logo Ontology for Biomedical Investigations

An integrated ontology for the description of life-science and clinical investigations

The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of life-science and clinical investigations.

Products

obi.owl OBI The full version of OBI in OWL format
obi.obo OBI in OBO The OBO-format version of OBI
obi/obi_core.owl OBI Core A collection of important high-level terms and their relations from OBI and other ontologies
obi/obi-base.owl OBI Base module Base module for OBI

Usages

User
https://www.iedb.org
Description
The Immune Epitope Database (IEDB) is funded by NIAID that catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation.
Examples
A specific assay curated in the IEDB using the OBI:1110180 '3H-thymidine assay measuring epitope specific proliferation of T cells' ('3H-thymidine')
User
https://www.encodeproject.org/
Description
ENCODE is 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.
Examples
A specific assay annotated in ENCODE using OBI:0000716 'ChiP-seq'
User
https://genelab-data.ndc.nasa.gov/genelab/projects
Description
The NASA GeneLab data repository hosts space biology and space-related datasets funded by multiple space agencies around the world.
Examples
A specific assay annotated in NASA GeneLab using OBI:0001271 'RNA-seq assay'
User
https://app.nih-cfde.org/
Description
The CFDE is providing a centralized metadata resource to allow search across data coordination centers from multiple Common Fund programs.
Examples
OBI is used in CFDE to captures types of experiments with assay terms such as OBI:0003094 'fluorescence in-situ hybridization assay'
User
http://www.neuinfo.org
Description
NIF is a dynamic inventory of Web-based neuroscience resources, data, and tools accessible via any computer connected to the Internet.
Examples
A specific OBI term used to autocomplete in NIF search OBI:0100026 'organism'