Preprint on Wikidata and the bibliography of life

Last week I submitted a manuscript entitled "Wikidata and the bibliography of life". I've been thinking about the "bibliography of life" (AKA a database of every taxonomic publication ever published) for a while, and this paper explores the idea that Wikidata is the place to create this database. The preprint version is on bioRxiv (doi:10.1101/2021.05.04.442638). Here's the abstract:

Biological taxonomy rests on a long tail of publications spanning nearly three centuries. Not only is this literature vital to resolving disputes about taxonomy and nomenclature, for many species it represents a key source - indeed sometimes the only source - of information about that species. Unlike other disciplines such as biomedicine, the taxonomic community lacks a centralised, curated literature database (the “bibliography of life”). This paper argues that Wikidata can be that database as it has flexible and sophisticated models of bibliographic information, and an active community of people and programs (“bots”) adding, editing, and curating that information. The paper also describes a tool to visualise and explore bibliography information in Wikidata and how it links to both taxa and taxonomists.

The manuscript summarises some work I've been doing to populate Wikidata with taxonomic publications (building on a huge amount of work already done), and also describes ALEC which I use to visualise this content. I've made various (unreleased) knowledge graphs of taxonomic information (and one that I have actually released Ozymandias), I'm still torn between whether the future is to invest more effort in Wikidata, or construct lighter, faster, domain specific knowledge graphs for taxonomy. I think the answer is likely to be "yes".

Meantime, one chart I quite like from the submitted version of this paper is shown below.

It's a chart that is a bit tricky to interpret. My goal was to get a sense of whether bibliographic items added to Wikidata (e.g., taxonomic papers) were actually being edited by the Wikidata community, or whether they just sat there unchanged since they were added. If people are editing these publications, for example, by adding missing author names, linking papers to items for their authors, or adding additional identifiers (such as DOIs, ZooBank identifiers, etc.), then there is clear value in using Wikidata as a repository of bibliographic data. So I grabbed a sample of 1000 publications, retrieved their edit history from Wikidata, and plotted the creation timestamp of each item against the timestamps for each edit made to that item. If items were never edited then every point would fall along the diagonal line. If edits are made, they appear to the right of the diagonal. I could have just counted edits made, but I wanted to visualise those edits. As the chart shows, there is quite a lot of editing activity, so there his a community of people (and bots) curating this content. In many ways this is the strongest argument for using Wikidata for a "bibliography of life". Any database needs curation, which means people, and this is what Wikidata offers, a community of people who care about often esoteric details, and get pleasure from improving structured data.

There are still huge gaps in Wikidata's coverage of the taxonomic literature. Once you move beyond the "low hanging fruit" of publications with CrossRef DOIs the task of adding literature to Wikidata gets a bit more complicated. Then there is the reconciliation problem: given an existing taxonomic database with a list of references, how do we match those references to the corresponding items in Wikidata? There is still a lot to do.

Finding scientific articles in a large digital archive: BioStor and the Biodiversity Heritage Library

Yesterday I uploaded a manuscript to Nature Precedings that describes the inner workings of BioStor. The title is "Finding scientific articles in a large digital archive: BioStor and the Biodiversity Heritage Library", and you can grab it here: hdl:10101/npre.2010.4928.1.

Manuscripts describing databases are usually pretty turgid affairs, and this isn't an exception, despite my attempts to spice it up with the tale of Leviathan, oops, Livyatan (see doi:10.1038/nature09381 and Wikipedia). Plus, I can't escape the thought that BioStor would have been a lot more fun to write if I'd used a key-value database like CouchDB. I fear this is often the way of things. By the time it comes to writing something up, you realise that if you could start over you'd do it rather differently.

Elsevier Grand Challenge paper out

At long last the peer-reviewed version of the paper "Enhanced display of scientific articles using extended metadata" (doi:10.1016/j.websem.2010.03.004), in which I describe my entry in the Elsevier Grand Challenge, has finally appeared in the journal Web Semantics: Science, Services and Agents on the World Wide Web. The pre-print version of this paper has been online (hdl:10101/npre.2009.3173.1) for a year prior to appearance of the published version (24 April 2009 versus 3 April 2010), and the Challenge entry itself went online in December 2008. Unfortunately the published version has an awful typo in the title (that was in neither the manuscript nor the proofs).

Given this typo, the time lag between doing the work, writing the manuscript, and seeing it published, and the fact that I've already been to meetings where my invitation has been based the entry and the pre-print, I do wonder why on Earth would I bother with traditional publication (which is somewhat ironic, given the topic of the paper)?

Wikipedia manuscript

I've written up some thoughts on Wikipedia for a short invited review to appear (pending review) in Organisms, Environment, and Diversity (ISSN 1439-6092). The manuscript, entitled "Wikipedia as an encyclopaedia of life" is available as a preprint from Nature Precedings (hdl:10101/npre.2010.4242.1). The opening paragraph is:

In his 2003 essay E O Wilson outlined his vision for an "encyclopaedia of life" comprising "an electronic page for each species of organism on Earth", each page containing "the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits." Although the "quiet revolution” in biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson’s essay (e.g., http://ispecies.org, http://www.eol.org), we are still some way from the goal of having available online all relevant information about a species, such as its taxonomy, evolutionary history, genomics, morphology, ecology, and behaviour. While the biodiversity community has been developing a plethora of databases, some with overlapping goals and duplicated content, Wikipedia has been slowly growing to the point where it now has over 100,000 pages on biological taxa. My goal in this essay is to explore the idea that, largely independent of the efforts of biodiversity informatics and well-funded international efforts, Wikipedia (http://en.wikipedia.org/wiki/Main_Page) has emerged as potentially the best platform for fulfilling E O Wilson’s vision.

The content will be familiar to readers of this blog, although the essay is perhaps a slightly more sober assessment of Wikipedia than some of my blog posts would suggest. It was also the first manuscript I'd written in MS Word for a while (not a fun experience), and the first ever for which I'd used Zotero to manage the bibliography (which worked surprisingly well).

Paper published

Bit of a rarity these days. My paper on identifiers in biodiversity informatics, which I mentioned earlier when I deposited the preprint at Nature Precedings, has been published in Briefings in Bioinformatics (doi:10.1093/bib/bbn022).

Here's the abstract:

A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers [such as Digital Object Identifiers (DOIs) and Life Science Identifiers (LSIDs)], and the implementation of services that link those identifiers.

Nature Precedings

Nature precedings is pre-publication server launched by Nature a few months ago. To quote from the website:

Nature Precedings is a place for researchers to share pre-publication research, unpublished manuscripts, presentations, posters, white papers, technical papers, supplementary findings, and other scientific documents. Submissions are screened by our professional curation team for relevance and quality, but are not subjected to peer review. We welcome high-quality contributions from biology, medicine (except clinical trials), chemistry and the earth sciences.

Unable to resist, I've uploaded three manuscripts previously languishing as "Technical Reports" on my old server. The three I uploaded now have bright shiny DOIs, which may take a little while to register with CrossRef. The manuscripts are:

Treemap Versus BPA (Again): A Response to Dowling doi:10.1038/npre.2007.1030.1 (a response to a critique of my ancient TreeMap program).

On The Dangers Of Aligning RNA Sequences Using "Conserved" Motifs doi:10.1038/npre.2007.1029.1 (a short note on Hickson et al.'s (2000) use of conserved motifs to evaulate RNA alignment).

Towards a Taxonomically Intelligent Phylogenetic Database doi:10.1038/npre.2007.1028.1 (a paper written for DBiBD 2005, basically a rewrite of a grant proposal).

All three are under the evolution and ecology subject heading. Visitors to Nature precedings can comment on papers, and vote for which ones they like. The fact that I've uploaded some manuscripts probably says nothing good about me, but I'll be checking every so often to see if anybody has anything to say...