ICIC 2014 Semantic Integration of Pharmaceutical Content : Blueprint and Examples

Copyright © 2014 TEMIS - All Rights Reserved - Slide 1
Semantic Integration of Pharmaceutical Content : Blueprint and Examples
ICIC Heidelberg, October 15, 2014
Stefan Geißler, TEMIS Deutschland GmbH
www.temis.com

A pioneer in Content Enrichment since 2000
70

We‘re from Heidelberg
And since we are from Heidelberg, this is not the first time I visit the Stadthalle…
„Ball der Vampire“ 2014

TEMIS @ Publishing

TEMIS @ Industry Accounts

TEMIS Mission: Structuring the unstructured
We report a 52 year-old man presenting an acute hair loss induced by carbamazepine (CBZ) in concentration of 8.6 microg/ml.
Extract domain-specific information from text
Relations
We report a 52 year-old man presenting an acute hair loss induced by carbamazepine (CBZ) in concentration of 8.6 microg/ml.
Verb
Patient
Verb
Symptom
Verb
Dosage information
Subj
Entities
Drug Name
Terms
Pro
Verb
Num
Art
N-P
Noun
Verb
Art
Adj
Nn
Nn
Verb
Pp
PropNn
Pp
Noun
Pp
Num
Unit
Abbr
Attributes
Roles
Adverse Event
Side Effect Alopecia
Cause Carbamazepine
Dosage 8.6 mg/ml
Patient 52 year old male

Delivery of Analysis Results
Luxid WebFrontend: Highlighting, Linking, Charts, Graphs, …

Observation
Luxid Webfrontend: Powerful, rich tool for experienced expert users
Some users express the demand for a simpler, less sophisticated system
Quote from one client:
„The aim is not to make 5% of my staff 80% smarter, but 80% of my people 5% smarter!“

Introducing Luxid Navigator
TEMIS acquisition of „I3 Analytics“ from Columbia, USA, in 2013
Large-scale crawling, enrichment, indexing and delivery of Life Science content in an intuitive web application
Design and implementation in close cooperation with BigPharma pilot client
Deployments at INSERM and Prometic Life Sciences

Fierce Bio
Fierce Pharma
Marketwire
PrNewswire
Biospace
Reuters
Linkoph
DrugDiscoveryNews
NewsMedical.net
pr.com
Medline
ChemIDPlus
MeSH
NCT
WHO
FDA
NIH …
Excel
HTML
XML
PDF
Streamlines experts & competitive intelligence efforts by :
•Aggregating, Enriching and Integrating multiple sources of open but unstructured data on these topics
•Presenting information in structured yet easy-to-use interfaces
Biopharma Edition
Luxid® Navigator
Extract key items of
interest
Interconnect items with Linked Data
Portal application
Content Aggregation
Information Extraction
Knowledge Integration
Presentation
Content merged into a single template

BioExpert Navigator:
Assists users in identifying experts and their published content in life sciences research.
ClinicalTrials Navigator:
Assists users in identifying competitive intelligence related to clinical trials.
BioNews Navigator:
Continuously scans news feeds to pick up every possible news story for target discovery, drug approvals, trial initiation, trial results, regulatory news and variety of other news.
Pharmacovigilance (Beta) Provide overview over Adverse Events
Toxicology (in preparation)
Biopharma Edition
Luxid® Navigator

Biopharma Navigator Modules

Copyright © 2014 TEMIS - All Rights Reserved
Data Breakdown
❖~750,000 News Articles (1,000 new per day)
❖~270,000 Clinical Trials (WHO + CT.gov)
❖~13,600,000 Medline Articles (1992-Today)
❖~18,000,000 FDA Adverse Events
❖~5,100,000 US Patents
❖~390,000 NIH Grants
❖~11,000 Conference Documents
Biopharma Edition
Luxid® Navigator

Refreshing Documents
❖ClinicalTrials.gov fully recrawled daily
❖Takes less than an hour
❖Bionews refreshed weekly
❖Takes a few hours
❖Medline (13.6 million) refreshed monthly
❖Takes about 30 hours
❖Multiple refreshes in parallel with little time difference
Selective refreshes can be done for real time results and are recommended
Biopharma Edition
Luxid® Navigator

Process: Capture, Extract, Normalize & Integrate Data
Extract, Normalize, and Integrate
(Vocabularies)
Clinical Trials
News releases
Scientific Publications
Adverse Events
Drug Profile: Integrated Information View
Factor Xa
Vocabularies
•Drugs
•MOA
•Diseases
•Organizations
•Adverse Reactions
•….

Multiple Terminology & Multiple Values
Drug/Intervention/ Product
•BAY59-7939 (molecule name)
•Rivaroxaban (chemical name)
•Xarelto (brand name)
Sponsor/Co-sponsor/ Manufacturer/ Organization/Affiliation
•Bayer
•Bayer Healthcare
•Berlex
•Berlis AG
Condition/Disease/ Indication
•AF
•Atfb1
•Atrial Fibrillation
•Auricular Fibrillations
•Familial Atrial Fibrillation

Multiple Data Sources
Case Study: Xarelto
•BAY59-7939 in Atrial Fibrillation Once Daily (OD)
•Oral Direct Factor Xa Inhibitor BAY59-7939 in Patients With Acute Symptomatic Proximal Deep Vein Thrombosis(ODIXa-DVT)
•Rivaroxaban for Antiphospholipid Antibody Syndrome (RAPS)
Clinical Trials
•Xarelto Lawsuit Alleges Uncontrollable Bleeding Nearly Cost California Woman Her Life, Bernstein Liebhard LLP Reports
•Anticoagulant therapy Rivaroxaban for patients with AF undergoing cardioversion
•Xarelto is Alleged to Cause Serious and Uncontrolled Internal Bleeding
News Releases
•Development of new anticoagulant highly honoured: Bayer's Xarelto recognised with 2010 international Prix Galien award.
•The discovery and development of Rivaroxaban, an oral, direct factor Xa inhibitor
•Antagonists of activated factor Xa and thrombin: innovative antithrombotic agents
Scientific Publications
•An adverse event of cerebral hemorrhage leading to death was reported to FDA while patient was on Xarelto for the treatment of atrial fibrillation
FDA Adverse Events

Normalized Yet Granular
Search for BAY59-7939
Non-Normalized
•105 publications
Normalized
•2055 publications
Search for Rivaroxaban
Non-Normalized
Normalized
Search for Xarelto
Non-Normalized
•216 publications
Normalized
Source Data: Medline Publications
Granular Search
Normalized Search

Sample Analysis: Expert Finder
Find experts & documents based on Medline publications

Behind the scenes: Named Entity Recognition
Name Disambiguation
•Name ambiguity is a big challenge when we bring data from multiple sources – not only the naming schemes differ, but the form of the record often differs.
•Our name disambiguation algorithms overcome this challenge.
Why it Matters?
•It is critical to present a holistic view when identifying experts across different data sources.
•Example: a person may be represented as
–“Smith J.” in Medline
–“Smith J., MD” in clinicaltrials.gov and
–“john Smith” in Patent database
Our system is able to make such connections.

Behind the scenes: Metadata creation from fulltext
Missing Information
•Data elements in trial registries (e.g. trial phase in WHO) are not always populated under designated xml fields. However, such data elements could be buried under textual descriptions.
•Algorithms have been developed to extract such elements from textual description: Enrollment Country location Phase level data Principal Investigator Inclusion and Exclusion Criteria
•In addition, algorithms have been developed to extract pre-clinical and other Phase I trials (not mandatory to be included in trial registries) from news releases
Why it Matters?
•Missing data can give an incomplete picture when analyzing the competitive landscape. We seek to bring the full picture to our end users.

Alerts
Staying up to date with your topics of interest

Comparison
Search Query: “Glucagon-like Peptide-1 (GLP-1) Agonists”
Clinicaltrials.gov returns 96 trials
Clinical Trials Navigator returns 231 trials
Mechanism of action (MoA) search

Comparison
Search Query: “RG7652 AND PCSK9”. RG7652 (MPSK3169A) is an Anti-PCSK9 Antibody in development for the treatment of Coronary diseases by Roche.
Clinicaltrials.gov returns no trial
Clinical Trials Navigator returns 1 trial

Comparison
Search Query: “NCT00460265 AND Bulgaria”. NCT00460265: phase 3 trials conducted at multiple location across world. Health Authority field specifies the country locations.
Clinicaltrials.gov returns no trial
Clinical Trials Navigator brings the relevant trial
Country Search

Document Processor
High Level Architecture
Glossaries
Management UIs
Apache Load Balancer
Front End
Front End
Users
Clinical Trials
FDA AERS
Medline
News RSS
NIH Grants
US Patents
Crawlers
Backend MongoDB
Frontend
MongoDB
ReplicaSet
Solr
Luxid

Luxid Biopharma Navigator
Sign up for a free trial at
www.biopharmanavigator.com

Thank you
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ICIC 2014 Semantic Integration of Pharmaceutical Content : Blueprint and Examples

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ICIC 2014 Semantic Integration of Pharmaceutical Content : Blueprint and Examples