Jan 21st, 2016 Ontology Working Group Meeting: Difference between revisions

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=Update on browsers=  
=Update on browsers=  
* Main Planteome website: http://planteome.org/
* Main Planteome website: http://planteome.org/
** drupal front pages and AmiGO2 browser serving ontologies and annotation data


* Development site: http://dev.planteome.org/amigo
* Development site: http://dev.planteome.org/amigo
** Currently just ontology files but can also load annotations on there to test
** loads nightly with all the ontologies


Issues being sorted out:  
==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)
* 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
** only showing up- is_a, part_of and occurs_inthis is an issues for the Gene Ontology as well  
** this is an issues for the Gene Ontology as well  
** Gene Ontology tracker:


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


=
From MAL:  
From MAL:  
   - the CO terms are showing up as subclasses, but they get confused with other things that are subclasses
   - the CO terms are showing up as subclasses, but they get confused with other things that are subclasses

Revision as of 19:55, 21 January 2016

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

- 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/
    • drupal front pages and AmiGO2 browser serving ontologies and annotation data
  • Development site: http://dev.planteome.org/amigo
    • Currently just ontology files but can also load annotations on there to test
    • loads nightly with all the ontologies

Issues being sorted out:

From MAL:

 - the CO terms are showing up as subclasses, but they get confused with other things that are subclasses
   - they should be 'taxonomic equivalents'
     - perhaps you can have double-relationships
   - AND subclasses
   - perhaps color coding in combination with changing CO_### to the correct
 - Need a better way to view trees.  Choices now are broken OLSvis, or static .png
 - TD will change, but we have a script to auto-update and provide updated CO.owl ontologies (read only) for specific crops

Upcoming meetings and workshops