Jan 21st, 2016 Ontology Working Group Meeting - Revision history

Cooperl: /* Issues being sorted out: */

2017-02-07T21:51:01Z

Issues being sorted out:

← Older revision		Revision as of 21:51, 7 February 2017
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	** Choices now are OLS-vis, or the static .png display (note: OLS-Vis is currently only on the dev site)		** Choices now are OLS-vis, or the static .png display (note: OLS-Vis is currently only on the dev site)
	** OLS-Vis tool (http://ols.wordvis.com/)- pulls all the ontologies from the urls, so it is the Release version.		** OLS-Vis tool (http://ols.wordvis.com/)- pulls all the ontologies from the urls, so it is the Release version.
	** Could this be modified to display the planteome ones specifically on our browser?? ''Does not appear to be available for local install.''		** Could this be modified to display the planteome ones specifically on our browser?? ''Does not appear to be available for local install.''

	==Trait vs descriptors- from EA- breeder terminology is important==		==Trait vs descriptors- from EA- breeder terminology is important==

Cooperl: /* Next meetings: */

2016-01-26T18:25:24Z

Next meetings:

← Older revision		Revision as of 18:25, 26 January 2016
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	* can use SPQL		* can use SPQL

	===Next meetings:===		==Next meetings:==
	* need to break up the calls into:		* need to break up the calls into:
	** Ontology- Tuesday Feb 2nd		** Ontology- Tuesday Feb 2nd

Cooperl: /* Next meetings: */

2016-01-26T18:25:05Z

Next meetings:

← Older revision		Revision as of 18:25, 26 January 2016
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	===Next meetings:===		===Next meetings:===
	* need to break up the calls into:		* need to break up the calls into:
	** Ontology- Tuesday ~~Jan 26th~~		** Ontology- Tuesday Feb 2nd
	** technical things (mappings and such)??		** technical things (mappings and such)??
	** Browser/annotation ??		** Browser/annotation ??

Cooperl: /* AberOWL- Georgios V. Gkoutos */

2016-01-26T18:24:41Z

AberOWL- Georgios V. Gkoutos

← Older revision		Revision as of 18:24, 26 January 2016
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	** evaluation: happens at multiple times		** evaluation: happens at multiple times

	===AberOWL- Georgios V. Gkoutos===		==AberOWL- Georgios V. Gkoutos==
	* An ontology repository and semantic search engine- link to paper on PubMed: http://www.ncbi.nlm.nih.gov/pubmed/25627673		* An ontology repository and semantic search engine- link to paper on PubMed: http://www.ncbi.nlm.nih.gov/pubmed/25627673

Cooperl: /* Trait vs descriptors- from EA- breeder terminology is important */

2016-01-26T18:24:30Z

Trait vs descriptors- from EA- breeder terminology is important

← Older revision		Revision as of 18:24, 26 January 2016
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	** Could this be modified to display the planteome ones specifically on our browser?? ''Does not appear to be available for local install.''		** Could this be modified to display the planteome ones specifically on our browser?? ''Does not appear to be available for local install.''

	=== Trait vs descriptors- from EA- breeder terminology is important===		==Trait vs descriptors- from EA- breeder terminology is important==
	* Descriptors (need to avoid this word), these are not traits		* Descriptors (need to avoid this word), these are not traits
	** Usually measured on a small number of plants, and locations, with no stress		** Usually measured on a small number of plants, and locations, with no stress

Cooperl: /* Update on Planteome browsers */

2016-01-25T17:37:45Z

Update on Planteome browsers

← Older revision		Revision as of 17:37, 25 January 2016
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	** How could this be done?		** How could this be done?

	~~==From PJ: ==~~
	* Merged version of TO will contain all the mappings to the Crop specific ontologies, so they will not have to be loaded individually		* Merged version of TO will contain all the mappings to the Crop specific ontologies, so they will not have to be loaded individually (From PJ)
	* The breeders and data managers from the CG centers will maintain their Trait Dictionaries (TDs), which should include the mappings to the TO		* The breeders and data managers from the CG centers will maintain their Trait Dictionaries (TDs), which should include the mappings to the TO
	* MAL's script will convert from the TD to the ontology file		* MAL's script will convert from the TD to the ontology file

Cooperl: /* Issues being sorted out: */

2016-01-25T17:36:55Z

Issues being sorted out:

← Older revision		Revision as of 17:36, 25 January 2016
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	** How could this be done?		** How could this be done?

	* From PJ: Merged version of TO will contain all the mappings to the Crop specific ontologies, so they will not have to be loaded individually		==From PJ: ==
			* Merged version of TO will contain all the mappings to the Crop specific ontologies, so they will not have to be loaded individually
	* The breeders and data managers from the CG centers will maintain their Trait Dictionaries (TDs), which should include the mappings to the TO		* The breeders and data managers from the CG centers will maintain their Trait Dictionaries (TDs), which should include the mappings to the TO
	* MAL's script will convert from the TD to the ontology file		* MAL's script will convert from the TD to the ontology file

Cooperl: /* Issues being sorted out: */

2016-01-25T17:36:25Z

Issues being sorted out:

← Older revision		Revision as of 17:36, 25 January 2016
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	From MAL:		From MAL:
	* '''The CO terms are showing up as subclasses, but they get confused with other things that are subclasses'''		* '''The CO terms are showing up as subclasses, but they get confused with other things that are subclasses'''- We need special relationship to link the CO and TO classes
	** need special relationship to link the CO and TO classes		* Currently, the method_of, scale_of and variable_of relations are not being displayed- MAL will post a comment on the tracker: (https://github.com/Planteome/planteome-ontology-browsers/issues/20)
	** Perhaps they should be 'taxonomic equivalents' AND subclasses; perhaps you can have double-relationships??? (Suggestion from BS)		** Perhaps they should be 'taxonomic equivalents' AND subclasses? ; perhaps you can have double-relationships??? (Suggestion from BS)

	''This requires further discussion''		''This requires further discussion''

Cooperl: /* Update on Planteome browsers */

2016-01-25T17:33:45Z

Update on Planteome browsers

← Older revision		Revision as of 17:33, 25 January 2016
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	<big> Main Planteome website: http://planteome.org/</big>		<big> Main Planteome website: http://planteome.org/</big>
	* drupal front pages and AmiGO2 browser serving ontologies and annotation data		* drupal front pages and AmiGO2 browser serving ontologies and annotation data


	<big> Development site: http://dev.planteome.org/amigo</big>		<big> Development site: http://dev.planteome.org/amigo</big>
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	** loads nightly with all the ontologies		** loads nightly with all the ontologies
	** would be good if it was a different color or if there was a banner to alert users that it is the dev site. '''Done'''		** would be good if it was a different color or if there was a banner to alert users that it is the dev site. '''Done'''


	==Issues being sorted out:==		==Issues being sorted out:==

Cooperl: /* Issues being sorted out: */

2016-01-25T17:33:18Z

Issues being sorted out:

← Older revision		Revision as of 17:33, 25 January 2016
Line 78:		Line 78:
	** need special relationship to link the CO and TO classes		** need special relationship to link the CO and TO classes
	** Perhaps they should be 'taxonomic equivalents' AND subclasses; perhaps you can have double-relationships??? (Suggestion from BS)		** Perhaps they should be 'taxonomic equivalents' AND subclasses; perhaps you can have double-relationships??? (Suggestion from BS)

			''This requires further discussion''

	* '''Suggestions for improving the display:'''		* '''Suggestions for improving the display:'''
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	* From PJ: Merged version of TO will contain all the mappings to the Crop specific ontologies, so they will not have to be loaded individually		* From PJ: Merged version of TO will contain all the mappings to the Crop specific ontologies, so they will not have to be loaded individually
	* The breeders and data managers from the CG centers will maintain their Trait Dictionaries (TDs), which should include the mappings ~~tot he~~ TO		* The breeders and data managers from the CG centers will maintain their Trait Dictionaries (TDs), which should include the mappings to the TO
	* MAL's script will convert from the TD to the		* MAL's script will convert from the TD to the ontology file
	* We should work on creating and testing a merged version with cassava, rice and lentil		* We should work on creating and testing a merged version with cassava, rice and lentil

	* Visualization: need a better way to view the ontology trees		* '''Visualization: need a better way to view the ontology trees '''
	** Choices now are OLS-vis, or the static .png display (note: OLS-Vis is currently only on the dev site)		** Choices now are OLS-vis, or the static .png display (note: OLS-Vis is currently only on the dev site)
	** OLS-Vis tool (http://ols.wordvis.com/)- pulls all the ontologies from the urls, so it is the Release version.		** OLS-Vis tool (http://ols.wordvis.com/)- pulls all the ontologies from the urls, so it is the Release version.
	** Could this be modified to display the planteome ones specifically on our browser??		** Could this be modified to display the planteome ones specifically on our browser?? ''Does not appear to be available for local install.''

	=== Trait vs descriptors- from EA- breeder terminology is important===		=== Trait vs descriptors- from EA- breeder terminology is important===
	* Descriptors (need to avoid this word), these are not traits?		* Descriptors (need to avoid this word), these are not traits
	** Usually measured on a small number of plants, and locations, with no stress		** Usually measured on a small number of plants, and locations, with no stress
	** qualitative scale, but may be converted to ???		** qualitative scale, but may be converted to ???