BioStor so far

My BioStor project has reached over 13,000 articles, making it a sizeable respository of open access articles on biodiversity. It's still a tiny fraction of what could be extracted from the Biodiversity Heritage Library (BHL), but perhaps it's worth taking stock of what's there.

Coverage

One pleasing discovery is that, despite the 1923 cut-off due to U.S. copyright, BHL contains a lot of post-1923 articles. Indeed, a sparkline of the number of articles over time shows that the bulk of the articles I've extracted from BHL are from the second half of the twentieth Century. These include journals such as Entomological News, and major herbaria and museum publications, such as Annals of the Missouri Botanical Garden, Breviora, Bulletin of the British Museum (Natural History). Zoology, and Proceedings of the United States National Museum.

This distribution partly reflects my own biased harvesting of BHL, but perhaps it also reflects a transition in publishing (from books and monographs to journals).

Exhibit

The interface to BioStor is still pretty rough, but one thing I've had fun adding is the SIMILE Exhibit widget to the author pages. Exhibit enables faceted browsing, so you can filter an author's list of publications by the journal they published, what year the article was published, and who was a coauthor.

One use I've found is that you can quickly filter out purely nomenclatural papers by select an author's publications in the Bulletin of Zoological Nomenclature.

Sparklines

I'm a fan of sparklines, and I'm a starting to add some to various pages. For example, you can now see a graph of how many papers an author has published over time, the example below is for the prolific Charles P Alexander:

Search

This pretty much sums up search in BioStor at the moment:

Harvesting

The rate of growth of BioStor has been pretty steady, partly because I keep managing to find (or are alerted to, or are given) sources of bibliographic metadata. I'm also adding individual papers as I come across them, either using the Reference finder form directly, or by using OpenURL from within Endnote. But there's still a crying need for large bibliographies that can be harvested.

Export

Individual references can be exported in a range of formats, and there is a RSS feed, but I need to add bulk export (including the ability to dump the whole database).

Viewer

The viewer I developed earlier is working reasonably well, but could do with sprucing up. I'm also toying with using other viewers as well as (or instead of) mine. One possibility is iPaper (although this is Flash-based, and I'd like to avoid Flash wherever possible).

Taxonomic names

One thing I've discovered to my horror is just how common it is for the BHL taxon finder to miss obvious taxonomic names. I need to investigate this a bit more, but this is potentially a major issue as taxonomic indexing is one of the primary ways people will find content in BioStor

Future

There's still so much to do. For one thing, the visualisations that originally got me seriously thinking about playing with BHL aren't in BioStor yet. And there's a long to-do list.

EOL hyperbole

The latest post on the EOL blog (Biodiversity in a rapidly changing world) really, really annoys me. It claims that

The case of the red lionfish exemplfies how EOL can provide information for science-based decision making. Red lionfish are native to coral reef ecosystems in the Indo-Pacific. Yet, probably due to human release of the fish from aquariums, a large population has found itself in the waters near the Bahamas.

Nope, I suggest it demonstrates just how limited EOL is. If I view the page for the red lionfish I get an out of date map from GBIF that shows a very limited distribution, and doesn't show the introductions in Florida and the Bahamas (I have to wade through text to find reference to the Florida introduction, and the page doesn't mention the Bahamas!). The blog entry states that

In this senerio[sic], EOL and its data partners provide up to date information about the lionfish, or pterois[sic] volitans, in a species page.

Well, the GBIF map is old (a more recent map is available from GBIF itself), the bibliography omits key references such as "Biological invasion of the Indo-Pacific lionfish Pterois volitans along the Atlantic coast of North America" (useful reading for a "science-based decision", one would think). Most of this information I got from Wikipedia, GBIF, and Google Scholar via an iSpecies search.

In other words, EOL in it's present state is serving limited, out of date information. The gap between hype and delivery shows no sign of narrowing. How can this help "science-based decision making"? Surely there will come a point when people will tire of breathless statements about how EOL will be useful, and they will start to ask "where's the beef?"

Encyclopedia of Life - first impressions

Some thoughts on the first release of the Encyclopedia of Life. I am being deliberately critical. This is a high profile project with tens of millions of dollars in funding, lots of people involved, and is accompanied by some of the most overblown hype in organismal biology. In a sense I think EOL has set itself up by over promising and under delivering.

Before continuing, I should point out that I am involved in EOL in an advisory capacity, but not in actually making anything. Some of the tools I've blogged about have made there way into EOL, such as Pygmybrowse and reference parsing (see David Shorthouse's excellent work on this).

Lack of content
I think the first release of EOL should have, at a minimum, provided at least as much information that I can get from iSpecies and Wikipedia. Other projects, such as Freebase, have pre-populated their databases with content from Wikipedia and other sources. Why didn't EOL? If the argument is that they want authenticated content, then this doesn't wash. Their authenticated content is minimal, and waiting for authentication will, in my view, cripple EOL.

Exemplars are incomplete
The first release contains 25 exemplars. Pages for these taxa

...show the kind of rich environment, with extensive information, to which all the species pages will eventually grow. The information on the exemplar pages has been authenticated (endorsed) by the scientists whose names are listed on these pages.

Well, I hope this isn't the standard EOL aspires to. The pages are incomplete and not interlinked. One of the 25 chosen exemplars is Anolis carolinensis. EOL lists its distribution as:

Widely-distributed throughout the southeastern United States: North Carolina to Key West, Florida, and west to southest Oklahoma and central Texas.

However, the GBIF map EOL displays shows lots of dots in Hawaii:


The EOL account is silent on this interesting distribution pattern. It will come as no suprise that the Wikipedia account of the same species tells us that it has been introduced into Hawaii. Wikipedia 1, EOL 0.

Links

If two pages talk about species that are ecologically associated, then surely those pages should be linked? Among the exemplars is Pissodes strobi, the white pine weevil. In the EOL account, among the hosts listed is Pinus strobus, another exemplar taxon. The accounts of these two taxa are not linked. No hyperlink, nothing. The reader has no idea that there is an exemplar account for Pinus strobus. Furthermore, when reading the account for Pinus strobus there is no indication that it is host to the white pine weevil.
Surely the point of having all this information in one place is so that it can be linked together?

BHL
EOL also exposes some limitations of the Biodiversity heritage Library. Consider the exemplar page for Pinus strobus L. The "L." indicates that this species was described by Linnaeus. Among the many references listed by BHL, none are by Linnaeus. What gives?

Well, the IPNI record reveals that this species was described on p. 1001 of Species Plantarum. BHL has digitised Species Plantarum, and page 1001 has Pinus strobus:



Now, BHL relies on uBio's tools to extract names, and Linnaeus didn't make this easy (the specific epithet strobus is in the right hand margin, separate from Pinus), but one would have thought that for the exemplar taxa an effort would have been made to link Linnaean names to BHL content -- what better place to showcase the link between a name and its publication? It's quite easy to do, given that IPNI has page numbers for plant names. Just map page numbers to BHL URLs, and you're done.

Inconsistency
Going down the taxonomic hierarchy weird things happen. When viewing the plant genus Morus if I can see a picture of Morus nigra (presumably this is "authenticated" content). If I drill down to the species Morus nigra, I'm told there is no authenticated content for this species. Either the image is Morus nigra or it isn't. If it is, why not show it, if it isn't, why claim that it is?



Logos

Way too much space is devoted to logos of various contributors, BHL being the worst offender (it doesn't help that the BHL content is incomplete, lacking links for Linnaean names). I don't care about logos. Contributors may care about getting their logos displayed, but users couldn't care less. They get in the way. On some pages, there's more screen space devoted to logos than information (e.g., the page for Apomys datae). This is, frankly, ridiculous, and reflects a warped set of priorities.

What's worse, all these logos are associated with links that take people away from EOL. Hence EOL becomes little more than a collection of web links to other sites.

Search
The search is based on the Catalogue of Life, and inherits the same problems. For example, if I search for "Morus" I get a list in alphabetical order of taxonomic names that contain the string "morus". The two names that are an exact match occur as items three and four on the list -- they should be first and second.

It gets worse if I search on "Tyrannosaurus rex". EOL doesn't do dinosaurs, and so doesn't contain anything on T. rex, but the search results tell me that The following 116 search results contain 'Tyrannosaurus rex'. Nope, none of them do.

The search engine is poorly done, it fails to rank results sensibly, incorrectly reports what it does find, and has no support for spelling mistakes.

Authenticated content
This is probably the thing that, if left as it is, will strangle EOL. The insistence on "authenticated (endorsed)" content places a severe brake on what EOL can offer.

It's a web site
EOL's web site has no mechanism for people to extract data (e.g., RSS feeds, microformats, links to RDF, etc.). It's intended to be read by humans, not machines. This greatly diminishes its utility.

So, I've got that off my chest. The first release was always going to be a disappointment, especially given the hype. What frustrates me, however, is just how far the first release is from what it could have been.

The real question is how much the issues I've raised are things which are easy to fix given time, or whether they reflect underlying problems with the way the project is conceived.