Mar 15th, 2016 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

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

• Links to recordings:
• File:Planteome-IRRI Meeting 3-10-16 audio only.m4a
• File:Planteome-IRRI Meeting 3-10-16-video.mp4

Planteome Ontology WG Zoom Meeting:

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

Agenda

The main topics of discussion will be:

Update and report on the visit to IRRI by Austin, Marie-Angelic and Leo

        Austin: annotations- progress report and issues with webservices and dbxref urls
           Test files on dev.planteome see awn color: http://dev.planteome.org/amigo/search/bioentity?q=awn%20color 
       Leo/ MAL: Update on the revisions to the Rice Trait dictionary

   AmiGO2 issues continued.. 

   Resolving issues between PO and TO- e.g stem/ culm, grain/kernel/caryopsis and fruit, pistil/carpel etc 

Upcoming Meetings and Workshops

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

• MAL is going
  • 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

Recent updates on the TO

• revisions to equivalence axioms- occurs_in and composition
• Stem and culm
• anther morphology traits, incl. anther number
• biochemical branch

• Resolving issues between PO and TO- e.g stem/ culm, grain/kernel/caryopsis and fruit, pistil/carpel etc

• revisions to the equivalence axioms etc

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

• MAL is going
  • 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: [2]

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