Modeling biomedical experimental processes with OBI

By R. Brinkman, Mélanie Courtot, D. Derom, J. Fostel, Yongqun Oliver He, Phillip W. Lord, J. Malone, H. Parkinson, Björn Peters, Philippe Rocca-Serra and 7 more. Journal of Biomedical Semantics, 2010

306 citations recorded by the source corpus.

BackgroundExperimental 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.ResultsThe 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.ConclusionWe 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.AvailabilityOBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl

Subfields: Artificial Intelligence, Information Systems and Management, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/38eb611384cd2d3083ec0a04658615f7466a46d6

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Mauno Vihinen

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Citations in the corpus

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability (2016, background): “…of the CL, Cell Line Ontology (CLO) [25], Reagent Ontology (ReO) [26], the Gene Ontology [9], and Ontology for Biomedical Investigations (OBI) [27], have agreed that the root class ‘ cell ’ (CL:0000000) in CL should be regarded as the root of all cell type classes in OBO Foundry ontologies…”
Uberon, an integrative multi-species anatomy ontology (2012, background): “Such an ontology would also form a vital building block in the modular development of a number of ontologies, such as Gene Ontology (GO), the Cell Ontology (CL) and the Ontology of Biomedical Investigations (OBI), each of which has a need to reference anatomical terms representing multiple species o”
Finding Our Way through Phenotypes (2015, background): “The prospects of computable phenotype data have slowly improved over the past several years, with several domain-specific initiatives yielding results [21,30,32,94,95] and a larger framework of data integration resources [96–100].”
Standardized description of scientific evidence using the Evidence Ontology (ECO) (2014, background): “php/OBO_Foundry_Wo rkshop_2009) including (i) inconsistent mixing of ‘is_a’ relations based on experimental methodology, commercial platform, types of reagents used, measurement objective and analyte being measured; (ii) incomplete or entirely lacking term definitions; (iii) a lack of active develop”