Extracting museum specimen codes from text

Quick note about a tool I've cobbled together as part of the phyloinformatics course, which addresses a long standing need I and others have to extract specimen codes from text. I've had this code kicking around for a while (as part of various never-finished data mining projects), but never got around to releasing it, until now. It is very crude (basically a bunch of regular expressions), and there's a lot which could be done to improve it (not least starting with a complete list of museum specimen codes, rather than just those I've come across in, say Zootaxa and BioStor).

You can try the tool at http://iphylo.org/~rpage/phyloinformatics/services/specimenparser.php. Paste in some text and it will try and extract museum codes. The tool tries to handle ranges of specimens (e.g., MHNSM 1808-09), and some of the more common specimen numbering schemes.

Comments welcome. If you are looking for a source of text, papers in Zookeys or Zootaxa are a good place to start (especially papers on vertebrates where specimen numbers are often used). BioStor is also a good source: if you're looking at a paper in BioStor click on the "Text" link to get the OCR text for an article and paste that into the form at . For example, the text for Systematics of the Bufo coccifer complex (Anura: Bufonidae) of Mesoamerica is available at http://biostor.org/reference/97426.text.

The extraction tool can also be called as a web service using POST to get back the results in JSON.

Talks at The Natural History Museum and British Library

Vince Smith has produced a nice flyer for my forthcoming talk at The Natural History Museum on March 17th (11-12).



It will be a busy day as I'm also talking at the British Library in the evening (6pm - 8:30pm), for which Sarah Kemmitt has produced a flyer, and set up a discussion forum on Nature Network. With all this effort going into the artwork, I'd better actually come up with something useful to say.

iPhone, barcodes, and natural history museums

One of my pet peeves is how backward natural history museums are in grasping the possibilities the Internet raises. Most electronic displays in museums have low information content, and are doomed to obsolescence. Traditional media (plaques, labels) have limited space, and also date quickly. For example, the Natural History Museum in London has a skeleton of Diplodocus carnegiei (see photo below by EmLah). This is one of many replicas distributed around the world.


The plaque describing this fossil has fairly minimal information. Wikipedia, however, has a nice article on Diplodocus, which includes a public domain image of the replica skeleton being presented to the trustees of the British Museum of Natural History in 1905.

Given the limitations of physical media, museum labels and plaques will always be small, and will often be out of date. Wikipedia, of course, can be kept current, and anybody can contribute.

So, the trick is to link the physical object to the Internet. This is now trivial thanks to mobile tagging. By pointing a mobile phone with a camera at a 2D barcode, one can go from physical object to web site.


Here is a 2D barcode for the URL of the Wikipedia article on Diplodicus. Imagine taking your iPhone, pointing it at this barcode, and being taken to the Wikipedia page. If museums were clever, they could set out their own Wiki, and mobilise the combined skills of the museum staff, volunteers, and visitors to populate it.

Now that the iPhone has applications, imagine creating an application that read these barcodes. Kevin Chiu at Columbia has a made one, and there are others out there. Museums could build on this, brand it with their logo, and greatly enhance visitor experience.

Wonder if anyone is doing this...?