Feb 18th, 2016 Ontology Working Group Meeting - Revision history

Cooperl: /* How to model count information: has_number_of vs amount */

2016-07-07T22:50:27Z

How to model count information: has_number_of vs amount

← Older revision		Revision as of 22:50, 7 July 2016
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	* We should annotate to the upper-level "molecular entity"; being consistent is more important than being correct (ontologically)		* We should annotate to the upper-level "molecular entity"; being consistent is more important than being correct (ontologically)
	e.g. iron molecular entity		e.g. iron molecular entity

			* concentration: has increased concentration in a mixture, either increased amount in a mixture

	=== Discussion of PATO ''Composition''===		=== Discussion of PATO ''Composition''===

Cooperl: /* How to model count information: has_number_of vs amount */

2016-07-07T22:50:10Z

How to model count information: has_number_of vs amount

← Older revision		Revision as of 22:50, 7 July 2016
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	* how to describe "number_of"		* how to describe "number_of"


	* concentration: has increased concentration in a mixture, either increased amount in a mixture
	* has_number_of molecules, that's why has-number-of		* has_number_of molecules, that's why has-number-of

Cooperl: /* How to model count information: has_number_of vs amount */

2016-07-07T22:36:15Z

How to model count information: has_number_of vs amount

← Older revision		Revision as of 22:36, 7 July 2016
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	* Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant		* Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
	* alternative term: unfolds in; unfolds_in; occurs_in		* alternative term: unfolds in; unfolds_in; occurs_in




	===How to model count information: ''has_number_of'' vs ''amount''===		===How to model count information: ''has_number_of'' vs ''amount''===

Cooperl: /* Need to clarify when to use occurs_in and when to use inheres_in in the equivalence axioms */

2016-07-07T22:35:58Z

Need to clarify when to use occurs_in and when to use inheres_in in the equivalence axioms

← Older revision		Revision as of 22:35, 7 July 2016
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	** ''The BFO definition (see below) of "occurs_in" does not fit the current understanding of PATO.''		** ''The BFO definition (see below) of "occurs_in" does not fit the current understanding of PATO.''
	** ''In a trait ontology you are interested in looking at the changes in a trait over time, but you are looking at a limit case at an instance in time.''		** ''In a trait ontology you are interested in looking at the changes in a trait over time, but you are looking at a limit case at an instance in time.''
			** It is OK to use 'occurs_in' as the issue is currently under discussion between PATO and BFO


	* BFO_0000066: occurs_in is specific to biological processes		* BFO_0000066: occurs_in is specific to biological processes

Cooperl: /* Display of the Crop Ontologies in AmiGO2 */

2016-06-29T22:19:46Z

Display of the Crop Ontologies in AmiGO2

← Older revision		Revision as of 22:19, 29 June 2016
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	* Crop-specific names have been added to the rice, cassava and lentil files		* Crop-specific names have been added to the rice, cassava and lentil files
	* Names should be in lower case		* Names should be in lower case




	==Visit to IRRI==		==Visit to IRRI==

Cooperl: /* Discussion of PATO Composition */

2016-06-29T22:19:34Z

Discussion of PATO Composition

← Older revision		Revision as of 22:19, 29 June 2016
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	* See diagram: [[File:PATO composition.png\|thumbnail\|PATO_composition.png]]		* See diagram: [[File:PATO composition.png\|thumbnail\|PATO_composition.png]]

	*		* composition vs. amount: composition (PATO) cannot be used for non-morphology things (like blood, or sap)
			** composition is in the structure branch, and should be renamed "structural composition" or "structure composition"
			** - ''Need to open tracker for this''

Cooperl: /* How to model count information: has_number_of vs amount */

2016-06-29T22:19:10Z

How to model count information: has_number_of vs amount

← Older revision		Revision as of 22:19, 29 June 2016
Line 97:		Line 97:
	* We should annotate to the upper-level "molecular entity"; being consistent is more important than being correct (ontologically)		* We should annotate to the upper-level "molecular entity"; being consistent is more important than being correct (ontologically)
	e.g. iron molecular entity		e.g. iron molecular entity

	* composition vs. amount: composition (PATO) cannot be used for non-morphology things (like blood, or sap)
	** composition is in the structure branch, and should be renamed "structural composition" or "structure composition"
	** - ''Need to open tracker for this''

	=== Discussion of PATO ''Composition''===		=== Discussion of PATO ''Composition''===

Cooperl: /* How to model count information: has_number_of vs amount */

2016-06-29T22:17:57Z

How to model count information: has_number_of vs amount

← Older revision		Revision as of 22:17, 29 June 2016
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	* PATO - smaller entity has an amount (or towards)		* PATO - smaller entity has an amount (or towards)

			* 'has_number_of' is a relational quality
			* CM: Some trait ontologies are using the older, more simple pattern PATO ''number (ie amount)'' that inheres in the thing that is being counted.
			** ''inheres_in'' the thing you're counting, ''occurs_in'' whatever larger entity
			* Example: To describe the number of seeds in a pod: quality = amount, entity = seed, occurs_in pod

	* PATO ''has_number_of'' that inheres in the thing that is being counted. Instead of number_of petals inhering in
	** ''inheres_in'' the thing you're counting, ''occurs_in'' whatever larger entity
	** quality = amount, entity = seed, occurs_in pod
	** don't use relational qualities (eg: has_number_of)		** don't use relational qualities (eg: has_number_of)
	** ''occurs_in'' == ''towards''		** ''occurs_in'' == ''towards''

	* amount can inhere in the object being counted, where as has_number_of, is a quality of the larger entity		* amount can inhere in the object being counted, where as has_number_of, is a quality of the larger entity

			* how to describe "number_of"


	* concentration: has increased concentration in a mixture, either increased amount in a mixture		* concentration: has increased concentration in a mixture, either increased amount in a mixture
	* has_number_of molecules, that's why has-number-of		* has_number_of molecules, that's why has-number-of
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	** composition is in the structure branch, and should be renamed "structural composition" or "structure composition"		** composition is in the structure branch, and should be renamed "structural composition" or "structure composition"
	** - ''Need to open tracker for this''		** - ''Need to open tracker for this''

	* how to describe "number_of"

	=== Discussion of PATO ''Composition''===		=== Discussion of PATO ''Composition''===

Cooperl: /* Discussion of PATO Composition */

2016-06-29T19:11:21Z

Discussion of PATO Composition

← Older revision		Revision as of 19:11, 29 June 2016
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	=== Discussion of PATO ''Composition''===		=== Discussion of PATO ''Composition''===
	Currently, PATO term composition (PATO_0000025) is subclass of structure (PATO_0000141), in the morphology branch of physical object quality. ~~See diagram~~		* We are using composition (PATO_0000025) to describe the content classes, since amount actually means "number_of"
			* Currently, PATO term composition (PATO_0000025) is subclass of structure (PATO_0000141), in the morphology branch of physical object quality.

	[~~[File~~:~~PATO composition.png\|thumbnail\|PATO_composition.png]~~]		* composition (PATO_0000025): A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. [ PATOC:GVG ]

			* See diagram: [[File:PATO composition.png\|thumbnail\|PATO_composition.png]]

			*


	* PJ: suggestion to move composition out of subclass of structure, need to be able to describe the composition of entities such as ''xylem sap''.		* PJ: suggestion to move composition out of subclass of structure, need to be able to describe the composition of entities such as ''xylem sap''.
	** this would make it a physical object quality		** this would make it a physical object quality
			* Comment from BS: The content /composition terms should be a subclass of the morphology of the structure, rather than being in a separate branch. ''This would actually make sense in a way, since it is in the physical object quality branch.
			** For example:

	* View on PATO on http://www.ebi.ac.uk/ols/ontologies/pato		* View on PATO on http://www.ebi.ac.uk/ols/ontologies/pato

Cooperl: /* Discussion of PATO Composition */

2016-06-29T18:57:11Z

Discussion of PATO Composition

← Older revision		Revision as of 18:57, 29 June 2016
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	=== Discussion of PATO ''Composition''===		=== Discussion of PATO ''Composition''===
			Currently, PATO term composition (PATO_0000025) is subclass of structure (PATO_0000141), in the morphology branch of physical object quality. See diagram

	[[File:PATO composition.png\|thumbnail\|PATO_composition.png]]		[[File:PATO composition.png\|thumbnail\|PATO_composition.png]]



	* PJ: suggestion to move composition out of subclass of structure, need to be able to describe the composition of entities such as ''xylem sap''.		* PJ: suggestion to move composition out of subclass of structure, need to be able to describe the composition of entities such as ''xylem sap''.
	** this would make it a physical object quality		** this would make it a physical object quality