Self-Service Knowledge Discovery for Drug Discovery Research

1. Amgen Research Connected Data
Landscape – Enabling Self-
Service Knowledge Discovery
Filip Pattyn, PhD
filip@ontoforce.com - Scientific Lead & Product Manager
www.ontoforce.com - www.disqover.com
Track 4 - May 24, 2017

2. Islands of information

3. Islands of information

4. Islands of information

5. Conversion & Update Pipeline
• Aggregation
• Semantic Conversion
• Interlinking
Smart Data

6. Conversion & Update Pipeline
• Aggregation
• Semantic Conversion
• Interlinking
Smart Data

7. Conversion & Update Pipeline
• Aggregation
• Semantic Conversion
• Interlinking
Smart Data

8. FAIR Data
Ü Findable
Ü Accessible
Ü Interoperable
Ü Reusable
Booth #100
Wednesday
• assess how FAIR is your data
• make your data more FAIR
Thursday
• 12:55 – 1:45 Exhibit Hall Vendor
Theater
• demos and jury deliberation

9. www.disqover.com
• free to use platform
• 120+ data sources
• semantic search capabilities
• linked data
• provenance
• export your search results
• keep track of and share searches

10. www.disqover.com
• free to use platform
• 120+ data sources
• semantic search capabilities
• linked data
• provenance
• export your search results
• keep track of your searches

11. www.disqover.com
• free to use platform
• 120+ data sources
• semantic search capabilities
• linked data
• provenance
• export your search results
• keep track of your searches

12. www.disqover.com
• free to use platform
• 120+ data sources
• semantic search capabilities
• linked data
• provenance
• export your search results
• keep track of and share searches

14. www.disqover.com
• free to use platform
• 120+ data sources
• semantic search capabilities
• linked data
• provenance
• export your search results
• keep track of and share searches

16. www.disqover.com
• free to use platform
• 120+ data sources
• semantic search capabilities
• linked data
• provenance
• export your search results
• keep track of and share searches

18. www.disqover.com
• free to use platform
• 120+ data sources
• semantic search capabilities
• linked data
• provenance
• export your search results
• keep track of and share searches

19. www.disqover.com
• free to use platform
• 120+ data sources
• semantic search capabilities
• linked data
• provenance
• export your search results
• keep track of and share searches

22. www.disqover.com
• free to use platform
• 120+ data sources
• semantic search capabilities
• linked data
• provenance
• export your search results
• keep track of and share searches

23. www.disqover.com
• free to use platform
• 120+ data sources
• semantic search capabilities
• linked data
• provenance
• export your search results
• keep track of and share searches

24. www.disqover.com
• free to use platform
• 120+ data sources
• semantic search capabilities
• linked data
• provenance
• export your search results
• keep track of and share searches

25. Public and Third Party data federation
Remote DISQOVER
www.disqover.com
• 120+ data sources
• automated update pipeline
• third party data store
Local DISQOVER
• internal data
• enriched with remote
(public/third party) data

26. CONNECTED DATA LANDSCAPES:
ENABLING SELF-SERVICE
KNOWLEDGE DISCOVERY
IN EARLY RESEARCH
WITH
WOLFGANG HOECK, PHD DANIEL GSCHWEND, PHD
PRINCIPAL BUSINESS ANALYST,
RESEARCH INFORMATICS
DIRECTOR, INFORMATION ARCHITECTURE
R&D INFORMATICS
BIO IT - MAY 24, 2017

27. 2
Provided May 24th, 2017, as part of an oral presentation and is qualified by
such, contains forward-looking statements, actual results may vary
materially; Amgen disclaims any duty to update.
Improved drug target knowledge awareness
Scientists must be able to find comprehensive
internal and external knowledge about a
Gene/Drug Target
We aim to ensure drug target assessments are
fully informed, facilitating efficient progression
through the Discovery pipeline
GENE KNOWLEDGE DISCOVERY (GKD)
AGGREGATES AND CONNECTS RESEARCH DATA
• Enable knowledge discovery by connecting scientific concepts and allowing “data to talk to data”
A data-centric view, not system-centric
Research scientists can focus on the data
they need for decisions, without having to
think about which system contains it.
We facilitate self-service knowledge
discovery by linking available data together,
increasing visibility, and neutralizing
boundaries.
Can’t we have a single
place for Amgen and public
data about a Gene/Target?
Have we
ever worked
on “X” as a
target?
What’s the relevance
of this target to
disease indications?

28. 3
Provided May 24th, 2017, as part of an oral presentation and is qualified by
such, contains forward-looking statements, actual results may vary
materially; Amgen disclaims any duty to update.
Molecule Registration
Systems
In-vitro/In-vivo Assay
Data Systems
Omics Data Systems
Translational Research
Information Platform
GKD ENHANCES FINDABILITY AND DISCOVERY WITHIN
A RESEARCH DATA LANDSCAPE
Structured Data
Unstructured Data
PUBLIC
DATA
Consumer Producer & Consumer
search
filter
explore
discover
•••
Link
to
details

29. 4
Provided May 24th, 2017, as part of an oral presentation and is qualified by
such, contains forward-looking statements, actual results may vary
materially; Amgen disclaims any duty to update.
GKD IS A SELF-SERVICE KNOWLEDGE DISCOVERY
PLATFORM BUILT ON SEMANTIC INTEGRATION
Spotfire
Research
Gateway
Reagent
ordering
Public data
Experiment
Metadata
Institutional
Knowledge
Omics
Metadata
Amgen
DISQOVER
Ontoforce
DISQOVER
Semantic
Transformation
Terminology &
Reference Data
Graph
Visualizer
analytics &
visualization drilldown
Other Amgen
systems
Public Data
information model
dataintegrationdecisions
Molecules &
Reagents
Gene & Drug
Target Catalogs

30. 5
Provided May 24th, 2017, as part of an oral presentation and is qualified by
such, contains forward-looking statements, actual results may vary
materially; Amgen disclaims any duty to update.
VISUAL CUES IDENTIFY AMGEN CANONICAL TYPES AND
DISTINGUISH PRIVATE FROM PUBLIC DATA
logo indicates presence of Amgen data
Deep integration of Public and Amgen data
Areas of deep integration in progress

31. 6
Provided May 24th, 2017, as part of an oral presentation and is qualified by
such, contains forward-looking statements, actual results may vary
materially; Amgen disclaims any duty to update.
A COHESIVE, CONNECTED KNOWLEDGE LANDSCAPE
EMERGES FROM LINKED DATA (data-source independent!)

32. 7
Provided May 24th, 2017, as part of an oral presentation and is qualified by
such, contains forward-looking statements, actual results may vary
materially; Amgen disclaims any duty to update.
A SEMANTIC FOUNDATION EMPOWERS
KNOWLEDGE DISCOVERY
1
2
3
4
5

33. 8
Provided May 24th, 2017, as part of an oral presentation and is qualified by
such, contains forward-looking statements, actual results may vary
materially; Amgen disclaims any duty to update.
WE HEAR CONSISTENTLY ABOUT THE VALUE GKD BRINGS
With GKD I can easily find
out what I and others know
about a Gene/Target. Previously I had to know who
to ask before an answer could
be gained. Now I can easily
learn about a Project, the
People that are involved and
the Resources which have
been created.
I always had to rely on experts
to find gene expression data.
GKD gives me the tools to do
this myself.
To run experiments I need
reagents. Antibodies are a good
example. GKD makes it easy to
find antibodies at Amgen or
from commercial sources.
Cell Lines are a work horse
for initial experiments around
a Target. GKD brings all data
about Cell Lines within reach.

34. 9
Provided May 24th, 2017, as part of an oral presentation and is qualified by
such, contains forward-looking statements, actual results may vary
materially; Amgen disclaims any duty to update.
• Access available to staff across all
Research sites
• Team of Data Stewards from Research
help to drive adoption and
requirements
GKD IMPACT AT AMGEN CONTINUES TO GROW
• Supports key Research activities:
– Target Identification & Validation
– Molecule Development & Testing
– Safety Assessments
– In/out-licensing opportunities
new user registrations over time usage over timeusage by location

35. 10
Provided May 24th, 2017, as part of an oral presentation and is qualified by
such, contains forward-looking statements, actual results may vary
materially; Amgen disclaims any duty to update.
• Close partnership and alignment with scientists’ needs is required to establish an
underlying information model that is both pragmatic for users yet pure to the data
• Data quality and transparency are critical in exploration and decision-making, particularly
for data sources over which we have limited control
• Domain-specific searching, e.g. by chemical structure or DNA/protein sequence, will open
valuable new discovery paths
• API access for querying across public and private data would facilitate more complex
analytics and insights
• Clarification of the boundary between a knowledge discovery environment and
analytics/visualization solutions is challenging, but will help guide user experience and
architectural design decisions
KEYS FOR CONTINUED SUCCESS
• GKD/DISQOVER enables fluid exploration of our Research connected data landscape
• and offers a key capability for preserving and sharing institutional knowledge

36. 11
Provided May 24th, 2017, as part of an oral presentation and is qualified by
such, contains forward-looking statements, actual results may vary
materially; Amgen disclaims any duty to update.
Executive
Sponsorship
Therapeutic Areas
Steering
Committee
Therapeutic Areas
CBSS
Research Informatics
Research
Data
Stewards
Sean Caenepeel
Lauren Mihalcik
Becky Pferdehirt
Neil Rampal
Lisa Sherman
YuMei Xiong
Oncology TA
CBSS
GAU
Neuroscience TA
Inflammation TA
CardioMetabolic Disorders TA
RESEARCH/IS PARTNERSHIP DELIVERS
SELF-SERVICE KNOWLEDGE DISCOVERY WITH GKD
Amgen IS
Team
Bill Craven
Shishir Dube
Dan Gschwend
Wolfgang Hoeck
Arun Nayar
Larry Rodriguez
Ariela Shofaro
Ingrid Skei
Vishaka Sriniwasan
Research Informatics
Ontoforce
Team
Hans Constandt
Kenny Knecht
Filip Pattyn
Peter Verrykt