Open PHACTS for BDE SC1.1

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Big data perspectives on building open semantic data services for life sciences Open PHACTS Foundation [email protected]

Transcript of Open PHACTS for BDE SC1.1

Page 1: Open PHACTS for BDE SC1.1

Big data perspectives on building open semantic data services for life

sciences

Open PHACTS Foundation

[email protected]

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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?

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Public Domain Drug Discovery Data

LiteraturePubChem

GenbankPatents Databases

Downloads

Data Analysis Data Integration Firewalled Databases

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Public Domain Drug Discovery Data - The Current Situation

Pfizer

AZ

Roche

n

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Open PHACTS Mission:

Integrate Multiple Research Biomedical Data Resources

Into A Single Open & FreeAccess Point

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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

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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

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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

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P12047X31045P1

2047

GB:29384RS

_2353

Names and standards in biomedical science

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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

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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?

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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

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Literature Patents NewsPipeline SAR CSRs SafetyIn vivo Etc

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Rapidly Evolving Pharmaceutical EcosystemProprietary

contentproviderPublic

contentprovider

Academicgroup

Software vendor

CRO

Service provider

Regulatoryauthorities

Pharma

Patient organization

Big Life Science

Company

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The data world is changing fast

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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 !!!

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Bioscience and the 4Vs of big data

Big Data

Variety

Velocity

Volume

Veracity

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[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