Here's a collection of links about the Open Biological and Biomedical Ontologies (OBO), and related topics.
If you're completely new to OBO, I suggest starting with Ontologies 101:
- Unit 1: Controlled Vocabularies, Ontologies, and Data Linking (PowerPoint Slides)
- Unit 2: An Introduction to OWL (Powerpoint Slides)
- Unit 3: Ontology Community (Powerpoint Slides)
- BDK14 Ontologies 101 repository
If you're new to scientific computing more generally, then I strongly recommend Software Carpentry, which provides a set of very pragmatic introductions to the Unix command line, git, Python, Make, and other tools widely used by OBO developers.
Open Biological and Biomedical Ontologies¶
OBO is a community of people collaborating on open source ontologies for science. We have a set of shared principles and best practises to help people and data work together effectively.
- OBO Foundry Homepage
- The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration (journal article)
- OBO Discuss mailing list
Here is a very incomplete list of some excellent services to help you find an use OBO terms and ontologies.
- Bioportal provides ontology browsing, search, mapping, etc.
This is the suite of open source software that most OBO developers use.
- OBO Tools mailing list
- GitHub is where most OBO projects are hosted and what we use to manage code, issues, etc.
- Protégé is a graphical user interface for editing OWL ontologies. (Java)
- ROBOT is a command-line tool for automating ontology tasks. (Java)
- DOS-DP is a command-line tool for working with ontology design patterns. (Python)
- ODK: Ontology Development Kit
is a collection of tools for building and maintaining an OBO project. (Docker)
- OBO Tools and Workflows (Google Slides) A good overview of technical and advanced topics of OBO practises, including the Ontology Development Kit.
- OWLAPI is a Java library for working with ontologies, and is the foundation for Protégé and ROBOT.
- OBO PURL System is used to redirect OBO terms from their IRIs to the right resource
This section is for technical reference, not beginners.
OBO projects use Semantic Web and Linked Data technologies:
These standards form layers:
- IRI: Internationalized Resource Identifiers are a superset of the familiar URLs used to locate resources on the web. Every ontology term has a globally unique IRI.
- RDF: Resource Description Format is a standard for combining IRIs into subject-predicate-object "triples" that make a statement about some thing. Sets of triples form a graph (i.e. network), and graphs can easily be merged to form larger graphs. SPARQL is the language for querying RDF graphs.
- RDFS: RDF Schema 1.1 extends RDF with classes, hierarchies, and other features.
- XSD: W3C XML Schema Definition Language (XSD) 1.1 Part 2: Datatypes is the common standard for datatypes in RDF
- OWL: Web Ontology Language extends RDF and RDFS to provide more powerful logic
Other useful resources on technical topics:
- Monkeying around with OWL Chris Mungall's blog, mostly on technical topics for ontologies.