1. Spotfire in Amgen Research
@ Spotfire Life Science Industry Forum
Sept. 23rd, 2008
Wolfgang G. Hoeck, Ph.D.
Sr.Manager, Research & Development Informatics

2. Agenda
A bit about Amgen
Spotfire in Research
The Spotfire Cockpit
Example guides and visualizations
Transitioning to TIBCO Spotfire
Managing complex data relationships
Final thoughts and Acknowledgments

3. Amgen: A Biotechnology Pioneer
Founded in 1980, Amgen was
one of the first biotechnology
companies to successfully
discover, develop and make
protein-based medicines
Today, we’re leading the
industry in its next wave of
innovation by:
– Developing therapies in
multiple modalities
– Driving cutting-edge
research and development
– Continuing to advance the
science of biotechnological
manufacturing

4. Our Worldwide Presence
Cambridge, MA Norway Denmark
Luxembourg Finland
Toronto, ON
West Greenwich, RI Sweden
The Netherlands
Washington, DC Belgium
Estonia
Ireland
Burnaby, BC Latvia
Lithuania
Bothell, WA Russia
England
Seattle, WA
Czech Republic
Longmont, CO France
Poland
Boulder, CO Switzerland
Slovakia
Hungary
Fremont, CA India
United Arab Emirates
South San Francisco, CA Hong Kong
Greece
Slovenia
Austria
Thousand Oaks, CA
Germany
Mexico City, Mexico
Italy
Louisville, KY Spain Australia
New Zealand
Juncos, Puerto Rico Portugal

5. Our Products
For additional information about Amgen products, including
important safety information, please visit www.amgen.com

6. Spotfire is used across many departments in
Research
High Throughput Screening Research Informatics
Therapeutic Areas Medicinal Chemistry
Investigative Toxicology DMPK
Pathology

7. Why Spotfire?
Interactivity
– Enable “what if” scenarios, Ad-hoc analysis
– Zoom-in & zoom-out capability
– Details-on-demand
– Assemble data: Add columns & rows
Visualizations
– Bar charts, scatter plots, heat maps, cross tables, profile
charts
Web-based Data Sharing
Server-based Data Access
– Multiple data sources
– Easy set-up of queries, information links

8. Where does the data come from and
where does it need to go?
File-based
Star-schema Transactional
Data Sources
warehouse Database
Data Layer
ActivityBase
Assay Data
Warehouse
Assay Data
Store
Layer
App
Sharing
Layer

9. The Spotfire Platform at Amgen
Spotfire DecisionSite 9.1
Spotfire Posters
Spotfire Analytics Server 10.1 on Solaris (prod,
test/dev)
Spotfire Computation Services (Scitegic)
***************************************
TIBCO Spotfire Professional
TIBCO Spotfire Web Player

10. The Spotfire Cockpit for Lead Discovery

11. Guide Example #1: Lead Discovery
What IC50 and POC screening data do we have available for compound X?
Panel of biochemical and cell-based assays

12. Integration with Scitegic Pipeline Pilot
Scientist
Initiate query
Initiate
Initiate query
To add assay
visualizations
With compound ID
annotations
Spotfire
Integrate
Invoke Scitegic
Invoke information
dataset
connector
link
warehouse
Data
Execute SQL
Pipeline Pilot
Scitegic
Query Excel
spreadsheet

13. Guide Example #2: Toxicology
Panel of biochemical profiling assays

14. Data about Data – that’s a key …
Type of experimental result: IC50, POC
Type of assay: biochemical, cell-based
Type of target screened: target classification
Type of samples tested: cell lines, tissues
Source of samples tested: colon, liver, skin, etc.
Stage of disease: metastatic or non-metastatic

15. Sharing data via Spotfire Webplayer
Small Molecule Screening Data
Panel of biochemical and cell-based dose-response assays

16. Sharing data via Spotfire Webplayer
Gene Expression Profiling Data

17. Switching gears a bit …

18. Increased interest in ontologies in biomedical
literature
PubMed search for “ontology” on
May, 2nd 2008 yields 2430 articles
2004-GoPubMed
2000-Gene Ontology

19. What is an Ontology ?
--Thesauri
- Taxonomies
Lists
Ontologies
IS EXPRESSED IN
Targets Diseases Anatomy
Synonyms
IS UP REGULATED IN
AFFECTS
IS EXPRESSED IN
AFFECTS
An ontology is a controlled vocabulary that describes
IS UP REGULATED IN
objects and the relations between them in a formal
IS A TARGET FOR
way, and has a grammar for using the vocabulary
terms to express something meaningful within a
specified domain of interest. AFFECTS
IS DOWN REGULATED IN

20. Selecting Items of Interest

21. Selecting items of interest from a network of
relationships

22. Future
Accessing data via SOA rather than direct DB access
Integration, integration, integration
Network visualizations
Segmenting user groups according to development,
configuration, analysis and decision-making needs
Retaining features available in DecisionSite: Heatmap,
Clustering methods, computation services