May 24th, 2016 Ontology Working Group Meeting - Revision history

Cooperl: /* Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop */

2017-02-07T21:57:20Z

Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop

← Older revision		Revision as of 21:57, 7 February 2017
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	===Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop===		===Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop===
	* '' 9 participants, 7 crop species:''		* '' 9 participants, 7 crop species:''
	* Nordine El- Hassouni - CIRAD - rice		** Nordine El- Hassouni - CIRAD - rice
	** Trushar Shah- IITA, Kenya - cassava, cowpea, and banana		** Trushar Shah- IITA, Kenya - cassava, cowpea, and banana
	** Jeffery Detras - IRRI - rice		** Jeffery Detras - IRRI - rice

Cooperl: /* 1. Update from PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France */

2016-05-24T19:24:53Z

1. Update from PhenoHarmonIS 2016, May 9th-13th, 2016; Montpellier, France

← Older revision		Revision as of 19:24, 24 May 2016
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	* ''PJ offered to talk to Leo about options if he is interested''		* ''PJ offered to talk to Leo about options if he is interested''

	* Weds afternoon- Visit to https://www6.montpellier.inra.fr/lepse_eng/M3P/PHENOARCH-platform		* '''Weds afternoon- Visit to https://www6.montpellier.inra.fr/lepse_eng/M3P/PHENOARCH-platform'''
	** High throughput phenotyping platform		** High throughput phenotyping platform, rotate through different crop experiments
			** Pascal's database,
			** should try to access the list of evaluation data and the traits
			** Analyzed final data, to test on
			** how to address HTP phenotyping experiments?
			** Follow-up with Astrid Junker, list of traits? :
			** Francois Tardieu - leader at PhenoArch- LC will contact


	===Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop===		===Thursday afternoon: Hands-on Session (2.5 hours)-AM, LC: "Planteome: Bring Your Own Data Annotation Mini-Workshop===
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	** Ashley DuVal - Mars, Inc USA - cacao		** Ashley DuVal - Mars, Inc USA - cacao
	** Anthony Bolger - RWTH Aachen University - Institute for Biology 1, Germany		** Anthony Bolger - RWTH Aachen University - Institute for Biology 1, Germany
	** Astrid Junker - IPK Gatersleben, Germany - HTP phenotyping		** Astrid Junker - IPK Gatersleben, Germany - HTP phenotyping
	* '' Outcomes: ''		* '' Outcomes: ''
	** No matter how hard you try to streamline the process, the uniqueness of people's data will continue to require expert intervention.		** No matter how hard you try to streamline the process, the uniqueness of people's data will continue to require expert intervention.

Cooperl: /* Planteome Presentations: */

2016-05-24T19:19:10Z

Planteome Presentations:

← Older revision		Revision as of 19:19, 24 May 2016
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	''Leo is leaving the project as of May 30th- lack of funds and moving on to other things''		''Leo is leaving the project as of May 30th- lack of funds and moving on to other things''
	** Leo working on the guide lines for the TDs		* Leo working on the guide lines for the TDs
	** ''Who will Continue work on TD, or is it dying?- Julian taking a few crops over,		* ''Who will Continue work on TD, or is it dying?- Julian taking a few crops over,
	** ''EA, and MAL will be working on the remainder in their free time.		* ''EA, and MAL will be working on the remainder in their free time.
	** ''EA wants to hire someone new, but no funds, is applying for several grants. Agroportal has no funding ''.		* ''EA wants to hire someone new, but no funds, is applying for several grants. Agroportal has no funding ''.
	** H2020 program not too secure funding		* H2020 program not too secure funding
	** Genticin (??) Platform more reliable		* Genticin (??) Platform more reliable
	** ''PJ offered to talk to Leo about options if he is interested''		* ''PJ offered to talk to Leo about options if he is interested''

	* Weds afternoon- Visit to https://www6.montpellier.inra.fr/lepse_eng/M3P/PHENOARCH-platform		* Weds afternoon- Visit to https://www6.montpellier.inra.fr/lepse_eng/M3P/PHENOARCH-platform

Cooperl: /* Planteome Presentations: */

2016-05-24T19:18:52Z

Planteome Presentations:

← Older revision		Revision as of 19:18, 24 May 2016
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	** Wheat TD version #5 was uploaded just prior to the PhenoHarmonis meeting (to where?)		** Wheat TD version #5 was uploaded just prior to the PhenoHarmonis meeting (to where?)
	** Rosemary shared the validated mappings duringt he workshop, so MAL will be able to upload onto the Planteome Github		** Rosemary shared the validated mappings duringt he workshop, so MAL will be able to upload onto the Planteome Github
			** Rice almost done
			** Reinhard is almost done with the TDs for the potato, sweet potato

	''Leo is leaving the project as of May 30th- lack of funds and moving on to other things''		''Leo is leaving the project as of May 30th- lack of funds and moving on to other things''
			** Leo working on the guide lines for the TDs
	** ''Who will Continue work on TD, or is it dying?- Julian taking a few crops over,		** ''Who will Continue work on TD, or is it dying?- Julian taking a few crops over,
	** ''EA, and MAL will be working on the remainder in their free time.		** ''EA, and MAL will be working on the remainder in their free time.
	** ''EA wants to hire someone new, but no funds, is applying for several grants''		** ''EA wants to hire someone new, but no funds, is applying for several grants. Agroportal has no funding ''.
			** H2020 program not too secure funding
			** Genticin (??) Platform more reliable
	** ''PJ offered to talk to Leo about options if he is interested''		** ''PJ offered to talk to Leo about options if he is interested''

Cooperl: /* Planteome Presentations: */

2016-05-24T19:14:38Z

Planteome Presentations:

← Older revision		Revision as of 19:14, 24 May 2016
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	* '''Tuesday afternoon: Hands-on Session (2.5 hours)- LV:'''		* '''Tuesday afternoon: Hands-on Session (2.5 hours)- LV:'''
	** Progressing on the Trait Dictionaries: Groups: Tree species (cacao), Musa, barley~~, wheat, rice~~, sorghum, potato, sweet potato, yam		** Progressing on the Trait Dictionaries: Groups: wheat, rice, maize, Tree species (cacao), Musa, barley, sorghum, potato, sweet potato, yam
	** Feedback on the TD template		** Feedback on the TD template

Cooperl: /* Planteome Presentations: */

2016-05-24T19:13:55Z

Planteome Presentations:

← Older revision		Revision as of 19:13, 24 May 2016
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	* Notes:		* Notes:
	** Wheat TD version #5 was uploaded just prior to the PhenoHarmonis meeting		** Wheat TD version #5 was uploaded just prior to the PhenoHarmonis meeting (to where?)
	** Rosemary shared the mappings		** Rosemary shared the validated mappings duringt he workshop, so MAL will be able to upload onto the Planteome Github

	''Leo is leaving the project as of May 30th- lack of funds and moving on to other things''		''Leo is leaving the project as of May 30th- lack of funds and moving on to other things''

Cooperl: /* Planteome Presentations: */

2016-05-24T19:12:33Z

Planteome Presentations:

← Older revision		Revision as of 19:12, 24 May 2016
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	* Tuesday afternoon: oral presentation (10 min)- MAL: "Ontology Mapping Techniques for traits"		* Tuesday afternoon: oral presentation (10 min)- MAL: "Ontology Mapping Techniques for traits"

	* Tuesday afternoon: Hands-on Session (2.5 hours)- LV:		* '''Tuesday afternoon: Hands-on Session (2.5 hours)- LV:'''
	** Progressing on the Trait Dictionaries: Groups: Tree species (cacao), Musa, barley, wheat, rice, sorghum, potato, sweet potato, yam		** Progressing on the Trait Dictionaries: Groups: Tree species (cacao), Musa, barley, wheat, rice, sorghum, potato, sweet potato, yam
	** Feedback on the TD template		** Feedback on the TD template

	* Notes:		* Notes:
	**''Leo is leaving the project as of May 30th- lack of funds and moving on to other things''		** Wheat TD version #5 was uploaded just prior to the PhenoHarmonis meeting
			** Rosemary shared the mappings

			''Leo is leaving the project as of May 30th- lack of funds and moving on to other things''
	** ''Who will Continue work on TD, or is it dying?- Julian taking a few crops over,		** ''Who will Continue work on TD, or is it dying?- Julian taking a few crops over,
	** ''EA, and MAL will be working on the remainder in their free time.		** ''EA, and MAL will be working on the remainder in their free time.

Cooperl: /* 3. Planning for Post-ICBO Curator Workshop */

2016-05-24T19:09:39Z

3. Planning for Post-ICBO Curator Workshop

← Older revision		Revision as of 19:09, 24 May 2016
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	* Who is interested in attending?- Ideally 5-6 people		* Who is interested in attending?- Ideally 5-6 people
	** Indian researcher has contacted - working to get TO terms added, rice gene annotations, PJ will send his info to LC		** Indian researcher has contacted - working to get TO terms added, rice gene annotations, PJ will send his info to LC
	** Target wheat and maize researchers, primarily from [http://www.cimmyt.org/ CIMMYT] ?, also rice
	*** [http://cropgenebank.sgrp.cgiar.org/index.php/crops-mainmenu-367/maize-mainmenu-361/characterization-mainmenu-377 CIMMYT/CGIAR Characterization of Maize Page]		* Target wheat and maize researchers, primarily from [http://www.cimmyt.org/ CIMMYT] ?, also rice
			** [http://cropgenebank.sgrp.cgiar.org/index.php/crops-mainmenu-367/maize-mainmenu-361/characterization-mainmenu-377 CIMMYT/CGIAR Characterization of Maize Page]
			* EA: Are you interested in genebank data or evaluation data? It is managed differently- starting with genebank data and can also work with evaluation data- different people- should discuss with Kate, CIMMYT will refer to the data managers, Kate could suggest a person from scientific team.

	* Focus on the people who are developing the TDs, annotations to germplasm, gene bank repositories, traits		* Focus on the people who are developing the TDs, annotations to germplasm, gene bank repositories, traits
	* Good to set the standards,		* Good to set the standards,
	** Julian Pietragalla- IBP, Mexico		** Julian Pietragalla- IBP, Mexico
	** Kate - maize data manager		** Kate - maize data manager, entry point to
	** Rosemary Shrestha - wheat data manager		** Rosemary Shrestha - wheat data manager
	** Need an additional wheat/Maize breeder- ask Julian??		** Need an additional wheat/Maize breeder- ask Julian??

			* Could also go through the Wheat IS to find people with data sets...

	==4.Planteome Ontology Updates==		==4.Planteome Ontology Updates==

Cooperl: /* 3. Planning for Post-ICBO Curator Workshop */

2016-05-24T19:03:56Z

3. Planning for Post-ICBO Curator Workshop

← Older revision		Revision as of 19:03, 24 May 2016
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	* Proposed Dates: Three days: Monday Aug 8th to Weds Aug 10th, (or possibly right before the ICBO mtg?), or maybe Friday May 5th to Sunday May 7th??		* Proposed Dates: Three days: Monday Aug 8th to Weds Aug 10th, (or possibly right before the ICBO mtg?), or maybe Friday May 5th to Sunday May 7th??
	** ''Lol out Sunday Aug 7th for family responsibilities''		** ''Lol out Sunday Aug 7th for family responsibilities''
			* If people come for the week of ICBO, are they able to stay for an additional 5 days to a week? BS: no, MAL: ?

	* People can come for the ICBO meeting and then stay for the plant-specific, more hand's on session		* People can come for the ICBO meeting and then stay for the plant-specific, more hand's on session

Cooperl: /* 3. Planning for Post-ICBO Curator Workshop */

2016-05-24T19:03:19Z

3. Planning for Post-ICBO Curator Workshop

← Older revision		Revision as of 19:03, 24 May 2016
Line 115:		Line 115:
	** Indian researcher has contacted - working to get TO terms added, rice gene annotations, PJ will send his info to LC		** Indian researcher has contacted - working to get TO terms added, rice gene annotations, PJ will send his info to LC
	** Target wheat and maize researchers, primarily from [http://www.cimmyt.org/ CIMMYT] ?, also rice		** Target wheat and maize researchers, primarily from [http://www.cimmyt.org/ CIMMYT] ?, also rice
	** ~~focus on the people who are developing the TDs, annotations to germplasm, gene bank repositories, traits~~		*** [http://cropgenebank.sgrp.cgiar.org/index.php/crops-mainmenu-367/maize-mainmenu-361/characterization-mainmenu-377 CIMMYT/CGIAR Characterization of Maize Page]
	** Good to set the standards,
	*** Julian Pietragalla- ~~IBP, Mexico~~
	*** Kate - maize ~~data manager~~
	*** Rosemary Shrestha - ~~wheat data manager~~
	*** Need an additional wheat/Maize ~~breeder- ask Julian??~~

	* If people ~~come for~~ the ~~week of ICBO~~, ~~are they able~~ to ~~stay for~~ an additional ~~5 days to a week~~?		* Focus on the people who are developing the TDs, annotations to germplasm, gene bank repositories, traits
			* Good to set the standards,
			** Julian Pietragalla- IBP, Mexico
			** Kate - maize data manager
			** Rosemary Shrestha - wheat data manager
			** Need an additional wheat/Maize breeder- ask Julian??

	==4.Planteome Ontology Updates==		==4.Planteome Ontology Updates==