BEL Update

October 30th, 2014

© 2012, Open BEL Community 1

Agenda

• What is OpenBEL?• Updates• New Tools

© 2012, Open BEL Community 2

What is OpenBEL?

© 2012, Open BEL Community 3

What Is OpenBEL?

• BEL - The Biological Expression Language– A triple-based language– Represents causal and correlative relationships

between biological entities with context

• The BEL Framework - Software Tools for BEL– Knowledge acquisition & Management– Computable graph knowledge bases from BEL

Statements– APIs, other support

BEL Was Designed to Capture and Use Scientific Findings

5

Scientific Literature

Original Research

“RNA expression of RBL2 is directly mediated via activation of the FOXO3 transcription factor”

“LY294002 inhibits the activity of the PI3K alpha catalytic subunit”

XYZ Corp Document 12345

J Biol Chem 2002 Nov 22 277(47) 45276-84

tscript(p(HGNC:FOXO3)) => r(HGNC:RBL2)

a(CHEBI:LY294002) -| kin(p(HGNC:PIK3CA))

BEL Statements Are Assembled Into Computable Knowledge Networks

BEL Functions Provide a Granular Representation• BEL Functions provide

representation of different types of biological measurements– E.g., AKT1 (EGID:207) can

be represented as a• Gene• RNA• Protein• Modified Protein• Activity

7

BEL Statements and Annotations

8

Term Expression Relationship Term Expression

a(CHEBI:dexamethasone) increases r(MGI:Cdkn1a)

"The abundance of p21 mRNA increases about 5-fold within 2 h after addition of dexamethasone."

Supporting Text

{"PubMed", "Mol Endocrinol", "9139801", "1997-05-11","Ramalingam A|Hirai A|Thompson EA",""}

Citation

10090

Species

fibroblast

Cell Type

Updates

© 2012, Open BEL Community 10

BEL v2.0

• Major language update• Will be supported by next generation of BEL Framework• Summary of changes:

– Variant representation• Include gene, RNA• Adopt HGVS notation

– Protein cleavage fragments added– Post-translational modifications and activities updated to adopt

external vocabularies– Translocations updated to include location as an abundance

modifier function– Regulates relationship added

BEL Resources (Namespaces, Equivalences)

• v20131211 released – Updated values and equivalences– Consolidation of namespaces

• Affymetrix, Selventa protein families, Selventa named complexes

– Tools to upgrade BEL documents from v1 to v20131211

• Pipeline to generate .belns and .beleq data from source files

• New data formats to support next generation BEL Framework

New Tools

© 2012, Open BEL Community 13

Motivation

• Principles– Configurable layers that adapt to a deployment (i.e. RDF

Store, Cache, etc.).– Scales linearly with BEL knowledge. Iterative processing of

BEL knowledge to avoid buffering data in memory.

• Technology– Leverage RDF model as the single source of truth.– Cache access to immutable data like namespaces and

annotations.– Create BEL Networks from filtered, transformed RDF

© 2013, Open BEL Community 14

© 2012, Open BEL Community 15

Landscape