bel update october 30 th, 2014 © 2012, open bel community1
TRANSCRIPT
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
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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
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BEL Statements and Annotations
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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