The DOI matches its Crossref record; 51 of the 51 references it cites were found in a registry or an index.
The Ontology for Biomedical Investigations
Open accessAbstract
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.
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Cites
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
Database resources of the National Center for Biotechnology Information: update
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Pellet: A practical OWL-DL reasoner
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The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
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Self-citationThe minimum information about a genome sequence (MIGS) specification
Field, D., Garrity, G., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T., Thomson, N., Allen, M. J., Angiuoli, S. V., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt1360 · Cited by 1,141
Self-citationChEBI: a database and ontology for chemical entities of biological interest
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The immune epitope database (IEDB) 3.0
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Self-citationSweetening Ontologies with DOLCE
Gangemi, A., Guarino, N., Masolo, C., Oltramari, A., & Schneider, L. (2002) · Lecture Notes in Computer Science · doi:10.1007/3-540-45810-7_18 · Cited by 1,032
Relations in biomedical ontologies
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Self-citationUberon, an integrative multi-species anatomy ontology
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“Several subclasses of material entity are imported from external ontologies: Classes under organism are imported from the NCBI Taxonomy[18], gross anatomical part and its subclasses from the Uber anatomy ontology (UBERON)[24] or the Common Anatomy Reference Ontology (CARO)[25], and the molecular entity hierarchy from…”
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Cited by
Mungall, C. J., McMurry, J. A., Köhler, S., Balhoff, J. P., Borromeo, C., Brush, M., Carbon, S., Conlin, T., Dunn, N., Engelstad, M., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1128 · Cited by 441
Self-citationThe Immune Epitope Database (IEDB): 2024 update
Vita, R., Blazeska, N., Marrama, D., IEDB Curation Team Members, Shackelford, D., Zalman, L., Foos, G., Zarebski, L., Chan, K., Reardon, B., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1092 · Cited by 274
Self-citationMichie, S., West, R., Finnerty, A. N., Norris, E., Wright, A. J., Marques, M. M., Johnston, M., Kelly, M. P., Thomas, J., & Hastings, J. (2020) · Wellcome Open Research · doi:10.12688/wellcomeopenres.15902.1 · Cited by 76
Cell type discovery and representation in the era of high-content single cell phenotyping
Bakken, T., Cowell, L., Aevermann, B. D., Novotny, M., Hodge, R., Miller, J. A., Lee, A., Chang, I., McCorrison, J., Pulendran, B., et al. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1977-1 · Cited by 55
Self-citationOntologies and Knowledge Graphs in Oncology Research
Silva, M. C., Eugénio, P., Faria, D., & Pesquita, C. (2022) · Cancers · doi:10.3390/cancers14081906 · Cited by 46
Metadata
- Authors
- Bandrowski, A., Brinkman, R., Brochhausen, M., Brush, M. H., Bug, B., Chibucos, M. C., Clancy, K., Courtot, M., Derom, D., Dumontier, M., Fan, L., Fostel, J., Fragoso, G., Gibson, F., Gonzalez-Beltran, A., Haendel, M. A., He, Y., Heiskanen, M., Hernandez-Boussard, T., Jensen, M., Lin, Y., Lister, A. L., Lord, P., Malone, J., Manduchi, E., McGee, M., Morrison, N., Overton, J. A., Parkinson, H., Peters, B., Rocca-Serra, P., Ruttenberg, A., Sansone, S.-A., Scheuermann, R. H., Schober, D., Smith, B., Soldatova, L. N., Stoeckert, C. J., Taylor, C. F., Torniai, C., Turner, J. A., Vita, R., Whetzel, P. L., & Zheng, J.
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2016-04-29
- Volume
- 11
- Issue
- 4
- Pages
- e0154556
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2021074129
- Cited by
- 386
- References
- 51
- FWCI
- 17.91
- Type
- journal article
- Language
- en
- Open access
- gold
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- Bandrowski, A., Brinkman, R., Brochhausen, M., Brush, M. H., Bug, B., Chibucos, M. C., Clancy, K., Courtot, M., Derom, D., Dumontier, M., Fan, L., Fostel, J., Fragoso, G., Gibson, F., Gonzalez-Beltran, A., Haendel, M. A., He, Y., Heiskanen, M., Hernandez-Boussard, T., . . . Zheng, J. (2016). The Ontology for Biomedical Investigations. PLOS ONE. https://doi.org/10.1371/journal.pone.0154556
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