Feb 4th, 2016 Ontology Working Group Meeting
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.
https://docs.google.com/document/d/1oPJ-U86so9H621oRMpSO9ztOXXbH-v8cX9dKuZuIn3c/edit?usp=sharing
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
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).
Upcoming meetings and workshops
- Phenotype RCN meeting Feb 2016
- Biocuration 2016 (https://www.isb-sib.ch/events/biocuration2016/home)
- GARNet/Egenis Workshop: Integrating Large Data into Plant Science
- April 21st-22nd 2016 (Link)
- Meeting in Montpellier, May 2016
- Intelligent Systems for Molecular Biology (ISMB) http://www.iscb.org/ismb2016; BioOntologies SIG
- ICBO and Biocreative 2016 Corvallis