Ontology Tutorials and Resources

Ontology Browsers

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

Tutorials

• Introduction to Ontologies: slides from Cold Spring Harbor workshop, October 2018.
• Ontology 101 Tutorial from International Conference on Biological Ontology (ICBO) 2018
• Ontology 101 Open Educational Resource. Funded by NIH BD2K Initiative.

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.
• VOCOL: An Integrated Environment for Collaborative Vocabulary Development.
• Karma Data Integration: A data integration tool.

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
• Ontology Development 101: A Guide to Creating Your First Ontology by Natalya F. Noy and Deborah L. McGuinness.
• 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, First Edition by Dean Allemang and James Hendler
• Semantic Web for the Working Ontologist, Second Edition by Dean Allemang and James Hendler (2nd ed. is better than the 1st)
• Linked Data Patterns: A pattern catalogue for modelling, publishing, and consuming Linked Data by Leigh Dodds and Ian Davis
• Learning SPARQL by Bob DuCharme