TreeBASE meets NCBI, again

Déjà vu is a scary thing. Four years ago I released a mapping between names in TreeBASE and other databases called TBMap (described here: doi:10.1186/1471-2105-8-158). Today I find myself releasing yet another mapping, as part of my NCBI to Wikipedia project. By embedding the mapping in a wiki, it can be edited, so the kinds of problems I encountered with TbMap, recounted here, here, and here. The mapping in and of itself isn't terribly exciting, but it's the starting point for some things I want to do regarding how to visualise the data in TreeBASE.

Because TreeBASE 2 has issued new identifiers for its taxa (see TreeBASE II makes me pull my hair out), and now contains its own mapping to the NCBI taxonomy, as a first pass I've taken their mapping and added it to http://iphylo.org/linkout. I've also added some obvious mappings that TreeBASE has missed. There are a lot more taxa which could be added, but this is a start.

The TreeBASE taxa that have a mapping each get their own page with a URL of the form http://iphylo.org/linkout/<TreeBase taxon identifier>, e.g. http://iphylo.org/linkout/TB2:Tl257333. This page simply gives the name of the taxon in TreeBASE and the corresponding NCBI taxon id. It uses a Semantic Mediawiki template to generate a statement that the TreeBASE and and NCBI taxa are a "close match". If you go to the corresponding page in the wiki for the NCBI taxon (e.g., http://iphylo.org/linkout/Ncbi:448631) you will see any corresponding TreeBASE taxa listed there. If a mapping is erroneous, we simply need to edit the TreeBASE taxon page in the wiki to fix it. Nice and simple.

At the time of writing the initial mapping is still being loaded (this can take a while). I'll update this post when the uploading has finished.

Why we need wikis

I've just spent a frustrating few minutes trying to find a reference in BioStor. The reference in question is

Heller, Edmund 1901. Papers from the Hopkins Stanford Galapagos Expedition, 1898-1899. WIV. Reptiles. Proc. Biol. Soc. Washington 14: 39-98

and comes from the Reptile Database page for the gecko Phyllodactylus gilberti HELLER, 1903. This is primary database for reptile taxonomy, and supplies the Catalogue of Life, which repeats this reference verbatim.
Thing is, this reference doesn't exist! Page 39 of Proc. Biol. Soc. Washington volume 14 is the start of Gerrit S Miller (1901) A new dormouse from Italy. Proc Biol Soc Washington 14: 39-40.
After much fussing with trying diferent volumes and dates for Proc. Biol. Soc. Washington, I searched BHL for Phyllodactylus gilberti, and discovered that this name was published in Proceedings of the Washington Academy of Sciences:

Edmund Heller (1903) Papers from the Hopkins Stanford Galapagos Expedition, 1898-1899. XIV. Reptiles. Proceedings of the Washington Academy of Sciences 5: 39-98

(see http://biostor.org/reference/20322). Three errors (wrong journal, wrong date, minor typo in title), but enough to break the link between a name and the primary source for that name.

Anybody who demands authoritative, expert-vetted resources, and thinks the Catalgoue of Life is a shining example of this needs to think again. Our databases are riddled with errors, which are repackaged over and over again, yet these would be so easy to fix if they were opened up and made easy to edit. It's time to get serious about wikis.