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 (as always)

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)

From JE: Can't really do it as the "download" is actually a direct query to the solr and can't add stuff to it. However, there is a "Gaf chunk download" button that should actually have the gaf format, but again for technical reasons, we can't add a header line to. But, that button currently doesn't work, and a ticket has been created for it. Apparently, that button is not used much as it is broken on their end as well: https://github.com/geneontology/amigo/issues/293

  • 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 Planteome 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
    • would be good if it was a different color or if there was a banner to alert users that it is the dev site. Done


Issues being sorted out:



  • Links to GitHub trackers are not functional-
    • Need to add these as dbxrefs in the AmiGO file- AM will do
    • CM has suggested going to using the url of the issue instead. LC will test, could write a script to implement this.


From MAL:

  • The CO terms are showing up as subclasses, but they get confused with other things that are subclasses- We need special relationship to link the CO and TO classes
  • Currently, the method_of, scale_of and variable_of relations are not being displayed- MAL will post a comment on the tracker: (https://github.com/Planteome/planteome-ontology-browsers/issues/20)
    • Perhaps they should be 'taxonomic equivalents' AND subclasses? ; perhaps you can have double-relationships??? (Suggestion from BS)

This requires further discussion

  • Suggestions for improving the display:
    • Perhaps color coding in the graph
    • Changing CO_### to the correct name- e.g. CO_334:0000432 Plant Height ---> lentil plant height
    • How could this be done?


  • Merged version of TO will contain all the mappings to the Crop specific ontologies, so they will not have to be loaded individually (From PJ)
  • The breeders and data managers from the CG centers will maintain their Trait Dictionaries (TDs), which should include the mappings to the TO
  • MAL's script will convert from the TD to the ontology file
  • We should work on creating and testing a merged version with cassava, rice and lentil
  • Visualization: need a better way to view the ontology trees
    • Choices now are OLS-vis, or the static .png display (note: OLS-Vis is currently only on the dev site)
    • OLS-Vis tool (http://ols.wordvis.com/)- pulls all the ontologies from the urls, so it is the Release version.
    • Could this be modified to display the planteome ones specifically on our browser?? Does not appear to be available for local install.

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

    • 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- Tuesday Feb 2nd
    • technical things (mappings and such)??
    • Browser/annotation ??
    • Planning

Upcoming meetings and workshops

  • Phenotype RCN meeting Feb 2016
  • GARNet/Egenis Workshop: Integrating Large Data into Plant Science: From Big Data to Discovery

April 21st-22nd 2016 (Link)

  • Meeting in Montpellier, May 2016
  • ICBO 2016 Corvallis
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