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== | |||
EA upcoming travel in May: | |||
* 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 | ||
** pigeon pea TD- Training was done with the breeders at the [https://www.integratedbreeding.net/15/breeding-management-system BMS], requested more traits, added 12 new | ** pigeon pea TD- Training was done with the breeders at the [https://www.integratedbreeding.net/15/breeding-management-system 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 ([https://www.integratedbreeding.net/8/about-us/governance-management]). Julian is at CIMMYT, deals with the data standards for the BMS. | Note: Discussion of the workflow: Working with Julian Pietragalla, Technical Support Officer of the BMS ([https://www.integratedbreeding.net/8/about-us/governance-management]). Julian is at CIMMYT, deals with the data standards for the BMS. | ||
* EA and LV are going to CIMMYT for all next week 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 | * 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 | * 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 [https://www.integratedbreeding.net/132/communities/genomics-crop-info/crop-information Crop Information & Genomics page] | |||
* Genebank staff will be gone, will be meeting with Rosemary 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: [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 ? | |||
** You can search for the descriptors for the different plant species: [https://npgsweb.ars-grin.gov/gringlobal/descriptors.aspx] | |||
* Would be good to have the Planteome ontologies integrated into the GRIN Global system | |||
[[File:Grin Global descriptors.png|thumbnail|Example of Grin Global descriptors for wheat]] | |||
==Data Harmonization Workshop, DC May 11-15th== | |||
* Pankaj will attend [http://www.agmip.org/events/data-harmonization-workshop/] | |||
* Organizer: Cheryl Porter ([http://www.agmip.org/AgMIP 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 | * Curator position: Interviews starting this week | ||
* CM offering to assist reviewing candidates | |||
* Software developer position under review, probably will start interviews mid-May | |||
==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- may need to revise names | ||
* Will remove from SVN | * Will remove from SVN | ||
==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: | |||
== Possible working meeting in Montpellier July 1,2?== | |||
== Next meeting date May 12th== | |||
* PJ will be in DC, EA? |
Latest revision as of 19:45, 7 May 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
EA upcoming travel in May:
- 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 Rosemary 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
Progress on transition to Github
- See: https://github.com/Planteome
- created repos for CGIAR rice, maize, wheat and cassava- may need to revise names
- Will remove from SVN
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?