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Other Resources

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:

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.

Services

Here is a very incomplete list of some excellent services to help you find an use OBO terms and ontologies.

  • EMBL-EBI
  • Onto-Animals
    • Ontobee is an ontology browser
    • Ontofox is an ontology extraction tool
  • Bioportal provides ontology browsing, search, mapping, etc.

Tools

This is the suite of open source software that most OBO developers use.

Technical

This section is for technical reference, not beginners.

OBO projects use Semantic Web and Linked Data technologies:

These standards form layers:

  1. 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.
  2. 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.
  3. RDFS: RDF Schema 1.1 extends RDF with classes, hierarchies, and other features.
  4. XSD: W3C XML Schema Definition Language (XSD) 1.1 Part 2: Datatypes is the common standard for datatypes in RDF
  5. OWL: Web Ontology Language extends RDF and RDFS to provide more powerful logic

Other useful resources on technical topics: