1. BEL Update October 30 th, 2014 © 2012, Open BEL Community1

2. Agenda What is OpenBEL? Updates New Tools © 2012, Open BEL Community2

3. What is OpenBEL? © 2012, Open BEL Community3

4. 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

5. 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))

6. BEL Statements Are Assembled Into Computable Knowledge Networks

7. 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

8. 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", "9139801", "1997-05- 11","Ramalingam A|Hirai A|Thompson EA",""} Citation 10090 Species fibroblast Cell Type

9. BEL History

10. Updates © 2012, Open BEL Community10

11. 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

12. 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

13. New Tools © 2012, Open BEL Community13

14. 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

15. © 2012, Open BEL Community15 Landscape