Ontology Tutorials and Resources

Ontology Browsers

• OBO Foundry
• BioPortal
• Ontology Lookup Service
• Ontobee
• QuickGO
• AmiGO
• Linked Open Vocabularies

Tutorials/Slides

• Introduction to Ontologies: slides from Cold Spring Harbor workshop, October 2018.
• Ontology Development 101: A Guide to Creating Your First Ontology by Natalya F. Noy and Deborah L. McGuinness.
• Ontology 101 Tutorial from International Conference on Biological Ontology (ICBO) 2018
• Ontology 101 Open Educational Resource. Funded by NIH BD2K Initiative.
• Learning SPARQL by Bob DuCharme
• ROBOT tutorial by Becky Jackson and James Overton
• Managing Ontologies with the Ontology Development Kit by Chris Mungall

Ontology tools

• Protege: An ontology development software application
• Ontology Development Kit: A toolkit to initialize an OBO library repository and associated files.
• Robot: ROBOT is a an tool for working with Open Biomedical Ontologies. See paper here.
• VOCOL: An Integrated Environment for Collaborative Vocabulary Development.
• Karma Data Integration: A data integration tool.
• Knotation: a notation for knowledge representation.

Relevant Publications

• An Intrepid Guide to Ontologies., by Mike Bergman, posted on May 16, 2007 in Adaptive Information, Description Logics, Ontologies, Semantic Web, Structured Web
• Monkeying around with OWL:, a technical blog on ontologies and ontology engineering by Chris Mungall.
• Feed your head:, a technical blog on ontologies and ontology engineering by Robert Stevens.
• MIRO: guidelines for minimum information for the reporting of an ontology by Nicolas Matentzoglu, James Malone, Chris Mungall and Robert Stevens, Journal of Biomedical Semantics20189:6, https://doi.org/10.1186/s13326-017-0172-7
• What are Ontologies?
• Semantic Web for the Working Ontologist, Second Edition by Dean Allemang and James Hendler
• Linked Data Patterns: A pattern catalogue for modelling, publishing, and consuming Linked Data by Leigh Dodds and Ian Davis
• Biomedical ontologies, data integration and annotation, British sense of humour: a technical blog on ontologies and ontology engineering by James Malone.
• ROBOT: A Tool for Automating Ontology Workflows by Rebecca C. Jackson, James P. Balhoff, Eric Douglass, Nomi L. Harris, Christopher J. Mungall & James A. Overton, BMC Bioinformaticsvolume 20, Article number: 407 (2019)
• How to use Ontologies to unlock the full potential of your Scientific Data