Ontology Browsers

  • OBO Foundry
  • BioPortal: has over 700 biomedical ontologies, including the OBO Foundry ontologies. Users can search for terms or browse individual ontologies. BioPortal also provides tools to aid in increasing ontology interoperability.
  • Ontology Lookup Service (OLS): lets users search for terms across all ontologies, or individual ontologies, as well as view term hierarchies. OLS also has an API so that ontologies can be browsed programmatically.
  • Ontobee: Part of the Onto-Animal tool collection. Users can search all available ontologies and browse detailed descriptions of individiual terms. OntoBee is the default server for most OBO Foundry ontology IRIs.
  • AberOWL: A repository of biological ontologies and access to reasoned versions of those ontologies. Ontolgies can be browsed by term labels or queried by Manchester OWL syntax statements.
  • QuickGO
  • AmiGO
  • Linked Open Vocabularies

Tutorials

Ontology Tools

  • Ontology Development Kit (ODK): A toolkit for initializing a new ontology repository. The template includes a structured directory, a Makefile with automated release workflows, continuous integration testing, and full documentation.
  • ROBOT: A command line tool to automate ontology workflows. It includes commands that can be used manually or integrated in automated processes to develop and release ontologies.
  • Protégé: An ontology editing environment for OWL ontologies. It allows developers to visualize the ontology hierarchy, add and edit ontology terms, reason over the ontology, and more.
  • Onto-Animals: Tools to extract external ontology terms, compare ontologies, edit ontology terms, query and visualize ontologies, and more.
  • VOCOL: An integrated environment for collaborative vocabulary development
  • Karma Data Integration: A data integration tool
  • Ontofox: An ontology term and relation extraction and reuse tool
  • Ubergraph: A sparql endpoint with many OBO ontologies loaded and pre-reasoned with simple triples materialized

Ontology Analysis

  • OBO Dashboard: An assesment of OBO Foundry ontologies’ conformance to OBO Foundry principles
  • OBO Community Health Report: A self-updating assessment of the quality of metadata, responsiveness of the maintainers, and the overall community engagement for each OBO Foundry ontology.
  • Ontology Quality Assessment: A self-updating assesment of the semantic quality of OBO Foundry ontologies and beyond (using known prefixes, using standard identifiers, etc.)

Relevant Publications/blogs