Jan 21st, 2016 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

• Date: Thursday Jan. 21st, 2016
• Time: 8:15am PST (GMT-8)
• Connection details: Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328

• Attendees: LC, AM, JE, PJ, EA, MAL, BS, GG.

File:Ontology WG Meeting 1-21-2016 video.mp4

File:Ontology WG Meeting 1-21-2016 audio.m4a

Report on PAG 2016

• strong emphasis on high throughput phenotyping, machine learning is hot right now
• data standardization, field scale measurements
• Utilization of ontologies for data annotation
• everyone wants specialized ontologies for THEIR data, not something predefined

- we need to demonstrate how ontologies are useful.

Planteome Collaborators Workshop Monday Jan 11th

- http://planteome.org/outreach/workshops/PAG_2016

• Goals of the Meeting:
  • Introduce the Planteome project and launch Planteome 1.0 beta
  • Provide an update on the progress of the collaboration with the Crop Ontology to map crop-specific trait dictionaries to the Reference Trait Ontology
  • Provide a summary report and overview of the Planteome Curators Workshop, held Nov 2015 in Corvallis, OR
  • Engage Planteome collaborators and the plant genomics community by demonstrating use cases of data annotation for rice, cassava and lentils
  • Seek engagement of the plant genomics community through tools and applications to integrate into your workflow

• Who attended?

- 29 attendees (link to spreadsheet: Participants list CO-Planteome Meeting PAG 2016)

- Representatives from: CG centers (IITA, CIP, CIMMYT, IRRI) and Bioversity; INRA, IRD, LIRMM, USDA-ARS databases (SoyBase, MaizeGDB, GDR, PeanutBase, LegumeInfo), EBI, Transplant, ELIXIR Consortium, Rothamsted Research.

Comments and feedback

• Takeaways

- people are concerned about the GAF2 format - hopefully will be expanding to more than 16 columns - we will develop standards for conversion TO GAF2 - worry about having people download in GAF2 - need a few use-cases for questions that researchers will be trying to answer. - figure out what format people want to download data in, allow for download in this format

Update on browsers

• Main Planteome website: http://planteome.org/

• Development site: http://dev.planteome.org/amigo

Issues being sorted out:

• Many of our relations are not being recognized and displayed in AmiGO 2.0 (https://github.com/Planteome/planteome-ontology-browsers/issues/20)
  • only showing up- is_a, part_of and occurs_in
  • this is an issues for the Gene Ontology as well

• Synonym scopes are not being displayed- all the broad, narrow, realted and exact synonyms are being lumped together- (https://github.com/Planteome/planteome-ontology-browsers/issues/17)