Feb 4th, 2016 Ontology Working Group Meeting - Revision history

Cooperl: /* Top level term: biochemical trait TO:0000277 */

2016-02-08T22:55:20Z

Top level term: biochemical trait TO:0000277

← Older revision		Revision as of 22:55, 8 February 2016
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	** ''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] ''		** ''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.''		** ''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 ''		* ''Similarly, the enzyme activity traits are traits chemical entities (CHEBI:24431) with role catalyst ''

Cooperl: /* Top level term: biochemical trait TO:0000277 */

2016-02-08T19:45:08Z

Top level term: biochemical trait TO:0000277

← Older revision		Revision as of 19:45, 8 February 2016
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	** ''How can we represent roles in the TO? Currently the has_role relations are not displayed.''		** ''How can we represent roles in the TO? Currently the has_role relations are not displayed.''

	* ''Similarly, the enzyme activity traits are chemical entities (CHEBI:24431) with role catalyst		* ''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)==		==biological process related trait (TO:0000283)==

Cooperl: /* Top level term: biochemical trait TO:0000277 */

2016-02-08T19:21:16Z

Top level term: biochemical trait TO:0000277

← Older revision		Revision as of 19:21, 8 February 2016
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	** ''How can we represent roles in the TO? Currently the has_role relations are not displayed.''		** ''How can we represent roles in the TO? Currently the has_role relations are not displayed.''

			* ''Similarly, the enzyme activity traits are chemical entities (CHEBI:24431) with role catalyst
	* ''Similarly, the enzyme activity traits chemical entities (CHEBI:24431)

	==biological process related trait (TO:0000283)==		==biological process related trait (TO:0000283)==

Cooperl: /* Top level term: biochemical trait TO:0000277 */

2016-02-08T19:17:54Z

Top level term: biochemical trait TO:0000277

← Older revision		Revision as of 19:17, 8 February 2016
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	* From LC:		* 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?''		* ''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] ''		** ''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.''		** ''How can we represent roles in the TO? Currently the has_role relations are not displayed.''

Cooperl: /* Top level term: biochemical trait TO:0000277 */

2016-02-08T19:17:34Z

Top level term: biochemical trait TO:0000277

← Older revision		Revision as of 19:17, 8 February 2016
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	* ''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?''		* ''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] ''		* ''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.''

Cooperl: /* Top level term: biochemical trait TO:0000277 */

2016-02-08T19:16:07Z

Top level term: biochemical trait TO:0000277

← Older revision		Revision as of 19:16, 8 February 2016
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	''Discussion Points:''		''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''		* ''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''
	* ''~~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?''		* 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] ''		* ''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] ''

Cooperl: /* Top level term: biochemical trait TO:0000277 */

2016-02-08T19:15:26Z

Top level term: biochemical trait TO:0000277

← Older revision		Revision as of 19:15, 8 February 2016
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	* ''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''		* ''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''
	* ''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?''		* ''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)''		* ''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] ''
	* ''Similarly, the enzyme activity traits


			* ''Similarly, the enzyme activity traits chemical entities (CHEBI:24431)

	==biological process related trait (TO:0000283)==		==biological process related trait (TO:0000283)==

Cooperl: /* Top level term: biochemical trait TO:0000277 */

2016-02-08T19:03:02Z

Top level term: biochemical trait TO:0000277

← Older revision		Revision as of 19:03, 8 February 2016
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	* 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''
			* ''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)''
			* ''Similarly, the enzyme activity traits

	==biological process related trait (TO:0000283)==		==biological process related trait (TO:0000283)==

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

2016-02-08T18:46:31Z

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

← Older revision		Revision as of 18:46, 8 February 2016
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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.

	https://docs.google.com/document/d/1oPJ-U86so9H621oRMpSO9ztOXXbH-v8cX9dKuZuIn3c/edit?usp=sharing		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==

Cooperl: /* biological process related trait (TO:0000283) */

2016-02-05T04:30:15Z

biological process related trait (TO:0000283)

← Older revision		Revision as of 04:30, 5 February 2016
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	''Moved biological process related trait (TO:0000283) to be is_a plant trait:		''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).''		''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=