The ABCD of primary biodiversity data access

Abstract

Within the context of the Global Biodiversity Information Facility (GBIF), the Biological Collections Access Service (BioCASe) has been set up to foment data provision by natural history content providers. Products include the BioCASe Protocol and the PyWrapper software, a web service allowing to access rich natural history data using complex schemas like ABCD (Access to Biological Collection Data). New developments include the possibility to produce DarwinCore-Archive files using PyWrapper, in order to facilitate the indexing of large datasets by aggregators such as GBIF. However, BioCASe continues to be committed to distributed data access and continues to provide the possibility to directly query the web service for up-to-date data directly from the provider's database. ABCD provides comprehensive coverage of natural history data, and has been extended to cover DNA collections (ABCD-DNA) and geosciences (ABCD-EFG, the extension for geosciences). BioCASe also developed web portal software that allows to access and display rich data provided by special interest networks. We posit that the XML-based networking approach using a highly standardised data definition such as ABCD continues to be a valuable approach towards mobilising natural history information. Some suggestions are made regarding further improvements of ABCD.

Keywords:

• ABCD
• BioCASe
• XML
• primary biodiversity data networks
• GBIF
• open access

Abbreviations:

• ABCD, Access to Biological Collections Databases; ABCD-EFG, ABCD-Extension for Geosciences; BGBM, Botanic Garden and Botanical Museum Berlin-Dahlem; BioCASe, Biological Collection Access Service; BioCASE, Biological Collection Access Service for Europe; BOLD, Barcode of Life Data Systems; DwC, DarwinCore; EDIT, European Distributed Institute of Taxonomy; ENHSIN, European Natural History Specimen Information Network; GBIF, Global Biodiversity Information Facility; GBRDS, Global Biodiversity Resource Discovery System; GeoCASe, Geosciences Collection Access Service; GUID, Globally Unique Identifier; HISPID, Herbarium Information Standards and Protocols for Interchange of Data; HTTP, Hypertext Transfer Protocol; IPT, Integrated Publishing Toolkit; ISO, International Organization for Standardization; MaNIS, Mammal Networked Information System; RDF, Resource Description Framework; REMIB, Red Mundial de Informatióbre Biodiversidad; TAPIR, TDWG Access Protocol for Information Retrieval; TDWG, Taxonomic Databases Working Group; XML, eXtensible Markup Language

Acknowledgements

The authors would like to thank all scientists who have contributed their knowledge to the design and improvement of the ABCD data schema, particularly Charles Copp. The initial BioCASE project has been funded by the European Union under grant number EVR1-2001-00003 BioCASE.