The RDF foundry: call for an initiative to build enhanced RDF resources for biological data integration

  • Authors:

  • Aravind Venkatesan;Ward Blondé;Erick Antezana;Mats Skillingstad;M Scott Marshall;Bernard De Baets;Vladimir Mironov;Martin Kuiper

  • Affiliations:

  • Norwegian University of Science and Technology (NTNU), Høgskoleringen, Trondheim, Norway;Ghent University, Ghent, Belgium;Norwegian University of Science and Technology (NTNU), Høgskoleringen, Trondheim, Norway;Norwegian University of Science and Technology (NTNU), Høgskoleringen, Trondheim, Norway;University of Amsterdam, The Netherlands;Ghent University, Ghent, Belgium;Norwegian University of Science and Technology (NTNU), Høgskoleringen, Trondheim, Norway;Norwegian University of Science and Technology (NTNU), Høgskoleringen, Trondheim, Norway

  • Venue:
  • Proceedings of the International Conference on Web Intelligence, Mining and Semantics
  • Year:
  • 2011

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Abstract

Currently, the OBO Foundry plays an important role by setting guidelines to formalise the concepts within the biomedical domain. The ontologies within the OBO Foundry are usually represented in the OBO ontology language. While being human-readable, this language lacks the computational rigour required for the Semantic Web (SW). Consequently, the RDF and OWL languages, both fundamental components of the SW technology stack, are being increasingly adopted by the biomedical community to exchange biological knowledge in a computer intelligible form. Some of the OBO- formatted ontologies have been made available in OWL, thus signalling a move towards the SW. OWL provides support for automated reasoning, which is its raison d'être. Unfortunately, automated reasoning on the massive volumes of data that are typical of the biomedical domain is riddled with performance limitations. Due to consistent support for the SPARQL specification in triple store implementations, as well as the ability to simulate some types of reasoning with pre-computed closures, RDF has evolved into a language of choice for knowledge exchange within the framework of the SW. Here, we discuss the need to establish a foundry charged with the task of harmonizing biomedical RDF resources, acting along the same lines as the OBO Foundry. To substantiate the need for an RDF Foundry, we provide the outcome of a small survey we have conducted to highlight the domain coverage, redundancies, and comprehensiveness of results obtained from a few representative distributed resources available today.