BEL Update October 30 th, 2014 © 2012, Open BEL Community1
Agenda What is OpenBEL? Updates New Tools © 2012, Open BEL Community2
What is OpenBEL? © 2012, Open BEL Community3
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” “LY inhibits the activity of the PI3K alpha catalytic subunit” XYZ Corp Document J Biol Chem 2002 Nov (47) 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 ExpressionRelationshipTerm 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", " ", " ","Ramalingam A|Hirai A|Thompson EA",""} Citation Species fibroblast Cell Type
BEL History
Updates © 2012, Open BEL Community10
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) v released – Updated values and equivalences – Consolidation of namespaces Affymetrix, Selventa protein families, Selventa named complexes – Tools to upgrade BEL documents from v1 to v Pipeline to generate.belns and.beleq data from source files New data formats to support next generation BEL Framework
New Tools © 2012, Open BEL Community13
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 Community14
© 2012, Open BEL Community15 Landscape