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Beyond Text Mining: BRAIN
August 11th, 2014/ACS
2
Market Drivers
Euretos
BRAIN
Use cases
Close
Topics
The Data Tsunami
Datarrhoeia
Standards?
Needle Transport
DIY Data
Key drivers
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* 2013: Ann Winblad legendary investor and senior partner at Hummer-Winblad
“Data is just like crude. It’s valuable, but if unrefined it cannot
really be used. It has to be changed into gas,
plastic, chemicals, etc., to create a valuable
entity that drives profitable activity.”
Data: The new oil
Is anyone really ‘doing it’?
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Life sciences – the perfect storm?
Phenome
Metabolome
Transciptome
Proteome
Genome
The easy ‘low hanging fruit’ medical discoveries have been madeNew ‘higher hanging fruit’ research is orders of magnitude more complexDrowning in data
1.5 new article published every minuteMassive multi-omics output data (genome data alone doubles per 8 months)
Lost in dataMany databases are consulted dailyEach only have a fragment of the puzzleEach have specific classifications, termsGoogle as the only integrative tool
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Market Drivers
Euretos
BRAIN
Use cases
Close
Topics
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Addressing researchers’ needs
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Many online resources
Look through data
Discover new relations
Instantly evaluate evidence
Personalise alerts
Minimise Time to knowledge
Euretos Product Solution:
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Products & Services
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KaaS
Overview
• Knowledge as a Service• User friendly application• Instant access• Public & private data• Secure• Up to date• Easy collaboration• Alerts
Private Instance
Overview
• On-site BRAIN install• Behind own firewall• Public & private data• Frequent updates• Tailored pricing• Full integration into local
environment
Reports
Overview
• Standard reports• Custom reports
API
Overview
• Access to BRAIN database• Develop own applications
License
• Fixed price per report /• Subscription
License
• Monthly subscription• Integration services
License
• Annual base license &• Per transaction fee
License
• Annual base license &• Support fee &• Professional services
Selected references
11Copyright Euretos b.v. 2014
We provide
• BRAIN KaaS to the pre-clinical research team
We provide
• Target dossiers for target owners and internal review panel
We provide
• API for in-house solution development including project support
We provide
• In-house installation of key elements of BRAIN to support data indexing & publishing
KaaS
Overview
• HQ Kopenhagen, DK• Listed company• Development of human
antibody therapeutics for cancer treatment
Private Instance
Overview
• HQ Hinxston, UK• Official EU infrastructure
for life sciences data • ‘FAIR’ datapublishing of
public research data
Reports
Overview
• Based in Leiden, NL• Bayer, Lundbeck, Merck,
AstraZeneca, Janssen, Sanofi, UCB Consortium
• Target screening
API
Overview
• HQ San Diego, US• Agricultural, industrial
and healthcare markets• Plant and yeast genetics
& trait development
Market Drivers
Euretos
BRAIN
Use cases
Close
Topics
12Copyright Euretos b.v. 2014
A STATEMENT: [Term A - relates to - Term B] & it’s SOURCE
R. Yamaguchi, 2008, Journal of Systems
Biology
Term ‘A’
KLK2 gene
‘relates to’
Causes
Term ‘B’
Prostate Cancer
Source
BRAIN knowledge refinery process
We refine data to the smallest unit of knowledge (a Nanopublication)
Disambiguation – By knowing all terms, their synonyms and storing them as a single concept. Whatever term you enter, we always find what you meanLook through data – By connecting these Nanopublications and thus ‘look through’ all the data sources at onceData reduction – By taking only Nanopublications from raw data and ‘zip up’ all identical ones in a single ‘Cardinal Assertion’. Performance – the result: high performance at a very low footprint
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SEEINGTHROUGH
DATA
Connected
Is inPMID: 22869380 PMID: 22869380
Binds
PMID: 20164304
PMID: 22869380
beta parvin Akt1
BindsPMID: 20164304
paxilin
Leucine aspartic repeat motifs
14Copyright Euretos b.v. 2014
Biological pathways
Genetics
Proteins
Phenotypes
Chemical/Pharmacology
Other
H1 2014 H2 2014
Pubmed
Uniprot
ChEMBL
EntrezGene
WikiPW
Drugbank
EnzymeProtein Data bank
Genes /Diseases
Reactome
LOVDENCODESNP db
HMDB
GWAS Jaspar DB TigerEpigenomics
Secreted Protein db
Binding db
DBGaP
BioGRID
SuperLigandsPubChem
NCIClinicaltrial USPTO
GeneOntology
Protein Atlas
CTD
H1 2015
KEGG
Foodb
TD3B
NCI/UMLS
Comprehensive
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In summary: Value to the researcher
First to Knowledge…
Create a single view on private & public dataSee all existing knowledge in all sources at onceDiscover ‘potential’ relationsCollaborate on specific hypothesesKeep up to date via alerts
….First to Market
Find more leads for researchIncrease quality of researchDecrease late stage attrition of leadsAccelerate end to end development processSave time, cost & money
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Market Drivers
Euretos
BRAIN
Use cases – Time to knowledge
Close
Topics
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Based on meticulous reading of 221 articles
Time to knowledge
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Using BRAIN Path predictor function
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Using BRAIN Shortest Path function
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Detail statement and provenance
Not mentioned in the Miedema paper.
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Significant Time-to-Knowledge saving
4 minutes….in BRAINReading 221 papers: WEEKS
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Market Drivers
Euretos
BRAIN
Use cases – Knowledge Prediction
Close
Topics
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“Also just saw this article on ALS and
Retigabine, a drug that affects Potassium
channels and might work for ALS.
Would BRAIN have predicted this relationship?
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Knowledge prediction
Store terms and statements in project folder
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Select statements with relevant relations
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Before this paper was published,
BRAIN contained sufficient indirect
relationships between
Retigabine and ALS to predict it as a potential drug.
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Discovery that several mutations associated with ALS cause abnormally high activity in motor neurons > early degradation. There is a deficit in open potassium channels in ALS motor neurons. Retigabine, a drug that opens potassium channels and approved for human use, seems to normalize ALS cells in vitro, reducing their hyperexcitability > clinical trials in preparation.
Then visualize statements
Location of
Causes
Stimulates
Interacts with
Causes
Associated with
Location of
Stimulates
Location of
Stimulates
Stimulates
Interacts with Causes
Causes
Location of
Affects
Market Drivers
Euretos
BRAIN
Use cases – Target dossier
Close
Topics
28Copyright Euretos b.v. 2014
P14735
One click target dossiers
29Copyright Euretos b.v. 2014
We provide
• Target dossiers for target owners and internal review panel
Reports
Overview
• Based in Leiden, NL• Bayer, Lundbeck, Merck,
AstraZeneca, Janssen, Sanofi, UCB Consortium
• Target screening
Key functions
Target – disease association (predict function)
Drugability analysis of a compound
Indepth compound analysis ranked by QeD
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Market Drivers
Euretos
BRAIN
Use cases – Adverse Drug Reaction
Close
Topics
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Adverse drug reaction assessment
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Rosiglitazone (trade name Avandia, GlaxoSmithKline) is an antidiabetic drug in the thiazolidinedione class of drugs.
A meta-analysis of 16 observational studies released in March, 2011, provides evidence that rosiglitazone is associated with a higher risk of heart failure, myocardial infarction and death than a similar agent, pioglitazone in real life.
Connect the key concepts
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Review the evidence
2006
2010
2008
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Market Drivers
Euretos
BRAIN
Use cases
Close
Topics
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