Planteome Curator workshop Fall 2015: Difference between revisions

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Discussions from
= Note: This page is under development, so check back frequently=
= Goals of the meeting: Strategic planning, and ontology curation, and Protege training=
    
- Can be just for curators without preexisting training
See link to [http://planteome.org/curation_workshop_2015 Planteome Curation Workshop Webpage]
- wants a group of ontology developers to meet, and face-to-face    
* Form a strategic plan on how to build each ontology and how they fit together.
* Get curators together for some hands-on development


* Who should attend: Planteome Ontology team: developers and software team and experts from various crops: e.g. Medicago, soybean, legume
== Dates: Week of Monday, Nov. 9th to Friday Nov. 13th==
* People could arrive Sunday Nov 8th.  See below for more info on the logistics
* Who should attend? Planteome Ontology team: developers and software team and experts from various crops
** Barry Smith- (will attend Nov 9th-10th)
** Dennis will attend remotely on Mon Nov 9th and Tues Nov 10th
** Chris Mungall and Seth Carbon
** Marie-Angelique LaPorte
** LC, JE, AM


'''* PJ's vision: Distributed ontology development and maintenance'''
* Not able to attend: Elizabeth, George and John
- Ontology Developers- areas of focus- maybe a dedicated group for each crop group?


* Possible collaborators to be included:
* Will invite the CO curators who are interested, can have another session at the PAG meeting for those who cannot attend
** legumes- soybean, Medicago, peanut, lentils (?)
** tubers- cassava, potato
** rice
** maize
** wheat


* Which of the curators from the CO ready to be involved in ontology development??
== Goals and Agenda of the meeting==


* Logistics: Planned to be in Corvallis- plan to fly into Portland (PDX) ~1.5hrs drive, or Eugene (EUG) ~ 50 mins drive
=== 1. Strategic Planning ===
* Dates: October-November- "2-3 days(core), with a few days more for outside ontologists"
* Goal: Form a strategic plan on '''how to build each ontology''' and '''how they fit together in the Planteome'''
* Who: Core Ontology Working Group:
** PJ, LC, AM, JE, DWS, CM, BS, EA, MAL, GG, SC


* Doodle poll will be circulated (LC)
===2.  GitHub, TermGenie and Protege Training===
- Barry: "Any 3 days in Nov 3-16 would work (this includes 2 half days for travel), preferred in Nov 4-15"
* Lead by Chris Mungall, Marie-Angelique can assist
* Goal: Train curators in using the GitHub Repositories and Protege software for ontology curation - collect their feedback
* Jenkins and Continuous integration


* Who: Ontology Curators
** Planteome team: LC, AM, MAL, NYBG postdoc?, GG postdoc?, OSU undergrad students- Megan and Ethan
** Any of the CO curators are ready to be involved in ontology development
===3. Ontology Curation and Data Annotation===
* '''Planteome Vision: Distributed ontology development and maintenance'''
* Wants a group of ontology developers to meet face-to-face
* Get curators together for some hands-on development and Data Annotation
* Possible Ontology Developers- collaborators to be included based on areas of focus- maybe a dedicated group for each crop group?
** legumes- soybean, Medicago (Rex Nelson), peanut, lentils (Scott Kalber)
** tubers- cassava (Afola Agbona, [http://www.iita.org/ IITA]), potato (Reinhard Simon) and sweet potato (Vilma Huela): both from CIP
** wheat, rice and
** maize Mary Schaeffer
==Logistics:==
* Location: Oregon State University Corvallis- plan to fly into Portland (PDX) ~1.5hrs drive, or Eugene (EUG) ~ 50 mins drive
** Hut Shuttle service from Portland Airport: http://www.hutshuttle.com/
===Accommodations: ===
* On campus housing is available in dorm-style suites at [http://oregonstate.edu/uhds/bloss Bloss Hall] (on-campus)
* Private room with shared bathroom facility (separate men's and women's).
** Link to more information about the facilities: [http://oregonstate.edu/uhds/scholar-housing Scholar Housing- OSU]
* Link to information about hotels in Corvallis: [http://www.tripadvisor.com/Hotels-g51817-Corvallis_Oregon-Hotels.html Corvallis_Oregon-Hotels].
** Closest hotel to campus is the [http://hiltongardeninn3.hilton.com/en/hotels/oregon/hilton-garden-inn-corvallis-CVOCHGI/index.html Hilton Garden Inn]
===Other info===
Dates of OSU Home Games: http://www.osubeavers.com/SportSelect.dbml?SPSID=750125&SPID=127145
Dates of OSU Home Games: http://www.osubeavers.com/SportSelect.dbml?SPSID=750125&SPID=127145

Latest revision as of 20:02, 22 October 2015

Note: This page is under development, so check back frequently

See link to Planteome Curation Workshop Webpage

Dates: Week of Monday, Nov. 9th to Friday Nov. 13th

  • People could arrive Sunday Nov 8th. See below for more info on the logistics
  • Who should attend? Planteome Ontology team: developers and software team and experts from various crops
    • Barry Smith- (will attend Nov 9th-10th)
    • Dennis will attend remotely on Mon Nov 9th and Tues Nov 10th
    • Chris Mungall and Seth Carbon
    • Marie-Angelique LaPorte
    • LC, JE, AM
  • Not able to attend: Elizabeth, George and John
  • Will invite the CO curators who are interested, can have another session at the PAG meeting for those who cannot attend

Goals and Agenda of the meeting

1. Strategic Planning

  • Goal: Form a strategic plan on how to build each ontology and how they fit together in the Planteome
  • Who: Core Ontology Working Group:
    • PJ, LC, AM, JE, DWS, CM, BS, EA, MAL, GG, SC

2. GitHub, TermGenie and Protege Training

  • Lead by Chris Mungall, Marie-Angelique can assist
  • Goal: Train curators in using the GitHub Repositories and Protege software for ontology curation - collect their feedback
  • Jenkins and Continuous integration
  • Who: Ontology Curators
    • Planteome team: LC, AM, MAL, NYBG postdoc?, GG postdoc?, OSU undergrad students- Megan and Ethan
    • Any of the CO curators are ready to be involved in ontology development

3. Ontology Curation and Data Annotation

  • Planteome Vision: Distributed ontology development and maintenance
  • Wants a group of ontology developers to meet face-to-face
  • Get curators together for some hands-on development and Data Annotation
  • Possible Ontology Developers- collaborators to be included based on areas of focus- maybe a dedicated group for each crop group?
    • legumes- soybean, Medicago (Rex Nelson), peanut, lentils (Scott Kalber)
    • tubers- cassava (Afola Agbona, IITA), potato (Reinhard Simon) and sweet potato (Vilma Huela): both from CIP
    • wheat, rice and
    • maize Mary Schaeffer

Logistics:

  • Location: Oregon State University Corvallis- plan to fly into Portland (PDX) ~1.5hrs drive, or Eugene (EUG) ~ 50 mins drive

Accommodations:

  • On campus housing is available in dorm-style suites at Bloss Hall (on-campus)
  • Private room with shared bathroom facility (separate men's and women's).

Other info

Dates of OSU Home Games: http://www.osubeavers.com/SportSelect.dbml?SPSID=750125&SPID=127145

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