Description:

Genetic variation data is an important data type, but consistency across datasets is poor. This group will assess current variation standards, discuss challenges from improving reference genomes and emerging pan-genomes, as well as the adoption of persistent standard identifiers in agricultural research.

With the loss of NCBI’s dbSNP for non-human data the challenge of adopting standard identifiers for genetic variants has increased. Fortunately, the EBI European Variation Archive (EVA) accepts non-human data, and hence -at present- it is the most reasonable long-term repository for agricultural variation data. This working group aims to address coordination and access of genetic variation through the EVA; establish recommendations, best practices and resources to submit genetic variation to the EVA repository.

 

Main goals:

  1. Survey the community on existing and anticipated genetic variation data sets.

  2. Survey the community on the need for genetic variation.

  3. Review existing software for calling genetic variation.

  4. Recommendation on standards for samples nomenclature metadata accompanying VCF files (genetic variation data) review across different species. 

  5. Develop a plan to disseminate the recommended standards using existing resources (or write a newly expanded user guide).

  6. Training community members on best practices.

  7. Apply the concept with a minimum of 5 new submissions to the EVA. 

  8. Write a report on the four activities (2-5 above).

  9. Documentation on outcomes of targets above.  Potential for contributions to the whitepaper, based on outcomes.

 

Time a member dedicates to this working group on average (including meetings and assigned tasks):
 

  • Minimum 2 hours per month to attend a monthly meeting. 

  • Up to 6 extra hours if participating in specifically targeted meetings (e.g., biocuration, survey, documentation, review of workflows meetings). 
     

Benefits of joining this working group:
 

  • Professional development; 

  • Learning new resources; 

  • Developing a community of best practices;

  • Networking with others; 

  • Developing partnerships for future funding opportunities;  

  • Education/training experience; 

  • Potential authorship in reporting out, representation at meetings, and consulting.

 

 

Chair: Marcela Karey Tello-Ruiz

Co-Chair: Timothee Cezard

Members:

  • Alexey Sokolov
  • Andria Harkey
  • Doreen Ware
  • Emily Grau
  • Jill Bushakra
  • Jodi Humann
  • Kazim Wazir
  • Kelly Vining
  • Marcela K. Tello-Ruiz
  • Maria Skrabisova
  • Mazdak Salavati
  • Melanie Harrison
  • Moira Sheehan
  • Nahla Bassil
  • Nicholas Gladman
  • Osman Gutierrez
  • Raja Nandety
  • Rajdeep Singh Khangura
  • Rex Nelson
  • Sarah Dyer
  • Sebastian Beier
  • Sharon Wei
  • Shaun Clare
  • Timothee Cezard
  • Yogendra Khedikar
  • Victoria DeLeo
  • Vivek Kumar

 

Deliverables:

 

Meeting Schedule: Please contact us for more details.

For more information, please email agbiodata@gmail.com.

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