1. sampleminded Ontology and the Future of Laboratory Information Could it be any Clearer?

2. sampleminded General Game Plan for Discussion LIMS – Changing nature Industry trends Industry slight of hand etc.. Protocol Driven Research Early experiences at ITN Shaping approach at IRF Ontologies as the mediation wrapper Where Why

3. sampleminded LIMS Landscape Types LIMS, LIS, ELN, CTMS, SDMS, LES.. Changing but not as fast as one would think Big dollar investment (Lab or Org.. CIO or COO ) Increasing domain specificity, or narrowing functional objectives (Genelogics, SDMS ) Moving toward distributed science or is it

4. sampleminded Specification, Configuration, Execution and Delivery Specification – The operational description of entities that are created, consumed or altered as part the supported laboratory workflows. Configuration – The conversion of the operational description into the technical paradigm of the system Execution – the automated conduct of operational workflows leveraging data capture and reuse of data and data structures defined in the system Delivery - The extraction of the system data in support of the operational management and or data delivery.

5. sampleminded Where is the Specification Mapping and to what value ?

6. sampleminded Specify From What Perspective ?

7. sampleminded Life is Good…… Don’t dig here

8. sampleminded E-Science…( old news ?? ) 2006 National Science and Technology Council report by the Interagency Working Group on Digital Data (IWGDD), Charles Humphreys

9. sampleminded Scientific Data Lifecycle- Operationalized Data Use and Dissemination Data Structure and Storage Data Collection and Annotation Hypothesis Refinement Process Refinement Protocol Design Data Collection Data Processing Data Access Data Discovery Data Analysis Data Archiving

10. sampleminded Immune Tolerance Network

11. sampleminded ITN Early Days: Epoch Ontologies -

12. sampleminded Attempt 1 … Data Operations vs. Knowledge Management

13. sampleminded The Study Designer at the ITN Knowledge Representation Knowledge Acquisition Expert Knowledge Specification Data Representation Data Value Set Specification CaDSR Metadata Repository Local Metadata Repository BRIDG Entity Framework Local Library Knowledge Acquisition Data ConceptsStructure Content

14. sampleminded NIAID Integrated Research Facility

15. sampleminded Operations Protocol Design and Development Research Support Preliminary Data Workspace Document Management Regulatory Review and Approval Animal Facility Management Animal Inventory Animal Housing Animal Procedures Study Conduct Study Design Study Activity Laboratory Management Anatomical Pathology Histology Virology Clinical Pathology Immunology Support and Housekeeping Functionality Experiment Design and Development Experiment Definition Experiment Conduct Methods Annotation Document Results Electronic Lab Notebook SharePoint InStem Provantis LIMS

16. sampleminded Study Lifecycle Full Proposal Pipeline Development and Program Commitment Initial Review Project Approval Project Review Define Study Review Impact Optimize Configure Study Definition and Management Study Conduct ROMS Systems Study Monitoring Review, Analysis and Archive Complied Data Data Review Data Archive Schedule SharePoint Document Workflow Study Planning and Definition Interactive Reporting Data Processing Provantis LabWare SharePoint Portal

17. sampleminded Groups Study Definition Activity Sample Type(s) Study Subjects Timeline Assay Process Observation Intervention Study Definition Data Package PV LIMS Core Services Requests Study Conduct Operational Reporting Study Reports Manuscript(s) Product(s) Study Close Letter of Intent Study Plan Concept Proposal Full Proposal MTA CRADA Approval Review and Approval Strategic Study Calendar Cost Model Return of Investment Analysis Specification Structure

18. sampleminded Project Review and Approval Create Study Plan Review and Approval Study Plan Study Conduct Close and Archive Study Project approved and SharePoint project sub-site established Study Plan template instantiated producing a physical document (the plan) and a computable representation of study activities Optimize and align with IRF resources and priorities with study design Configure Provantis and LabWare based on the study plan. Extract and create the data deliverables and upload to study portal based on milestones or structure defined in the study plan SharePoint Project MER-01 Study MER-01- 001 Docs SharePoint Project MER-01 Study MER-01-001 Study Doc Study Data Methods Reports Base Site Study Site (structure no content) SharePoint Project MER-01 Study MER-01-001 Study Doc Study Data Methods Reports Study Site (instantiated ) Study Plan Template Study Plan Study Data Provantis LabWare Study Definition

19. sampleminded Study Definition We are manually creating the data management plan which includes the sequence of activities (SOA) and sampling plan tables that will ultimately drive LIMS configuration and specimen management Data management plan is an integral part of creating the study plan Data management plan submitted as part of the study plan for IRF approval Establish a single computable representation of the study structure; including required activities and timing of those activities Project components: Controlled list of activities Application to define study structure and assign activities to study day

20. sampleminded The IRF ROMS Process Automation Protocol Design Clinical Operations Study Execution Sample Collection and Processing Inventory and Location Management Electronic Laboratory Notebook Process Documentation SOP and Methodology Instrument / Assay QC Data Auditability Scheduling and Resource Management

21. sampleminded LIMS Data 594 Tables 192 have data 6 define the core elements Project Patient Sample Orders Test Result Auditing and Workflows No understanding of the what SampleTest

22. sampleminded Leveraging information models in ROMS configuration

23. sampleminded

24. IRF Unified Model Enough to: Define study structure Define activity types and association Establish data expectations

25. sampleminded IRF Unified Model Enough to: Define study structure Define activity types and association Establish data expectations

26. sampleminded IRF Unified Model Enough to: Define study structure Define activity types and association Establish data expectations

27. sampleminded IRF Unified Model Enough to: Define study structure Define activity types and association Establish data expectations

28. sampleminded IRF Unified Model Enough to: Define study structure Define activity types and association Establish data expectations

29. sampleminded IRF Unified Model Enough to: Define study structure Define activity types and association Establish data expectations

30. sampleminded

31. Configuration

32. sampleminded Configuration

33. sampleminded Ontologies as a Mediation Layer When viewed at an industry or organization wide, these types of semantic based system integration and knowledge management efforts can be overwhelming and often fail because of the prevalence of organizations to respond in one of two ways; Do nothing. Data silos continue to exist with no metadata, no basic dictionary, no context, no “mapability” and, hence, no practical capability for flexible reuse… or Do everything. Implement a perfect enterprise dictionary with agreed- upon definitions, and model a perfect ontology to describe the complex relationships between concepts for every aspect of the organization —an ideal that when started is rarely completed.

34. sampleminded Incremental Adoption

35. sampleminded Representation Of Biomedical Investigations Using OBI Jie Zheng University of Pennsylvannia

36. sampleminded

37. Summary The Study Designer + 8 years Knowledge Representation Knowledge Acquisition Expert Knowledge Specification Data Value Set Specification ISO 21090? Local Metadata Repository OBI LSDAM Local Library Knowledge Acquisition Data ConceptsStructure Content Configuration Specification Study Data Set