Ontology for Biomedical Investigations
Abbreviation: OBI
This record replaces or incorporates the following deprecated resources:
Homepage http://obi-ontology.org/
Countries that developed this resource European Union , United Kingdom , United States
Created in 2008
Taxonomic range
Knowledge Domains
Subjects
How to cite this record FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Feb. 8, 2021, 1:22 p.m.; Last accessed: Apr 17 2021 1 p.m.
Publication for citation The Ontology for Biomedical Investigations. Bandrowski A, Brinkman R, Brochhausen M et al; PLoS One ; 2016; 10.1371/journal.pone.0154556;
Record updated: Feb. 8, 2021, 1:06 p.m. by The FAIRsharing Team.
forum | GitHub Issue Tracker |
Mailing List | OBI Users Mailing List |
Mailing List | OBI Development Mailing List |
online documentation | OBI Development Call Agenda |
online documentation | OBI Term Guidelines |
online documentation | OBI Wiki |
online documentation | GitHub Repository |
Additional Information
Contact | Bjoern Peters ORCID |
External Links
Bioportal | http://bioportal.bioontology.org/ontologies/OBI |
OBO | http://obofoundry.org/ontology/obi.html |
No XSD schemas defined
Conditions of Use
Applies to: Data useData Release
download | http://purl.obolibrary.org/obo/obi.owl |
Data Access
Browse (Ontobee) | http://www.ontobee.org/ontology/OBI |
Browse (OLS) | https://www.ebi.ac.uk/ols/ontologies/obi |
Query enhancement through the practical application of ontology: the IEDB and OBI.
Vita R,Overton JA,Greenbaum JA,Sette A,Peters B
J Biomed Semantics 2013
Modeling biomedical experimental processes with OBI.
Brinkman RR,Courtot M,Derom D,Fostel JM,He Y,Lord P,Malone J,Parkinson H,Peters B,Rocca-Serra P,Ruttenberg A,Sansone SA,Soldatova LN,Stoeckert CJ Jr,Turner JA,Zheng J
J Biomed Semantics 2010
Minimum Information about a Genotyping Experiment (MIGEN).
Huang J,Mirel D,Pugh E,Xing C,Robinson PN,Pertsemlidis A,Ding L,Kozlitina J,Maher J,Rios J,Story M,Marthandan N,Scheuermann RH
Stand Genomic Sci 2011
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.
Rocca-Serra P,Walls R,Parnell J,Gallery R,Zheng J,Sansone SA,Gonzalez-Beltran A
Database (Oxford) 2015
The Ontology for Biomedical Investigations.
Bandrowski A, Brinkman R, Brochhausen M et al
PLoS One 2016
View in BioPortal.
View in OBO Foundry.
Reporting Guidelines
Terminology Artifacts
- Chemical Entities of Biological Interest
- Cell Ontology
- Neural ElectroMagnetic Ontologies
- Evidence and Conclusion Ontology
- CHEMical INFormation Ontology
- Ontology of Medically Related Social Entities
- Information Artifact Ontology
- Gene Ontology
- Basic Formal Ontology
- Vaccine Ontology
- Neuroscience Information Framework Standard Ontology
- Adverse Event Reporting ontology
- Ontology for Drug Discovery Investigations
- Semanticscience Integrated Ontology
- Ontology of Core Data Mining Entities
- Bioinformatics Web Service Ontology
- Ontology of Experimental Variables and Values
- eagle-i Research Resource Ontology
- Ontology for Genetic Interval
- Ontology of Immune Epitopes
- UBER anatomy ONtology
- VIVO Integrated Semantic Framework Ontology
- Microarray and Gene Expression Data Ontology
- Influenza Ontology
- The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology
- NGS ontology
- VIVO Ontology
- Ontology of Biological and Clinical Statistics
- Genomic Epidemiology Ontology
- Obstetric and Neonatal Ontology
- Chemical Methods Ontology
- Ontology for Nutritional Studies
- Subject Resource Application Ontology
- Domain Resource Application Ontology
- Blood Ontology
- Ontology of Prokaryotic Phenotypic and Metabolic Characters
Models and Formats
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
Comparison system for cancer stem cell analysis
Virus Pathogen Database and Analysis Resource
The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. The database is available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.
Influenza Research Database
The Influenza Research Database (IRD) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization, and comparative genomics analysis, together with personal login- protected ‘workbench’ spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature.
Eukaryotic Pathogen, Vector and Host Informatics Resource
The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB) focuses on eukaryotic pathogens and invertebrate vectors of infectious diseases, , encompassing data from prior resources devoted to parasitic species (EuPathDB), fungi (FungiDB) and vector species (VectorBase). While each of the taxonomic groups within this resource is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all of these resources, and the opportunity to leverage orthology for searches across genera.
Neuroscience Information Framework (NIF)
NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web.
Immunology Database and Analysis Portal
The Immunology Database and Analysis Portal (ImmPort) data repository was created for the exploration of clinical and basic research data on immunology and associated findings. ImmPort intends to promote effective data sharing across the basic, clinical and translational research communities. It collects data both from clinical and mechanistic studies on human subjects and from immunology studies on model organisms. The ImmPort ecosystem consists of four components: private data, shared data, data analysis, and resources-for data archiving, dissemination, analyses, and reuse.
ENCODE Project
The ENCODE (Encyclopedia of DNA Elements) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. ENCODE results from 2007 and later are available from this project. This covers data generated during the two production phases 2007-2012 and 2013-present.
Gemma
Gemma is a database for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize co-expression and differential expression results.
Immune Epitope Database
The IEDB provides the scientific community with a central repository of freely accessible epitope data and epitope prediction and analysis resources. The IEDB is a publicly accessible, comprehensive immune epitope database containing peptidic linear and conformational epitopes and non peptidic epitopes such as lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody, T cell, MHC binding or MHC ligand elution experimental assays. Epitope data related to infectious diseases, allergy, autoimmunity and transplant tested in humans, non human primates, and any other species can be found in the IEDB.
Harvard Dataverse
Harvard Dataverse is a research data repository running on the open source web application Dataverse. Harvard Dataverse is fully open to the public, and allows upload and browsing of data from all fields of research, and is free for all researchers worldwide (up to 1 TB). Links to related grants, authors, software and research products are provided. Harvard Dataverse supports managed access (with an access request workflow) as well as embargoing generally and during peer review. Dataverse allows users to share, preserve, cite, explore, and analyse research data. It facilitates making data available to others, and allows you to replicate others' work more easily. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive academic credit and web visibility. The Harvard Database receives support from Harvard University, public and private grants, and an emergent consortium model.
Alliance of Genome Resources
The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.
OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.
Portail Data INRAE
Portail Data INRAE is offered by INRAE as part of its mission to open the results of its research. INRAE is Europe’s top agricultural research institute and the world’s number two centre for the agricultural sciences. Data INRAE will share research data in relation to food, nutrition, agriculture and environment. It includes experimental, simulation and observation data, omics data, survey and text data. Only data produced by or in collaboration with INRAE will be hosted in the repository, but anyone can access the metadata and the open data. Data INRAE is built on software from the Dataverse Project.
Metabolomic Repository Bordeaux
MeRy-B is a plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants.
e-cienciaDatos
e-cienciaDatos is a multidisciplinary data repository that houses the scientific datasets of researchers from the public universities of the Community of Madrid and the UNED, members of the Consorcio Madroño, in order to give visibility to these data. The purpose of this repository is to ensure data preservation and to facilitate data access and reuse. e-cienciaDatos collects datasets from of each of the member universities. e-cienciaDatos offers the deposit and publication of datasets, assigning a digital object identifier DOI to each of them. The association of a dataset with a DOI will facilitate data verification, dissemination, reuse, impact and long-term access. In addition, the repository provides a standardized citation for each dataset, which contains sufficient information so that it can be identified and located, including the DOI.
DataverseNO
DataverseNO (https://dataverse.no/) is a national, generic repository for open research data, owned and operated by UiT The Arctic University of Norway. DataverseNO is aligned with the FAIR Guiding Principles for scientific data management and stewardship. The technical infrastructure of the repository is based on the open source application Dataverse, which is developed by an international developer and user community led by Harvard University. DataverseNO is CoreTrustSeal certified.
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Record Maintainer
Funds
California Institute for Regenerative Medicine (Government body)
European Network of Excellence (Consortium)
Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
European Commission (Government body)
European Network of Excellence (ENFIN), Hinxton, Cambridgeshire, UK (Government body)
National Science Foundation (NSF), USA (Government body)
Engineering and Physical Sciences Research Council (EPSRC), UK (Government body)
National Institute of Allergy and Infectious Diseases (NIAD), Bethesda, MD, USA (Government body)
National Institutes of Health (NIH), Bethesda, MD, USA (Government body)
Maintains
OBI consortium (Consortium) Lead
Grant Number(s)
1458400 (National Science Foundation (NSF), USA)
1U19AI118626 (National Institutes of Health (NIH), Bethesda, MD, USA)
503630 (European Network of Excellence (ENFIN), Hinxton, Cambridgeshire, UK)
BB/C008200/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/E025080/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/E025080/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/G000638/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/G000638/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/I000917/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
BB/L024101/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)
EP/K030582/1 (Engineering and Physical Sciences Research Council (EPSRC), UK)
EP/M015661/1 (Engineering and Physical Sciences Research Council (EPSRC), UK)
GC1R-06673-B (California Institute for Regenerative Medicine)
H2020-EU.1.4.1.3 654241 (European Commission)
H2020-EU.3.1 634107 (European Commission)
HHSN272201200010C (National Institutes of Health (NIH), Bethesda, MD, USA)
HHSN272201400028C (National Institutes of Health (NIH), Bethesda, MD, USA)
HHSN272201400030C (National Institutes of Health (NIH), Bethesda, MD, USA)
P41 HG003619 (National Institutes of Health (NIH), Bethesda, MD, USA)
R01AI081062 (National Institute of Allergy and Infectious Diseases (NIAD), Bethesda, MD, USA)
R01GM093132 (National Institutes of Health (NIH), Bethesda, MD, USA)
U01 DK 072473 (National Institutes of Health (NIH), Bethesda, MD, USA)