Video Tip of the Week: iDigBio for access to historical specimens and more

idigbio_logoUsually for Thanksgiving week posting is light. In the past, we’ve all done turkey breeding and genomics, cranberry genome, and some people have included apples, potatoes, and more. But another key aspect of the holiday is to remember the past and thank those who came before. And as I was watching this video that crossed my desk, I was thinking about our really ancient ancestors and their companions on the planet. And those who have created and preserved specimens in museum collections documenting the planet’s history. Increasingly those things are being digitized when appropriate, and sometimes even sequenced now when possible.

Some people think of these types of things as “stamp collecting”. But I think we are going to find these resources increasingly valuable as more folks can access and explore them.

So I want to thank folks who have been collecting, curating, and documenting our planet and its species over the millennia. This week I highlight iDigBio and their specimen portal that will provide access to these important curated collections for researchers to take into the future.

This week’s video is only one of the presentations at their iDigBio Summit V. They have a great Vimeo channel with other talks, but this one on Digitized Data in Biodiversity Research caught my attention first. It talks about work in wrangling information in biodiversity, making it available for further work with tools and workflows. It’s a nice overview of the goals and umbrella of topics they are interested in. And also mentions PhyloJIVE, which can integrate phylogeny data and available specimens. That’s a very cool bridge, it seems to me.

iDigBio Summit V: Digitized Data in Biodiversity Research from iDigBio on Vimeo.

So as you are eating and drinking a diverse range of species over the next few days, thank evolution. And thank folks who have been monitoring biodiversity in the past, and moving the studies into the future, on this pale blue dot we share.

Quick links:

iDigBio Portal:



Nelson, G., Sweeney, P., Wallace, L., Rabeler, R., Allard, D., Brown, H., Carter, J., Denslow, M., Ellwood, E., Germain-Aubrey, C., Gilbert, E., Gillespie, E., Goertzen, L., Legler, B., Marchant, D., Marsico, T., Morris, A., Murrell, Z., Nazaire, M., Neefus, C., Oberreiter, S., Paul, D., Ruhfel, B., Sasek, T., Shaw, J., Soltis, P., Watson, K., Weeks, A., & Mast, A. (2015). Digitization Workflows for Flat Sheets and Packets of Plants, Algae, and Fungi Applications in Plant Sciences, 3 (9) DOI: 10.3732/apps.1500065

Nelson, G., Paul, D., Riccardi, G., & Mast, A. (2012). Five task clusters that enable efficient and effective digitization of biological collections ZooKeys, 209, 19-45 DOI: 10.3897/zookeys.209.3135

Jolley-Rogers, G., Varghese, T., Harvey, P., dos Remedios, N., & Miller, J. (2014). PhyloJIVE: Integrating biodiversity data with the Tree of Life Bioinformatics, 30 (9), 1308-1309 DOI: 10.1093/bioinformatics/btu024