Merck’s Information Landscape
Knowledgebase
Kelly Clark & Charisma Eugenio
June 10, 2014
Modeling Merck’s Information Landscape
(MRL = Merck Research Laboratories)
Metabolomics
Gene expression
Sequencing
Pharmac...
Information Types/Taxonomies from Merck’s 
Information Landscape Knowledgebase (ILK)
3
Marketing
Regulatory
Clinical
Molec...
R&D decisions rely on high quality information to steer 
programs and the pipeline
Knowledge Artifacts
“Target validation ...
5
Today Next 2-3 Years Beyond
Culture of Single Use
“Find & Access”
DecisionMaking
Quality
Vocabulary
Management
Embedded
...
Clinical
Development
Consumer
Care
Research
Formulation
Safety
Regulatory
Manufacturing
Enterprise Business Analysis and I...
“Google Street View” for information flows…
Merck
Analysts need a way to collaborate on mapping information flows
from different domains without explicit coordination...
Is a method of documenting and modeling the flow of information through an enterprise 
that allows both targeted and holis...
Discovering the Information Flow Modeling 
Ontology
Mind Map for Merck’s “Patients Like Me” collaboration hand‐drawn by Jy...
Data
Sources
Organizations
Business
Processes
Decisions
KM
Artifacts
Initiatives
/ Projects
Use
Cases
People Roles
Informa...
Collaboration without Coordination
The use of an information modeling ontology allows multiple informatics and 
business a...
Leveraging the Information Landscape  Knowledgebase 
to enable Information Management and Search
By encoding this knowledg...
Semantic Information Flow Modeling 
–Tools
Role
(from
Information
Modeling
Framework)
«informatio...
Information type
(fro...
Information Landscape Knowledgebase (ILK)
Information Landscape Knowledgebase –
Entity Explorer for Ad Hoc Analysis
Joe Smith
Jane Doe
Information Landscape Knowledgebase –
Data Sources
Drill down by faceting on any entity type
18
Feedback/Pain Point Analysis
19
MRL Search Survey 2013
Example Pain Point Categories:
• Access provisioning
• Business Pro...
Summary – Merck’s Information Landscape 
Knowledgebase
• Volume and complexity of scientific information is accelerating
•...
Acknowledgements
• Merck Research Laboratories – Information Technology
– Karen Conrad
– Charisma Eugenio
– John Koch
– El...
Merck’s Information Landscape
Knowledgebase
Charisma Eugenio
June 10, 2014
23
Information Landscape Knowledgebase (ILK)
Role
(from
Information
Modeling
Framework)
«informatio...
Information type
(f...
24
Anzo Express is a complete spreadsheet data management solution. It enables
users to link data from multiple Excel spre...
25
Anzo Ontology Editor
26
Anzo Ontology Editor
27
Information Flow Model (IFM)
28
IFM Oracle Database Schema
29
Anzo Connect
30
Anzo Connect
31
Anzo Connect
32
Anzo Connect
33
Anzo Connect
34
Anzo Connect
35
Information Landscape Knowledgebase (ILK)
36
Information Landscape Knowledgebase (ILK)
37
Information Landscape Knowledgebase (ILK)
38
Information Landscape Knowledgebase (ILK)
39
Information Landscape Knowledgebase (ILK)
40
Information Landscape Knowledgebase (ILK)
41
ILK – Entity Explorer
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ILK – Entity Explorer
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ILK – Entity Explorer
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ILK – Entity Explorer
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ILK – Entity Explorer
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ILK – Entity Explorer
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ILK – Entity Explorer
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ILK – Entity Explorer
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ILK – Systems
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ILK – Systems
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ILK – Systems
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Information Landscape Knowledgebase (ILK)
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Merck's Information Landscape Knowledgebase - Eugenio, Clark

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Merck’s Informatics IT team has developed the Information Landscape Knowledgebase, a semantically rich, intuitively accessible model of information types and sources across Merck. In this presentation, we discuss how the solution takes advantage of underlying semantic models and novel visualizations to address the needs of both scientists and data stewards while providing valuable insights for IT resourcing.

Pharmas of all sizes possess a wealth of information across hundreds of data sources at all levels of the organization from basic and clinical research to drug safety and commercial competitive intelligence. Without a cohesive understanding of which data sources include which types of information, how they are used and who uses them, the potential value of this information is far from realized. IT organizations have used traditional enterprise data management solutions to track data sources as best they can. However, complexity of these tools does not allow the data stewards to provide first-hand insight about their data sources or scientists to explore and discover new sources. The results are under-utilization and duplication of data, leading to undiscovered knowledge and inefficient IT spending. By leveraging semantic models and visualizations, our Information Landscape Knowledgebase overcomes these traditional challenges to weave together an easily understood, discoverable, and analyzable view into a huge diversity of information sources across Merck.

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Merck's Information Landscape Knowledgebase - Eugenio, Clark

  1. 1. Merck’s Information Landscape Knowledgebase Kelly Clark & Charisma Eugenio June 10, 2014
  2. 2. Modeling Merck’s Information Landscape (MRL = Merck Research Laboratories) Metabolomics Gene expression Sequencing Pharmacogenetics Imaging Safety/PV Real world data Clinical trials Global EMRs & registries Social networks / patient communities Monitoring Behavior/ adherence /compliance Vaccine production RNAi HTS Pathways Biological lit. / Targets Chemistry / Chemical lit Disease Competitive intelligence Pharmacology Epidemiology  Target Class Mechanism of Action Toxicity Outcomes EHR Stage gate decisions External partners Indication Targeted institutions Engagement programs Formulary Market access / channels Batch records Labeling Quality Assurance Manufacturing & process design 2011 – “Retina Diagram“ - Concept
  3. 3. Information Types/Taxonomies from Merck’s  Information Landscape Knowledgebase (ILK) 3 Marketing Regulatory Clinical Molecules /  Compounds Pharmacology Toxicology PK/PD Studies Gene Competitive  Intelligence Animals Biological  Specimens Assays Real World  Evidence Targets Protein ExperimentsLaboratory Programs Biomarkers Modeling &  Simulation 2014 – “Retina Diagram” - Real This graphic created using Gephi: Bastian M., Heymann S., Jacomy M. (2009). Gephi: an open source software for exploring and manipulating networks. International AAAI Conference on Weblogs and Social Media.
  4. 4. R&D decisions rely on high quality information to steer  programs and the pipeline Knowledge Artifacts “Target validation plan” Business Groups “Early Development team” People “John Smith” Information Types “Clinical Trial Name” Organization Units “Analytical Chemistry” Sources “Electronic Lab Notebook” Business Processes “Integrative assessment of liver  toxicity” Activities “Refine model” Roles “Statistician” Decisions/ Gateways “Determine Patient  Stratification Biomarkers” R&D Information Landscape >27,000 entities and 70,000 relationships defined The volume and variety of internal information and external scientific information continues to  grow at a rapid and accelerating rate The ability to readily find, access, and use information is absolutely critical Capabilities “Biomarker  Validation” Feedback Surveys, VoC
  5. 5. 5 Today Next 2-3 Years Beyond Culture of Single Use “Find & Access” DecisionMaking Quality Vocabulary Management Embedded Stewardship Information Flows Modeled Effective Search Integrated Information Architecture IM Challenges Characterized Fragmented tools, processes Systematic categorization of data Information ManagementMaturity As knowledge workers understand and embrace improved information management practices, better decision making can be enabled by better access to information Organization-Wide Information Re-Use ? Better Information Management  Better Decision Making: Better analysis, more transparency and collaboration, better workflow management, faster decisions DecisionQualityAdoption,Maturity Improving R&D Decision Making  Information Flows Modeled
  6. 6. Clinical Development Consumer Care Research Formulation Safety Regulatory Manufacturing Enterprise Business Analysis and IT Resource planning  tends to focus on organizational domains separately “Every system is perfectly designed to get exactly the results it gets.” --
  7. 7. “Google Street View” for information flows…
  8. 8. Merck Analysts need a way to collaborate on mapping information flows from different domains without explicit coordination http://www.dwalls.com/Nature/Nature-World-Travel/Aerial+View+of+Downtown+Boston
  9. 9. Is a method of documenting and modeling the flow of information through an enterprise  that allows both targeted and holistic analysis across the information continuum. Sales &  Marketing MCC •Regulatory R&D Manufacturing Merck Semantic Information Flow Modeling (sIFM)… Regulatory
  10. 10. Discovering the Information Flow Modeling  Ontology Mind Map for Merck’s “Patients Like Me” collaboration hand‐drawn by Jyoti Shah Used with permission from PatientsLikeMe ®
  11. 11. Data Sources Organizations Business Processes Decisions KM Artifacts Initiatives / Projects Use Cases People Roles Information Types Capabilities Business Groups Activities We determined the types of things (entities) and the types of relationships that we were trying to understand and model them using a common  semantic framework
  12. 12. Collaboration without Coordination The use of an information modeling ontology allows multiple informatics and  business analysts to collaborate on the same model without explicit coordination Analyst 1 Analyst 2 Analyst 3 Compound structure  ELN Medicinal Chemist uses ChemCart Pharm Sci uses ELN Program Biologist uses ELN Compound Structure  ChemCart Active Pharmaceutical Ingredient  ELN Toxicologist uses ELN Medicinal Chemist member-of Lead optimization team Compound Structure ELN
  13. 13. Leveraging the Information Landscape  Knowledgebase  to enable Information Management and Search By encoding this knowledge in a searchable semantic knowledgebase, we can discover details about Merck’s information landscape on the fly, that were previously difficult to uncover. Project Information Types Data Sources KM Artifacts Translational PK/PD Modeling ?Information Types ?KM Artifacts ?Data Sources includes flow flow What are the types of information and data sources associated with Translational PKPD Modeling?
  14. 14. Semantic Information Flow Modeling  –Tools Role (from Information Modeling Framework) «informatio... Information type (from Information Modeling Framework) «business gr... Team (fromInformation Modeling Framework) «informatio... Information class (from Information Modeling Framework) BusinessProcess1 (from Information Modeling Framework) Activity2 Decision Business Division (from Information Modeling Framework) «initiative» Initiativ e (fromInformation Modeling Framework) Internal Data Source «view» View (fromInformation Modeling Framework) Document (from Information Modeling Framework) «organizati... Organization Unit (from Information Modeling Framework) «business enterp... Enterprise (fromInformation Modeling Framework) «organization... Organization Unit 2 (from Information Modeling Framework) «organization... Organization Unit 3 (from Information Modeling Framework) Role 2 (from Information Modeling Framework) Role 4 (from Information Modeling Framework) External Data Source Unstructured Document Repository «informatio... information type 2 (from Information Modeling Framework) «informatio... information type 3 (from Information Modeling Framework) «information c... information class 2 (fromInformation Modeling Framework) Person Name 2 Person name 3 Person Name Person Name 4 Person Name 5 «information c... Information class 3 (from Information Modeling Framework) Specialization of Role (from Information Modeling Framework) Specialization 2 of role (from Information Modeling Framework) Decision 2 «business gr... Committee (fromInformation Modeling Framework) «business gr... Governance Body (from Information Modeling Framework) «initiative» Initiativ e 2 (from Information Modeling Framework) «initiative» Initiativ e 3 (from Information Modeling Framework) Person name 6 Person Name 7 StartEvent1 EndEvent1 «informatio... Information type 5 (from Information Modeling Framework) «informatio... Information type 6 (fromInformation Modeling Framework) Internal Data Source 2Internal Data Source 3 «information c... Information class 4 (fromInformation Modeling Framework) «Capability» Capability (from Information Modeling Framework) (fromInformation Modeling Framework) «use case» Use Case «external or... External Organization (from Information Modeling Framework) «problem» Pain Point / Problem (from Information Modeling Framework) Information Modeling Framework:: Database Table 1 «Field» Database Field 1 (from Information Modeling Framework) «Field» Database Field 2 (from Information Modeling Framework) Information Modeling Framework:: Database Table 2 «Field» Database Field 3 (from Information Modeling Framework) «dataset» Dataset 1 (fromInformation Modeling Framework) part-of member-of participates-in «flow»«flow» «flow» decides «flow» includes includes «flow» part-of enables enables part-of includes-role part-of includes-role includes-role provides member-of member-of «flow» «flow» «flow» «flow» «flow» «flow» «flow» has-role has-role has-role part-of «flow» performs decides decides part-of has-role «stewards» uses «flow» «flow» «flow»«flow» «includes» «includes» «flow» hasContact «identified-by» «owns» «participates-in» «provides» «identified-by» «includes» «includes» «includes»«includes» «flow» sIFM starts with the work  business analysts do to  assess the current state,  elicit requirements, pain  points, and informatics  opportunities • Stakeholder analysis • Interviews / Req. Elicitation • Surveys / Diagnostics • Review of existing artifacts • Brainstorming / Concept mapping Information‐related  entities and concepts are  graphically represented  using an ontological model  with the help of the EA  business and information  modeling software Anzo software provides  semantic web structuring  of the IFM model, and an  intuitive interface to allow  ad hoc querying,  visualization and analytics Information Landscape Knowledgebase Information Flow – Knowledge Gathering Information Flow Modeling
  15. 15. Information Landscape Knowledgebase (ILK)
  16. 16. Information Landscape Knowledgebase – Entity Explorer for Ad Hoc Analysis Joe Smith Jane Doe
  17. 17. Information Landscape Knowledgebase – Data Sources
  18. 18. Drill down by faceting on any entity type 18
  19. 19. Feedback/Pain Point Analysis 19 MRL Search Survey 2013 Example Pain Point Categories: • Access provisioning • Business Process/Workflow management • Data Quality and Completeness • Data Security • Data Vizualzation/Analysis Capabilities • Federated Search • Knowledge Management and organization • Platform / Database • Tags / Keywords • Training / Awareness
  20. 20. Summary – Merck’s Information Landscape  Knowledgebase • Volume and complexity of scientific information is accelerating • It is critical that scientists can seamlessly find and access that information • Traditional analysis makes it difficult to understand how information is actually stewarded across the organization, and perpetuates the establishment of siloed solutions • Semantic Information Flow Modeling and the Information Landscape Knowledgebase allows analysts and architects to collaborate on a common representation of information flow across the organization to enable: – Linked-data approach to analysis – Identification of high impact scientific information management solutions – Stewardship of Merck’s knowledge assets 20
  21. 21. Acknowledgements • Merck Research Laboratories – Information Technology – Karen Conrad – Charisma Eugenio – John Koch – Ellie Norris – Jyoti Shah – Kim Wilson • Cambridge Semantics Inc. – Ben Szekely – Lee Feigenbaum 21
  22. 22. Merck’s Information Landscape Knowledgebase Charisma Eugenio June 10, 2014
  23. 23. 23 Information Landscape Knowledgebase (ILK) Role (from Information Modeling Framework) «informatio... Information type (from Information Modeling Framework) «business gr... Team (from Information Modeling Framework) «informatio... Information class (from Information Modeling Framework) BusinessProcess1 (from Information Modeling Framework) Activity2 Decision Business Division (from Information Modeling Framework) «initiative» Initiative (from Information Modeling Framework) Internal Data Source «view» View (from Information Modeling Framework) Document (from Information Modeling Framework) «organizati... Organization Unit (from Information Modeling Framework) «business enterp... Enterprise (fromInformation Modeling Framework) «organization... Organization Unit 2 (from Information Modeling Framework) «organization... Organization Unit 3 (from Information Modeling Framework) Role 2 (from Information Modeling Framework) Role 4 (from Information Modeling Framework) External Data Source Unstructured Document Repository «informatio... information type 2 (from Information Modeling Framework) «informatio... information type 3 (from Information Modeling Framework) «information c... information class 2 (from Information Modeling Framework) Person Name 2 Person name 3 Person Name Person Name 4 Person Name 5 «information c... Information class 3 (from Information Modeling Framework) Specialization of Role (from Information Modeling Framework) Specialization 2 of role (from Information Modeling Framework) Decision 2 «business gr... Committee (from Information Modeling Framework) «business gr... Gov ernance Body (from Information Modeling Framework) «initiative» Initiative 2 (from Information Modeling Framework) «initiative» Initiativ e 3 (from Information Modeling Framework) Person name 6 Person Name 7 StartEvent1 EndEvent1 «informatio... Information type 5 (from Information Modeling Framework) «informatio... Information type 6 (from Information Modeling Framework) Internal Data Source 2Internal Data Source 3 «information c... Information class 4 (from Information Modeling Framework) «Capability» Capability (from Information Modeling Framework) (from Information Modeling Framework) «use case» Use Case «external or... External Organization (from Information Modeling Framework) «problem» Pain Point / Problem (from Information Modeling Framework) Information Modeling Framework:: Database Table 1 «Field» Database Field 1 (from Information Modeling Framework) «Field» Database Field 2 (from Information Modeling Framework) Information Modeling Framework:: Database Table 2 «Field» Database Field 3 (from Information Modeling Framework) «dataset» Dataset 1 (from Information Modeling Framework) part-of member-of participates-in «flow»«flow» «flow» decides «flow» includes includes «flow» part-of enables enables part-of includes-role part-of includes-role includes-role provides member-of member-of «flow» «flow» «flow» «flow» «flow» «flow» «flow» has-role has-role has-role part-of «flow» performs decides decides part-of has-role «stewards» uses «flow» «flow» «flow» «flow» «includes» «includes» «flow» hasContact «identified-by» «owns» «participates-in» «provides» «identified-by» «includes» «includes» «includes»«includes» «flow» Anzo knowledgebase for Merck’s information landscape, including information-related concepts and entities captured via the Enterprise Semantic Information Flow Modeling (sIFM) initiative
  24. 24. 24 Anzo Express is a complete spreadsheet data management solution. It enables users to link data from multiple Excel spreadsheets and relational databases together in real-time for data collection, collaboration, and reporting. Anzo Express also includes a state-of-the-art Web dashboard tool so that you can easily share your integrated Excel data with your colleagues. • Anzo Ontology Editor • Anzo Connect • Anzo for Excel • Anzo on the Web Anzo Express
  25. 25. 25 Anzo Ontology Editor
  26. 26. 26 Anzo Ontology Editor
  27. 27. 27 Information Flow Model (IFM)
  28. 28. 28 IFM Oracle Database Schema
  29. 29. 29 Anzo Connect
  30. 30. 30 Anzo Connect
  31. 31. 31 Anzo Connect
  32. 32. 32 Anzo Connect
  33. 33. 33 Anzo Connect
  34. 34. 34 Anzo Connect
  35. 35. 35 Information Landscape Knowledgebase (ILK)
  36. 36. 36 Information Landscape Knowledgebase (ILK)
  37. 37. 37 Information Landscape Knowledgebase (ILK)
  38. 38. 38 Information Landscape Knowledgebase (ILK)
  39. 39. 39 Information Landscape Knowledgebase (ILK)
  40. 40. 40 Information Landscape Knowledgebase (ILK)
  41. 41. 41 ILK – Entity Explorer
  42. 42. 42 ILK – Entity Explorer
  43. 43. 43 ILK – Entity Explorer
  44. 44. 44 ILK – Entity Explorer
  45. 45. 45 ILK – Entity Explorer
  46. 46. 46 ILK – Entity Explorer
  47. 47. 47 ILK – Entity Explorer
  48. 48. 48 ILK – Entity Explorer
  49. 49. 49 ILK – Systems
  50. 50. 50 ILK – Systems
  51. 51. 51 ILK – Systems
  52. 52. 52 ILK – Systems
  53. 53. 53 ILK – Systems
  54. 54. 54 ILK – Systems
  55. 55. 55 ILK – Systems
  56. 56. 56 ILK – Systems
  57. 57. 57 ILK – Systems
  58. 58. 58 ILK – Systems
  59. 59. 59 ILK – Systems
  60. 60. 60 ILK – Systems
  61. 61. 61 ILK – Systems
  62. 62. 62 ILK – Systems
  63. 63. 63 ILK – Systems
  64. 64. 64 ILK – Systems
  65. 65. 65 Information Landscape Knowledgebase (ILK)
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