These resources are intended to give an introduction to the subject and provide information on how to begin working with ontologies.
Ontogenesis Knowledge Blog
This blog is a useful place to find out more about ontologies, find tutorials and gain insights from leading researchers in the field. It can be viewed as an equivalent to an academic text book. The site is a stable resource and not edited after publication. Many of the articles are peer-reviewed.
Useful articles include:
- "What is an ontology?" - by Robert Stevens
- "Components of an ontology" - by Philip Lord
- "Why use an ontology?" - by Robert Stevens
- "Ontologies for Sharing, Ontologies for Use" - David Shotton, Chris Catton and Graham Klyne
Finding Ontologies
The following resources provide extensive lists of ontologies for the biological and biomedical research community:
- Open Biomedical Ontologies (OBO) - This site includes a tightly defined set of ontologies. The ontologies are open, community efforts. They provide an orthogonal suite of ontologies for researchers.
- NCBO BioPortal - The BioPortal site includes the OBO ontologies plus many small, one-person efforts. If you are after an ontology to suit a particular purpose, then the search service is a quick and simple solution.
- Ontology Lookup Service - This EBI site is similar to BioPortal but only covers OBO ontologies. It can be used to search through an ontology for specific terms.
- Swoogle - The Swoogle site functions very much like an ontology search engine. It covers a - contains ontologies that aren’t in BioPortal and OLS; covers more than the biomedical domain. Behaves like a search engine for ontologies.
Things to consider
A couple of useful bits of advice from the workshop:
- Identify your needs first - don't do what you don't need
- There is no simple solution for dealing with the enormous amount of overlap between existing ontologies - it’s an ongoing issue in the field
- Think about potential use cases for your completed ontology
- Don’t worry about annotating to high levels of detail - see Terry Meehan’s slides - it is OK to annotate to 'kidney' and then have a kidney expert look at the annotations to differentiate different parts of kidney for you
- Things to consider when deciding to use an ontology or incorporate it into an application ontology
- 1. Does it provide coverage?
- 2. Is it actively developed?
- 3. Does it have textual definitions?
- 4. Do other data providers use it?