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Open Access Highly Accessed Short Report

The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions

Bernard de Bono13*, Robert Hoehndorf2, Sarala Wimalaratne1, George Gkoutos2 and Pierre Grenon1

Author Affiliations

1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK

2 Dept. of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK

3 Auckland Bioengineering Institute, University of Auckland, Symonds Street, Auckland 1010, New Zealand

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BMC Research Notes 2011, 4:313  doi:10.1186/1756-0500-4-313

Published: 30 August 2011

Abstract

Background

The practice and research of medicine generates considerable quantities of data and model resources (DMRs). Although in principle biomedical resources are re-usable, in practice few can currently be shared. In particular, the clinical communities in physiology and pharmacology research, as well as medical education, (i.e. PPME communities) are facing considerable operational and technical obstacles in sharing data and models.

Findings

We outline the efforts of the PPME communities to achieve automated semantic interoperability for clinical resource documentation in collaboration with the RICORDO project. Current community practices in resource documentation and knowledge management are overviewed. Furthermore, requirements and improvements sought by the PPME communities to current documentation practices are discussed. The RICORDO plan and effort in creating a representational framework and associated open software toolkit for the automated management of PPME metadata resources is also described.

Conclusions

RICORDO is providing the PPME community with tools to effect, share and reason over clinical resource annotations. This work is contributing to the semantic interoperability of DMRs through ontology-based annotation by (i) supporting more effective navigation and re-use of clinical DMRs, as well as (ii) sustaining interoperability operations based on the criterion of biological similarity. Operations facilitated by RICORDO will range from automated dataset matching to model merging and managing complex simulation workflows. In effect, RICORDO is contributing to community standards for resource sharing and interoperability.