Ontology Working Group Meeting, Tuesday June 9th, 2015

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Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada) Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/834566681

  • Who will attend: LC, MAL, DWS, PJ, BS
  • Others?: , CM, GG
  • Regrets: JE, EA

Agenda

Summary from last meeting May 26th:

  • Report form UN meeting- BS- need links to publication
  • Updates underway to the Trait Template (Leo)
  • Discussion of the id space for Crop Ontologies
  • Discussion of the hierarchy of the CO Vocabs- not a problem if the terms have logical def'ns, just import as flat file.
  • Mapping to TO with Agreement Maker Light - see below
  • Progress on AmiGO2 browser development: http://dev.planteome.org/amigo
  • Updates on the transition to Github: https://github.com/Planteome

Other Updates, etc

  • OSU: Offer has been made to postdoc, waiting for confirmation, hopefully will start around the end of June, undergraduate student hired for summer, another one joining in August
  • NYBG: - Offer to postdoc candidate has been made, waiting for confirmation, graduate student will be joining to help with the imaging work
    • Also working with the AISO-Bisque team to generate images. Idea to do a use case study involving in situ analysis- leaf development or procambium development

Report from Bioversity team

Introduce new Crop_Ontology_Pages on the wiki (MAL)

As a follow up from the discussion last week, Marie-Angelique has created an informative page on the wiki with information about the structure and format of the CO vocabularies.

  • Current structure of the Trait template (v.4)
  • Future structure of the Trait Template (v.5)

Updates on work on Plant Disease Ontology and future plans for Plant Stress Ontology (Laurel)

* Discussion Points:

  1. Started building a Plant Disease Ontology by adding diseases and pathogens causal agents from the APS "Common Names of Plant Diseases" pages. Currently has branches for the causal agents, host species and plant diseases, linked by relationships
  2. Adding in information from a number of additional sources now, as the APS is a bit outdated and not comprehensive e.g. NCBI, PHI-base, MaizeGDB, Rice SES, EOL
  3. Disease names are based on the common name in use with the host species and disease causal agent type added. e.g. "Bacterial blight (APS)" --> rice bacterial blight disease (PDO).
  4. Ideally we would like to have the disease causal agents and host plant species in a separate ontology or taxonomy that we would not be responsible for maintaining, such as NCBI from the , but it is too large to import into the AmiGO browser. In order to create a slim we need to have a list of the names of the pathogens. One suggestion was to use the NCBI Taxon ontology, but we would need to create a slim.
  • Suggestion from MAL after the call: There is also the Uniprot Taxonomy which has URIs for taxon along with some synonyms. Maybe it could be of interest :

Mappings from CO to TO: MAL

Tabled for next meeting....

Next Meeting Tuesday June 23rd

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