Scripting Life
Not really a blog post, more a note to self. If I ever did get around to writing a book again, I think Scripting Life would be a great title.
PLoS Biodiversity Hub launches
The PLoS Biodiversity Hub has launched today. There's a PLoS blog post explaining the background to the project, as well as a summary on the Hub itself:
The vision behind the creation of PLoS Hubs is to show how open-access literature can be reused and reorganized, filtered, and assessed to enable the exchange of research, opinion, and data between community members.
PLoS Hubs: Biodiversity provides two main functions to connect researchers with relevant content. First, open-access articles on the broad theme of biodiversity are selected and imported into the Hub. In time, the content will also be enhanced so that the articles are connected with data, and we will provide features to make the articles easier for people to use. These two functions - aggregation and adding value - build on the concept of open access, which removes all the barriers to access and reuse of journal article content.
Readers of iPhylo may recall my account of one of the meetings involved in setting up this hub, in which I began to despair about the lack of readiness of biodiversity informatics to provide much of the information needed for projects such as hubs. Despite this (or perhaps, because of it), I've become a member of the steering committee for the Biodiversity Hub. There's clearly a lot of interest in repurposing the content found in scientific articles, and I think we're going to see an increasing number of similar projects from the major players in science publishing, Open Access or otherwise. One of the challenges is going to be moving beyond the obvious things (such as making taxon names clickable) to enable new kinds of ways of reading, navigating, and querying the literature, and exploring ways to track the use that is made of the information in these articles. Biodiversity studies are ideally placed to explore this as the subject is data rich and much of that data, such as specimens and DNA sequences, persist over time and hence get reused (data citation gets very boring if the data is used just once). We also have obvious ways to enrich navigation, such as spatially and taxonomically.
For now the PLoS Biodiversity Hub is very pretty, but it's more a statement of intent than a real demonstration of what can be done. Let's hope our field gets its act together and seizes the opportunity that initiatives like the Hub represents. Publishers are desperate to differentiate themselves from their competitors by providing added value as part of the publication process, and they provide a real use case for all the data that the biodiversity projects have been accumulating over the last couple of decades.
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.
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.
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