The Ontology for Biomedical Investigations

By Anita E. Bandrowski, Ryan Remy Brinkman, M. Brochhausen, Matthew H. Brush, B. Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, D. Derom, M. Dumontier and 34 more. PLoS ONE, 2016

373 citations recorded by the source corpus.

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/205a6afb71c95a11aa1b7340f0012183142c31dd

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Citations in the corpus

The Immune Epitope Database (IEDB): 2018 update (2018, methodology): “For example, by using the Ontology of Biomedical Investigations (OBI) (11) to drive the IEDB Assay Finder, users can search for all T cell assays, all T cell assays measuring cytokines, or all T cell assays measuring a specific cytokine, such as IL2 because OBI logically defines its assay terms acco”
Human Disease Ontology 2018 update: classification, content and workflow expansion (2018, methodology): “ROBOT, developed in Java and available open source on GitHub (https://github.com/ ontodev/robot), has also been implemented in other OBO Foundry ontologies such as the Ontology for Biomedical Investigations (24), the Gene Ontology (25), the Evidence and Conclusion (ECO) ontology (26) and the Immune ”
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species (2016, methodology): “SEPIO will also integrate biological assays from the Ontology of Biomedical Investigations (61).”