ii-sdv 2016 stefan geißler navigating complex information landscapes – semantics in action in the...

Copyright © 2016 Expert System Enterprise - All Rights Reserved - Slide 1

Navigating complex information landscapes –Semantics in action in the Life Sciences

Stefan Geißler, Archna Bhandari, Dominique Noel,

Expert System

April 18 2016

II-SDV, Nice, France


We all know this situation


Drug DevelopmentDecisions in context : the 4 W’s

Drug PipelineDrug

Portfolio Drug

Approval

WHO ? WHAT ?

WHEN ? WHERE ?


The CI ProcessIn Practice

Clinical Trials

Publications

Regulatory Data

Grants

Patents

Experts

CI Experts/Analysts

Decision Makers

Sources

Reportingformats

News Releases


The CI processIn Practice

Publications

Grants

Patents

News Releases

Regulatory Data

Clinical Trials

Experts

PrioritiesChange

DataChanges

n n+1


The CI Process

• Data Gathering

• Data Selection

• Enrichment

• Presentation

Key Steps


The CI Process

• Data Gathering

• Data Selection

• Enrichment

• Presentation

Key Challenges

Constantchange


The CI ProcessOptions

Real-Time

SaaS

Cu

sto

m Do It Yourself

or

Outsource

static

standard

CustomAND

Real-time


Cockpits

Centralized up-to-date view of organization’s portfolio and competition

Value Proposition


Navigating Complex Information Landscapes …

… by using Semantic Approaches to

• normalize Entity Names

• use structured vocabularies

• Relation Extraction

• linking content items


Normalization: Example Company names

• This is what the user expects • This is the reality when looking at raw data

There are as we all know two companies „Merck“ (as there are many researchers with the same name) and the user expects them to bepresented in a disambiguated way.


LinkingData Linked Across Sources

Initial query on “Lymphoma”, trials on this topic …

… linked to other types of content (news, experts, …)


Entity Extraction and Normalization Data Linked Across Sources

Initial query on “Lymphoma”, trials on this topic …

… linked to other types of content (news, experts, …)


Data Sources

Area of Interest

Publications

MEDLINE

DailyGrants

NIH

Weekly

Patents

USPTO

Weekly

News Releases

Pharma Syndicated

Every 30 Minutes

Regulatory Data

FDA Adverse Events

FDA Release Schedule

Clinical Trials

USA, Europe, WHO, etc.

Daily to Weekly

Experts

Multiple Sources

Daily

Subscription and Internal Data

Sources

Other Sources


VocabulariesConditionDisease, Disorder, Syndrome

InterventionDrugs-Chemical

& Biological type

Mechanism of Action

OrganizationCompanies, Universities, Agencies, Institutions

Source: Medical Subject Headings (MeSH) subset

Source: ChemID Plus

Source: National Drug File Reference Terminology (NDFRT)

Source: ?? (compiled from public sources)

All vocabularies are subject to constant change and need to be constantly reviewed, curated and updated


Glossaries: Challenges

ConditionDisease, Disorder, Syndrome

InterventionDrugs-Chemical

& Biological type

Mechanism of Action

Challenge:• Limited MOA information available

for approved drugs• Controlled Vocabulary (e.g., NDFRT)

contains general terms such as Protease Inhibitors

• MOAs syntax may vary from company to company

• Almost all drug discovery now begins with activity of molecules on a molecular target

OrganizationCompanies, Universities, Agencies, Institutions

Challenge: • Pharma merger boom• Experts attribute it to a

combination of investor pressure and a narrowing window of opportunity Requires extensive

manual effort to gather this information


Drug

Activity

TargetMOA

Scientific Literature

News

Clinical Trials

Company’s Website

Target Database

(HGNC & IUPHAR)

Drug Activity RelationshipsHigh Level Process

HGNC = HUGO gene nomenclature committeeIUPHAR (International Union of Basic and Clinical Pharmacology)

3 Steps

Step1:Find relevant article; Relevant text in the

article

Step 2:Identify relevant

entities & relationships

Step 3:Populate glossaries

RP101 is a Phase II-stage Hsp27 inhibitor

Drug: RP101

Target: Hsp27

Action: Inhibits

Intervention: RP101

MoA: Hsp27 inhibitor


Drug Activity RelationshipsGoal: Make the process easier

Step1:Find relevant article and

text


entities and relationships

Step 3:Populate glossaries

RP101 is a Phase II-stage Hsp27 inhibitor

Drug: RP101

Target: Hsp27

Action: Inhibits

MoA: Hsp27 inhibitor

Intervention: RP101

Automated

Manual

Feed

bac

k

Drug Activity Relationship Skill Cartridge


Merger & Acquisition RelationshipsGoal: Make the process easier

Step1:Find relevant news

article and text


entities & relationships

Step 3:Populate glossary

Automated

Manual

Seragon Pharmaceuticals, … which was acquired by the Roche Group

Who: Roche

Whom: Seragon Phamaceuticals

Action: Acquisition

Parent: Roche

Subsidiary: Seragon Phamaceuticals

Competitive Intelligence Skill Cartridge

Feed

bac

k


Data Gathering One-stop Search

What is happening? Here :Trials on this therapeutic area in the

different phases

Where is is happening? Locate actor on this therapeutic area on

a map

When is is happening: Detect patterns of unusual activity

Simple query…


End-User View


Updated View


End-User View


Is that „just“ a nice chart?

Feedback fom a user:

„And you are telling me this chart is createdautomatically?

You know what: I regularly need to do these analysesfor my boss. And one such chart takes me days tocompile from the available sources!“


TestimonialMajor Pharma Client - User Adoption

Daily WorkflowExploration Adoption


Introducing Expert System

Copyright © 2016 TEMIS - All Rights Reserved - Company Confidential ( ) - Slide 27

• The leading pure-player in semantics & cognitive computing• More than 220 people – present in 7 countries• Multilingual Cognitive Computing, Natural Language Understanding, Information

Extraction and Document Categorization• Merged with TEMIS in 2015


Global Customers : By Vertical

28

ENERGY, OIL & GAS

GOVERNMENT

FEDERAL AGENCIES

MEDIA & PUBLISHING

COMMERCIAL

FINANCE

http://upload.wikimedia.org/wikipedia/it/1/1b/Finmeccanica-logo.gif


Science & HealthSTM Publishing Life Sciences


From theory to reality• The principles discussed in this talk guided also the design of a live system

• The Biopharma Navigator is online at https://www.biopharmanavigator.com/bpn

• Test account on request (see above)

• Currently ~800 experts from the industry are using the system

• Online presentation by Archna Bhandari & Stefan Geißler from Expert System with an Introduction from Matthias Staab, Global Head - PublishedInformation Access bei Sanofi, at https://vimeo.com/160332655

https://www.biopharmanavigator.com/bpn

https://vimeo.com/160332655

ii-sdv 2016 stefan geißler navigating complex information landscapes – semantics in action in the...

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