The Ontology for Biomedical Investigations

Anita Bandrowski; Ryan Brinkman; Mathias Brochhausen; Matthew H. Brush; Bill Bug; Marcus C. Chibucos; Kevin Clancy; Melanie Courtot; Dirk Derom; Michel Dumontier; Liju Fan; Jennifer Fostel; Gilberto Fragoso; Frank Gibson; Alejandra Gonzalez-Beltran; Melissa A. Haendel; Yongqun He; Mervi Heiskanen; Tina Hernandez-Boussard; Mark Jensen; Yu 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., Jr. Stoeckert; Chris F. Taylor; Carlo Torniai; Jessica A. Turner; Randi Vita; Patricia L. Whetzel; Jie Zheng

doi:10.1371/journal.pone.0154556

The Ontology for Biomedical Investigations

Anita Bandrowski^*, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Melanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. 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., Jr. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel, Jie Zheng

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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 language	English
Journal	PLOS ONE
Volume	11
Issue number	4
DOIs	https://doi.org/10.1371/journal.pone.0154556
Publication status	Published - 29 Apr 2016
Externally published	Yes

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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, 11(4). https://doi.org/10.1371/journal.pone.0154556

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title = "The Ontology for Biomedical Investigations",

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.",

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

year = "2016",

month = apr,

day = "29",

doi = "10.1371/journal.pone.0154556",

language = "English",

volume = "11",

journal = "PLOS ONE",

issn = "1932-6203",

publisher = "Public Library of Science",

number = "4",

}

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, MA, 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, S-A, Scheuermann, RH, Schober, D, Smith, B, Soldatova, LN, Stoeckert, CJJ, Taylor, CF, Torniai, C, Turner, JA, Vita, R, Whetzel, PL & Zheng, J 2016, 'The Ontology for Biomedical Investigations', PLOS ONE, vol. 11, no. 4. https://doi.org/10.1371/journal.pone.0154556

TY - JOUR

T1 - The Ontology for Biomedical Investigations

AU - Bandrowski, Anita

AU - Brinkman, Ryan

AU - Brochhausen, Mathias

AU - Brush, Matthew H.

AU - Bug, Bill

AU - Chibucos, Marcus C.

AU - Clancy, Kevin

AU - Courtot, Melanie

AU - Derom, Dirk

AU - Dumontier, Michel

AU - Fan, Liju

AU - Fostel, Jennifer

AU - Fragoso, Gilberto

AU - Gibson, Frank

AU - Gonzalez-Beltran, Alejandra

AU - Haendel, Melissa A.

AU - He, Yongqun

AU - Heiskanen, Mervi

AU - Hernandez-Boussard, Tina

AU - Jensen, Mark

AU - Lin, Yu

AU - Lister, Allyson L.

AU - Lord, Phillip

AU - Malone, James

AU - Manduchi, Elisabetta

AU - McGee, Monnie

AU - Morrison, Norman

AU - Overton, James A.

AU - Parkinson, Helen

AU - Peters, Bjoern

AU - Rocca-Serra, Philippe

AU - Ruttenberg, Alan

AU - Sansone, Susanna-Assunta

AU - Scheuermann, Richard H.

AU - Schober, Daniel

AU - Smith, Barry

AU - Soldatova, Larisa N.

AU - Stoeckert, Christian J., Jr.

AU - Taylor, Chris F.

AU - Torniai, Carlo

AU - Turner, Jessica A.

AU - Vita, Randi

AU - Whetzel, Patricia L.

AU - Zheng, Jie

PY - 2016/4/29

Y1 - 2016/4/29

N2 - 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.

AB - 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.

U2 - 10.1371/journal.pone.0154556

DO - 10.1371/journal.pone.0154556

M3 - Article

SN - 1932-6203

VL - 11

JO - PLOS ONE

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