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.
• Bioregistry provides metadata for ontologies and other semantic resources

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.
• curies is a Python library for working with prefix maps and extended prefix maps and converting between CURIEs and URIs.
• 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.
3. RDF 1.1 Primer
4. SPARQL 1.1 Overview
5. RDFS: RDF Schema 1.1 extends RDF with classes, hierarchies, and other features.
6. XSD: W3C XML Schema Definition Language (XSD) 1.1 Part 2: Datatypes is the common standard for datatypes in RDF
7. OWL: Web Ontology Language extends RDF and RDFS to provide more powerful logic
8. 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.