How Data Mining Drives Pharma: Information as a Raw

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How Data Mining Drives Pharma: Information as a Raw Material and Product

Dr. William Carroll ACS Board Chair

Dr. Wendy Cornell Head of Informatics IT Proprietary Information and Knowledge Management, Merck



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How Data Mining Drives Pharma: Information As Raw Material and Product Wendy Cornell, Ph.D. ACS Fellow Webinar October 10, 2013

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Information drives decision making at each stage of the drug discovery process

Target ID/Validation

Lead ID

Lead Optimization

Preclinical Development

Phase 1

Phase 2

Phase 3

Pharmacovigilance

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Different types of questions can be answered with data and text mining

Search for – Exact or similar matches – Consensus or trends – Novel information

New!!

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Question #1

Have you done a Google search in the last 24 hours?

1. Yes 2. No

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Mining of protein sequence and crystal structure databases supports target validation and lead finding and optimization

Protein Sequence Database Target protein sequence

Protein Databank (PDB)

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Proprietary compound databases contain the many compounds made in pursuit of the final drug

ISENTRESS

SINGULAIR

Query molecule

CRIXIVAN

CLARINEX

Proprietary Compound Database

JANUVIA

VICTRELIS

ZOCOR

Molecules to test in experimental assays

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Text mining for discovery and competitive intelligence

Targets

Medline Conference Abstracts

Compounds

Patents Company News Clinical Trials NIH Grants

Discovery of cyclic sulfoxide hydroxyethylamines as potent and selective β-site APP-cleaving enzyme 1 (BACE1) inhibitors: Structure based design and in vivo reduction of amyloid β-peptides. Rueeger H, Lueoend R, Machauer R, Veenstra SJ, Jacobson LH, Staufenbiel M, Desrayaud S, Rondeau JM, Möbitz H, Neumann U. Source Department of Global Discovery Chemistry, Institutes for BioMedical Research, Novartis Pharma AG, CH-4057 Basel, Switzerland. Electronic address: [email protected]. Abstract Previous structure based optimization in our laboratories led to the identification of a novel, high-affinity cyclic sulfone hydroxyethylamine-derived inhibitor such as 1 that lowers CNS-derived Aβ following oral administration to transgenic APP51/16 mice. Herein we report SAR development in the S3 and S2' subsites of BACE1 for cyclic sulfoxide hydroxyethyl amine inhibitors, the synthetic approaches employed in this effort, and in vivo data for optimized compound such as 11d.

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Natural language processing (NLP) Linguistic analysis of textual information with extraction of entities and assertions • Groups words into meaningful units • Morphology allows search for different forms of words

sentences

noun phrases match entities

verb groups match actions

SOCS-1 is a progression marker of human melanoma and may downregulate biological responses by endogenous and/or therapeutically administered cytokines.

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I2E presents extracted assertions in standardized format

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Question #2 The largest source of funding for ACS is: 1. Membership dues 2. National meeting registration fees 3. Bulk chemicals 4. ACS Publications and Chemical Abstracts Services (CAS) 5. Donations

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Text mining for FDA required adverse event monitoring of medical literature

Merck product list (400+)

Medline FDA

ICSR Embase

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Opportunities are emerging to mine real world health data

What co-morbidities are seen?

Why are patients switching treatments? How do factors such as diet, exercise, or sleep impact symptoms?

Electronic health records

Examples

Social Media

Reasons

Monitoring apps or devices

Trends

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Data and information are the foundations of informed decision making

Informed Decisions Visualization

Mining of external data starts with search and access

Predictive Modeling & Analytics Integration Search & Access

Mining of proprietary data starts with data creation and stewardship

Stewardship Data Creation & Acquisition Governance 23

Question #3 Do you use data mining or informatics in your job?

1. Yes every day

2. From time to time 3. Once or twice on special projects 4. Maybe 5. Never

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Career opportunities in informatics • Bioinformatics and medical informatics • Cheminformatics • Natural language processing (NLP) • Semantic engineering • Mathematical modeling and optimization • Statistics and “Data sciences” • Software Engineers (Big Data technologies/Hadoop ecosystem) 25

Thank you! Questions?

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Dr. Wendy Cornell


Head of Informatics IT Proprietary Information and Knowledge Management, Merck



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Dr. Wendy Cornell Head of Informatics IT Proprietary Information and Knowledge Management, Merck



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How Data Mining Drives Pharma: Information as a Raw

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