIRAD.<br /> <br /> * Some traits measured:<br /> ** TO:0000522 - stomatal conductance<br /> ** TO:0012001 - leaf area index<br /> ** TO:0000207 - plant height<br /> ** root traits: branching angle, depth, amount of branching/hairs<br /> <br /> * all software is in-house??<br /> * KOS ontology? says reference ontology<br /> * raw data to clean data -- this is your most difficult challenge. They are responsible for doing some of this, and providing an overview for what was done.<br /> <br /> * Don't actually do experiments, they just maintain the facilities - and the DATA<br /> * knime - some sort of workflow software.<br /> <br /> * linking to the source germplasm = QR code<br /> <br /> * no standards. They deliver data, and the users decide how to interpret it. This is frustrating, because it does the opposite of standardizing. However, the metadata is standardized. What cameras, what environmental conditions.<br /> <br /> * They would like to have some terms for groupings of plants (plot) because they measure data on plots, or stands, not always individual plants.<br /> * they would also like standardizing of the &quot;elements&quot; plot, field, plant, etc<br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Upcoming Events==<br /> * [http://phenome2018.org/ Phenome 2018], Tucson, AZ, Feb 14th-17th, 2018<br /> * Phenoharmonis May 14th-18th, 2018<br /> * ICBO 2018- Corvallis, OR, August 6-10th<br /> <br /> ==Next meeting: TBA==</div>

Cooperl https://wiki.planteome.org/index.php?title=Nov_14th,_2017_Ontology_Working_Group_Meeting&diff=3579 2018-02-10T21:07:42Z

<p>Cooperl: /* Request for Revisions to aroma TO:0000087 */</p> <hr /> <div>* Date: Tuesday Nov 14th, 2017<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Connection details: <br /> Topic: Planteome Ontology Working Group Meeting<br /> Time: Nov 14, 2017 8:15 AM PST<br /> <br /> Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/324208533<br /> * Meeting Recordings:<br /> ** [[File:Ontology WG meeting audio 11-14-17.m4a|thumb|Ontology WG meeting audio 11-14-17]]<br /> ** [[File:Ontology WG meeting video 11-14-17.mp4|thumbnail|Ontology_WG_meeting_video_11-14-17.mp4]]<br /> <br /> =Agenda and Notes= <br /> * Update on Changes to PECO- ''in progress''<br /> <br /> ==Presentation of PhenoArche data management by INRA==<br /> * Francois and Pascal are fully booked before end of the year so they propose the following dates: 23, 25 janvier et 6 février.<br /> * EA and MAL may be in Peru during the week - Lima is on eastern time zone<br /> <br /> == Request for Revisions to aroma TO:0000087==<br /> * From PJ; See tracker ([https://github.com/Planteome/plant-trait-ontology/issues/424 #424]) <br /> * Current definition: aroma ([http://dev.planteome.org/amigo/term/TO:0000087 TO:0000087]): The aroma of the cooked/uncooked grains.<br /> * aroma (TO:0000087) has dual parentage:<br /> ** is_a fruit flavor trait (TO:0002694)<br /> ** is_a seed composition quality trait (TO:0000488)<br /> *** ''This structure makes no sense.'' <br /> <br /> * Proposed <br /> ** Rename grain aroma trait (TO:0000087)- ''done''<br /> ** Move to be is_a grain quality trait TO:0000162 - ''done''<br /> ** Make it part_of: fruit flavor trait (TO:0002694) - ''done''<br /> <br /> * Comment from PJ: Needs repositioned as IS_A quality trait with two children seed and fruit aroma. with rice scent /aroma being a child of seed aroma.<br /> * Since rice grain is a caryopsis fruit (PO:0030104), rice grain aroma would be is_a fruit aroma<br /> * Aroma grouping term?, where to put it?<br /> * ''don't have to assert the aroma parent- since it will have the EA, it will be aroma inheres_in grain''<br /> * Aroma is a physical object quality in PATO- PATO:0000058<br /> <br /> ==Next Release==<br /> * Try for December befoer PAG<br /> <br /> ==Food Ontology meeting==<br /> * Involvement of industry and tech, informatics<br /> * Full spectrum of production<br /> * Agvoice company Bruce Rasa http://www.agvoiceglobal.com/- Alexa technology, <br /> <br /> * Food processing traits<br /> * Organoleptic traits- Integrate into TO at a high level? <br /> <br /> * Next IC Foods meeting in March in Dublin, Ireland<br /> ** http://foodontology.github.io/foodon/<br /> ** https://github.com/FoodOntology/foodon<br /> <br /> * Ask Matthew Lange about coming to future meeting <br /> * Phenoharmonis planned for mid-May 2018<br /> <br /> == Upcoming Events ==<br /> * Phenoscape Hackathon in Dec- LC and AM will attend<br /> * Plant and Animal Genome meeting January 2018<br /> * Phenoharmonis planned for mid-May 2018<br /> * ICBO 2018- in Corvallis, August 6-10th<br /> <br /> Next meeting: Dec 5th</div>

Cooperl https://wiki.planteome.org/index.php?title=Feb_27th,_2018_Ontology_Working_Group_Meeting&diff=3578 2018-02-10T20:42:21Z

<p>Cooperl: </p> <hr /> <div>* Date: Tuesday Feb 27th, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Connection details: <br /> Join from PC, Mac, Linux, iOS or Android: TBA<br /> <br /> Meeting recordings: TBA<br /> <br /> Link to notes: [https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing Ontology Meeting Notes]</div>

Cooperl https://wiki.planteome.org/index.php?title=Jan_23rd,_2018_Ontology_Working_Group_Meeting&diff=3577 2018-02-10T20:41:18Z

<p>Cooperl: </p> <hr /> <div>* Date: Tuesday Jan 23rd, 2018<br /> * Time: 8:15am PST (GMT-8)<br /> <br /> * Connection details: <br /> Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/831712725<br /> <br /> Meeting recordings: <br /> * [[File:Ontology Working Group Meeting-video- 1-23-18.mp4|thumb|Ontology Working Group Meeting-video- 1-23-18]]<br /> * [[File:Ontology Working Group Meeting audio-1-23-18.m4a|thumb|Ontology Working Group Meeting audio-1-23-18]]<br /> <br /> =Agenda=<br /> Special presentation on [https://www6.montpellier.inra.fr/lepse_eng/M3P/PHENOARCH-platform PhenoArch] Data Management at INRA by Pascal Neveu, INRA SupAgro- (data &amp; databases) and [http://jobs.inra.fr/en/Career-opportunities/Portraits/Francois-tardieu François Tardieu] (platform leader). <br /> <br /> * PhenoArch is a phenotyping platform aimed at analysing the genetic determinisms of plant responses to environmental conditions in particular drought, temperature and light. It is hosted in the LEPSE group (INRA), with users belonging to several groups in INRA and CIRAD.<br /> <br /> * Some traits measured:<br /> ** TO:0000522 - stomatal conductance<br /> ** TO:0012001 - leaf area index<br /> ** TO:0000207 - plant height<br /> ** root traits: branching angle, depth, amount of branching/hairs<br /> <br /> * all software is in-house??<br /> * KOS ontology? says reference ontology<br /> * raw data to clean data -- this is your most difficult challenge. They are responsible for doing some of this, and providing an overview for what was done.<br /> <br /> * Don't actually do experiments, they just maintain the facilities - and the DATA<br /> * knime - some sort of workflow software.<br /> <br /> * linking to the source germplasm = QR code<br /> <br /> * no standards. They deliver data, and the users decide how to interpret it. This is frustrating, because it does the opposite of standardizing. However, the metadata is standardized. What cameras, what environmental conditions.<br /> <br /> * They would like to have some terms for groupings of plants (plot) because they measure data on plots, or stands, not always individual plants.<br /> * they would also like standardizing of the &quot;elements&quot; plot, field, plant, etc<br /> <br /> <br /> <br /> <br /> <br /> <br /> ==Upcoming Events==<br /> * [http://phenome2018.org/ Phenome 2018], Tucson, AZ, Feb 14th-17th, 2018<br /> * Phenoharmonis May 14th-18th, 2018<br /> * ICBO 2018- Corvallis, OR, August 6-10th<br /> <br /> ==Next meeting: TBA==</div>

Cooperl https://wiki.planteome.org/index.php?title=Feb_27th,_2018_Ontology_Working_Group_Meeting&diff=3576 2018-02-10T20:40:44Z

<p>Cooperl: Created page with &quot; Link to notes: https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing&quot;</p> <hr /> <div><br /> <br /> Link to notes: https://docs.google.com/document/d/15pDTx_LjsY8kAFZYcLNPSgx4RF_QdpvKex3oKV-oWs4/edit?usp=sharing</div>

Cooperl https://wiki.planteome.org/index.php?title=Planteome_Ontology_Development_and_Coordination_Working_Group&diff=3575 2018-02-10T20:40:10Z

<p>Cooperl: /* Ontology Working Group Meetings: */</p> <hr /> <div>=Participants=<br /> * Jaiswal Lab (Oregon, OSU): Laurel Cooper (Project coordinator, Curator), Pankaj Jaiswal (PI), Justin Elser (System Admin), Austin Meier (Curator)<br /> * Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI, AmiGO2, Gene Ontology)<br /> * CGIAR Consortium (Montpellier, France and CG centers around the world): Elizabeth Arnaud (Co-PI, Crop Ontology), Marie Angelique Laporte (Ontology Engineer), Léo Valette* (former Curator, IBP + CO)<br /> ** Rosemary Shrestha (Wheat Traits, CIMMYT, Mexico, Curator), Kate Dreher (Maize Traits, CIMMYT, Mexico, Curator),<br /> * New York Botanic Garden (Bronx, NY): Dennis W. Stevenson (Co-PI), new curator to be added<br /> * Barry Smith, University at Buffalo (Ontology Consultant)<br /> * Georgios Gkoutos, University of Aberystwyth, UK (Senior Personnel, PATO), new curator to be added<br /> <br /> - Has left the project*<br /> <br /> =Ontology Working Group Meetings:=<br /> * Goal is to hold these meetings on a bi-weekly basis on Tuesday 8:15 am PST (GMT -8)/ PDT (GMT -7)<br /> * Please check for your specific local time, if you are not sure here is a handy site: http://www.timeanddate.com/worldclock/meeting.html. <br /> [[Ontology Working Group_Meetings- 2015]]<br /> <br /> [[Ontology Working Group_Meetings- 2016]]<br /> <br /> [[Jan 31st, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Feb 21st, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Mar 14th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Mar 21st, 2017 Ontology Working Group Meeting]]<br /> <br /> [[April 6th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[April 11th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[May 2nd, 2017 Ontology Working Group Meeting]]<br /> <br /> [[May 9th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Oct 5th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Oct 17th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Oct 31st, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Nov 14th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Dec 5th, 2017 Ontology Working Group Meeting]]<br /> <br /> [[Jan 23rd, 2018 Ontology Working Group Meeting]]<br /> <br /> [[Feb 27th, 2018 Ontology Working Group Meeting]]<br /> <br /> =Goals and Objectives:=<br /> ==1. Develop a set of common reference ontologies to describe major knowledge domains of plant biology, comprising plant phenotype and traits, environments, and biotic and abiotic stresses, including plant diseases.==<br /> The project will provide a suite of reference and interoperable ontologies (Figure-1) relevant to the knowledge domain of plant biology required for annotating and describing the experiments, data sets, tagging published papers, and images. <br /> <br /> These ontologies include the Plant Ontology (PO); Trait Ontology (TO), Environment Ontology (EO) and Plant Stress Ontology (PSO) to be developed by the cROP project and will associate them to the existing reference ontologies for relevant knowledge domains (Figure-1 Table-1) being developed and funded by other resources. <br /> <br /> The Planteome project will also contribute to and enhance the existing reference ontologies, developed and maintained by the proposal partners. A network of national and international collaborators, representing major plant genomics resources, large-scale phenotype and genome annotation projects (Appendix-A3), will apply the set of reference ontologies to empower researchers to build their hypotheses, query, discover and analyze the plant genomics and genetics data sets.<br /> <br /> * Plant Trait Ontology (TO)<br /> * Plant Environment Ontology (EO)<br /> * Plant Ontology (PO) <br /> * Plant Stress Ontology (PSO) <br /> * Coordination with the Phenotypic Qualities Ontology (PATO)<br /> * Building references with the Crop Ontology (CO) as a resource of concepts for cROP<br /> <br /> ==2. Develop standards, workflows and tools for ontology development, curation and improved annotation of genes, genomes, phenotype and germplasm.==<br /> ===2.1 Collaborative approaches on ontology development and annotation:=== <br /> * Transition to OWL Format<br /> * Introduction of Elk reasoner and Continuous Integration (CI) system<br /> * Development of TermGenie tool for TO and PO<br /> * Use of Inferred graph completion<br /> <br /> ===2.2 Improving ontology-based annotations for plant genomes and develop quality assessment matrix:===<br /> GOstruct method<br /> <br /> ===2.3 Annotating orphan plant genomes and maintaining reference genome annotations.===<br /> Details TBA<br /> <br /> ----<br /> =Ontology Development Workshops=<br /> [[Planteome Curator workshop Fall 2015]]<br /> ----<br /> <br /> =Links to current versions of the Ontologies:=<br /> [http://dev.planteome.org/amigo Planteome Development Browser] Updates nightly<br /> <br /> ==Plant Trait Ontology (TO)==<br /> Link to most recent changes on GitHub: <br /> [https://github.com/Planteome/plant-trait-ontology Plant Trait Ontology repository]<br /> ----<br /> <br /> ==Plant Ontology (PO)==<br /> <br /> ==Crop Ontology (TO)==<br /> * [[Crop Ontology Pages]] on wiki<br /> * Link to home page: [http://www.cropontology.org/ Crop Ontology Curation Tool]</div>

Cooperl