Apr. 5th, 2016 Ontology Working Group Meeting: Difference between revisions

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* Modeled after traits in trait dictionaries- is it crop specific then?  
* Modeled after traits in trait dictionaries- is it crop specific then?  
* Goal is to develop it in Owl using protege- currently not available
* 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==
== Progress on developing the rice annotation files from IRRI==

Revision as of 18:59, 6 April 2016

Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Mar. 29th, 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

Agenda

  • 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


ICBO 2016 Call for Papers is open

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..

http://tomodachi.berkeleybop.org/amigo/landing

Other Items- Tabled for next meeting

  • Presentation for Biocuration meeting- Marie-Angelique
  • Plant Trait Ontology updates- Recent revisions and changes to the equivalence axioms etc
  • Progress on the development of the V. 5 trait dictionaries- Marie-Angelique and/or Leo

OBA development- Chris Mungall

  • CM: If there is time I would like to walk through the procedure we use to develop OBA.
  • Part of this was covered in the tutorial on template-based ontology development, but we had to rush this part due to lack of time:

https://github.com/Planteome/protege-tutorial/tree/master/template-examples

  • For OBA, the source of the ontology is primarily in TSVs, found here:

https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/modules

  • The design patterns are specified here:

https://github.com/obophenotype/bio-attribute-ontology/tree/master/src/ontology/patterns

  • Together these are used to build the ontology with equivalence axioms, with the entire ontology hierarchy being inferred automatically, e.g:

http://www.ebi.ac.uk/ols/beta/ontologies/oba/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBA_VT0000017

Upcoming Meetings and Workshops

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

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

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