openbel.rb

Overview

• Some terminology
• The pitch
• RDF modeling
• The system design
• Talk is cheap, show me the code
• Questions / Help us!

Some terminology

A rose by any other name would smell as sweet.
~ William Shakespeare

BEL

Human readable, minimum syntax, language for capturing biological knowledge from scientific literature.

# Statement
tscript(p(HGNC:EGFR)) => g(EGID:207)

# Annotations
SET CellLine = "L6 cell line"
SET Species = "9606"
SET Evidence = "In this paper, we present a comprehensive pathway map of EGFR signaling and other related pathways."

# Citation
SET Citation = {"Other","Mol Sys Biol 2005 May msb4100014","Mol Sys Biol 2005 May msb4100014","","",""}
  

more on BEL...

Knowledge Network

A graph consisting of the effects (edges) between biological functions (nodes).

Subgraph of RDF knowledge graph.

The pitch

• Handles entity equivalences
• Manage BEL knowledge networks
• Connect to other networks using RDF

Entity equivalences - Disconnected

Entity equivalences - Connected

Entity equivalences - SKOS RDF

RDF modeling

Present RDF Model (Gephi)

System design

Talk is cheap, show me the code

Show some code

Questions

Questions? I have some:

• Is SKOS a good fit?
• Is it important to tie our BEL ontology (function types, relationship types) to other ontologies?
• How does OWL fit in?
• Is reifying a BEL statement a good idea in this context?
• SPARQL subgraphs vs. Property graph model (tinkerpop graph api)

Links

project - github://OpenBEL/openbel.rb

OpenBEL wiki

Discussion group

IRC: irc.freenode.net / #openbel