Genetic & Genomic Data Session
Our ability to link genetic sequence information with physical voucher specimens and tissue samples is essential for several reasons, including ensuring scientific reproducibility and legality in genetic studies, enabling future re/use of data, and providing attribution to those institutions that maintain these collections. This listening session will explore operational mechanisms and infrastructure needs that will facilitate data integration in this realm and beyond with both major existing initiatives such as NCBI, BOLD, and iBOL, and efforts of existing specimen collections. Discussions will revolve around the data requirements for linking specimen and sequence information, the legal implications of FAIR digital sequence information, and how best to coordinate efforts across existing platforms to achieve the goal of FAIR, integrated data.
Date: June 26, 2024
Time: 11:00 AM – 1:00 PM EDT; 3:00 – 5:00 PM GMT
Facilitated by:
Breda Zimkus, Andrew Bentley, John Bates, Nimanthi Abeyrathna, Mike Lomas
Key Domain Representatives:
- Conrad Schoch, NCBI
- Kevin Kerr, Centre for Biodiversity Genomics, University of Guelph
Read the session summary.
Please share your thoughts on the questions listed below. Each question is posted as a separate comment. You may respond to a specific question by posting a ‘reply’ to that particular comment.
Q1. How do we ensure ‘connectivity’ among all the various databases linked to a specimen in the face of federal agency priorities, requirements, and infrastructure?
It occurs to me that there is a “social contract” element at play here where we are relying on the good nature of researchers to make the connection between sequences and specimens through the metadata they are entering into NCBI and others. This is a flawed system exacerbated by the fact that we as collections managers do not have access to the sequence records to update or correct them. As such I am wondering whether we need a brokering or intermediary system like GEOME or the eventual Digital Extended Specimen (DES) infrastructure to make the connections for us so that interested parties could access the broker to provide all information about the specimen, sequence an any other related information. This could be done in a semi-automated fashion using unique identifiers or could be human-mediated much like what collection managers have been doing up to now to make those connections in their CMS databases.
Q2. How do we address access versus use?
Q3. Are there gaps in services? Is there something that we are missing that will allow us to link all this data (e.g., infrastructure, hardware, people, partnerships)?
Q4. How are we going to get people to comply after they are provided with the correct tools?
The hope is that they would not need to comply but that automated processes would make these linkages for us but without such a system I think it will be a case of putting guidelines or requirements into existing structures (like the specimen management plan, journal instructions to authors, editorial board review guidelines, collection loan policies, etc.) to educate the necessary people as to why this is a necessary part of “playing the game”.
Q5. How can we interactively address data accuracy issues in genetic data in an increasingly genomic world?
Q6. When is data restricted (not FAIR), how do we deal with it, and can we increase access in these situations? Three examples of restricting access for various reasons:
(a) Access to digital sequence information under access and benefit-sharing frameworks.
(b) Commercial use of public data/physical specimens.
(c) Federal agency use in promoting the “bioeconomy.”
Q7. Does limiting access to Digital Sequence Information harm provider countries?
Q8. What could be done with no, modest, and substantial funding?
The funding issue is tricky. I think a comprehensive solution will require some sort of funding to get the DES infrastructure in place and make all the connections across the disparate solutions we currently have. However, it needs to be a global solution and this is hard to do. Hopefully something like the Biological Collections Action Center will catalyze some of this stuff in the US (if it ever gets funded) and it sounds like DiSCCo will be doing a lot of this in Europe but what do we do about the rest of the world to ensure that it is not a pay to play environment and the rest get left by the wayside?