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The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web

Brian J Stucky1*, John Deck2, Tom Conlin3, Lukasz Ziemba4, Nico Cellinese4 and Robert Guralnick13

Author Affiliations

1 Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA

2 Berkeley Natural History Museums, University of California, Berkeley, California, USA

3 Museum of Natural History, University of Colorado, Boulder, Colorado, USA

4 Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA

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BMC Bioinformatics 2014, 15:257  doi:10.1186/1471-2105-15-257

Published: 29 July 2014

Abstract

Background

Recent years have brought great progress in efforts to digitize the world’s biodiversity data, but integrating data from many different providers, and across research domains, remains challenging. Semantic Web technologies have been widely recognized by biodiversity scientists for their potential to help solve this problem, yet these technologies have so far seen little use for biodiversity data. Such slow uptake has been due, in part, to the relative complexity of Semantic Web technologies along with a lack of domain-specific software tools to help non-experts publish their data to the Semantic Web.

Results

The BiSciCol Triplifier is new software that greatly simplifies the process of converting biodiversity data in standard, tabular formats, such as Darwin Core-Archives, into Semantic Web-ready Resource Description Framework (RDF) representations. The Triplifier uses a vocabulary based on the popular Darwin Core standard, includes both Web-based and command-line interfaces, and is fully open-source software.

Conclusions

Unlike most other RDF conversion tools, the Triplifier does not require detailed familiarity with core Semantic Web technologies, and it is tailored to a widely popular biodiversity data format and vocabulary standard. As a result, the Triplifier can often fully automate the conversion of biodiversity data to RDF, thereby making the Semantic Web much more accessible to biodiversity scientists who might otherwise have relatively little knowledge of Semantic Web technologies. Easy availability of biodiversity data as RDF will allow researchers to combine data from disparate sources and analyze them with powerful linked data querying tools. However, before software like the Triplifier, and Semantic Web technologies in general, can reach their full potential for biodiversity science, the biodiversity informatics community must address several critical challenges, such as the widespread failure to use robust, globally unique identifiers for biodiversity data.

Keywords:
Biocollections; Biodiversity informatics; Darwin core; Linked data; Ontology; RDF; Semantic web; SPARQL