The Ontology for Biomedical Investigations

Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark JensenYu Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel, Jie Zheng

Research output: Contribution to journalArticle

82 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article numbere0154556
JournalPLoS One
Volume11
Issue number4
DOIs
StatePublished - Apr 1 2016

Fingerprint

Biological Ontologies
Ontology
Strigiformes
immunology
planning
genomics
phenotype
methodology

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Bandrowski, A., Brinkman, R., Brochhausen, M., Brush, M. H., Bug, B., Chibucos, M. C., ... Zheng, J. (2016). The Ontology for Biomedical Investigations. PLoS One, 11(4), [e0154556]. https://doi.org/10.1371/journal.pone.0154556

The Ontology for Biomedical Investigations. / Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H.; Bug, Bill; Chibucos, Marcus C.; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L.; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A.; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna Assunta; Scheuermann, Richard H.; Schober, Daniel; Smith, Barry; Soldatova, Larisa N.; Stoeckert, Christian J.; Taylor, Chris F.; Torniai, Carlo; Turner, Jessica A.; Vita, Randi; Whetzel, Patricia L.; Zheng, Jie.

In: PLoS One, Vol. 11, No. 4, e0154556, 01.04.2016.

Research output: Contribution to journalArticle

Bandrowski, A, Brinkman, R, Brochhausen, M, Brush, MH, Bug, B, Chibucos, MC, Clancy, K, Courtot, M, Derom, D, Dumontier, M, Fan, L, Fostel, J, Fragoso, G, Gibson, F, Gonzalez-Beltran, A, Haendel, M, He, Y, Heiskanen, M, Hernandez-Boussard, T, Jensen, M, Lin, Y, Lister, AL, Lord, P, Malone, J, Manduchi, E, McGee, M, Morrison, N, Overton, JA, Parkinson, H, Peters, B, Rocca-Serra, P, Ruttenberg, A, Sansone, SA, Scheuermann, RH, Schober, D, Smith, B, Soldatova, LN, Stoeckert, CJ, Taylor, CF, Torniai, C, Turner, JA, Vita, R, Whetzel, PL & Zheng, J 2016, 'The Ontology for Biomedical Investigations', PLoS One, vol. 11, no. 4, e0154556. https://doi.org/10.1371/journal.pone.0154556
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC et al. The Ontology for Biomedical Investigations. PLoS One. 2016 Apr 1;11(4). e0154556. https://doi.org/10.1371/journal.pone.0154556
Bandrowski, Anita ; Brinkman, Ryan ; Brochhausen, Mathias ; Brush, Matthew H. ; Bug, Bill ; Chibucos, Marcus C. ; Clancy, Kevin ; Courtot, Mélanie ; Derom, Dirk ; Dumontier, Michel ; Fan, Liju ; Fostel, Jennifer ; Fragoso, Gilberto ; Gibson, Frank ; Gonzalez-Beltran, Alejandra ; Haendel, Melissa ; He, Yongqun ; Heiskanen, Mervi ; Hernandez-Boussard, Tina ; Jensen, Mark ; Lin, Yu ; Lister, Allyson L. ; Lord, Phillip ; Malone, James ; Manduchi, Elisabetta ; McGee, Monnie ; Morrison, Norman ; Overton, James A. ; Parkinson, Helen ; Peters, Bjoern ; Rocca-Serra, Philippe ; Ruttenberg, Alan ; Sansone, Susanna Assunta ; Scheuermann, Richard H. ; Schober, Daniel ; Smith, Barry ; Soldatova, Larisa N. ; Stoeckert, Christian J. ; Taylor, Chris F. ; Torniai, Carlo ; Turner, Jessica A. ; Vita, Randi ; Whetzel, Patricia L. ; Zheng, Jie. / The Ontology for Biomedical Investigations. In: PLoS One. 2016 ; Vol. 11, No. 4.
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