Transcript Slides

Repurposable and computable knowledge
from biological findings extracted from the literature
SLA PHT Winter Virtual Conference • 07 December 2012
William Hayes, Ph.D., Senior VP Platform Development
Ted Slater, CTO OpenBEL Consortium
Selventa, Inc.
Librarians  Information Analysts
No longer sufficient to
Provide documents or books
Run searches
Literature is only valuable if you can use it
Must help to build and curate mission-critical databases
and knowledge bases
Why is knowledge representation important?
What are issues that arise from using Excel as your only
database tech?
How does BEL fit?
“We are close to having
a $1,000
genome sequence,
this may be accompanied by
$1,000,000 interpretation.”
uce Korf, Former President of the American College of Medical Genetics
is important.
So, if you’re still doing it
the way you did 40 years
This is not
think about their
This is.
Linguamatics I2E BEL
I2E Pilot for BEL
Causal Biology?
It’s likely that, to this day, you haven’t been able to buy or
develop a single knowledge base of causal biology you
could use effectively to
Understand disease biology
Do pathway walking
Predict, describe, and leverage mechanisms of action
and biomarkers competitively
Overview of
What is OpenBEL?
The BEL Language
The BEL Tools
Biological Expression
Open source (Apache
triple-based, represents
causal relationships in
scientific findings
Knowledge acquisition &
Computable graph
knowledge bases from
BEL statements
APIs, other support
10 years of continuous
use and development at
The BEL Language
BEL Highlights
BEL Terms
Represent types of abundances or processes
Based on external vocabularies and ontologies
Can be derived as functions of other terms
BEL Statements
Correspond to a specific finding
Express a relationship between terms
Retain context and provenance via annotations
BEL Statements
Term Expression
Term Expression
a(CHEBI:corticosteroid) -| bp(NCI:”Tissue Damage”)
The abundance of molecules
designated by the name
“corticosteroid” in the CHEBI
The biological process
designated by the name
“Tissue Damage” in the NCI
Capture and Use Scientific
“RNA expression of RBL2 is directly mediated via
activation of the FOXO3 transcription factor”
Scientific Literature
tscript(p(HGNC:FOXO3)) => r(HGNC:RBL2)
J Biol Chem 2002 Nov 22 277(47) 45276-84
“LY294002 inhibits the activity of the
PI3K alpha catalytic subunit”
Original Research
a(PubChem:3973) -| kin(p(HGNC:PI3KCA))
XYZ Corp Document 12345
BEL Statement Annotations
Provide Context & Provenance
SET Citation = {“PubMed”, “J Mol Med (Berl). 2003
Mar;81(3):168-74.“ , “12682725”}
SET Evidence =
“high-dose steroid treatment decreases
vascular inflammation and ischemic tissue damage
after myocardial infarction and stroke through
direct vascular effects involving the
nontranscriptional activation of eNOS”
SET Tissue = “vascular system”
SET Disease = “Stroke”
a(CHEBI:corticosteroid) -| bp(NCI:”Tissue Damage”)
Assemble Facts as
Computable Models
into models…
…for use in
BEL and
“Reverse Causal Reasoning”
RCR – Using computable models
built from BEL sources to generate
mechanistic hypotheses based on
high-throughput data.
BEL Documents
Assembled Model
Hypothesis Network
The BEL Tools
The BEL Tools
A set of BEL-based applications and APIs that work
together to support
Knowledge acquisition and management
Knowledge publishing
Knowledge use
BEL Tools Components
BEL Framework v2.0 comprises
BEL Compiler/Assembler
Knowledge Assembly Models (KAMs)
Navigable networks (graphs) of biological facts
Creates KAMs from BEL documents
Java and Web Services Application Programming Interfaces for
interacting with KAMs stored in KAM Stores
Validating and converting BEL documents; managing KAMs;
format conversions; etc.
Eclipse-based BEL Editor for editing BEL documents
BEL Cytoscape plug-in for network visualization
The OpenBEL Consortium
Promote, Protect, Standardize
Members of the OpenBEL Consortium proudly support
Driving adoption and evolving the standards
Increasing the amount of BEL content and number of BEL tools available to the
Increasing the number of people knowledgeable about OpenBEL through training,
education, and publication
Facilitating crucial administrative, technical, and legal functions for the
community to enable them to continue to advance the platform
Serving as a proxy between the academic community, the healthcare and life
sciences industry, publishers, and tools & services providers to ensure everyone’s
needs are best understood and that collaboration solutions are optimized
Holding neutral collaboration and legal events to ensure the platform is advanced
and protected
Serving as the neutral voice for OpenBEL to ensure that it remains a successful,
thriving, and growing platform
OpenBEL Ecosystem
BEL for BioPharma
Library services - capturing causal biology for use in R&D (disease
biology, MoA, Toxicology, Clinical Trials, Drug Safety)
Integrating databases (Ingenuity, AriadneGenomics, GeneGo,
internal research requests) into single KB
Model Organism Translatability - e.g. how to check if mouse biology
maps well with human biology for pre-clinical drug studies
Disease vs Normal Biology Comparisons - comparing known
biological differences between disease and normal states in an
organism's tissue
Assay Development - add tool compound and drug/target relations
into BEL Network to aid development of biological assays
Example using
Demonstration of
Starting Questions
Does treating mouse model X with drug Y correlate to
human biology?
What is known biology for EGFR? Tissues expressed,
interacting proteins, associated disease conditions, …
What is found in the literature to associate kidney failure to
steatosis (liver adverse event)?
We need more detailed and highly contextualized
information for Pathway X than what is in
How could using drug X with MoA Y affect tissue Z?
Future Enhancements
BEL Statement/Script Creation
Dynamic Web-based Statement Editor (Q2 2013)
Curation Tool/PDF Reader Plugin (est Q4 2013)
Academic UIMA-based text mining workflows for KB
Thank You!
Questions? Contact
[email protected] or visit
Get OpenBEL at