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Ontologies: Technology | BioMedBridges

Ontologies: Technology

This page contains information on ontology technologies; including links to ontology research centres, APIs, tools and resources.


Ontology Resources

  • Bubastis -  tool to detect logical differences between ontologies, such as between versions of an ontology

  • ELKOWL - an ontology reasoner

  • EL-OWL - Lightweight description logic, a fragment of OWL
  • HermiT - OWL reasoner

  • OBO - Open Biomedical Ontologies; collaboration to create shared ontologies for biology and medicine

  • OBO-Foundry - collaborative resources for the OBO experiment
  • Listings of ontologies
  • Development principles
  • Technical infrastructure and support
  • OWL - Web Ontology Language; a semantic web processing language
  • an introduction can be found here: w3schools
  • a tutorial and other resources can be found here: CO-ODE Resources
  • Pellet - an OWL 2 reasoner for Java

  • Protege - Ontology Editor
  • Variants for OWL, RDF(S) and XML
  • SKOS - Simple Knowledge Organisation Systems, standardised representation of knowledge organisation systems
  • uses RDF
  • a tutorial for SKOS can be found here: SKOS Resources
  • Spreadsheets - yes, really! You can use spreadsheets to get data from domain experts that can then be sucked into OWL.

Annotation Tools

  • NCBO annotator - quick way of grabbing annotations for a piece of text; no scoring system though

  • Whatizit - simple text-mining tool with pre-defined tasks

  • Terminizer - tool to annotate ontological terms in text
  • limited to OBO ontologies

Ontology APIs

  • Jena - Java framework for creating Semantic Web applications

  • OntoCAT - Java and R api for programmatic ontology sources
  • OLS, BioPortal and OWL
  • project expertise at EBI and UMCG
  • OWL API - Java API for manipulating the OWL ontologies

  • URIgen - Java API tool to generate URIs for ontology terms

Editing Tools

  • Bamboo - a continuous integration framework
  • used to perform checks during code commits
  • perform build plans, such as releasing the EFO ontology
  • OBO-edit - open-source Java editor for OBO ontologies

  • Phenotator - phenotypes annotation tool; allows you to create ‘entity-quality’ pairs for each phenotype.