Jan 21st, 2016 Ontology Working Group Meeting

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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, but hopefully it will be expanding to more than 16 columns- modification of the GAF2 format
    • we will develop standards for conversion to GAF2

Data download functionality on the browser needs to be refined

  • PJ: Suggest to have the column headings displayed- that would help people (JE open issue @ column headings)
  • Modification and customization of the fields for download ( open issue @)


  • figure out what format people want to download data in, allow for download in this format
    • GeneBanks use the MCPD format (?)
    • Need a few use-cases for questions that researchers will be trying to answer

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
    • Perhaps they should be 'taxonomic equivalents' AND subclasses; perhaps you can have double-relationships??? (Suggestion from BS)
    • Perhaps color coding in combination with changing CO_### to the correct name
  • Visualization: Need a better way to view trees.

- Choices now are OLS-vis, or the static .png display

  • OLS-Vis tool (http://ols.wordvis.com/)- pulls all the ontologies from the urls
    • Could this be modified to display the planteome ones specifically on our browser??


Trait vs descriptors- from EA- breeder terminology is important

  • Descriptors (need to avoid this word), these are not traits?
    • Usually measured on a small number of plants, and locations, with no stress
    • qualitative scale, but may be converted to ???
    • Often used for taxonomic reasons, measured at their maximum
  • breeder evaluation of trait: done at multiple sites, multiple generations, include stress evaluations
    • are traits, looking for stability
    • indexed or quantitative, can be categorical scale
    • evaluation: happens at multiple times

AberOWL- Georgios V. Gkoutos

  • An ontology repository and semantic search engine.
    • semantic queries looking at relationships
  • can search over all ontologies in obo
  • reasoner is run, then query.
  • can use SPQL

=Next meetings:

  • need to break up the calls into:
  • ontology
  • technical things (mappings and such)
  • Browser/annotation

Upcoming meetings and workshops

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