From Plant Press, Vol. 20, No. 2, April 2017.
By Tom Hollowell and Vicki Funk
While modern systematics research usually involves genetic analyses, sequences such as those submitted by researchers to the National Center for Biotechnology Information’s (NCBI) public databases still rely on voucher specimens held in all biological collections (including herbaria) for identification and future reference.
Genetic sequences are usually submitted to NCBI in association with a researcher’s scientific publications. NCBI accession numbers are generated, but they are not automatically associated with data about voucher specimens, including National Museum of Natural History (NMNH) Botany records. While this is sure to improve going forward, there is a wealth of legacy data that need to be identified and integrated. We became aware of new possibilities once these data are united after the University of Alaska Museum Herbarium (ALA) brought their NCBI cross-linking efforts to our attention. Here at NMNH, and really at collections everywhere, we need to appeal through several channels to researchers holding these legacy data. So here we go!
Museum researchers: Are your GenBank or other NCBI sequence numbers in EMu, NMNH’s Research and Collections Information System? If so, you are already part of a Museum-wide project making our voucher and sample records accessible from NCBI. Although EMu records have included links from GenBank numbers to NCBI for a while, now it is a two-way street. NMNH now participates in NCBI’s LinkOut service so NCBI GenBank and BioSample records can also link back to our online EMu records, which increasingly includes Smithsonian Institution biorepository information, Global Genome Biodiversity Network (GGBN) links, and images of voucher specimens.
Would you like to see an example? Visit <http://collections.nmnh.si.edu>, select the Department of Botany link, and search for Funk 12700. Or better yet, follow this link: http://n2t.net/ark:/65665/3ad350607-c883-41b5-9eed-c3e1b270c52b directly to the EMu web record (Fig. 1). The GenBank numbers at the bottom of the page link directly to NCBI records. There you will see that the NCBI records include, in the column to the right, a return link to the EMu record (Fig. 2, see arrows).
All NMNH systematic biology departments have NCBI numbers in EMu, but many more numbers remain in researchers’ files waiting to be added. If you have NCBI numbers in a spreadsheet or other tabular file with any sort of collection record identifier for an NMNH specimen (ex. Collector + Collector number, Catalog number (= Sheet number), Barcode, etc.) they can probably be loaded to EMu. NCBI links can point back to both EMu Voucher and Sample records. Researchers from outside institutions who have submitted NMNH specimen based sequences to NCBI could also have their numbers added to EMu.
This is a wonderful opportunity to increase exposure of your research. In addition to sequence and publication information, each linked NCBI record will add easy access to your primary voucher specimen data. If interested contact a data manager from the appropriate NMNH department for advice or assistance as needed.