Linking multiple biodiversity informatics platforms with Darwin Core Archives

Abstract

We describe an implementation of the Darwin Core Archive (DwC-A) standard that allows for the exchange of biodiversity information contained within the Scratchpads virtual research environment with external collaborators. Using this single archive file Scratchpad users can expose taxonomies, specimen records, species descriptions and a range of other data to a variety of third-party aggregators and tools (currently Encyclopedia of Life, eMonocot Portal, CartoDB, and the Common Data Model) for secondary use. This paper describes our technical approach to dynamically building and validating Darwin Core Archives for the 600+ Scratchpad user communities, which can be used to serve the diverse data needs of all of our content partners.

Keywords: Darwin Core; Darwin Core Archive; Scratchpads; biodiversity; biodiversity informatics; taxonomy; virtual research environment.

Figure 1.

The star schema showing the relation of Darwin Core Archive extension files to the core file.

Figure 2.

Data flow from Scratchpad to Darwin Core Archive. The dwca_export module (orange) defines a number of custom Drupal Views (queries) that collect the data required for archive generation from the Scratchpad (blue) and combines them with the meta.xml which describes the information in the archive. For eMonocot Scratchpads the emonocot_dwca module (green) provides an intermediary function replacing the Scratchpads internal unique identifiers with those used throughout the eMonocot project (see eMonocot modifications section).

Figure 3.

A single Taxon Description node on a Scratchpad corresponds to one or more rows in the description.txt file.