Tools for the nascent CDM community

The Common Data Model (CDM) is at the heart of the EDIT Platform for Cybertaxonomy – based on the hard-won lessons from more than 10 years of modeling taxonomic data, it describes the information taxonomists process within the Platform.

EDIT has been working to ensure that the Common Data Model suits the needs of taxonomists working across the entire spectrum of biological data. Eventually, this could even result in taxonomic data from all participating institutions being accessed as one dataset. But even if these lofty heights are not reached, collaboration across geographic and disciplinary boundaries will be made easier.

To implement the CDM in as many contexts as possible, we have been collaborating with partners outside of EDIT. To date, we have been active with the CATE project in London, and with the upcoming European Key2Nature project, as well as with the EDIT-initiated PESI project (“Pan European Species-directories Infrastructure”), which starts mid 2008.

Crucial to the acceptance of our work within the wider scientific community is to provide tools that are easy to learn, and which are intuitive and pleasurable to use. These tools are after all the window through which most users will interact with the CDM. Our medium term goal is to release a number of data portals and a CDM taxonomic editor which are well-designed, quickly learned, and easy to adopt and to adapt.

Drupal – a common development platform

We would like to foster a community-wide culture of collaboration. We believe that one way to do so is to offer tools to institutions without the latest-and-greatest technical know-how at their disposal to develop their own web applications for the CDM (or indeed for any web applications they would like to make available to the EDIT community).

The open source standard we have chosen for this task is Drupal . It is a content management system which allows the creation of flexible websites adapted in look and functionality to the needs of each community. Drupal comes with custom webpages, forums, blogs, image galleries and much more out of the box. Drupal development has already begun within EDIT but outside the CDM sphere, including the EDIT Scratchpads , the BDTracker , and the WP2 Experts Database .

EDIT Portals

The first wave of web-enabled CDM applications to be developed using Drupal are currently available as mockups on the EDIT wiki site . These portals will make available to the public data from the EDIT WP6 exemplar groups responsible for the palm, Cichorieae, and Diptera datasets. Initially, these portals will be read-only, displaying data that has already been imported into the CDM; in future versions, simple forms will be created to allow remote contributors to quickly add new images, common names or personal text based annotations.

With the creation of these portals, we hope to build up within EDIT partner institutions both familiarity with the CDM and Drupal expertise, to enable the development of more complex applications in the future.

Taxonomic Editor

For the editing of CDM data, a desktop Taxonomic Editor application is in development, with which the taxonomist user can do anything from fine-tuning an imported checklist to compiling a complete dataset from scratch .

We chose to make the editor a desktop application for a number of reasons. The portals described above will display the data in so-called Community Stores, centralized CDM datasets that are shared by members of a discreet community, i.e. the Cichorieae group. A desktop application offers the ability to download either a complete copy or a slice of the data in a Community Store; it then uses the synchronizing components of the CDM programming library to save any changes done locally to the Community Store, and to resolve any resulting conflicts. Furthermore, with a desktop application, the user can also work entirely offline; with future releases, we hope to take advantage of this fact, for example, with modules designed for fieldwork and/or hand-held devices. This will also allow applications specializing in different areas of the CDM to work on the same dataset. Software for structured descriptions and keys are likely to be initial candidates.

Development on both the Taxonomic Editor and the CDM is being done in Java. The thinking was similar to that behind the adoption of Drupal: by focusing on as few technologies as possible, we hope to more quickly build up expertise within the European biodiversity informatics community. We have also tried to minimize the burden of IT administration on resource-constrained institutions; another reason for a desktop-based Taxonomic Editor is to avoid foisting yet another web server on our partners.