Talking about...

• BEL in the Semantic Web
• Processing BEL with Ruby

Why use an RDF model for BEL?

• Shared representation of biological data
• Publish BEL RDF vocabulary back to the community
• More easily connect knowledge graphs

Design guidelines

• Convert biological identifiers to canonical form
• HGNC:AKT1 maps to EGID:207
• MESHPP:Apoptosis maps to GOBP:"apoptotic process"
• Establish term and statement URIs using this canonical form
• Reuse standard vocabularies

Concepts: Schema

• Derived from the SKOS vocabulary
• Capture biological concepts
• identifiers, preferred names, and synonyms
• equivalences between concepts
• orthology between concepts

Concepts: BRAF example

BEL

• Describes Terms, Statement and Evidence
• Capture biological concepts

BEL Term

kin(p(HGNC:ATR))

BEL Term

p(HGNC:TP53, pmod(P, S, 15))

BEL Statement

kin(p(HGNC:ATR)) => p(HGNC:TP53, pmod(P, S, 15))

Evidence

kin(p(HGNC:ATR)) => p(HGNC:TP53, pmod(P, S, 15))

Summary

• Derived from the SKOS vocabulary
• Capture biological concepts
• identifiers, preferred names, and synonyms
• equivalences between concepts
• orthology between concepts

Learn More

• RDF build of namespaces
• Wiki space for BEL 2 RDF
• Public SPARQL endpoint with BEL corpora to follow soon

Why use Ruby?

• Simple, Elegant, and Expressive
• Conducive to domain-specific language
• Works on Java using JRuby

# No fuss
File.read 'small_corpus.bel'

# Expressive
3.times do say "Hello, OpenBEL!" end

# Domain-specific languages
tscript(p(HGNC['AKT1'])).increases p(HGNC['BRAF'])
  

Design

• Accessible and easy to use
• Fully featured
• Can support multiple versions of BEL (BEL 2.0!)

Capabilities

• Load BEL resource files
• Language specification and parser
• Write BEL in Ruby code
• Validation of BEL terms and statements
• Conversion of BEL to RDF triples

Where does it fit in OpenBEL?

Stand-alone library for creating, processing, and transforming BEL

Backbone of openbel-server

Demo of bel.rb

• Parsed and queried BEL
• Created BEL programmatically
• Validated semantics of kinase BEL term
• Upgraded BEL file to the latest namespaces
• Converted BEL file to RDF

So in summary, bel.rb is...

• Easy to get started
• Easy to use and understand
• Fully-featured

Learn More

• Installing Ruby
• Source on GitHub
• More examples of usage
• Tests
• Published Ruby Gem

Questions?