Pharma goes FAIR Herman van Vlijmen Janssen Pharmaceu9ca Beerse, - - PowerPoint PPT Presentation

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Pharma goes FAIR Herman van Vlijmen Janssen Pharmaceu9ca Beerse, - - PowerPoint PPT Presentation

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Pharma goes FAIR Herman van Vlijmen Janssen Pharmaceu9ca Beerse, Belgium What is FAIR? hIps://www.dtls.nl/fair-data/fair-data/ 23/11/2017 DTL mee9ng Utrecht 2 Sci Data. 2016, 3:160018 23/11/2017 DTL mee9ng Utrecht 3 Why is FAIR

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Pharma goes FAIR

Herman van Vlijmen

Janssen Pharmaceu9ca Beerse, Belgium

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What is FAIR?

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hIps://www.dtls.nl/fair-data/fair-data/

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Sci Data. 2016, 3:160018

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Why is FAIR important?

  • Many data sets and databases are s9ll siWng in

silos with

– Poor accessibility and/or findability of data – Absent or incomplete use of nomenclature standards

  • The amount and diversity of scien9fic data is

growing fast

  • Most valuable analysis involves data from

different domains/technologies

  • Machine learning and data mining require

unambiguous computer-readable data

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From molecule to medicine

5 FROM DISCOVERY OF A DRUG TO SUBMISSION OF REGISTRATION FILE FROM REGISTRATION TO LAUNCH FROM LAUNCH TO LOSS OF PATENT

0 YEAR 20y 4 6 12,5y

BASIC RESEARCH DEVELOPMENT CLINICAL TRIALS REGISTRATION COMMERCIALIZATION

è è

Basic Research/Discovery

  • Select Disease
  • Select Drug Target
  • IdenCfy Bioassay
  • Find compound hits
  • Find lead compound(s)
  • Select clinical candidate

Development

  • Drug metabolism and

PharmacokineCcs

  • Safety evaluaCon
  • Chemical producCon
  • PharmaceuCcal formulaCon

Clinical Trials

  • Safety (Phase I)
  • Efficacy & Dose (Phase II)
  • Efficacy (Phase III)
  • PostmarkeCng (Phase IV)

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Why is FAIR important to Janssen?

  • If the data is there but nobody (re)uses it…
  • Scien9sts at Janssen rarely use all data they have access to

– Difficult to access mul9ple databases – Lack of awareness of databases – LiIle experience with defini9on of cross-domain analysis

  • Data from mul9ple domains and sources (private, public,

commercial) is needed for best possible analysis

– Target iden9fica9on and valida9on – Hit finding, H2L, Lead Op9miza9on – Phenotypic screens, Omics experiments – Mechanis9c analysis tox, side effects, drug repurposing – Transla9onal analysis (cell phenotype <-> animal -> human) – Clinical and Real World Evidence analysis

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Answering more complex ques9ons

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Open PHACTS data sources

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Phenotypic Drug Discovery Workflows

Digles et al, MedChemComm, 7: 1237 (2016)

“Knowing the knowns”

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Open PHACTS developments: Patent Info

  • Huge amount of knowledge in patent corpus, most of

which will never be published elsewhere, but poten9ally great value to drug discovery

  • SureChEMBL system (EBI) already automa9cally extracts

compounds from these documents

  • Open PHACTS consor9um funded project to also extract

gene/disease informa9on (EMBL-EBI and SciBite)

  • ~4 million patents in total, 260 million annota9ons

(patent-compound, patent-gene or patent-disease associa9ons)

  • Example use cases:

– For a given target or disease, give me all the compounds that are linked to this through patents

  • Important to find new extrac9on tools to con9nue this

annota9on and make available at EBI

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A broad set of use cases can be addressed using a linked data system

Some examples:

Target idenCficaCon and validaCon

  • Give me all direct and indirect suppor9ng evidence linking a gene and disease
  • Are there examples of compounds targe9ng any member of this target family?
  • What are the relevant indirect links between a gene and a phenotypic assay?

Lead idenCficaCon and opCmizaCon

  • What compounds bind to this target or related targets (family, 3D similarity)?
  • What bioac9vi9es and pathways are associated to a compound?
  • Show the ac9vity of these compounds on all kinases involved in this pathway
  • What are poten9al side-effects of hiWng similar binding sites to our target?
  • What side effects have similar compounds ?

Biomarker discovery

  • What secreted proteins in a par9cular 9ssue are associated with this cellular pathway and might be

biomarkers?

  • New biomarkers: for which indirect biomarker-disease links there is no direct reported associa9on,

and which ones have the strongest level of data support?

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Querying higher level research ques9ons

What are the Janssen compounds ac9ve in this Janssen assay? Give me all internal/commercial/public data on compounds that are ac9ve on my target and other closely related targets. What is the difference in gene expression profile between tumor and normal 9ssue? Given the differences in expression profiles between these 9ssues, give me the compounds with biochemical acCvity profiles that resemble the difference profile most Search PubMed for poten9al target-disease associa9on: “bcl2 schizophrenia” Show me all possible direct and indirect links between bcl2 and schizophrenia, ranked by level of scienCfic data support I have a CDK7 lead compound. Is there anything known in PubMed on toxicity of CDK7 inhibitors? Given my CDK7 lead compound, what are the most likely mechanisms by which this compound class could cause toxicity

A comparison of the queries that are done today versus what will be possible

TODAY FUTURE

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Internal efforts in Discovery: Chem3

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  • SemanCc graph database of internal and

external data linked to chemistry

– Compound Ac9vity:

  • ABCD, Athena, PIRlab, CAPE (all internal Janssen)
  • ChEMBL, PubChem, GOSTAR, Clarivate
  • Pending:

– SureChEMBL – Etc. based on user needs

– Plasorm: Virtuoso – Fast chemical cartridge (internal)

  • Interface in 3DX, Pipeline Pilot, R

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Examples of Linked Data challenges in Pharma

Data types and units for pharmacological ac9vity in ChEMBL

Lee and Gobbi. J. Chem. Inf. Model. 2012, 52, 285−292

Stereochemistry Tautomerism

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Internal efforts in Discovery: Exploring use

  • f Euretos Knowledge Plasorm for TI/TV

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Step 1 Step 2 www.euretos.com

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Internal efforts in Discovery: Exploring use

  • f Euretos Knowledge Plasorm for TI/TV

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Step 3 Step 4 www.euretos.com

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  • Call launched in July 2017
  • Candidate consor9a are currently being

evaluated

  • Likely start project Q3 2018, dura9on 3 years
  • Budget: The financial contribu9on from IMI2 is a

maximum of EUR 4M

  • Pharma partners: Janssen, AZ, Bayer, Boehringer

Ingelheim, Eli Lilly, GSK, Novar9s

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Summary of FAIRifica9on Proposal

  • Select data sets and databases from finished and ongoing

IMI projects, based on:

– Scien9fic value of making this data accessible and interoperable – Complexity of making the data available

  • Select databases at individual EFPIA companies

– Selec9on based on value for companies – Consolida9on to limited set of data domains

  • FAIRify these data sets to enable the sustainable use of the

data in answering research ques9ons

– Work sessions with data owners and FAIRifica9on experts, including data domain experts (vocabularies, ontologies, use cases) and IT experts (conversion of data, database implementa9on) – Implementa9on of sustainable solu9on for storage and maintenance

  • f FAIRified IMI databases

– Iden9fica9on of sustainable solu9on for storage and maintenance of FAIRified EFPIA databases

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  • ELF

European Lead Factory

  • EMIF

European Medical Informa9on Framework

  • EMTRAIN

European Medicines Research Training Network

  • ENABLE

European Gram-nega9ve An9bacterial Engine

  • EPAD

European preven9on of Alzheimer’s demen9a consor9um

  • eTOX

Integra9ng bioinforma9cs and chemoinforma9cs approaches for the development of Expert systems allowing the in silico predic9on of toxici9es

  • eTRIKS

Delivering European Transla9onal Informa9on & Knowledge Management Services

  • EU-AIMS

European Au9sm Interven9ons - a Mul9centre Study for Developing New Medica9ons

  • Eu2P

European programme in Pharmacovigilance and Pharmacoepidemiology

  • EUPATI

European Pa9ents' Academy on Therapeu9c Innova9on

  • EUROPAIN

Understanding chronic pain and improving its treatment

  • FLUCOP

Standardiza9on and development of assays for assessment of influenza vaccines correlates of protec9on

  • GETREAL

Incorpora9ng real-life clinical data into drug development

  • iABC

Inhaled an9bio9cs in bronchiectasis and cys9c fibrosis

  • IMIDIA

Improving beta-cell func9on and iden9fica9on of diagnos9c biomarkers For treatment monitoring in diabetes

  • iPiE

Intelligent Assessment of Pharmaceu9cals in the Environment

  • K4DD

Kine9cs for Drug Discovery

  • MARCAR

Biomarkers and molecular tumour classifica9on for non-genotoxic carcinogenesis

  • MIP-DILI

Mechanism-Based Integrated Systems for the Predic9on of Drug- Induced Liver Injury

  • ND4BB

New Drugs for Bad Bugs

  • NEWMEDS

Novel methods leading to new medica9ons in depression and schizophrenia

  • Onco Track

Methods for systema9c next genera9on oncology biomarker development

  • Open PHACTS

The Open Pharmacological Concepts Triple Store

  • ORBITO

Oral biopharmaceu9cs tools

  • Pharma-Cog

Predic9on of cogni9ve proper9es of new drug candidates for neurodegenera9ve diseases in early clinical development

  • Pharmatrain

Pharmaceu9cal Medicine Training Programme

  • PRECISESADS

Molecular reclassifica9on to find clinically useful biomarkers for systemic autoimmune diseases

  • Predect

New models for preclinical evalua9on of drug efficacy in common solid tumours

  • PreDiCT-TB

Model-based preclinical development of an9-tuberculosis drug combina9ons

  • PRO-acCve

Physical Ac9vity as a Crucial Pa9ent Reported Outcome in COPD

  • ABIRISK

An9-Biopharmaceu9cal Immuniza9on: Predic9on and Analysis of Clinical Relevance to Minimize the Risk

  • ADVANCE

Accelerated development of vaccine benefit-risk collabora9on in Europe

  • AETIONOMY

Organising mechanis9c knowledge about neurodegenera9ve diseases for the improvement of drug development and therapy

  • BioVacSafe

Biomarkers for Enhanced Vaccine Immunosafety

  • BTCure

Be The Cure

  • CHEM21

Chemical manufacturing methods for the 21st century pharmaceu9cal industries

  • COMBACTE

CombaWng Bacterial Resistance in Europe

  • COMBACTE-CARE

CombaWng Bacterial Resistance in Europe - Carbapenem Resistance

  • COMBACTE-MAGNET

CombaWng bacterial resistance in Europe - molecules against Gram nega9ve infec9ons

  • COMPACT

Collabora9on on the op9misa9on of macromolecular pharmaceu9cal access to cellular targets

  • DDMoRe

Drug Disease Model Resources

  • DIRECT

Diabetes research on pa9ent stra9fica9on

  • DRIVE-AB

Driving re-investment in R&D and responsible an9bio9c use

  • EBiSC

European Bank for induced pluripotent Stem Cells

  • Ebola+

Ebola and other filoviral haemorrhagic fevers

  • EHR4CR

Electronic Health Records Systems for Clinical Research

  • PROTECT

Pharmacoepidemiological research

  • n outcomes of therapeu9cs by a

European consor9um

  • Quic-Concept

Quanta9ve imaging in cancer:connec9ng cellular process with therapy

  • RAPP-ID

Development of rapid point-of-care test plasorms for infec9ous diseases

  • SAFE-T

Safer and Faster Evidence-based Transla9on

  • SafeSciMET

European Modular Educa9on and Training Programme in Safety Sciences for Medicines

  • SPRINTT

Sarcopenia and physical frailty in

  • lder people: mul9-component

treatment strategies

  • STEMBANCC

Stem cells for biological assays of novel drugs and predic9ve toxicology

  • SUMMIT

Surrogate markers for micro- and macro-vascular hard endpoints for innova9ve diabetes tools

  • TRANSLOCATION

Molecular basis of the bacterial cell wall permeability

  • U-BIOPRED

Unbiased biomarkers for the predic9on of respiratory disease

  • utcomes
  • WEB-RADR

Recognising Adverse Drug Reac9ons

IMI Projects

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ProgrammeCall Project No Project Acronym Project Title Start Date End Date FAIRification legal Coordinator Short Name (A2.1) IMI1 1 115001 MARCAR bioMARkers and molecular tumor clas 1/01/2010 30/06/2015 Yes Novartis IMI1 1 115002 eTOX Integrating bioinformatics and chemo 1/01/2010 31/12/2016 Yes Novartis IMI1 1 115003 SAFE-T SAFER AND FASTER EVIDENCE-BASED 15/06/2009 14/06/2015 Yes Novartis IMI1 1 115004 PROTECT Pharmacoepidemiolocal Research on1/09/2009 30/04/2015 Yes EMA IMI1 1 115005 IMIDIA Improving beta-cell function and ident1/02/2010 30/09/2015 Yes SAD IMI1 1 115006 SUMMIT SUrrogate markers for vascular Micro1/11/2009 31/10/2015 Yes Boehringer Ingelheim IMI1 1 115007 EUROPAIN Understanding chronic pain and impro 1/10/2009 30/09/2015 Yes HLU IMI1 1 115008 NEWMEDS Novel Methods leading to New Medic 1/09/2009 28/02/2015 Yes HLU IMI1 1 115009 PHARMA-COG Prediction of cognitive properties of n 1/01/2010 31/12/2015 Yes GSK IMI1 1 115010 U-BIOPRED Unbiased Biomarkers for the Predicti 1/10/2009 30/09/2015 Yes NOV IMI1 1 115011 PRO- Active Physical Activity as a Crucial Patient1/09/2009 31/05/2016 Yes Chiesi IMI1 1 115012 SafeSciMET European Modular Education and Tra1/01/2010 31/08/2016 No ROCHE IMI1 1 115013 PharmaTrain Pharmaceutical Medicine Training Pr 1/05/2009 30/04/2014 No PharmaTrain Federation IMI1 1 115014 EU2P European programme in Pharmacovig1/09/2009 30/06/2016 Yes ROCHE IMI1 1 115015 EMTRAIN European Medicines Research Traini 1/10/2009 30/09/2016 No AstraZeneca IMI1 2 115142 BTCURE BeTheCuRE 1/04/2011 31/03/2017 Yes UCB IMI1 2 115151 QUIC-CONCEPT QUantitative Imaging in Cancer: CON1/09/2011 31/08/2016 Yes EORTC IMI1 2 115153 RAPP-ID Development of RApid Point-of-Care t1/04/2011 30/09/2016 Yes JNJ IMI1 2 115156 DDMoRe Drug Disease Model Resources 1/03/2011 31/08/2016 ? Pfizer IMI1 2 115188 PREDECT New Models for Preclinical Evaluation1/02/2011 30/04/2016 Yes Servier IMI1 2 115189 EHR4CR Electronic Health Record systems fo 1/03/2011 29/02/2016 Blank AZ IMI1 2 115191 Open PHACTS The Open Pharmacological Concepts1/03/2011 29/02/2016 Yes GSK IMI1 2 115234 OncoTrack OncoTrack - Methods for systematic1/01/2011 31/12/2016 Yes BHP IMI1 3 115300 EU-AIMS European Autism Interventions - A M 1/04/2012 31/03/2017 Yes ROCHE IMI1 3 115303 ABIRISK Anti-Biopharmaceutical Immunization1/03/2012 28/02/2017 Yes GSK IMI1 3 115308 BioVacSafe Biomarkers For Enhanced Vaccine Sa 1/03/2012 28/02/2017 Yes GSK Vaccines Srl IMI1 3 115317 DIRECT DIabetes REsearCh on patient sTratif1/02/2012 31/01/2017 Yes SAD IMI1 3 115334 EUPATI European Patients' Academy on Ther1/02/2012 31/01/2017 No VFA IMI1 3 115336 MIP-DILI Mechanism-Based Integrated Systems 1/02/2012 31/01/2017 Yes AstraZeneca IMI1 3 115337 PreDiCT-TB Model-based preclinical development 1/05/2012 30/10/2017 Yes GSK IMI1 4 115360 CHEM21 Chemical Manufacturing Methods for 1/10/2012 30/09/2016 ? GSK IMI1 4 115363 Compact Collaboration on the Optimisation of 1/11/2012 31/10/2017 ? SAD IMI1 4 115366 K4DD Kinetics for Drug Discovery (K4DD) 1/11/2012 31/10/2017 Yes Bayer IMI1 4 115369 OrBiTo Oral biopharmaceutics tools 1/10/2012 30/09/2017 Yes AstraZeneca IMI1 4 115372 EMIF European Medical Information Frame 1/01/2013 31/12/2017 Yes Janssen IMI1 4 115439 StemBANCC Stem cells for Biological Assays of N1/10/2012 30/09/2017 Yes ROCHE IMI1 4 115446 eTRIKS Delivering European Translational Inf1/10/2012 30/09/2017 Yes AstraZeneca IMI1 5 115489 EUC²LID European Lead Factory 1/01/2013 31/12/2017 ? Bayer IMI1 6 115523 COMBACTE Combatting Bacterial Resistance in E 1/01/2013 31/12/2019 ? AstraZeneca IMI1 6 115525 Translocation Molecular basis of the outer membran 1/01/2013 31/12/2017 Yes GSK IMI1 7 115546 GetReal Incorporating real-life clinical data into 1/10/2013 31/12/2016 Yes GSK IMI1 7 115557 ADVANCE Accelerated Development of Vaccine 1/10/2013 30/09/2018 Yes EMC IMI1 8 115565 PRECISESADS Molecular Reclassification to Find Cli1/02/2014 31/01/2019 Yes UCB IMI1 8 115568 AETIONOMY Aetionomy – Organising Mechanistic 1/01/2014 31/12/2018 Yes UCB IMI1 8 115582 EBiSC European Bank for induced pluripoten1/01/2014 31/12/2016 Yes Pfizer

Preliminary analysis of IMI projects for availability of FAIRifiable data sets (par9al list) Analysis done by Anthony Rowe (Janssen) and Colm Carroll (IMI)

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Expected Impact

  • The scien9fic community can maximally leverage data

from legacy and current IMI projects

  • Strengthening the capacity of crea9on, cura9on, and

stewardship of FAIR databases within IT communi9es

  • f academia, SME, and pharma
  • BeIer understanding of the complexity, structure, and

breadth of pharmaceu9cal data: Allow the SME community to make their data, analysis tools and services beIer connected and aligned to pharma

  • A long-las9ng value-adding impact on effec9ve

scien9fic data usage

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Building on IMI1 programmes, e.g. EHR4CR (Electronic Health Records for Clinical Research) EMIF (European Medical Informa9on Framework) ADVANCE (Data framework for vaccine risk/benefit analysis) GetReal (RWE collec9on and synthesis) and other FP7 programmes, we will be u9lising the outputs of those PPPs, the rela9onships and their contribu9ons (Big Data for BeIer Outcomes BD4BO)

  • Work Package 1: Methodological Research
  • Federated network crea9on
  • Data harmonisa9on, evalua9on and quality benchmark
  • Eviden9al linkage with Regulators, HTAs
  • From technology to RWE

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Conclusions

  • Pharma has strong interest and need for

implemen9ng FAIR data principles

  • Exper9se is usually lagging due to complex

legacy data systems and limited IT resources

  • Scien9fic acceptance of FAIRifica9on in

Pharma requires strong use case examples

  • Collabora9on with academia and SME

community catalyzes exper9se and acceptance of FAIR data

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