Apr. 5th, 2016 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

• Date: Tuesday Apr. 6th, 2016
• Time: 8:15am PDT (GMT-7)
• Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/762470789

- attendees: AM, MAL, LC, PJ, JE, CM, BS

File:Ontology WG Meeting 4-6-16 video.mp4

File:Ontology WG Meeting 4-6-16 audio.m4a

Agenda

Update on the plans for the PhenoHarmonIS Meeting in Montpellier, 9-13 May 2016

• Link to website: https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
• Cannot put the tinyurl here...

• About 70+ Participants are signed up:
  • PhenoHarmonIS_List-of-participants

Agenda

• Still finalizing the agenda, meeting weds, final version TBA
  • https://docs.google.com/a/cgxchange.org/document/d/1rRVEu8X-E_a5tgTFYMrC10Ag-cGE0mqUf_yICrU26QY/edit?usp=sharing

• First day- Plenary sessions, tool demos
  • GG will give an ontology 101 session
• Following days hands-on sessions

Agronomy Ontology- Medha Devare and Celine Aubert

• meta analysis across platforms for agronomic trials
• trials, variables, measurements, farming practices
• Modeled after traits in trait dictionaries- is it crop specific then?
• Goal is to develop it in Owl using protege- currently not available
• CM: should coordinate with the Food Ontology folks- they will be having a workshop at ICBO

Progress on developing the rice annotation files from IRRI

• Austin and Marie-Angelique
  • Problems- linking to the GRIMS database or linking to Genesys

• taxon is not showing up as it is not in our slim yet
• awnless is a type of awn color????

• add accession # to label

ICBO 2016 Call for Papers is open

• ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission

http://icbo.cgrb.oregonstate.edu/ICBO_submission

Deadline is April 25th

Proposed Topics, with suggested lead:

• Planteome paper- LC
• Mappings- MAL
• Annotations project on rice, cassava and lentil, etc - AM

Formats:

• Extended Abstract- up to 2 pages
• Short Papers- up to 4 pages
• Full Papers- up to 6 pages

https://easychair.org/conferences/?conf=icbo2016

Papers will be published in a book of proceedings, not in a journal

AmiGO2 issues continued..

• New version of AmiGO is in the works- you can preview it here: http://tomodachi.berkeleybop.org/amigo/landing

• Significant changes:
  • Actual browser functionality
  • Neighborhood tab (was ancestors and children)
  • All relations will be displayed
  • annotations by species

Plant Trait Ontology updates

• Recent revisions and changes to the equivalence axioms etc

• Planning to do release soon- by end of this month

Other Items- Tabled for next meeting

• Presentation for Biocuration meeting- Marie-Angelique

• Progress on the development of the V. 5 trait dictionaries- Marie-Angelique and/or Leo

• OBA development- Chris Mungall- moved to April 26th

Upcoming Meetings and Workshops

Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland

• MAL is going and will be presenting a talk
  • key dates
  • Abstract submitted: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703

GARNet/Egenis Workshop: Integrating Large Data into Plant Science, April 21st-22nd 2016, Dartington Hall, Totnes, Devon

• Elizabeth and George are going, EA will present Planteome as part of her talk

Meeting in Montpellier, 9-13 May 2016

Link to tentative agenda/website: [1]

BioOntologies SIG of the Intelligent Systems for Molecular Biology (ISMB); July 8-12, 2016, Orlando, Florida

• Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
  • Short papers, up to 4 pages (will be published in JBMS)
  • Poster abstracts, up to 1 page
  • Flash updates, up to 1 page

7th International Conference on Biological Ontology and BioCreative 2016 Aug 1st to 4th, Corvallis, OR

• Link to program: ICBO + BioCreative Program
• Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589