NDLI: The Ontology for Biomedical Investigations

Content Provider	PubMed Central
Author	Bandrowski, Anita Brinkman, Ryan Brochhausen, Mathias Brush, Matthew H. Bill, Bug Chibucos, Marcus C. Clancy, Kevin Courtot, Mélanie Dirk, Derom Dumontier, Michel Fan, Liju Jennifer, Fostel Fragoso, Gilberto Gibson, Frank Gonzalez-beltran, Alejandra Haendel, Melissa A. He, Yongqun Heiskanen, Mervi Tina, Hernandez-boussard 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. Carlo, Torniai Turner, Jessica A. Vita, Randi Whetzel, Patricia L. Zheng, Jie
Editor	Xue, Yu
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.
Related Links	http://dx.doi.org/10.1371/journal.pone.0154556
Starting Page	154556
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	4
Volume Number	11
Language	English
Publisher	Public Library of Science
Publisher Date	2016-04-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Measuring the Evolution of Ontology Complexity: The Gene Ontology Case Study

Cross-Ontology Multi-level Association Rule Mining in the Gene Ontology

TrOn: An Anatomical Ontology for the Beetle Tribolium castaneum

Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology

Representing Kidney Development Using the Gene Ontology

Construction of Ontology Augmented Networks for Protein Complex Prediction

On the Ontology Based Representation of Cell Lines

Standardization of assay representation in the Ontology for Biomedical Investigations

ProKinO: An Ontology for Integrative Analysis of Protein Kinases in Cancer

The Ontology for Biomedical Investigations

Similar Documents

Measuring the Evolution of Ontology Complexity: The Gene Ontology Case Study

Cross-Ontology Multi-level Association Rule Mining in the Gene Ontology

TrOn: An Anatomical Ontology for the Beetle Tribolium castaneum

Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology

Representing Kidney Development Using the Gene Ontology

Construction of Ontology Augmented Networks for Protein Complex Prediction

On the Ontology Based Representation of Cell Lines

Standardization of assay representation in the Ontology for Biomedical Investigations

ProKinO: An Ontology for Integrative Analysis of Protein Kinases in Cancer

The Ontology for Biomedical Investigations