Abstract
AbstractThe goal of OBI is to enable a formal representation of biomedical investigations that captures the experimental evidence on which their findings are based. The scope of OBI includes: materials made in and produced for investigations, research objectives, experimental protocols, roles of people in investigations and processing and publication of data gathered in investigations. Use of OBI will allow comparison of experimental data from the wide array of scientific disciplines represented by domain experts in the OBI consortium. OBI follows the principles laid out by the OBO foundry, and integrates tightly with other foundry candidate ontologies, such as GO (www.geneontology.org) and ChEBI (www.ebi.ac.uk/chebi/) whose terms are used to describe biological reality. The use of OBI by the scientific community to represent or annotate their investigations within electronic data resources will facilitate interdisciplinary data synthesis, enable access to their data on the semantic web and improve third-party understanding of information related to life-science and clinical investigations.
Highlights
Information derived from biomedical investigations is increasingly being captured in structured electronic formats and made available through public database resources as a complement to reporting in traditional journal publications
The upper level consists of the Basic Formal Ontology (BFO) classes material entity, process, role and function, and the Information Artifact Ontology (IAO) class information content entity
Ontology for Biomedical Investigations (OBI) was chosen as the basis for these forms because it provides a framework for modeling the generation of the desired data through its use of planned processes in which external ontologies can be referenced
Summary
Information derived from biomedical investigations is increasingly being captured in structured electronic formats and made available through public database resources as a complement to reporting in traditional journal publications. To support interoperability between different database systems, the key features of an investigation need to be described in a common, shared and unambiguous manner This requires standards for the representation of samples, assays and data analysis methods used in an investigation. Org/TR/owl2-overview/), which is a World Wide Web Consortium (W3C; http://www.w3.org) ontology language developed for the semantic web (see Methodology) It supports and augments existing community standards such as Microarray Gene Expression tab-delimited format (MAGE-TAB)[5], Functional Genomics Experiment (FuGE)[1] and Investigation, Study, Assay tab-delimited format (ISA-Tab)[4]. OBI is publicly and freely available under the Creative Commons Attribution (CC-by) 3.0 license It is a community based, globally distributed grass-roots project in the tradition of many standardization efforts that have joined forces in this endeavor[6,7,8,9]. Further enhancements of OBI in terms of breadth and depth of coverage are driven by the participating consortium members; we welcome and encourage broader community participation in this open, collaborative ontology development effort
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