README.md

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:

• 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

Services

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

• EMBL-EBI
  • OLS: Ontology Lookup Service is an excellent ontology browser and search service
  • OxO shows mappings between ontologies and terms
  • Zooma for mapping free text to ontology terms
• 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.

• OBO Tools mailing list
• GitHub is where most OBO projects are hosted and what we use to manage code, issues, etc.
  • GitHub tutorial
• Protégé is a graphical user interface for editing OWL ontologies. (Java)
• ROBOT is a command-line tool for automating ontology tasks. (Java)
  • ROBOT tutorial
  • ROBOT: A Tool for Automating Ontology Workflows (journal article)
  • ENVO ROBOT Template and Merge Workflow
• 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
  • String of PURLs – frugal migration and maintenance of persistent identifiers (journal article)

Technical

This section is for technical reference, not beginners.

OBO projects use Semantic Web and Linked Data technologies:

• W3C Semantic Web overview
• Search for W3C data standards
• W3C Data on the Web Best Practices

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.
   • RDF 1.1 Primer
   • SPARQL 1.1 Overview
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
   • OWL 2 Web Ontology Language Primer (Second Edition)

Other useful resources on technical topics:

• Monkeying around with OWL Chris Mungall's blog, mostly on technical topics for ontologies.