Big Data Europe SC1 workshop May 21st 2015 Open PHACTS perspectives on big data in drug discovery

1. Big data perspectives on building
open semantic data services for life
sciences
Open PHACTS Foundation
bryn@openphactsfoundation.org

2. Why is it so hard to….
Competitors?
What’s the
structure?
Are they in our
file?
What’s
similar?
What’s the
target?Pharmacology
data?
Known
Pathways?
Working On
Now?
Connections to
disease?
Expressed in right
cell type?
IP?

3. Public Domain Drug Discovery Data
Literature
PubChem
Genbank
Patents
Databases
Downloads
Data Analysis Data Integration Firewalled Databases

4. Public Domain Drug Discovery Data
- The Current Situation
Pfizer
AZ
Roche
n

5. Open PHACTS Mission:
Integrate Multiple Research
Biomedical Data Resources
Into A Single Open & Free
Access Point

6. ChEMBL DrugBank
Gene
Ontology
Wikipathways
UniProt
ChemSpider
UMLS
ConceptWiki
ChEBI
TrialTrove
GVKBio
GeneGo
TR
Integrity
“Find me compounds
that inhibit targets in
NFkB pathway
assayed in only
functional assays with
a potency <1 μM”
“What is the
selectivity profile of
known p38 inhibitors?”
“Let me compare
MW, logP and PSA
for known
oxidoreductase
inhibitors”
DisGeNet
neXtProt
ChEMBL
Target Class
ENZYME
FDA adverse
events
SureChEMBL

7. Nanopub
Db
VoID
Data Cache
(Virtuoso Triple Store)
Semantic Workflow Engine
Linked Data API (RDF/XML, TTL, JSON)
Domain
Specific
Services
Identity
Resolution
Service
Chemistry
Registration
Normalisation
& Q/C
Identifier
Management
Service
Indexing
CorePlatform
P12374
EC2.43.4
CS4532
“Adenosine
receptor 2a”
VoID
Db
Nanopub
Db
VoID
Db
VoID
Nanopub
VoID
Public Content Commercial
Public Ontologies
User
Annotations
Apps

8. http://dx.doi.org/10.1016/j.websem.2014.03.003
The Open PHACTS Discovery Platform
• Cloud-Based
“Production” Level
System. Secure & Private
• Guided By Business
Questions
• Uses Semantic Web
Technology But provides
a simple REST-ful API for
everyone else
http://dx.doi.org/10.1016/j.drudis.2013.05.008

9. P12047
X31045
GB:29384
Names and standards in biomedical science

10. Basic Semantic web standards
– SPARQL 1.1, RDF(S), SKOS
Dataset descriptions
– Vocabulary of Interlinked Datasets (VoID)
– VoID linkset descriptions
QUDT Quantities, Units, Dimensions and
Types
Provenance
– W3C PROV, PAV, Nanopublications
BioPortal, ConceptWiki, ChEMBL,
identifiers.org, Uniprot, ChemSpider
http://imgs.xkcd.com/comics/standards.png

11. Why is it so hard to….
Competitors?
What’s the
structure?
Are they in our
file?
What’s
similar?
What’s the
target?Pharmacology
data?
Known
Pathways?
Working On
Now?
Connections to
disease?
Expressed in right
cell type?
IP?

12. Information/Data Tombs...
Internal and external
Built to manage content
Built to meet primary use-case
Tailored indexes
Tailored GUIs
Unique language & metadata
Poor interoperability/integration
Proliferation of PowerPoint, Documents, excel, etc.
Many suppliers of systems and content in a single
workflow
Literature Patents NewsPipeline SAR CSRs SafetyIn vivo Etc

14. Literature Patents NewsPipeline SAR CSRs SafetyIn vivo Etc

15. Rapidly Evolving Pharmaceutical Ecosystem
Proprietary
content
providerPublic
content
provider
Academic
group
Software vendor
CRO
Service provider
Regulatory
authorities
Pharma
Patient
organization
Big Life
Science
Company

16. The data world is changing fast

17. The Standards Value Chain is disconnected…
Phase IIIPhase IIPhase ILead OptLead IDHit IDTarget ID
COSTARTUMLS
MedRA
ICD9 to ICD10
Snomed-
CT
Not meant to be exhaustive !!!

18. Bioscience and the 4Vs of big data
Big
Data
Variety
Velocity
Volume
Veracity

19. info@openphactsfoundation.org @Open_PHACTS
Open PHACTS Practical Semantics
Acknowledgements
GlaxoSmithKline – Coordinator
Universität Wien – Managing entity
Technical University of Denmark
University of Hamburg, Center for
Bioinformatics
BioSolveIT GmBH
Consorci Mar Parc de Salut de Barcelona
Leiden University Medical Centre
Royal Society of Chemistry
Vrije Universiteit Amsterdam
Novartis
Merck Serono
H. Lundbeck A/S
Eli Lilly
Netherlands Bioinformatics Centre
Swiss Institute of Bioinformatics
ConnectedDiscovery
EMBL-European Bioinformatics Institute
Janssen Esteve Almirall
OpenLink Scibite
The Open PHACTS Foundation
Spanish National Cancer Research Centre
University of Manchester
Maastricht University
Aqnowledge
University of Santiago de Compostela
Rheinische Friedrich-Wilhelms-Universität
Bonn
AstraZeneca
Pfizer