2008 Spotfire Life Science Forum


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2008 Spotfire Life Science Forum

  1. 1. Spotfire in Amgen Research @ Spotfire Life Science Industry Forum Sept. 23rd, 2008 Wolfgang G. Hoeck, Ph.D. Sr.Manager, Research & Development Informatics
  2. 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. 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. 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. 5. Our Products For additional information about Amgen products, including important safety information, please visit www.amgen.com
  6. 6. Spotfire is used across many departments in Research High Throughput Screening Research Informatics Therapeutic Areas Medicinal Chemistry Investigative Toxicology DMPK Pathology
  7. 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. 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. 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. 10. The Spotfire Cockpit for Lead Discovery
  11. 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. 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. 13. Guide Example #2: Toxicology Panel of biochemical profiling assays
  14. 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. 15. Sharing data via Spotfire Webplayer Small Molecule Screening Data Panel of biochemical and cell-based dose-response assays
  16. 16. Sharing data via Spotfire Webplayer Gene Expression Profiling Data
  17. 17. Switching gears a bit …
  18. 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. 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. 20. Selecting Items of Interest
  21. 21. Selecting items of interest from a network of relationships
  22. 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