Thursday, May 10, 2007


Following on from my earlier grumble about how the catalogue of Life handles literature, I've spent an afternoon mapping publications in the "itis".publications table in a copy of ITIS to external GUIDs, such as DOIs, Handles, and SICIs in JSTOR. The mapping is not complete by any means, but gives an idea of how many publications have GUIDs.You can view the mapping here. Many of the publications in ITIS are books, which don't have DOIs. A lot of the literature is also old (although this doesn't always mean it won't have a DOI).

Of 4296 records, 324 have DOIs (around 7.5%). Not a lot, but a still a reasonable chunk. At least 700 of the ITIS publications are books (based on having an ISBN), so the percentage is a little higher.

The point of this exercise (following on from my comments on the design flaw in the catalogue of life), is that I think taxonomic databases need to use GUIDs internally to maximise their stability and utility.

Indeed, this is another reason to be disappointed with ZooBank. In addition to a poor way to navigate trees (which prompted me to explore tools such PygmyBrowse), ZooBank does exactly what ITIS and the Catalogue of Life do when it comes to displaying literature -- it displays a text citation (albeit with an invitation to view that record in Zoological Record, a subscription-based service).

For example, the copepod Nitocrellopsis texana was described in ITIS publication 3072, which I've discovered has the the DOI doi:10.1023/A:1003892200897. Given a DOI we have a GUID for the publication, and a direct link to it. In contrast, ZooBank merely gives us:
Nitocrellopsis texana n. sp. from central TX (U.S.A.) and N. ahaggarensis n. sp. from the central Algerian Sahara (Copepoda, Harpacticoida). Hydrobiologia 418 (1-3) 15 January: 82

and a link to Zoological Record. Interesting, even with the resources of ISI behind it, the Zoological Record result doesn't have the DOI.

This for me is one reason ZooBank was so disappointing, it actually provided little of value.

What next? Well, with the 300 or so references mapped to DOIs, one could link those to the ITIS records for the corresponding taxonomic names, and serve these up through somehting like iSpecies, for example. These would be links to the literature, in many cases original descriptions, to supplement the other literature found by iSpecies.


Anonymous said...

Dear Dr. Page,

your link to Zoobank is broken, you forgot to add the .org at the end.

We have developed a butterfly database online. It is still in early development yet it's productive at least for us.

Eventually we will like to link it to other butterfly databases like

Any criticism and comments are very appreciated.

Rod Page said...


Thanks for spotting that. I stumbled across your voucher database the other day. Very nice.

One thing that would be useful is some way of getting information about a voucher in XML, for example, so it could aggregated. As part of my bioGUID project I'm looking at ways to link sequence and specimen data together, and HTML pages, while nice, aren't as useful as an XML feed.

Anonymous said...

thanks for your comments!,

I will look into the RDF stuff. I started very recently to get into web stuff and your blogs are very informative to me.

all the best,