Feb 4th, 2016 Ontology Working Group Meeting

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Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Feb 4th, 2016
  • Time: 8:15am PST (GMT-8)
  • Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/626362406

  • Attendees: LC, AM, PJ, MAL, BS, GG


Revisions to the upper-level categories of the biochemical trait TO:0000277 branch of the TO:

Current structure of the branch:

Goals: Align and define each of the biochemical-related trait classes to either GO or ChEBI classes.

Link to Google Doc: Biochem Trait Branch

Top level term: biochemical trait TO:0000277

biochemical trait TO:0000277

  • Current def’n: The traits associated with assay of either of the effected metabolite profile, enzymatic activity and biological processes which includes the physiological processes.
  • propose revised def’n: A plant trait (TO:0000387) which is a quality of a molecular function (GO:0003674), a plant metabolite (CHEBI:76924), or a chemical entity (CHEBI:24431), that is part of, or has participant a cellular component (GO:0005575), plant anatomical entity (PO:0025131) and/or a plant structure development stage (PO:0009012).

Note: this def’n is based on the biological process (GO:0008150) terms moving to a new branch of their own (see below).

Link to tracker: https://github.com/Planteome/plant-trait-ontology/issues/381

  • This will define the scope of the branch

Discussion Points:

  • BS- It is not good practice to build definitions like this, being "disjunctive". The problem is that this class is currently a grouping term, or a "bag" that holds various types of traits that are related to biochemicals in the plants. Ideally we should look at each of the upper-level categories and see if they belong here
  • From LC:
  • Goal is to categorize all the traits in this branch as either molecular function (GO:0003674), a plant metabolite (CHEBI:76924), or a chemical entity (CHEBI:24431). Could we define the whole branch as chemical entity traits?
    • What we call 'plant metabolites' are chemical entities (CHEBI:24431) that have_role plant metabolite (CHEBI:76924). See this page for a list has_role plant metabolite
    • How can we represent roles in the TO? Currently the has_role relations are not displayed.
    • See BFO role: it is a realizable entity, similar to disposition


  • Similarly, the enzyme activity traits are traits chemical entities (CHEBI:24431) with role catalyst
  • All the enzymes are represented in the Protein Ontology, e.g alcohol dehydrogenase PR_000034540

biological process related trait (TO:0000283)

Current def’n: The trait associated with assay to determine the affected biological process. Source: GR:pj

Propose it would be better to be split out into a separate branch, rather than being in the "Biochemical traits" branch:

Link to tracker: “Move biological process related trait (TO:0000283) and relevant subclasses out of the biochemical trait (TO:0000277) branch”

  • GO definition:
    • biological process (GO:0008150): Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
  • All the terms in this branch should reference the associated GO BP term.


Moved biological process related trait (TO:0000283) to be is_a plant trait:

Revised def'n: A plant trait (TO:0000387) which is a quality of a biological process (GO:0008150) that occurs in a plant anatomical entity (PO:0025131), a cellular component (GO:0005575), or during a plant structure development stage (PO:0009012).

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