University of Glasgow

Roderic Page

Time (just) for a Friday folly. A couple of days ago the latest edition
of the [Catalogue of Life](http://www.catalogueoflife.org) (CoL) arrived
in my mailbox in the form of a DVD and booklet:  
  
![photo.JPG](http://lh4.ggpht.com/_Gct8lVAxKqQ/TKYeNNzFCOI/AAAAAAAAAxU/NNB6GVIoG4g/photo.JPG?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="300"}  
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](https://cloudant.com/)) 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](http://www.eol.org),
[GBIF](http://www.gbif.org), and
[iNaturalist.org](http://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is horribly out of date.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](http://github.com/), 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>:  
  
![croc.png](http://lh5.ggpht.com/_Gct8lVAxKqQ/TKYeOMQieII/AAAAAAAAAxY/DqnZNrWerWc/croc.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="383"}  
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.


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.

Messaggi di Rogue Scholar

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