Apr. 5th, 2016 Ontology Working Group Meeting
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
Agenda
- Update on the plans for the Meeting in Montpellier, 9-13 May 2016
- Update on the progress on developing the rice annotation files from IRRI by Austin and Marie-Angelique
- Progress on the development of the V. 5 trait dictionaries- Marie-Angelique and/or Leo
- ICBO call for papers is open- http://icbo.cgrb.oregonstate.edu/ICBO_submission
- Presentation for Biocuration meeting- Marie-Angelique
- Plant Trait Ontology updates- Recent revisions and changes to the equivalence axioms etc
- Other items?
- AmiGO2 issues continued..
- OBA presentation- CM?
Other items:
Update on the plans for the Meeting in Montpellier, 9-13 May 2016
See link to website:
https://sites.google.com/a/cgxchange.org/cropontologycommunity/home
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
Proceedings will be published in XYZ journal????
AmiGO2 issues continued..
tba..
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:
Upcoming Meetings and Workshops
Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland
- MAL is going and will be presenting a talk
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