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-Angelique 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: GRIMS System: 124,000 germplasm accessions (http://www.irgcis.irri.org:81/grc/IRGCISHome.html)

- Genesys, accessing the database- in MS access

- IR64 mutant lines- database not being maintained.

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

- Leo has completed cleaning the TD and will post to GH soon. MAL will create the OBO file with the mapping to the TO on the CO traits

- All the traits from IRIS - so genebank traits are covered

- some traits from GRiSP, next version will have the core traits from the Breeding for Rice - BPI(?)

- the variable will be a subclass of so that it shows up in the browser

• Mapping issues:

- apiculus traits in the TO are linked to the lemma apiculus, but the PO only includes palea apiculus.

- shouldn't be "paleal", should be non-adjective form

- add lemma apiculus to the PO

• Discussion of how to express the scale, esp the categorical ones- CO rice trait file does not have the scale info in it. MAL will fix it the next time.

• Link to summary report (https://docs.google.com/document/d/1SYt5MC4kw87UxMsCOElg2yJQaE4nsEzVuXdNYq30ixU/edit?ts=56e6fbb5)

Photo of rice grain from AM (from IRRI)

Recent updates on the TO

• revisions to equivalence axioms- occurs_in and composition
• anther morphology traits, incl. anther number
• biochemical branch
• revisions to the equivalence axioms etc
• Resolving issues between PO and TO- e.g stem/ culm, grain/kernel/caryopsis and fruit, pistil/carpel etc
  • Go ahead and make a "culm" term -PJ or not... Stay out of the granularity

- panicle traits- inflorescence - annotation to the trait- CO/TO - prefer to annotate to the CO trait, not to the variable

- can we use relationships, or annotation extension column eg: CO_320:0000184("2") - not sure how, or if this will work. Try with the cassava data set (where is this data?) - the relationships between CO traits, variables, scales, and methods are not working in the Planteome browser yet, but they should eventually. - traits for cassava- data set.Play with the annotations to get them to fit into GAF

Other items:

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

Tabled for next meeting

AmiGO2 issues continued..

Tabled for next meeting

OBA development- Chris Mungall

Tabled for next meeting...

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