A ViBRANT time for biodiversity

Think of the countless ecological interactions that occur in nature, from the environmental impacts of an elephant roaming the Serengeti savanna to the swimming of a ciliate protozoa in the Amazon.

Now, imagine the problem faced by biological researchers trying to categorize data about millions of species and adding them to the evolutionary tree.

Enter Scratchpads. These free web-based tools enable research communities to input, store, search for and share data sets that are hard to generalize. They act as a type of social network for academic researchers and could streamline the scholarly communication process, which is often expensive and complicated.

Scratchpads are run by ViBRANT (Virtual Biodiversity Research and Access Network for Taxonomy), an European Commission FP7 funded project to enable better collaboration between research communities through e-infrastructure services. More than just notepads, the technology is a sophisticated virtual interface for  academics, students and amateur ‘citizen scientists’ to collaborate via the web. Users ‘scratch-out’ their ideas or publish research about biodiversity, albeit digitally. All one needs to use them is information to share and some web development skills.

So far, the ViBRANT community has amassed 2,340 users from over 40 countries. Vincent Smith, a cybertaxonomist coordinating the project, commented: “A good number are professional amateurs.”

One such community is the Encyclopedia of Life (EOL) project which seeks to be the online resource for data about living species. They currently host 500,000 webpages of detailed species descriptions, and work with ViBRANT’s Scratchpads in a symbiotic relationship.

EOL has created APIs (Application-Programming-Interfaces) to enable Scratchpads to download data from them in order to share with other Scratchpad communities. And they are also developing tools to allow species information on Scratchpads to be published on EOL. “I believe functional integration between the two projects will produce something larger than the sum of its parts,” said Robert Corrigan, product manager and acting deputy director of EOL.

If you thought Scratchpads sound similar to the EpiCollect project, think again. Smith said that the principle of EpiCollect is for people in the field to upload biological observations via a smartphone application. In contrast, most of the research within Scratchpads is collected in the laboratory. But there are similarities; a Smartphone app for field researchers is being developed by ViBRANT.

In order to provide a user-friendly system, Scratchpad developers have made a standardized interface, supporting set taxonomies (parent-child structures). Smith and his team pre-program the most likely displays a user will need when inputting data using common recording standards.

Because there are still many specialized data sets (e.g. host-parasite relationships) that require the creation of custom content types, users are also able to set up their own interface to display custom data. This does have a drawback, however -- “This data cannot easily be aggregated across different Scratchpads, because it is hard to put structures on top that make it findable and usable” commented Smith.

Scratchpads have an open-source anatomy as Drupal provides their underlying framework. They are run on a ‘virtual machine,’ one-step behind a cloud service. (They only use a single virtual machine, whereas cloud services typically use many virtual machines.)

ViBRANT is also developing a framework that will connect communities of scientists to the public who are willing to contribute their time to projects. For example, marine divers in Greece could annotate digitized specimen images from natural history collections. The hope is to make these projects available through Zooniverse, a ‘crowd-sourcing’ website for anyone to get involved in citizen science projects. The BOINC system may also be used to garner volunteers’ idle computing power to analyze genetic datasets.

A new form of communication?

Academic publishing of biodiversity data is not as widespread as it should be because literature is not in an easily accessible format. Scratchpads could streamline this by automating the process of fusing biological information into academic publications. Formal species descriptions and images can be easily inserted into open-access journals. Therefore, users can transfer their findings to other websites or integrate them into scientific publications without losing their information hierarchies.   

Smith said, “We are changing the scholarly communication process, and moving away from traditional journal articles as the only metric of scholarly achievement.” Today, biological taxonomy is still fragmented and primarily recorded on paper-based literature, across countless institutions, with a handful of living experts. Meanwhile, the data continues to grow and the experts dwindle. Developing more Scratchpads suited to people’s needs could be one way for this digital adaptation to evolve biological taxonomy.

A detailed description of scratchpads can be found here.                                                           Scratchpads use common standards for data recording such as the ‘Darwin Core’ (a standard enabling easy exchange of information about the geographic occurrence of species) and the ‘Taxon Concept Schema’(each TCS container has a marker that briefly describes the data contained within). All images courtesy Vincent Smith.