Dec 8th, 2015 Ontology Working Group Meeting - Revision history

Cooperl at 20:46, 16 December 2015

2015-12-16T20:46:50Z

← Older revision		Revision as of 20:46, 16 December 2015
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	Time: 8:15am PST (GMT-8)		Time: 8:15am PST (GMT-8)
	* Connection details: '''Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/600315375'''		* Connection details: '''Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/600315375'''
			* Attendees: LC, AM, PJ, DWS, BS

			* [[File:Ontology WG Meeting 12-08-2015 audio.m4a\|thumb\|Ontology WG Meeting 12-08-2015 audio]]
			* [[File:Ontology WG Meeting 12-08-2015 video.mp4\|thumb\|Ontology WG Meeting 12-08-2015 video]]


	* Attendees: LC, AM, PJ, DWS, BS
	==Updates==		==Updates==
	- DWS is working on a plant anatomy glossary- images can be linked to the PO terms in the digital version.		- DWS is working on a plant anatomy glossary- images can be linked to the PO terms in the digital version.

Cooperl: /* Proposed Revisions to Biochemical Traits */

2015-12-08T22:11:05Z

Proposed Revisions to Biochemical Traits

← Older revision		Revision as of 22:11, 8 December 2015
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	** concentration = amount/ VOLUME		** concentration = amount/ VOLUME
	** content = amount/MASS		** content = amount/MASS
	* Reference about content vs concentration: http://www.ncbi.nlm.nih.gov/pubmed/23894859		* Reference about content vs concentration: http://www.ncbi.nlm.nih.gov/pubmed/23894859
	~~e.g.~~
	* 'copper content'		* 'copper content'
	** 'copper concentration'		** 'copper concentration'
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	* upper level: biochemical traits		* upper level: biochemical traits

			* BS: suggestion to include all biochem traits in the morphology branch as properties of the structure

	- include all biochem traits in the structure ~~branch~~

	== Planteome Curator Workshop at PAG ==		== Planteome Curator Workshop at PAG ==

Cooperl: /* Discussion about modified variables with scale info */

2015-12-08T22:09:37Z

Discussion about modified variables with scale info

← Older revision		Revision as of 22:09, 8 December 2015
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	== Discussion about modified variables with scale info ==		== Discussion about modified variables with scale info ==
	- MAL has been working on implementing the suggestion from PJ to add additional variable ids which are specific to each of the categorical scales. That way there is a unique id to assign to a data annotation. From this you can determine the trait, method, and the scale.		- MAL has been working on implementing the suggestion from PJ to add additional variable ids which are specific to each of the categorical scales. That way there is a unique id to assign to a data annotation. From this you can determine the trait, method, and the scale.

	- ID scale- each scale has a specific ID, these IDs are not linked to TO, but to each specific CO-variables		- ID scale- each scale has a specific ID, these IDs are not linked to TO, but to each specific CO-variables

	- color: can be measured using a color wheel, or subjective 1-10, or whatever breeders have used.		- color: can be measured using a color wheel, or subjective 1-10, or whatever breeders have used.

	- The CO curators/breeders have their own system for quality control, somewhat subjective. Comparison within the crop species it is fine, but would be difficult to compare across species. At that point, we should just compare at the level of the TO trait term.		- The CO curators/breeders have their own system for quality control, somewhat subjective. Comparison within the crop species it is fine, but would be difficult to compare across species. At that point, we should just compare at the level of the TO trait term.

Cooperl: /* Proposed Revisions to Biochemical Traits */

2015-12-08T22:09:06Z

Proposed Revisions to Biochemical Traits

← Older revision		Revision as of 22:09, 8 December 2015
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	** 'sodium concentration'		** 'sodium concentration'

	* 'zinc ~~concentration~~'		* 'zinc content'
	** 'zinc ~~content~~'		** 'zinc concentration'

Cooperl: /* Trait Ontology Revisions */

2015-12-08T21:39:25Z

Trait Ontology Revisions

@@ Line 67: / Line 67: @@
 * Reference about content vs concentration: http://www.ncbi.nlm.nih.gov/pubmed/23894859
 e.g.
 * 'copper content'
 ** 'copper concentration'
@@ Line 90: / Line 89: @@
 ** 'zinc content'
 * discussion of content vs. concentration

Cooperl: /* Proposed Revisions to Biochemical Traits */

2015-12-08T21:38:54Z

Proposed Revisions to Biochemical Traits

@@ Line 67: / Line 67: @@
 * Reference about content vs concentration: http://www.ncbi.nlm.nih.gov/pubmed/23894859
 e.g.
 * 'arsenic concentration'
 * 'ash content'
@@ Line 74: / Line 97: @@
 * 'carbon content'
 * 'cobalt concentration'
 *'hydrogen peroxide content'
 * 'lithium concentration'
 * 'magnesium concentration'
 * 'molybdenum concentration'
 * 'nickel concenteration'
 * 'nitrogen content'
 * 'phosphate content'
 * 'selenium concentration'
 * 'sulfur concentration'
 * discussion of content vs. concentration

Cooperl: /* Proposed Revisions to Biochemical Traits */

2015-12-08T21:36:49Z

Proposed Revisions to Biochemical Traits

← Older revision		Revision as of 21:36, 8 December 2015
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	===Proposed Revisions to Biochemical Traits===		===Proposed Revisions to Biochemical Traits===
	* Issue exists that we have a number of traits that are duplicated for the content and concentration, and many others that are just on concentration		* Issue exists that we have a number of traits that are duplicated for the content and concentration, and many others that are just on concentration
			- link to google doc: [https://docs.google.com/document/d/1oPJ-U86so9H621oRMpSO9ztOXXbH-v8cX9dKuZuIn3c/edit?usp=sharing Biochemical Traits]
	** concentration = amount/ VOLUME		** concentration = amount/ VOLUME
	** content = amount/MASS		** content = amount/MASS

Cooperl: /* Proposed Revisions to Biochemical Traits */

2015-12-08T21:35:25Z

Proposed Revisions to Biochemical Traits

← Older revision		Revision as of 21:35, 8 December 2015
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	* 'carbon content'		* 'carbon content'
	* 'cobalt concentration'		* 'cobalt concentration'
	* 'copper ~~concentration'''~~'		* 'copper content'
	** 'copper ~~content~~'		** 'copper concentration''''
	*'hydrogen peroxide content'		*'hydrogen peroxide content'
	* 'iron ~~concentration~~'		* 'iron content'
	** 'iron ~~content~~'		** 'iron concentration'
	* 'lithium concentration'		* 'lithium concentration'
	* 'magnesium concentration'		* 'magnesium concentration'
	* 'manganese ~~concentration~~'		* 'manganese content'
	** 'manganese ~~content~~'		** 'manganese concentration'
	* 'molybdenum concentration'		* 'molybdenum concentration'
	* 'nickel concenteration'		* 'nickel concenteration'

Cooperl: /* Proposed Revisions to Biochemical Traits */

2015-12-08T21:34:15Z

Proposed Revisions to Biochemical Traits

← Older revision		Revision as of 21:34, 8 December 2015
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	* 'arsenic concentration'		* 'arsenic concentration'
	* 'ash content'		* 'ash content'
	*'boron concentration'		* 'boron concentration'
	* 'cadmium concentration'		* 'cadmium concentration'
	* 'calcium concentration'		* 'calcium concentration'
	* 'carbon content'		* 'carbon content'
	* 'cobalt concentration'		* 'cobalt concentration'
	* 'copper concentration'		* 'copper concentration''''
	** 'copper content'		** 'copper content'
	*'hydrogen peroxide content'		*'hydrogen peroxide content'

Cooperl: /* Trait Ontology Revisions */

2015-12-08T21:33:38Z

Trait Ontology Revisions

@@ Line 60: / Line 60: @@
 == Trait Ontology Revisions  ==
-* Proposed Revisions to Biochemical Traits:
+===Proposed Revisions to Biochemical Traits===
-Issue exists that we have a number of traits that are duplicated for the content and concentration, and many others that are just on concentration
+* Issue exists that we have a number of traits that are duplicated for the content and concentration, and many others that are just on concentration
 e.g.
-*'arsenic concentration'
+* 'arsenic concentration'
 *'boron concentration'
 * 'cadmium concentration'
 * 'calcium concentration'
 * 'cobalt concentration'
 * 'copper concentration'
 ** 'copper content'
-'iron concentration'
+* discussion of content vs. concentration
-'iron content'
+- should we merge the content and concentration terms? Or put all concentration terms as subclasses of content?
-'lithium concentration'
+* from PATO
-'molybdenum concentration'
+* upper level: biochemical traits
      - include all biochem traits in the structure branch