Showing posts with label Wikispecies. Show all posts
Showing posts with label Wikispecies. Show all posts

Towards the bibliography of life

David King et al.'s paper "Towards the bibliography of life" http://dx.doi.org/10.3897/zookeys.150.2167 has just appeared in a special issue of ZooKeys. I've written a number of posts on this topic, so I've a few comments.

King et al. survey some of the issues, but don't really tackle the big issue of how we're going to build this. If we define the "bibliography of life" somewhat narrowly as the list of all papers that have published a scientific name (or a new combination, such as moving a species from one genus to another), then this is a large, but measurable undertaking. According to ION's metrics page, these are the numbers involved (for animals and protozoa):

Total New Names1,510,402
Total New Genera / Subgenera215,242
Total New Species / Subspecies1,192,366
Total Other New Names102,794
Total New Combinations241,296
Total New Synonyms260,544


Even in the worse case scenario of one name per publication (clearly not the case) this is big, but not insurmountable, task.

Publications not taxa
Part of the challenge is figuring out the best way to tackle the problem. In the past, most efforts at building taxonomic bibliographies have focussed on specific taxa, which is natural — the bibliographies are being built by taxonomists and they specialise in particular groups. But I'd argue that this is not the most efficient way to tackle the problem. Because the taxonomic literature is so widely dispersed, after the obvious "low hanging fruit" have been collected, considerable effort must be spent tracking down the harder to find citations. There are few economies of scale in this approach. In contrast, if we focus on publications at, say, the level of journal, then we can build a bibliography much more quickly. Once we've found the source, say, for one article, often we could use that information to harvest many articles from the same source (e.g., write scripts to harvest from a digital repository such as a DSpace server, or a digital library such as Gallica). But if we are focussed on a particular taxon, we will ignore the other articles in that journal ("what do I care about fish, I like turtles").

Put another way, if we imagine a taxa × publication matrix, then we can either go after rows (i.e., a bibliography for a specific taxonomic group), or columns (a list of articles in a specific journal). The article-based approach will be faster, albeit at the cost of finding articles that aren't necessarily relevant to taxonomy. This is why I'm spending what feels like far too much time harvesting article lists and uploading these to Mendeley. It is also one reason BHL has been so successful. They've simply gone after scanning the literature wholesale, rather than focussing on particular taxonomic groups.

TaxapublicationmatrixWikispecies logo enCrowd sourcing and Wikispecies
Crowd sourcing often strikes me as a euphemism for "we can't be bothered doing the tedious stuff, lets get the public to do it for us (plus it will look like we're engaged with the public)." I'm not denying can work, but I suspect it's not a magic bullet. Perhaps the best crowd sourcing is not to try and bring the crowd to a project, but go where the crowd has already gathered. In this case, an obvious crowd is the Wikispecies community. Working with the ION database for my Sherborn presentation, it's clear that the quality of bibliographic data in ION is variable, and rather poor for older references. In contrast, the reference lists on Wikispecies can be very good (e.g., the bibliography for George Boulenger). There are some issues with Wikispecies, notably the lack of a decent bibliographic template (unlike Wikipedia) so parsing references can be *cough* interesting, but there is scope here to use it to improve other databases. Citation matching can be a challenge, but in this case we have citations indexed by taxonomic name (in both ION and Wikispecies), which greatly reduces the scope of possible matches.

Summary
I think building the "bibliography of life" needs a combination of aggressive data gathering, and avoiding building additional tools unless absolutely needed. There are great tools and communities that can already be leveraged (e.g., Mendeley, Wikispecies), let's make use of them.

More BHL app ideas

Hero rosellasFollowing on from my previous post on BHL apps and a Twitter discussion in which I appealed for a "sexier" interface for BHL (to which @elywreplied that is what BHL Australia were trying to do), here are some further thoughts on improving BHL's web interface.
Build a new interface
A fun project would be to create a BHL website clone using just the BHL API. This would give you the freedom to explore interface ideas without having to persuade BHL to change its site. In a sense, the app would be provide the persuasion.

Third party annotations
It would be nice if the BHL web site made use of third party annotations. For example, BHL itself is extracting some of the best images and putting them on Flickr. How about if you go to the page for an item in BHL and you see a summary of the images from that item in Flickr? At a glance you can see whether the item has some interesting content. For example, if you go to http://biodiverritylibrary.org/item/109846 you see this:

N2 w1150

which gives you no idea that it contains images like this:

n24_w1150Tables of contents
Another source of annotations is my own BioStor project, which finds articles in scanned volumes in BHL. If you are looking at an item in BHL it would be nice to see a list of articles that have been found in that item, perhaps displayed in a drop down menu as a table of contents. This would help provide a way to navigate through the volume.

Who links to BHL?
When I suggested third party annotations on Twitter @stho002chimed in asking about Wikispecies, Species-ID, ZooBank, etc. These resources are different, in that they aren't repurposing BHL content but are linking to it. It woud be great if a BHL page for an item could display reverse links (i.e., the pages in those external databases that link to that BHL item).

Implementing reverse links (essential citation linking) can be tricky, but two ways to do it might be:
  1. Use BHL web server logs to find and extract referrals from those projects
  2. Perhaps more elegantly, encourage external databases to link to BHL content using an OpenURL which includes the URL of the originating page. OpenURL can be messy, but especially in Mediawiki-based projects such as Wikispecies and Species-ID it would be straightforward to make a template that generated the correct syntax. In this way BHL could harvest the inbound links and display them on the item page.