Oct 5th, 2017 Ontology Working Group Meeting - Revision history

Cooperl: /* Planteome Ontology WG Zoom Meeting */

2017-10-05T19:27:59Z

Planteome Ontology WG Zoom Meeting

← Older revision		Revision as of 19:27, 5 October 2017
Line 5:		Line 5:

	* Meeting Recordings:		* Meeting Recordings:
	**		** [[File:Ontology WG Meeting 10-5-17 audio only.m4a\|thumb\|Ontology WG Meeting 10-5-17 audio]]
	**		** [[File:Ontology WG Meeting video 10-5-17.mp4\|thumb\|Ontology WG Meeting video 10-5-17]]

	=Agenda and Notes=		=Agenda and Notes=

Cooperl: /* Agenda */

2017-10-05T19:20:58Z

Agenda

← Older revision		Revision as of 19:20, 5 October 2017
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	**		**

	=Agenda=		=Agenda and Notes=
	PJ		PJ
	* Applying for no cost extension, should be planning to start applying for renewal by spring		* Applying for no cost extension, should be planning to start applying for renewal by spring
Line 27:		Line 27:

	EA		EA
	phenotyping platforms, automating annotations		* phenotyping platforms, automating annotations
	MIAPPE meeting, concern about having ontology terms for the environment and experimental conditions		* MIAPPE meeting, concern about having ontology terms for the environment and experimental conditions
			* Setting up collaboration with groups doing High Throughput Phenotyping
			** French group at Agropolis in Montpellier
			** John Doonan
			** PODD- Australian group
			* Invite them to one of our calls

	~~Setting up collaboration with groups doing High Throughput Phenotyping~~
	~~French group at Agropolis in Montpellier~~
	~~John Doonan~~
	~~PODD- Australian group~~
	~~Invite them to one of our calls~~
	GG: - most of the data is proprietary		GG: - most of the data is proprietary
	Can we partner with them? Use the data/images with the sources removed, feed back to them?		* Can we partner with them? Use the data/images with the sources removed, feed back to them?
	Find phenotypic features		* Find phenotypic features
	Machine learning as an approach		* Machine learning as an approach

	PJ: Set up separate call with George and John to see what we can get working on		PJ: Set up separate call with George and John to see what we can get working on
	Need the data		* Need the data
	Also would like to have Bjorn Usadel come to one of our meetings		* Also would like to have Bjorn Usadel come to one of our meetings

	EA:		EA:
	HTP work going on at IRRI and other sites, that data may be more available		* HTP work going on at IRRI and other sites, that data may be more available
	Will work on setting up a conf call with the folks French group at Agropolis in Montpellier		* Will work on setting up a conf call with the folks French group at Agropolis in Montpellier



	MAL:		MAL:
	Breeding API		* Breeding API
	Mapping CO to TO will facilitate finding the data		* Mapping CO to TO will facilitate finding the data
	Next two CO vocabs are groundnut and Musa		* Next two CO vocabs are groundnut and Musa
	Working with Ethy Cannon on traits from PeanutBase, follow up with Steve Cannnon as well		* Working with Ethy Cannon on traits from PeanutBase, follow up with Steve Cannnon as well
	Do we have any peanut data?- Not at this time		* Do we have any peanut data?- Not at this time

	PJ: demo of the Ontology Enrichment Tool http://planteome.org/oat/		PJ: demo of the Ontology Enrichment Tool http://planteome.org/oat/
	Demo of the tool,		* Demo of the tool,
	test with the input gene example sets available from the bottom right hand side of the gene list box. Or add your own gene IDs from another species to test.		* test with the input gene example sets available from the bottom right hand side of the gene list box. Or add your own gene IDs from another species to test.
	Similar to AgriGO, but revised the methods		* Similar to AgriGO, but revised the methods

	Collaboration with software development company Sanmita		* Collaboration with software development company Sanmita
	Developing the ability to edit genes, add info etc		* Developing the ability to edit genes, add info etc
	May be able to merge with Noctua at some point in the future		* May be able to merge with Noctua at some point in the future
	Community engagement portal		* Community engagement portal

	AM: Update on OoPS		AM: Update on OoPS
	Samara scrape for APS and germplasm		* Samara scrape for APS and germplasm
	GRIN descriptors converted to gaf files		* GRIN descriptors converted to gaf files
	Mapping files,		* Mapping files,
	Using INCA tool -https://planteome.github.io/planteome-inca-form		* Using INCA tool -https://planteome.github.io/planteome-inca-form
	Some steps need to be done manually- like pushing to GH		* Some steps need to be done manually- like pushing to GH
	Plant disease patterns, issues with names that are obtained from script		* Plant disease patterns, issues with names that are obtained from script
	Probably need to have meeting with Dan Keith and CM to see what needs to be done on the INCA tool to get it configured		* Probably need to have meeting with Dan Keith and CM to see what needs to be done on the INCA tool to get it configured
	Scrape of diseases had about 11,000 lines, narrowed down to about 7000 as there are redundancies		* Scrape of diseases had about 11,000 lines, narrowed down to about 7000 as there are redundancies
	GG interested in doing text mining on the data set, or maybe a test set		* GG interested in doing text mining on the data set, or maybe a test set
	MAL- Crop dictionaries may also be helpful		* MAL- Crop dictionaries may also be helpful

	LC:		LC:
	NAR paper in review		* NAR paper in review
	Collaboration with Hong Cui and James Macklin- they have digitized the flora of North America descriptions		* Collaboration with Hong Cui and James Macklin- they have digitized the flora of North America descriptions
	Working on TO and PECO revisions		* Working on TO and PECO revisions

Cooperl: /* Agenda */

2017-10-05T19:17:27Z

Agenda

← Older revision		Revision as of 19:17, 5 October 2017
Line 9:		Line 9:

	=Agenda=		=Agenda=
			PJ
			* Applying for no cost extension, should be planning to start applying for renewal by spring
			* Ideally should include people who may have their own sources of funding
			* Planning for a database release by Dec 15th, in advance of PAG 2018
			* Metadata annotations automated,
			* Neural network approach
			* Using the images- recognition of leaf, flower, stem- ~ 60% accuracy
			* Need to bring in engineering/computing folks, people doing high throughput phenotyping

			GG
			* Working to develop Plant PhenomeNet further, but need a good source of annotated data
			* Qualities vs values in the data annotations
			* New person hired…
			* Luke Slater working on AberOwl
			* Also focusing on updating PATO
			* How to convert quantitative data to qualitative data??

			EA
			phenotyping platforms, automating annotations
			MIAPPE meeting, concern about having ontology terms for the environment and experimental conditions

			Setting up collaboration with groups doing High Throughput Phenotyping
			French group at Agropolis in Montpellier
			John Doonan
			PODD- Australian group
			Invite them to one of our calls
			GG: - most of the data is proprietary
			Can we partner with them? Use the data/images with the sources removed, feed back to them?
			Find phenotypic features
			Machine learning as an approach

			PJ: Set up separate call with George and John to see what we can get working on
			Need the data
			Also would like to have Bjorn Usadel come to one of our meetings

			EA:
			HTP work going on at IRRI and other sites, that data may be more available
			Will work on setting up a conf call with the folks French group at Agropolis in Montpellier



			MAL:
			Breeding API
			Mapping CO to TO will facilitate finding the data
			Next two CO vocabs are groundnut and Musa
			Working with Ethy Cannon on traits from PeanutBase, follow up with Steve Cannnon as well
			Do we have any peanut data?- Not at this time

			PJ: demo of the Ontology Enrichment Tool http://planteome.org/oat/
			Demo of the tool,
			test with the input gene example sets available from the bottom right hand side of the gene list box. Or add your own gene IDs from another species to test.
			Similar to AgriGO, but revised the methods

			Collaboration with software development company Sanmita
			Developing the ability to edit genes, add info etc
			May be able to merge with Noctua at some point in the future
			Community engagement portal

			AM: Update on OoPS
			Samara scrape for APS and germplasm
			GRIN descriptors converted to gaf files
			Mapping files,
			Using INCA tool -https://planteome.github.io/planteome-inca-form
			Some steps need to be done manually- like pushing to GH
			Plant disease patterns, issues with names that are obtained from script
			Probably need to have meeting with Dan Keith and CM to see what needs to be done on the INCA tool to get it configured
			Scrape of diseases had about 11,000 lines, narrowed down to about 7000 as there are redundancies
			GG interested in doing text mining on the data set, or maybe a test set
			MAL- Crop dictionaries may also be helpful

			LC:
			NAR paper in review
			Collaboration with Hong Cui and James Macklin- they have digitized the flora of North America descriptions
			Working on TO and PECO revisions

Cooperl: /* Planteome Ontology WG Zoom Meeting */

2017-10-05T19:15:53Z

Planteome Ontology WG Zoom Meeting

← Older revision		Revision as of 19:15, 5 October 2017
Line 3:		Line 3:
	* Time: 8:15am PDT (GMT-7)		* Time: 8:15am PDT (GMT-7)

	*
	* Meeting Recordings:		* Meeting Recordings:
	** ~~[[File:Ontology WG Meeting audio 5-9-17.m4a\|thumb\|Ontology WG Meeting audio 5-9-17]]~~		**
	** ~~[[File:Ontology WG Meeting video 5-9-17.mp4\|thumb\|Ontology WG Meeting video 5-9-17]]~~		**


	=Agenda=		=Agenda=

Cooperl: Created page with "=Planteome Ontology WG Zoom Meeting= * Date: Thursday Oct 5th, 2017 * Time: 8:15am PDT (GMT-7) * * Meeting Recordings: ** File:Ontology WG Meeting audio 5-9-17.m4a|thumb|O..."

2017-10-05T19:15:24Z

Created page with "=Planteome Ontology WG Zoom Meeting= * Date: Thursday Oct 5th, 2017 * Time: 8:15am PDT (GMT-7) * * Meeting Recordings: ** File:Ontology WG Meeting audio 5-9-17.m4a|thumb|O..."

New page

=Planteome Ontology WG Zoom Meeting=
* Date: Thursday Oct 5th, 2017
* Time: 8:15am PDT (GMT-7)

*
* Meeting Recordings:
** [[File:Ontology WG Meeting audio 5-9-17.m4a|thumb|Ontology WG Meeting audio 5-9-17]]
** [[File:Ontology WG Meeting video 5-9-17.mp4|thumb|Ontology WG Meeting video 5-9-17]]

=Agenda=