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

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

• Links to recordings:
• Planteome Ontology WG Zoom Meeting:
  • File:Ontology WG Meeting 3-15-2016 video.mp4
  • File:Ontology WG Meeting 3-15-2016 audio only.m4a

• Planteome IRRI meeting Thursday March 10th:
  • File:Planteome-IRRI Meeting 3-10-16 audio only.m4a
  • File:Planteome-IRRI Meeting 3-10-16-video.mp4

Agenda

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

- Currently we have a small test set of the annotations from The Rice SNP-Seek database (http://oryzasnp.org/iric-portal/index.zul).

Test files on dev.planteome see awn color: http://dev.planteome.org/amigo/search/bioentity?q=awn%20color - AM will see if they can add the dashes in from their end at IRRI, otherwise we need to just link to the generic Home page we the user could run the search

- IRIC site is very slow- Amazon cloud issue? - Accessing the API- AM can from here, MAL cannot

- Sources: GRIN System: 124,000 germplasm accessions - Genesys, accessing the database- in MS access - IR64 mutant lines- database notbeing maintained.

• MAL/Leo: Update on the revisions to the Rice Trait dictionary

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

AmiGO2 issues continued..

Tabled for next meeting

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: [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

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