70,000 articles extracted from the Biodiversity Heritage Library

Just noticed that BioStor now has just over 70,000 articles extracted from the Biodiversity Heritage Library. This number is a little "soft" as there are some duplicates in the database that I need to clean out, but it's a nice sounding number. Each article has full text available, and in most cases reasonably complete metadata.

Most of the articles in BioStor have been added using semi-automated methods, but there's been rather more manual entry than I'd like to admit. One task that does have to be done manually is attaching plates to papers. This is largely an issue for older publications, where printing text and figures required different processes, resulting in text and figures often being widely separated in the publication. Technology evolved, and the more recent literature doesn't have this problem.

Future plans include adding the ability to download the articles as searchable PDFs, and to support OCR correction, amongst other things. BioStor also underpins some of my other projects, such as the EOL Challenge entry, which as of now has around 80,000 animal names linked to their original description in BioStor (and some 300,000 in total linked to some form of digital identifier). One day I may also manage to get the article locations into BHL itself, so that when you browse a scanned item in BHL you can quickly find individual articles. Oh, and it would be cool to have all this on the iPad...

Sherborn presentation on Open Taxonomy

Here is my presentation from today's Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond meeting.

Open taxonomy

View more presentations from Roderic Page

All the presentations will be posted online, along with podcasts of the audio. Meantime, presentations by Dave Remsen and Chris Freeland are already online.

The top-ten new species described in 2010 and the failure of taxonomy to embrace Open Access publication

Each year the grandly titled International Institute for Species Exploration (IISE) publishes list of the top 10 species described in the previous year. This year's list is reproduced below, to which I've added the links to the original publications (why do people think still it's OK to omit links to the primary literature when all of these articles are online?).

The striking thing is that only 2 of the 10 species were described in Open Access publications (and I use that term loosely as as Arthropod Systematics & Phylogeny PDFs are freely available, but the licensing isn't clear). Sadly much of our knowledge of the planet's diversity is still locked up behind a paywall.

Species		Reference	DOI/PDF	Open Access
	Darwin's Bark Spider	Kuntner, M. and I. Agnarsson. 2010. Web gigantism in Darwin's bark spider, a new species from Madagascar (Araneidae: Caerostris). The Journal of Arachnology 38(2):346-356	10.1636/B09-113.1	No
	Bioluminescent Mushroom	Desjardin, D.E., B.A. Perry, D.J. Lodge, C.V. Stevani, and E. Nagasawa. 2010. Luminescent Mycena: new and noteworthy species. Mycologia 102(2):459-477	10.3852/09-197	No
	Bacterium	Sanchez-Porro, C., B. Kaur, H. Mann and A. Ventosa. 2010. Halomonas titanicae sp. nov., a halophilic bacterium isolated from the RMS Titanic. International Journal of Systematic and Evolutionary Microbiology 60(12):2768-2774	10.1099/ijs.0.020628-0	No
	Monitor Lizard	Welton, L.J., C.D. Siler, D. Bennett, A. Diesmos, M.R. Duya, R. Dugay, E.L.B. Rico, M. van Weerd and R.M. Brown. 2010. A spectacular new Philippine monitor lizard reveals a hidden biogeographic boundary and a novel flagship species for conservation. Biology Letters 6(5):654-658	10.1098/rsbl.2010.0119	No
	Pollinating cricket	Hugel, S., C. Micheneau, J. Fournel, B.H. Warren, A. Gauvin-Bialecki, T. Pailler, M.W. Chase and D. Strasberg. 2010. Glomeremus species from the Mascarene islands (Orthoptera, Gryllacrididae) with the description of the pollinator of an endemic orchid from the island of Réunion. Zootaxa 2545:58-68	PDF	No
	Duiker	Colyn, M., J. Hulselmans, G. Sonet, P. Oudé, J. de Winter, A. Natta, Z.T. Nagy and E. Verheyen. 2010. Discovery of a new duiker species (Bovidae: Cephalophinae) from the Dahomey Gap, West Africa. Zootaxa 2637:1-30	PDF	No
	Leech	Phillips, A.J., R. Arauco-Brown, A. Oceguera-Figueroa, G.P. Gomez, M. Beltran, Y.-T. Lai and M.E. Siddall. 2010. Tyrannobdella rex n. gen. n. sp. and the evolutionary origins of mucosal leech infestations. PLoS ONE 5(4):e10057	10.1371/journal.pone.0010057	Yes
	Underwater mushroom	Frank, J.L., R.A. Coffan and D. Southworth. 2010. Aquatic gilled mushrooms: Psathyrella fruiting in the Rogue River in southern Oregon. Mycologia 102(1):93-107	10.3852/07-190	No
	Jumping cockroach	Bohn, H., M. Picker, K.-D. Klass and J. Colville. 2010. A jumping cockroach from South Africa, Saltoblattella montistabularis, gen. nov., spec. nov. (Blattodea: Blattellidae). Arthropod Systematics and Phylogeny 68(1):53-39/td>	PDF	Yes
	Pancake Batfish	Ho, H.-C., P. Chakrabarty and J.S. Sparks. 2010. Review of the Halieutichthys aculeatus species complex (Lophiiformes: Ogcocephalidae), with descriptions of two new species. Journal of Fish Biology 77(4):841-869	10.1111/j.1095-8649.2010.02716.x	No

ZooKeys publishes articles of the future

The open access taxonomic journal ZooKeys has published a special issue with four papers, each available in HTML, PDF, and XML, the later being extensively marked up. Penev et al. ("Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples", doi:10.3897/zookeys.50.538) describes the process involved in creating these XML files. Two papers (doi:10.3897/zookeys.50.506 and doi:10.3897/zookeys.50.505) were created using authoring tools available in Scratchpads, as outlined by Blagoderov et al. ("Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys", doi:10.3897/zookeys.50.539). When you view the HTMl for these articles you can toggle on or off the highlighting citations, taxonomic names, and geographic co-ordinates. Mousing over a taxonomic name, for example, a popup appears with links to GBIF, NCBI, EOL, BHL, Wikipedia, etc.):



I think these papers represent one view of the future of scientific publishing ("article 2.0"), and I'm flattered that Penev et al. cite my Elsevier challenge work (doi:10.1016/j.websem.2010.03.004, preprint at hdl:10101/npre.2009.3173.1) as one of the sources of inspiration (along with the landmark Shotton et al. "Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article" doi:10.1371/journal.pcbi.1000361, which I've discussed previously). It is also good to see the TaxPub XML schema used by a publisher, and Scratchpads being a part of the process of publishing taxonomic information.

Deep linking

My initial impression is that there is huge of potential here, although I think there is still lots to do. I'm not totally convinced that popups are they way to go (although I've dabbled with them as well), and we need to move beyond simply linking to other sites to a deeper form of integration. For example, a Zookeys article might link to BHL via a taxonomic name, but how about deeper linking? For example, the paper by Brake and von Tschirnhaus (doi:10.3897/zookeys.50.505) contains the following citations:

Biró L (1899) Commensalismus bei Fliegen. Természetrajzi füzetek 22: 198–204.

Kertész K (1899) Verzeichnis einiger, von L. Biró in Neu-Guinea und am Malayischen Archipel gesammelten Dipteren. Természetrajzi füzetek 22: 173–19

Neither reference has any links in the HTML, so the user is under the impression that they aren't available online, but both references have been scanned by BHL. You can see full text for these articles in BioStor (references 52005 and 52004, respectively -- note that the pagination for Biró 1899 is given incorrectly in the paper). This is one area where BHL has a lot to offer publishers, and it would be great to see BHL provide the services publishers need to add these links to their articles.

This integration should go both ways. It's odd that the paper by Brake and von Tschirnhaus contains LSID used by the ZooBank for this paper (urn:lsid:zoobank.org:pub:DABB03F4-A128-43BB-990C-02F25D656B00, see the <self-uri> tag in the XML), but ZooBank doesn't know about the DOI for the paper, hence the ZooBank page for this article has no link to the article itself. It's time to join this stuff together.

What's next?

What I'd really like to see is article XML repurposed as, say, RDF, and used to populate a database so that we can query it. In this way we can start to atomise the article into useful parts, and recombine them in new and interesting ways. Might be something to play with over the summer.

On a practical level, I'm somewhat bemused by the variety of XML formats being used by open access publishers. PLoS use version 2.0 of the NLM Journal Archiving and Interchange Tag Suite, and I wrote a XSLT style sheet to transform PLoS articles for viewing on an iPad. TaxPub is based on version 3.0 of the NLM DTD, which breaks quite a bit of my code relating to citations, so I'll have to tweak this to get it to display Zookeys articles correctly. Handling TaxPub itself will also require some additional work. Then there are the BMC journals, which have their own flavour of XML (based on something called the "KETON DTD"). It's all a bit messy. But I guess it'd be no fun if it was too easy...