Mar 15th, 2016 Ontology Working Group Meeting - Revision history

Cooperl: /* Update and report on the visit to IRRI by Austin, Marie-Angelique and Leo */

2016-03-15T22:53:55Z

Update and report on the visit to IRRI by Austin, Marie-Angelique and Leo

← Older revision		Revision as of 22:53, 15 March 2016
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	=Agenda=		=Agenda=
	=='''Update and report on the visit to IRRI by Austin, Marie-Angelique and Leo'''==		=='''Update and report on the visit to IRRI by Austin, Marie-Angelique and Leo'''==
	* '''Austin: annotations- progress report and issues with webservices and dbxref urls~~'''~~		=== Austin: annotations- progress report and issues with webservices and dbxref urls===
	- Currently we have a small test set of the annotations from The Rice SNP-Seek database (http://oryzasnp.org/iric-portal/index.zul).		- Currently we have a small test set of the annotations from The Rice SNP-Seek database (http://oryzasnp.org/iric-portal/index.zul).

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	* '''MAL/Leo: Update on the revisions to the Rice Trait dictionary~~'''~~		=== MAL/Leo: Update on the revisions to the Rice Trait dictionary===
	- Leo has completed cleaning the TD and will post to GH soon. MAL will create the OBO file with the mapping to the TO on the CO traits		- Leo has completed cleaning the TD and will post to GH soon. MAL will create the OBO file with the mapping to the TO on the CO traits

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	- some traits from GRiSP, next version will have the core traits from the Breeding for Rice - BPI(?)		- some traits from GRiSP, next version will have the core traits from the Breeding for Rice - BPI(?)

	- the variable will be a ~~sbclass~~ of so that it shows up in the browser		- the variable will be a subclass of so that it shows up in the browser

	* Mapping issues:		* Mapping issues:
	- apiculus traits in the TO are linked to the lemma apiculus, but the PO only includes palea apiculus.		- apiculus traits in the TO are linked to the lemma apiculus, but the PO only includes palea apiculus.

	- shouldn't be "~~plaleal~~", should be non-adjective form		- shouldn't be "paleal", should be non-adjective form

	- add lemma apiculus to the PO		- add lemma apiculus to the PO

	* Discussion of how to express the scale, esp the categorical ones		* Discussion of how to express the scale, esp the categorical ones- CO rice trait file does not have the scale info in it. MAL will fix it the next time.
	-
	* Link to summary report (https://docs.google.com/document/d/1SYt5MC4kw87UxMsCOElg2yJQaE4nsEzVuXdNYq30ixU/edit?ts=56e6fbb5)		* Link to summary report (https://docs.google.com/document/d/1SYt5MC4kw87UxMsCOElg2yJQaE4nsEzVuXdNYq30ixU/edit?ts=56e6fbb5)

Cooperl: /* Update and report on the visit to IRRI by Austin, Marie-Angelique and Leo */

2016-03-15T21:58:17Z

Update and report on the visit to IRRI by Austin, Marie-Angelique and Leo

← Older revision		Revision as of 21:58, 15 March 2016
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	* Discussion of how to express the scale, esp the categorical ones		* Discussion of how to express the scale, esp the categorical ones
	-		-
			* Link to summary report (https://docs.google.com/document/d/1SYt5MC4kw87UxMsCOElg2yJQaE4nsEzVuXdNYq30ixU/edit?ts=56e6fbb5)

	Photo of rice grain from AM (from IRRI)		Photo of rice grain from AM (from IRRI)

Cooperl: /* Update and report on the visit to IRRI by Austin, Marie-Angelique and Leo */

2016-03-15T21:56:24Z

Update and report on the visit to IRRI by Austin, Marie-Angelique and Leo

← Older revision		Revision as of 21:56, 15 March 2016
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	- Accessing the API- AM can from here, MAL cannot		- Accessing the API- AM can from here, MAL cannot

	- Sources: ~~GRIN~~ System: 124,000 germplasm accessions		- Sources: GRIMS System: 124,000 germplasm accessions (http://www.irgcis.irri.org:81/grc/IRGCISHome.html)

	- Genesys, accessing the database- in MS access		- Genesys, accessing the database- in MS access

Cooperl: /* Update and report on the visit to IRRI by Austin, Marie-Angelic and Leo */

2016-03-15T19:04:18Z

Update and report on the visit to IRRI by Austin, Marie-Angelic and Leo

← Older revision		Revision as of 19:04, 15 March 2016
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	=Agenda=		=Agenda=
	=='''Update and report on the visit to IRRI by Austin, Marie-~~Angelic~~ and Leo'''==		=='''Update and report on the visit to IRRI by Austin, Marie-Angelique and Leo'''==
	* '''Austin: annotations- progress report and issues with webservices and dbxref urls'''		* '''Austin: annotations- progress report and issues with webservices and dbxref urls'''
	- Currently we have a small test set of the annotations from The Rice SNP-Seek database (http://oryzasnp.org/iric-portal/index.zul).		- Currently we have a small test set of the annotations from The Rice SNP-Seek database (http://oryzasnp.org/iric-portal/index.zul).

Cooperl: /* Upcoming Meetings and Workshops */

2016-03-15T18:59:26Z

Upcoming Meetings and Workshops

← Older revision		Revision as of 18:59, 15 March 2016
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	==DivSeek Partner Assembly, Friday, June 17th, Saskatoon, Canada==		==DivSeek Partner Assembly, Friday, June 17th, Saskatoon, Canada==

	==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==
	* Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
	** Short papers, up to 4 pages (will be published in JBMS)
	** Poster abstracts, up to 1 page
	** Flash updates, up to 1 page

	~~== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==~~
	* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
	* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

	~~= Upcoming Meetings and Workshops=~~
	~~==[https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th, 2016; Geneva, Switzerland]==~~
	* MAL is going
	** [https://www.isb-sib.ch/events/biocuration2016/key-dates key dates]
	** Abstract submitted: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703

	==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ GARNet/Egenis Workshop: Integrating Large Data into Plant Science], April 21st-22nd 2016, Dartington Hall, Totnes, Devon==
	* Elizabeth and George are going, EA will present Planteome as part of her talk

	~~== Meeting in Montpellier, 9-13 May 2016 ==~~
	~~Link to tentative agenda/website: [https://sites.google.com/a/cgxchange.org/cropontologycommunity/home]~~

	==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==		==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==

Cooperl: /* Other items: */

2016-03-15T18:58:47Z

Other items:

← Older revision		Revision as of 18:58, 15 March 2016
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	==Other items:==		==Other items:==
			=== Update on the plans for the Meeting in Montpellier, 9-13 May 2016===
			''Tabled for next meeting''

	===AmiGO2 issues continued.. ===		===AmiGO2 issues continued.. ===

Cooperl: /* Update on the plans for the Meeting in Montpellier, 9-13 May 2016 */

2016-03-15T18:58:04Z

Update on the plans for the Meeting in Montpellier, 9-13 May 2016

← Older revision		Revision as of 18:58, 15 March 2016
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	* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]		* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
	* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589		* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

	~~== Update on the plans for the Meeting in Montpellier, 9-13 May 2016==~~

	= Upcoming Meetings and Workshops=		= Upcoming Meetings and Workshops=

Cooperl: /* Agenda */

2016-03-15T18:57:11Z

Agenda

← Older revision		Revision as of 18:57, 15 March 2016
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	- traits for cassava- data set.Play with the annotations to get them to fit into GAF		- traits for cassava- data set.Play with the annotations to get them to fit into GAF

	==AmiGO2 issues continued.. ==		==Other items:==

			===AmiGO2 issues continued.. ===
	''Tabled for next meeting''		''Tabled for next meeting''

	=~~=Other items?==~~		===OBA development- Chris Mungall===

	==OBA development- Chris Mungall==
	Tabled for next meeting...		Tabled for next meeting...

Cooperl: /* Update and report on the visit to IRRI by Austin, Marie-Angelic and Leo */

2016-03-15T18:56:16Z

Update and report on the visit to IRRI by Austin, Marie-Angelic and Leo

← Older revision		Revision as of 18:56, 15 March 2016
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	* '''MAL/Leo: Update on the revisions to the Rice Trait dictionary'''		* '''MAL/Leo: Update on the revisions to the Rice Trait dictionary'''
	- Leo has completed cleaning the TD and will post to GH soon. MAL will create the OBO file with the mapping to the TO on the CO traits		- Leo has completed cleaning the TD and will post to GH soon. MAL will create the OBO file with the mapping to the TO on the CO traits

	- All the traits from IRIS - so genebank traits are covered		- All the traits from IRIS - so genebank traits are covered

	- some traits from GRiSP, next version will have the core traits from the Breeding for Rice - BPI(?)		- some traits from GRiSP, next version will have the core traits from the Breeding for Rice - BPI(?)

	- the variable will be a sbclass of so that it shows up in the browser		- the variable will be a sbclass of so that it shows up in the browser

Cooperl: /* Update and report on the visit to IRRI by Austin, Marie-Angelic and Leo */

2016-03-15T18:55:47Z

Update and report on the visit to IRRI by Austin, Marie-Angelic and Leo

← Older revision		Revision as of 18:55, 15 March 2016
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	- Test files on dev.planteome see awn color: http://dev.planteome.org/amigo/search/bioentity?q=awn%20color		- Test files on dev.planteome see awn color: http://dev.planteome.org/amigo/search/bioentity?q=awn%20color

	- AM will see if they can add the dashes in from their end at IRRI, otherwise we need to just link to the generic Home page we the user could run the search		- AM will see if they can add the dashes in from their end at IRRI, otherwise we need to just link to the generic Home page we the user could run the search

	- IRIC site is very slow- Amazon cloud issue?		- IRIC site is very slow- Amazon cloud issue?

	- Accessing the API- AM can from here, MAL cannot		- Accessing the API- AM can from here, MAL cannot

	- Sources: GRIN System: 124,000 germplasm accessions		- Sources: GRIN System: 124,000 germplasm accessions

	- Genesys, accessing the database- in MS access		- Genesys, accessing the database- in MS access

	- IR64 mutant lines- database not being maintained.		- IR64 mutant lines- database not being maintained.