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.

Replicating and forking data in 2010: Catalogue of Life and CouchDB

Time (just) for a Friday folly. A couple of days ago the latest edition of the Catalogue of Life (CoL) arrived in my mailbox in the form of a DVD and booklet:


While in some ways it's wonderful that the Catalogue of Life provides a complete data dump of its contents, this strikes me as a rather old-fashioned way to distribute it. So I began to wonder how this could be done differently, and started to think of CouchDB. In particular, I began to think of being able to upload the data to a service (such as Cloudant) where the data could be stored and replicated at scale. then I began to think about forking the data. The Catalogue of Life has some good things going for it (some 1.25 million species, and around 2 million names), and is widely used as the backbone of sites such as EOL, GBIF, and iNaturalist.org, but parts of it are broken. Literature citations are often incomplete or mangled, and in places it is horribly out of date.

Rather than wait for the Catalogue of Life to fix this, what if we could share the data, annotate it, correct mistakes, and add links? In particular, what if we link the literature to records in the Biodiversity Heritage Library so at we can finally start to connect names to the primary literature (imagine clicking on a name and being able to see the original species description). We could have something akin to github, but instead of downloading and forking code, we download and fork data. CouchDB makes replicating data pretty straightforward.

So, I've started to upload some Catalogue of Life records to a CouchDB instance at Cloudant, and write a simple web site to display these records. For example, you can see the record for at http://iphylo.org/~rpage/col/?id=e9fda47629c1102b9a4a00304854f820:


The e9fda47629c1102b9a4a00304854f820 in this URL is the UUID of the record in CouchDB, which is also the UUID embedded in the (non-functional) CoL LSIDs. This ensures the records have a unique identifier, but also one that is related to the original record. You can search for names, or browse the immediate hierarchy around a name. I hope to add more records over time as I explore this further — at the moment I've added a few lizards, wasps, and conifers while I explore how to convert the CoL records into a sensible JSON object to upload to CouchDB.

The next step is to think about this as a way to distribute data (want a copy of CoL, just point your CouchDB at the Cloudant URL and replicate it), and to think about how to build upon the basic records, editing and improving them, then thinking about how to get that information into a future version of the Catalogue.