standards > terminology artifact > DOI:10.25504/FAIRsharing.284e1z
Help us curate and collate the databases and standards useful for COVID-19 research. Our COVID-19 Collection (https://fairsharing.org/collection/COVID19Resources) is growing, but not yet complete. Join our community curatathon and tell us what's missing. Email contact@fairsharing.org to join!


ready Ontology for Biomedical Investigations

Abbreviation: OBI


Recommended
General Information
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 fosters clear communication about scientific investigations by defining more than 2500 terms for assays, devices, objectives, and more.


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



In the following recommendations:



How to cite this record FAIRsharing.org: OBI; Ontology for Biomedical Investigations; DOI: https://doi.org/10.25504/FAIRsharing.284e1z; Last edited: Aug. 5, 2019, 1:22 p.m.; Last accessed: Apr 06 2020 6:53 a.m.

Publication for citation  The Ontology for Biomedical Investigations. 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 SA,Scheuermann RH,Schober D,Smith B,Soldatova LN,Stoeckert CJ Jr,Taylor CF,Torniai C,Turner JA,Vita R,Whetzel PL,Zheng J; PLoS One ; 2016; 10.1371/journal.pone.0154556;


This record is maintained by bpeters  ORCID

Record updated: July 11, 2019, 3:23 p.m. by The FAIRsharing Team.

Show edit history


In Collections
Cell Migration Standardisation Organisation
bioCADDIE
eTRIKS Standards Starter Pack


Support

General

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

Tools

    No tools defined


Schemas

No XSD schemas defined


Access / Retrieve Data

Conditions of Use

Applies to: Data use

Data 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



Publications

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

View Paper (PubMed) View Publication

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

View Paper (PubMed) View Publication

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

View Paper (PubMed) View Publication

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

View Paper (PubMed) View Publication

The Ontology for Biomedical Investigations.

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 SA,Scheuermann RH,Schober D,Smith B,Soldatova LN,Stoeckert CJ Jr,Taylor CF,Torniai C,Turner JA,Vita R,Whetzel PL,Zheng J
PLoS One 2016

View Paper (PubMed) View Publication

OBI Ontology Display

View in BioPortal.


Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.

View in OBO Foundry.




Implementing Databases (11)
Stem Cell Discovery Engine
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 Database Resources
EuPathDB is an integrated database covering the eukaryotic pathogens. 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 ImmPort system serves as a long-term, sustainable archive of immunology research data generated by investigators mainly funded through the NIAID/DAIT. The core component of the ImmPort system is an extensive data warehouse containing an integration of experimental data and clinical trial data. The analytical tools created and integrated as part of the ImmPort system are available to any researcher within ImmPort after registration and approval by DAIT. Additionally, the data provided mainly by NIAID/DAIT funded researchers in ImmPort will be available to all registered users after the appropriate embargo time. ImmPort, is the data submission portal where researchers upload, QC, and curate their data prior to sharing in OpenImmPort.
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.
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.
Metabolomic Repository Bordeaux
MeRy-B is a plant metabolomics platform allowing the storage and visualisation of Nuclear Magnetic Resonance (NMR) metabolic profiles from plants.

Scroll for more...



Credit

Record Maintainer

Funds

Maintains

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)