I wrote that: asserting authorship using the Mendeley API

Inspired by the forthcoming Hack4Knowledge I've put together a service that enables you to assert that you are the author of a paper using the Mendeley API.

If you are impatient, give it a try at:

http://iphylo.org/~rpage/hack4knowledge/iwrotethat/

To use it you need a Mendeley account. When you go to I wrote that you will be asked to connect to your Mendeley account. Once you've done that, enter the DOI or PubMed ID of a paper and, if the paper is in your Mendeley library and flagged as a paper you've authored, you should see something like this:



The site can be a little sluggish as it needs to go through all of your publications one by one until it finds a match.

Why?
Imagine you have a web database that includes publications, and you want people to join your site as users. If they have publications in your database, you'd like your users to be able to say "I'm the author of those papers" or, more generally, the author you have as "Roderic D. M. Page" is me.

One way to do this would be to enable the users to sign in to your site using Mendeley (see my blog post Mendeley connect). Once they've done that, the user could select a publication and say "that's mine". How do we test this assertion? Well, if the user is indeed the author it is likely that they will have added it to their "My Publications" section in their Mendeley library. So, we can use the Mendeley API to get a list of the author's publications and see whether the publication they claim is, in fact, one of theirs.

The inspiration for this came from tools like Google Analytics, where in order to add the tool to your web site you need to convince Google that you own the site. One way to do this is to add some text supplied by Google to the HTML on for site, on the assumption that only you can do this (because it's your site). In the same way, only you can add papers to your Mendeley library. Of course, I'm assuming that Mendeley users are being trustworthy when they and papers to "My Publications" (i.e., they're not claiming authorship on papers they didn't write).

How?
This hack uses Mendeley's OAuth support (the same technology used by Twitter and Facebook to connect to other sites) to enable you to connect your Mendeley account to the "I wrote that" application (note that my app never sees your account name or password). I use the Mendeley API user authored method to get a list of your publications, and user library document details to retrieve details of each publication. I then compare the DOI or PMID you supplied with each publication, until I find one that matches. If none matches, then I've no evidence you authored that paper.

Moan
No post about the Mendeley API would be complete without a moan about the state of the API. Apart from the fact that there is no function to directly find a publication in your library by DOI or PMID (hence I have to look at them all), there is virtually no support for retrieving any details about the user. For example, I wanted to brighten the web page up a little by adding a picture of the Mendeley user once they've logged in. There is no API function for this, nor a function to retrieve an identifier or URL for the user. Hence, in order to get a picture I screen scrape (yes, screen scrape) the Mendeley web page for the reference to get the URL for the linked author of the paper, then scrape the author's profile page and extract the URL for the image. This is insane. Please, please can we have a better API?

Would you give me a grant? An experiment in Open Science

I would like to know what you think of a grant proposal I plan to submit to the UK Natural Environment Research Council at the end of the month. The proposal takes the notion of "dark taxa" explored in an earlier blog post and outlines three things I'd like to do:

1. Quantify the extent of dark taxa (taxa in GenBank that don't have scientific names)
2. Determine how many dark taxa are genuinely new species (as opposed to taxa that are known to science but simply haven't been labelled with their proper names)
3. Explore what we can learn about a taxon's biology even if it lacks a scientific name (e.g., the "symbiome")

Given that I discuss most of my ideas on this blog, and deposit preprints in Nature Precedings before the corresponding manuscript is published, it seems a logical extension to make grant proposals open as well. So you view the proposal on Google Docs, and you can add comments, if you wish.

Any feedback or suggestions are welcome. Do you think this is fundable? Have I made a good case for the proposed research? Is it interesting, or is it obvious, or has it already been done? Let me know what you think.

ZooBank on CouchDB: UUIDs, replication, and embedding the literature in taxonomic databases

Last December I released a web site called Australian Faunal Directory on CouchDB, which was part of my ongoing exploration of how to build a simple yet useful database of taxonomic names. In particular, I want to link names directly to the primary taxonomic literature. No longer is it adequate to simply list names, or list names with mangled bibliographic details (I'm looking at you, Catalogue of Life). This is the 21st century, so I expect one click from name to literature, or at the most two (via, say, a DOI). Nothing else will cut it.

The Australian Faunal Directory (AFD) was an eye opener as it was the first serious use I'd made of CouchDB (now CouchBase). I'd played with replicating and forking data in 2010: Catalogue of Life and CouchDB, but the AFD project was bigger, and also inspired me to use web hooks to make the database editable. Suddenly this stuff started to look easy: no schema, simple web services, and tiny amounts of code.

ZooBank
So then my attention turned to ZooBank, which is "the official registry of Zoological Nomenclature, according to the International Commission on Zoological Nomenclature (ICZN)." ZooBank was proposed by Polaszek et al. (2005) in a short piece in Nature ("A universal register for animal names", doi:10.1038/437477a). By providing a registry of names for animals, ultimately it aims to help avoid embarrassing situations such as the example I recount in my paper on BioStor (doi:10.1186/1471-2105-12-187): a recent paper in Nature published the name Leviathan for an extinct sperm whale with a giant bite (doi:10.1038/nature09067), only for authors to have to publish an erratum with a new name (doi:10.1038/nature09381) when it was discovered that Leviathan had already been used for an extinct mammoth.

ZooBank is developed and run by Rich Pyle, and has some nice features, such as RDF export (via LSIDs), but like most taxonomic databases it doesn't link directly to the literature. Where are the DOIs? Where are links to BHL? Where is the ability to add these links? And why is it almost entirely about fish? (OK, I know the answer to that one).

CouchDB
But the thing which really got me thinking about using CouchDB to create a version of ZooBank was Rich Pyle's vision of having a distributed ZooBank, and his insistence on using ugly UUIDs in ZooBank identifiers (e.g., urn:lsid:zoobank.org:act:6BBEF50E-76B4-42EF-97B1-7029DBCD8257). As much as they are ugly, Rich has always argued that they make distributed systems easy because you don't need a centralised system to assign unique identifiers.

Anybody who has played with CouchDB will know that CouchDB uses UUIDs by default to create identifiers for database documents. It also excels at data synchronisation, and can run on platforms large and small (including mobile such as Android and iOS). This means a database could be updated on an iPhone or iPad without an Internet connection, then the data could be synchronised with other databases. Indeed, I developed this CouchDB clone of ZooBank on my MacBook, then pointed it at CouchDB running on my server and within minutes had an exact copy of the database running on the server. This ease of replication, together with the joy of schema-less design makes CouchDB seem an obvious fit to ZooBank.

Demo
You can see the ZooBank on CouchDB demo here. It's not a complete copy of ZooBank, but has most of it. I reuse the UUIDs issued by ZooBank, so that

http://zoobank.org:80/?uuid=6bbef50e-76b4-42ef-97b1-7029dbcd8257

becomes

http://iphylo.org/~rpage/zoobank/6bbef50e-76b4-42ef-97b1-7029dbcd8257

As usual it's all a bit crude, but has some nice features, such as links to BHL content with a built in article viewer I wrote for the AFD project:

What's next?
At present only a fraction of the ZooBank references have external links, I hope to add more in the next few days, using both automatic scripts and the web hook interface. The search interface needs work, and being that ZooBank is about nomenclature and not taxonomy, it might be useful to add a classification (say from the Catalogue of Life) so that users can navigate around the names (and get a sense of how many are *cough* fish).

At present to display a reference I do one of four things:

1. If reference is in BHL I use my article viewer
2. If there is a freely available PDF online I display that using Google Docs PDF viewer
3. If 1 and 2 don't apply, but there is a DOI then I resolve the DOI and display the result in an IFRAME (yuck)
4. If none of 1-3 apply I display a blank rectangle

There are a couple ways we could improve this. The first is to enhance the display of BHL content by making use of the structure of the source DjVu files. Another is to make use of the XML now being made available by the journal Zookeys (see my blog post, and Pensoft's announcement that ZooKeys is now being archived by PubMed Central, complete with taxonomic markup). There are a lot of ZooKeys articles in ZooBank, so there's a lot of potential for embedding an article viewer that takes Zookeys XML and redisplays it with taxonomic names and references as clickable links that link to other ZooBank content. That way we approach the point where taxonomic literature becomes a first class citizen of a taxonomic database.