Dear all,
The AgBioData Standards for Genetic Variation Working Group (SGV) is preparing a white paper to support the adoption of rsIDs for agriculture and seeks your valuable input and data to further our research efforts.
They invite the AgBioData community to join them on* July 18 at 11:00 ET *to review the material and *discuss collaboration opportunities*. In particular, the SGV is looking for the following information:
1. Genetic Markers Linked to Traits: -
A list of genetic markers associated with specific traits used by the breeding and research community across various agricultural species, including plants, animals, and insects. See an example here https://docs.google.com/spreadsheets/d/167DaYxbdKejoL0l6UhGqMPu-GbGsW6vIok7raZEf6HU/edit?usp=sharing . -
Information on the species and traits these markers are linked to and the methodologies/platforms employed for genotyping in your community. 2. Functional Validation and Fitness Outcomes: -
Examples of genetic variations that have been functionally validated, including descriptions of the phenotypic differences these variations lead to. -
Case studies or data demonstrating these genetic variations have resulted in measurable fitness outcomes for the species in question. -
Information on related publications and any supporting data available. -
We would like to request examples from each of the different species/database providers for review at the upcoming GV working group meeting in July. 3. Standards and Data Access for Genetic & Phenotypic Variation: FAIR/ Interoperability -
Standard formats for exchanging information, identifiers, formats, and controlled vocabulary on: - Germplasm - Genetic Variation - Phenotypes -
Types of views and files provided for data access. -
Future targets for operating, displaying, or providing access to these data types. -
Usage of rsIDs and potential barriers to their adoption in your resource. -
For more information on RSIDs, please look at the following document RefSNPs: Clustered Variants https://docs.google.com/document/d/1PHXqW7M50mE5SSl4Zprd904KCr9nWzSR4L8sx3UHa_0/edit
4. Collaboration Opportunities: -
Barriers encountered when working with these data types. -
Opportunities for collaboration or data standards, sharing, and interoperability.
We really appreciate your support and look forward to your positive response to the request for information in any of the four categories.
*If you are willing to participate or are interested in contributing to our initiative and would like to collaborate, please complete this form (https://forms.gle/jcjWnLibHEKuESJe6 https://forms.gle/jcjWnLibHEKuESJe6) by July 16. *We will follow up with you with the Zoom link and other resources.
Best,
The AgBioData Standards for Genetic Variation WG