open phacts for bde sc1.1
TRANSCRIPT
Big data perspectives on building open semantic data services for life
sciences
Open PHACTS Foundation
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?
Public Domain Drug Discovery Data
LiteraturePubChem
GenbankPatents Databases
Downloads
Data Analysis Data Integration Firewalled Databases
Public Domain Drug Discovery Data - The Current Situation
Pfizer
AZ
Roche
n
Open PHACTS Mission:
Integrate Multiple Research Biomedical Data Resources
Into A Single Open & FreeAccess Point
ChEMBL DrugBankGene
OntologyWikipathways
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
ChEMBLTarget Class ENZYME FDA adverse
eventsSureChEMBL
RDFNanopub
Db
VoID
Data Cache (Virtuoso Triple Store)
Semantic Workflow Engine
Linked Data API (RDF/XML, TTL, JSON)DomainSpecificServices
Identity Resolution
Service
Chemistry RegistrationNormalisation & Q/C
IdentifierManagement
Service
Indexing
Co
re P
latf
orm
P12374EC2.43.4
CS4532
“Adenosine receptor 2a”
RDF
VoID
Db
RDFNanopub
Db
VoID
RDF
Db
VoID
RDFNanopub
VoID
Public Content Commercial
Public Ontologies
User Annotations
Apps
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
P12047X31045P1
2047
GB:29384RS
_2353
Names and standards in biomedical science
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 TypesProvenance– W3C PROV, PAV, Nanopublications
BioPortal, ConceptWiki, ChEMBL, identifiers.org, Uniprot, ChemSpider
http://imgs.xkcd.com/comics/standards.png
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?
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
Literature Patents NewsPipeline SAR CSRs SafetyIn vivo Etc
Rapidly Evolving Pharmaceutical EcosystemProprietary
contentproviderPublic
contentprovider
Academicgroup
Software vendor
CRO
Service provider
Regulatoryauthorities
Pharma
Patient organization
Big Life Science
Company
The data world is changing fast
The Standards Value Chain is disconnected…
Phase III Phase II Phase I Lead Opt Lead ID Hit IDTarget ID
COSTARTUMLS
MedRA
ICD9 to ICD10
Snomed-CT
Not meant to be exhaustive !!!
Bioscience and the 4Vs of big data
Big Data
Variety
Velocity
Volume
Veracity
[email protected] @Open_PHACTS
Open PHACTS Practical SemanticsAcknowledgements
GlaxoSmithKline – CoordinatorUniversität 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 AmsterdamNovartisMerck SeronoH. Lundbeck A/SEli LillyNetherlands Bioinformatics CentreSwiss Institute of BioinformaticsConnectedDiscoveryEMBL-European Bioinformatics InstituteJanssen Esteve AlmirallOpenLink ScibiteThe Open PHACTS FoundationSpanish National Cancer Research Centre University of Manchester Maastricht University AqnowledgeUniversity of Santiago de Compostela Rheinische Friedrich-Wilhelms-Universität BonnAstraZenecaPfizer