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Title: Modeling biomedical experimental processes with OBI
Authors: Brinkman, RR
Courtot, M
Derom, D
Fostel, JM
He, Y
Lord, P
Malone, J
Parkinson, H
Peters, B
Rocca-Serra, P
Ruttenberg, A
Sansone, S-A
Soldatova, LN
Stoeckert, CJ
Turner, JA
Zheng, J
Keywords: Ontology for Biomedical Investigations (OBI);Biomedical experiments;Data exchange;Data integration;Semantic Web
Issue Date: 2010
Publisher: Biomed Central
Citation: Journal of Biomedical Semantics, 1(Suppl 1): Article no. S7, 2010
Abstract: Background: Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange and information retrieval. Results: The Ontology for Biomedical Investigations (OBI), developed as a global, cross-community effort, provides a resource that represents biomedical investigations in an explicit and integrative framework. Here we detail three real-world applications of OBI, provide detailed modeling information and explain how to use OBI. Conclusion: We demonstrate how OBI can be applied to different biomedical investigations to both facilitate interpretation of the experimental process and increase the computational processing and integration within the Semantic Web. The logical definitions of the entities involved allow computers to unambiguously understand and integrate different biological experimental processes and their relevant components. Availability: OBI is available at
Description: © 2010 Soldatova et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
ISSN: 2041-1480
Appears in Collections:Computer Science
Dept of Computer Science Research Papers

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