Feb 4th, 2016 Ontology Working Group Meeting: Difference between revisions

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* Connection details:  Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/626362406
* Connection details:  Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/626362406
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* Attendees: TBA
* Attendees: LC, AM, PJ, MAL, BS, GG


* [[File:|thumb|]]
* [[File:Ontology WG Meeting 2-4-2016 audio.m4a|thumb|Ontology WG Meeting 2-4-2016_audio.m4a]]
* [[File:|thumb| ]]
* [[File:Ontology WG Meeting 2-4-2016 video.mp4|thumb|Ontology WG Meeting 2-4-2016 video]]




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


 
Link to Google Doc: [https://docs.google.com/document/d/1oPJ-U86so9H621oRMpSO9ztOXXbH-v8cX9dKuZuIn3c/edit?usp=sharing Biochem Trait Branch]


==Top level term: biochemical trait  TO:0000277==
==Top level term: biochemical trait  TO:0000277==
'''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.
* 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.
* 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
Link to tracker: https://github.com/Planteome/plant-trait-ontology/issues/381


* This will define the scope of the branch:
* 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 [http://www.ebi.ac.uk/ols/beta/ontologies/chebi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_76924 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 [http://www.ebi.ac.uk/ols/beta/ontologies/pr/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPR_000034540 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: 
[https://github.com/Planteome/plant-trait-ontology/issues/378  “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:''


==biological process (GO:0008150)==
''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=
= Upcoming meetings and  workshops=

Latest revision as of 22:55, 8 February 2016

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).

Upcoming meetings and workshops

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