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

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Planteome Ontology WG Zoom Meeting
Planteome Ontology WG Zoom Meeting
* Date: Tuesday Jan. 26th, 2016
* Date: Tuesday Feb 4th, 2016
* Time: 8:15am PST (GMT-8)
* Time: 8:15am PST (GMT-8)
* Connection details:  TBA
* Connection details:  Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/626362406
'''
'''
* 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]]




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


==Revisions to the upper-level categories ==
Current structure of the branch:


[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png|thumbnail|Biochemical branch TO]]
[[File:Screen Shot 2016-01-15 at 4.10.18 PM.png]]


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


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


*TO:0000283 biological process related trait
==Top level term: biochemical trait TO:0000277==
*TO:0000282 enzymatic activity and protein content related trait
'''biochemical trait TO:0000277'''
*TO:0000281 metabolite content related trait
* 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.
*TO:0000465 mineral and ion content related trait
*TO:0020080 stover organic matter digestability


Suggest reducing to:
* 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).     


*mineral and ion content trait
Note: this def’n is based on the  biological process (GO:0008150) terms moving to a new branch of their own (see below).
*metabolite content trait ([https://en.wikipedia.org/wiki/Metabolite definition of 'metabolite' is sufficiently vague])
*biological process trait


metabolite content branch to be divided further in parallel to ChEBI
Link to tracker: https://github.com/Planteome/plant-trait-ontology/issues/381


[[File:biochemical branch TO.png]]
* This will define the scope of the branch


== content/concentration/amount==
''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''


Previously mentioned [http://wiki.planteome.org/index.php/Dec_8th,_2015_Ontology_Working_Group_Meeting December 8th meeting]


24 “concentration” terms
* ''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]


45 “content” terms
==biological process related trait (TO:0000283)==
Current def’n:  The trait associated with assay to determine the affected biological process.          Source: GR:pj


9 both
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”]


Biochemists definitions:
* 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.         


*concentration = amount/ VOLUME
* All the terms in this branch should reference the associated GO BP term.


*content = amount/MASS


PATO defs:
''Moved biological process related trait (TO:0000283) to be is_a plant trait:''
 
*‘concentration of’ -A quality inhering in a substance by virtue of the '''amount''' of the bearer's there is mixed with another substance.
 
*'amount' -The number of entities of this type that are part of the whole organism.
 
-[https://github.com/pato-ontology/pato/issues/65 Requested a revision] of the 'amount' definition
 
*The number of entities of this type that are part of another entity.
 
 
=== Options: ===
 
'''Merge content and concentration terms - new terms would be "amount"'''
*this would allow for an overall reduction of terms.
 
*Keeps the TO "measurement agnostic", in the reference ontology sense
 
*Might be problematic due to changing definitions of terms with existing annotations (none found on Planteome browser)
 
'''Add new parent term 'amount'.  Make content and concentration terms children of this parent (see image)'''
 
*Results in an overall addition of terms
 
*Adds unnecessary parent to cases where both content and concentration terms don't exist
 
[[File:Content concentration amount.jpg]]


''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=
* Phenotype RCN meeting Feb 2016
* Phenotype RCN meeting Feb 2016
* GARNet/Egenis Workshop: Integrating Large Data into Plant Science: From Big Data to Discovery
* Biocuration 2016 (https://www.isb-sib.ch/events/biocuration2016/home)
April 21st-22nd 2016 ([http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ Link])
* GARNet/Egenis Workshop: Integrating Large Data into Plant Science
** April 21st-22nd 2016 ([http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ Link])
* Meeting in Montpellier, May 2016
* Meeting in Montpellier, May 2016
* ICBO 2016 Corvallis
* Intelligent Systems for Molecular Biology (ISMB) http://www.iscb.org/ismb2016; [http://www.bio-ontologies.org.uk/home BioOntologies SIG]
* ICBO and Biocreative 2016 Corvallis

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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