Thursday Aug 20th, 2015 - Revision history

Cooperl: /* C. Update from IT group- Data Store, AmiGO2- Justin Elser */

2015-08-28T19:38:09Z

C. Update from IT group- Data Store, AmiGO2- Justin Elser

← Older revision		Revision as of 19:38, 28 August 2015
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	* Association files: moving to iPlant eventually?		* Association files: moving to iPlant eventually?
	** Where are we going to put the association files?- the association files are too big for Github		** Where are we going to put the association files?- the association files are too big for Github
	** They are cluttered within the SVN- JE will move them all to a new SVN repository		** They are cluttered within the SVN- JE will move them all to a new SVN repository- ''Done''

			* New link to SVN repo: http://palea.cgrb.oregonstate.edu/viewsvn/associations/

	** Keep association files on SVN, but keep them alone, not mixed with things that have migrated to Github.		** Keep association files on SVN, but keep them alone, not mixed with things that have migrated to Github.

Cooperl: /* Mapping between Crop Ontologies and the Ref Ontologies: */

2015-08-28T19:36:22Z

Mapping between Crop Ontologies and the Ref Ontologies:

← Older revision		Revision as of 19:36, 28 August 2015
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	* Pankaj: Ideal goal is to have a tool available for the workflow by the curators		* Pankaj: Ideal goal is to have a tool available for the workflow by the curators
	** Suggestion ~~to each~~ run a common panel of files through and compare the results- e.g. rice and maize		** Suggestion: Each run a common panel of files through and compare the results- e.g. wheat, rice and maize

	''LC: Need to get the most recent version of the CO ~~file~~- Updated TT version 5. Wheat is on the GH repository, MAL and Leo will add rest''		''LC: Need to get the most recent version of the CO files- Updated TT version 5. Wheat is on the GH repository, MAL and Leo will add rest''

	* Goal is to map back to reference ontologies (TO) through the XPs. If the terms are composed in the XPs then we are able to generate the mapping automatically.		* Goal is to map back to reference ontologies (TO) through the XPs. If the terms are composed in the XPs then we are able to generate the mapping automatically.

Cooperl: /* Updates from Bioversity: Marie-Angelique */

2015-08-28T19:34:34Z

Updates from Bioversity: Marie-Angelique

← Older revision		Revision as of 19:34, 28 August 2015
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	* New version of the TT has more information than the older version		* New version of the TT has more information than the older version

	* From CM: Prospective mapping is better than retrospective mapping- by creating logical definitions		* From CM: Prospective mapping is better than retrospective mapping- by creating logical definitions- ''All agree!''
	* It would be good to work with CM to develop a workflow, power comes from the cross products		* It would be good to work with CM to develop a workflow, power comes from the cross products
	* Will review the workflow at the next ontology call		* Will review the workflow at the next ontology call

Cooperl: /* Other items: */

2015-08-28T19:33:08Z

Other items:

← Older revision		Revision as of 19:33, 28 August 2015
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	=== Other items:===		=== Other items:===
	* GG and JD could show their data structure at a future meeting- When, next all hands ~~meeeting~~		* GG and JD could show their data structure at a future meeting- When? Could be on next all hands meeting

	* Chris could demo update of new AmiGO curation NGS Annotation for the GO annotation with pathway curation, possibly in the next week		* Chris could demo update of new AmiGO curation NGS Annotation for the GO annotation with pathway curation, possibly in the next week

Cooperl: /* Roots, Tubers, Banana Development (TRB) meeting in Montpellier: */

2015-08-28T16:34:08Z

Roots, Tubers, Banana Development (TRB) meeting in Montpellier:

← Older revision		Revision as of 16:34, 28 August 2015
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	* Cassava has been uploaded, but it is not the up to date version, still needs to be finalized and now has a Read-Me file		* Cassava has been uploaded, but it is not the up to date version, still needs to be finalized and now has a Read-Me file

	''Question: which of the CO species does this include? cassava, potato, banana, others? '' BTI only works so far on the Cassava ontology. The other RTB crops that will be used by BTI nextgen project, will be the Crop Ontologies (~~Sweat~~ Potato, Yam, Banana, Potato)		''Question: which of the CO species does this include? cassava, potato, banana, others?

			''BTI only works so far on the Cassava ontology. The other RTB crops that will be used by BTI nextgen project, will be the Crop Ontologies (Sweet Potato, Yam, Banana, Potato)

	== C. Update from IT group- Data Store, AmiGO2- Justin Elser==		== C. Update from IT group- Data Store, AmiGO2- Justin Elser==

Cooperl: /* Mapping between Crop Ontologies and the Ref Ontologies: */

2015-08-28T16:33:22Z

Mapping between Crop Ontologies and the Ref Ontologies:

← Older revision		Revision as of 16:33, 28 August 2015
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	* Will review the workflow at the next ontology call		* Will review the workflow at the next ontology call

	''Ask CM to show us the mapping tool and if he has a more up to date version of the XP file, the one on the SVN is quite old''		''LC: Ask CM to show us the mapping tool and if he has a more up to date version of the XP file, the one on the SVN is quite old''

	* Pankaj: Ideal goal is to have a tool available for the workflow by the curators		* Pankaj: Ideal goal is to have a tool available for the workflow by the curators
	** Suggestion to each run a common panel of files through and compare the results- e.g. rice and maize		** Suggestion to each run a common panel of files through and compare the results- e.g. rice and maize
	''Need to get the most recent version of the CO file- Updated TT version 5. ~~Are these~~ on the GH repository?''
	* Goal is to map back to reference ontologies through the XPs. If the terms are composed in the XPs then we are		''LC: Need to get the most recent version of the CO file- Updated TT version 5. Wheat is on the GH repository, MAL and Leo will add rest''
	* Suggestion: A Term Genie instance for the generation of the terms for the CO vocabs.
			* Goal is to map back to reference ontologies (TO) through the XPs. If the terms are composed in the XPs then we are able to generate the mapping automatically.

			* PJ: Suggestion: A Term Genie instance for the generation of the terms for the CO vocabs.
			** Issue is that the terms must be in the ref ontologies
			** This would be only be helpful if it generates the XP- need to review TG

	* MAL will share her slides to illustrate, that were presented for the RTB meeting.		* MAL will share her slides to illustrate, that were presented for the RTB meeting.

Cooperl: /* Updates from Bioversity: Marie-Angelique */

2015-08-28T16:22:59Z

Updates from Bioversity: Marie-Angelique

← Older revision		Revision as of 16:22, 28 August 2015
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	* wheat, rice, cassava, soybean, groundnut, chickpea, lentil, cowpea, pigeon pea		* wheat, rice, cassava, soybean, groundnut, chickpea, lentil, cowpea, pigeon pea

			*'' Wheat TT5 uploaded 8-28. Need to look at a script to convert cleanly to csv or tsv.''

	====Mapping between Crop Ontologies and the Ref Ontologies:====		====Mapping between Crop Ontologies and the Ref Ontologies:====
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	* MAL has tried tools, CM has tools, need to find out what tool works best		* MAL has tried tools, CM has tools, need to find out what tool works best
	* New version of the TT has more information		* New version of the TT has more information than the older version

	* From CM: Prospective mapping is better than retrospective mapping- by creating logical definitions		* From CM: Prospective mapping is better than retrospective mapping- by creating logical definitions

Cooperl: /* Mapping between Crop Ontologies and the Ref Ontologies: */

2015-08-28T16:12:30Z

Mapping between Crop Ontologies and the Ref Ontologies:

← Older revision		Revision as of 16:12, 28 August 2015
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	''For details of the mapping algorithm- see the Ontology working group meeting June 21st''		''For details of the mapping algorithm- see the Ontology working group meeting June 21st''

	* Need to check on which of the files have been updated... ''not sure what this is referring to''		* The CO vocabs are being revised to include fields in TT spreadsheet for the entity and attribute

	* The CO vocabs are being revised to include fields in TT spreadsheet for the ~~enttiy~~ and attribute
	* Mappings will be added as they are developed, based on the E + A		* Mappings will be added as they are developed, based on the E + A

Cooperl: /* Updates from Bioversity: Marie-Angelique */

2015-08-28T16:10:59Z

Updates from Bioversity: Marie-Angelique

← Older revision		Revision as of 16:10, 28 August 2015
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	* Crop Ontology webpage: http://www.cropontology.org/		* Crop Ontology webpage: http://www.cropontology.org/
	** Curation efforts have been going on during the summer to update them to the new Trait Template Ver. 5		** Curation efforts have been going on during the summer to update them to the new Trait Template Ver. 5
	** Nine of the CO vocabs are done- will be uploaded - ''Where, to the CO site or to GH??'' We are planning to upload the curated ontologies on both Github (probably the rdf version, maybe the Excel Template even if changes cannot be tracked) and CO website.		** Nine of the CO vocabs are done- will be uploaded -
			* ''Where, to the CO site or to GH??'' We are planning to upload the curated ontologies on both Github (probably the rdf version, maybe the Excel Template even if changes cannot be tracked) and CO website.

			* wheat, rice, cassava, soybean, groundnut, chickpea, lentil, cowpea, pigeon pea

	====Mapping between Crop Ontologies and the Ref Ontologies:====		====Mapping between Crop Ontologies and the Ref Ontologies:====

Marieangelique.laporte: /* Updates from Bioversity: Marie-Angelique */

2015-08-27T08:29:53Z

Updates from Bioversity: Marie-Angelique

← Older revision		Revision as of 08:29, 27 August 2015
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	* Crop Ontology webpage: http://www.cropontology.org/		* Crop Ontology webpage: http://www.cropontology.org/
	** Curation efforts have been going on during the summer to update them to the new Trait Template Ver. 5		** Curation efforts have been going on during the summer to update them to the new Trait Template Ver. 5
	** ~~Twelve~~ of the CO vocabs are done- will be uploaded - ''Where, to the CO site or to GH??''		** Nine of the CO vocabs are done- will be uploaded - ''Where, to the CO site or to GH??'' We are planning to upload the curated ontologies on both Github (probably the rdf version, maybe the Excel Template even if changes cannot be tracked) and CO website.

	====Mapping between Crop Ontologies and the Ref Ontologies:====		====Mapping between Crop Ontologies and the Ref Ontologies:====