Ontology Working Group Meeting, Tuesday April 28th, 2015: Difference between revisions
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* [[File:Ontology WG 4-28-15 video.mp4|thumb|Ontology WG 4-28-15 video]] | * [[File:Ontology WG 4-28-15 video.mp4|thumb|Ontology WG 4-28-15 video]] | ||
Who: LC, PJ, EA, LV, CM, DWS | Who: LC, PJ, EA, LV, CM, DWS | ||
== Updates from CO team== | |||
* LV has been progressing on several crop trait dictionaries, working with the plant breeders: | * LV has been progressing on several crop trait dictionaries, working with the plant breeders: | ||
** cowpea TD - discussing with the users, waiting for feedback | ** cowpea TD - discussing with the users, waiting for feedback | ||
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* BMS is being tested for use at CIMMYT, new initiative, integrated with the | * BMS is being tested for use at CIMMYT, new initiative, integrated with the | ||
==GRIN Global System == | |||
* Also, CIMMYT is implementing the GRIN Global system: [https://npgsweb.ars-grin.gov/gringlobal/descriptors.aspx]- the USDA system for tracking and cataloging germplasm, been deployed for past 2 years | * Also, CIMMYT is implementing the GRIN Global system: [https://npgsweb.ars-grin.gov/gringlobal/descriptors.aspx]- the USDA system for tracking and cataloging germplasm, been deployed for past 2 years | ||
* GRIN Global- Peter Brettling, developer Peter ? | * GRIN Global- Peter Brettling, developer Peter ? | ||
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* Would be good to have the Planteome ontologies integrated into the GRIN Global system | * Would be good to have the Planteome ontologies integrated into the GRIN Global system | ||
==Data Harmonization Workshop, DC May 11-15th== | |||
* Pankaj will attend: [http://www.agmip.org/events/data-harmonization-workshop/] | * Pankaj will attend: [http://www.agmip.org/events/data-harmonization-workshop/] | ||
* Organizer: Cheryl Porter ([http://www.agmip.org/ AgMIP]) | * Organizer: Cheryl Porter ([http://www.agmip.org/ AgMIP]) | ||
* Has been working with EA on the variables for crop modeling, would be good to have the Planteome ontologies integrated into the AgMIP variables | * Has been working with EA on the variables for crop modeling, would be good to have the Planteome ontologies integrated into the AgMIP variables | ||
==DivSeek Update== | |||
* EA elected to the Steering Committee. | * EA elected to the Steering Committee. | ||
* One of the main focuses will be data standards, information management | * One of the main focuses will be data standards, information management | ||
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* Ruth Bastow will be taking part as well | * Ruth Bastow will be taking part as well | ||
== Updates from OSU- Positions== | |||
* Curator position: Interviews starting this week | * Curator position: Interviews starting this week | ||
* CM offering to assist reviewing candidates | * CM offering to assist reviewing candidates | ||
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* Possible candidate will | * Possible candidate will | ||
==Progress on transition to Github== | |||
* See: https://github.com/Planteome | * See: https://github.com/Planteome | ||
* created repos for CGIAR rice, maize, wheat and cassava | * created repos for CGIAR rice, maize, wheat and cassava | ||
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* Where to link the CO trait definitions to? - mapped to Gramene right now. Need annotations | * Where to link the CO trait definitions to? - mapped to Gramene right now. Need annotations | ||
==Updates on Amigo 2.0== | |||
See link: [http://dev.planteome.org dev.planteome.org] | See link: [http://dev.planteome.org dev.planteome.org] | ||
Tabled for next meeting: | Tabled for next meeting: | ||
=== Next meeting date May 12th | == Possible working meeting in Montpellier July 1,2?== | ||
== Next meeting date May 12th== | |||
* PJ will be in DC, EA? | * PJ will be in DC, EA? | ||
Revision as of 22:10, 28 April 2015
Planteome Ontology Working Group Meeting
- Time: Apr 28, 2015 8:30 AM (GMT-7:00) Pacific Time (US and Canada)
- Connection: Join from PC, Mac, iOS or Android: https://zoom.us/j/666739728
Who: LC, PJ, EA, LV, CM, DWS
Updates from CO team
- LV has been progressing on several crop trait dictionaries, working with the plant breeders:
- cowpea TD - discussing with the users, waiting for feedback
- pigeon pea TD- Training was done with the breeders at the BMS, requested more traits, added 12 new, submitted revisions to Preasad, then it will be uploaded. Done offline, via email and dropbox
- rice- no news from RH
Note: Discussion of the workflow: Working with Julian Pietragalla, Technical Support Officer of the BMS ([1]). Julian is at CIMMYT, deals with the data standards for the BMS.
- EA and LV are going to CIMMYT for all next week (May 3-8th?) to meet with the BMS folks and make revisions to the Trait Dictionaries. All the crops are on the list, wheat, maize, the legumes, etc
- Also will be working on better guidelines to fill in the TDs
PJ Question: Are there already vocabularies in place to annotate the germplasm/GWAS datasets, etc? Is there a list of traits that we can get to match with the TDs and the ref TO?. CIMMYT researchers are part of TCAP/maizeCAP projects? How can we address the needs for the top priority traits that are needed.
- Link to Crop Information & Genomics page
- Genebank staff will be gone, will be meeting with Rosemanry and Kate: their role is the harmonization of the metadata
- BMS is being tested for use at CIMMYT, new initiative, integrated with the
GRIN Global System
- Also, CIMMYT is implementing the GRIN Global system: [2]- the USDA system for tracking and cataloging germplasm, been deployed for past 2 years
- GRIN Global- Peter Brettling, developer Peter ?
- You can search for the descriptors for the different plant species: [3]
- Would be good to have the Planteome ontologies integrated into the GRIN Global system
Data Harmonization Workshop, DC May 11-15th
- Pankaj will attend: [4]
- Organizer: Cheryl Porter (AgMIP)
- Has been working with EA on the variables for crop modeling, would be good to have the Planteome ontologies integrated into the AgMIP variables
DivSeek Update
- EA elected to the Steering Committee.
- One of the main focuses will be data standards, information management
- They are aware of the Planteome ontologies,
- Ruth Bastow will be taking part as well
Updates from OSU- Positions
- Curator position: Interviews starting this week
- CM offering to assist reviewing candidates
- Software developer position under review, probably will start interviews mid-May
- Possible candidate will
Progress on transition to Github
- See: https://github.com/Planteome
- created repos for CGIAR rice, maize, wheat and cassava
- Will remove from SVN
- Where to link the CO trait definitions to? - mapped to Gramene right now. Need annotations
Updates on Amigo 2.0
See link: dev.planteome.org Tabled for next meeting:
Possible working meeting in Montpellier July 1,2?
Next meeting date May 12th
- PJ will be in DC, EA?