Wednesday, April 15, 2015

Linking specimen codes to GBIF

I've put together a working demo of some code I've been working on to discover GBIF records that correspond to museum specimen codes. The live demo is at and code is on GitHub.

To use the demo, simply paste in a specimen code (e.g., "MCZ 24351") and click Find and it will do it's best to parse the code, then go off to GBIF and see what it can find. Some examples that are fun include MCZ 24351, KU:IT:00312, MNHN 2003-1054, and AMS I33708-051


It's proof of concept at this stage, and the search is "live", I'm not (yet) storing any results. For now I simply want to explore how well if can find matches in GBIF.

By itself this isn't terribly exciting, but it's a key step towards some of the things I want to do. For example, the NCBI is interested in flagging sequences from type specimens (see ), so we could imagine taking lists of type specimens from GBIF and trying to match those to voucher codes in GenBank. I've played a little with this, unfortunately there seem to be lots of cases where GBIF doesn’t know that a specimen is, in fact, a type.

Another thing I’m interested in is cases where GBIF has a georeferenced specimen but GenBank doesn’t (or visa versa), as a stepping stone towards creating geophylogenies. For example, in order to create a geophylogeny for Agnotecous crickets in New Caledonia (see GeoJSON and geophylogenies ) I needed to combine sequence data from NCBI with locality data from GBIF.

It’s becoming increasingly clear to me that the data supplied to GBIF is often horribly out of date compared to what is in the literature. Often all GBIF gets is what has been scribbled in a collection catalogue. By linking GBIF records to specimen codes cited that are cited in the literature we could imagine giving GBIF users enhanced information on a given occurrence (and at the same time get citation counts for specimens The impact of museum collections: one collection ≈ one Nobel Prize).

Lastly, if we can link specimens to sequences and the literature, then we can populate more of the biodiversity knowledge graph