Sampleminded Ontology and the Future of Laboratory Information Could it be any Clearer?
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Transcript of Sampleminded Ontology and the Future of Laboratory Information Could it be any Clearer?
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sampleminded
Ontology and the Future of Laboratory Information
Could it be any Clearer?
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General Game Plan for Discussion LIMS –
Changing nature Industry trends Industry slight of hand etc..
Protocol Driven Research Early experiences at ITNShaping approach at IRF
Ontologies as the mediation wrapperWhere Why
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LIMS Landscape Types LIMS, LIS, ELN, CTMS, SDMS, LES ..
Changing but not as fast as one would thinkBig dollar investment (Lab or Org .. CIO or
COO )Increasing domain specificity, or narrowing
functional objectives (Genelogics, SDMS ) Moving toward distributed science or is it
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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.
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Where is the Specification Mapping and to what value ?
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Specify From What Perspective ?
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Life is Good……
Don’t dig here
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E-Science…(old news ??)
2006 National Science and Technology Council report by the Interagency Working Group on Digital Data (IWGDD), Charles Humphreys
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Scientific Data Lifecycle- Operationalized
Data Use and Dissemination
Data Structure and Storage
Data Collection and Annotation
Hypothesis Refinement
Process Refinement
ProtocolDesign
Data Collection
Data Processing
Data Access
Data Discovery
Data Analysis
Data Archiving
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Immune Tolerance Network
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ITN Early Days: Epoch Ontologies -
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Attempt 1 … Data Operations vs. Knowledge Management
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The Study Designer at the ITN
Knowledge Representation
Knowledge Acquisition
Expert
KnowledgeSpecification
Data Representation
Data Value Set Specification CaDSR Metadata
Repository
Local Metadata Repository
BRIDG
Entity Framework
Local Library
Knowledge Acquisition Data
Concepts Structure
Content
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NIAID Integrated Research Facility
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Operations
Protocol Design and Development
Research Support
Preliminary Data
Workspace
Document Managemen
t
Regulatory Review and Approval
Animal Facility Management
Animal Inventory
Animal Housing
Animal Procedures
Study Conduct
Study Design Study Activity
Laboratory Management
Anatomical Pathology
Histology VirologyClinical
Pathology Immunology
Support and Housekeeping Functionality Experiment Design and Development
ExperimentDefinition
ExperimentConduct
Methods Annotation
Document Results
Electronic Lab Notebook
SharePoint
InStem Provantis
LIMS
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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
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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
MTACRADA
Approval
Review and Approval
StrategicStudy
Calendar
Cost Model
Return of Investment
Analysis
Specification Structure
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Project Review
and Approv
al
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
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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
Activity Day -2 Day 0 Day 2 Day 4 Day 6 Day 8 Day 10 Day 12 Day 14At
Necropsy
Clinical Observations Innoculation Blood Collection Swab Collection Bronchial Lavage Euthanasia ABG
Chest CT
Clinical ChemistryHematologyHemostasis
Flow Cytometry Truecount TBNKLymphoid Meyloid
TaqMan qPCRNP Swab BAL Plaque assay
Blood Culture Tissue
Necropsy Histology EM
Pathology
Immunology
Comparative Medicine
Imaging
Clinical Laboratory
Virology
Bacteriology
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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
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LIMS Data 594 Tables
192 have data 6 define the core elements
Project PatientSample Orders Test Result
Auditing and Workflows No understanding of the what
Sample Test
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Leveraging information models in ROMS configuration
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IRF Unified Model Enough to:
Define study structure Define activity types and
association Establish data
expectations
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IRF Unified Model Enough to:
Define study structure Define activity types and
association Establish data
expectations
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IRF Unified Model Enough to:
Define study structure Define activity types and
association Establish data
expectations
![Page 27: Sampleminded Ontology and the Future of Laboratory Information Could it be any Clearer?](https://reader035.fdocuments.in/reader035/viewer/2022062515/56649f4f5503460f94c71ca5/html5/thumbnails/27.jpg)
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IRF Unified Model Enough to:
Define study structure Define activity types and
association Establish data
expectations
![Page 28: Sampleminded Ontology and the Future of Laboratory Information Could it be any Clearer?](https://reader035.fdocuments.in/reader035/viewer/2022062515/56649f4f5503460f94c71ca5/html5/thumbnails/28.jpg)
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IRF Unified Model Enough to:
Define study structure Define activity types and
association Establish data
expectations
![Page 29: Sampleminded Ontology and the Future of Laboratory Information Could it be any Clearer?](https://reader035.fdocuments.in/reader035/viewer/2022062515/56649f4f5503460f94c71ca5/html5/thumbnails/29.jpg)
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IRF Unified Model Enough to:
Define study structure Define activity types and
association Establish data
expectations
![Page 30: Sampleminded Ontology and the Future of Laboratory Information Could it be any Clearer?](https://reader035.fdocuments.in/reader035/viewer/2022062515/56649f4f5503460f94c71ca5/html5/thumbnails/30.jpg)
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Activity Day -2 Day 0 Day 2 Day 4 Day 6 Day 8 Day 10 Day 12 Day 14At
Necropsy
Clinical Observations Innoculation Blood Collection Swab Collection Bronchial Lavage Euthanasia ABG
Chest CT
Clinical ChemistryHematologyHemostasis
Flow Cytometry Truecount TBNKLymphoid Meyloid
TaqMan qPCRNP Swab BAL Plaque assay
Blood Culture Tissue
Necropsy Histology EM
Pathology
Immunology
Comparative Medicine
Imaging
Clinical Laboratory
Virology
Bacteriology
![Page 31: Sampleminded Ontology and the Future of Laboratory Information Could it be any Clearer?](https://reader035.fdocuments.in/reader035/viewer/2022062515/56649f4f5503460f94c71ca5/html5/thumbnails/31.jpg)
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Configuration
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Configuration
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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.
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Incremental Adoption
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Representation Of Biomedical Investigations Using OBI
Jie ZhengUniversity of Pennsylvannia
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Summary The Study Designer + 8 years
Knowledge Representation
Knowledge Acquisition
Expert
KnowledgeSpecification
Data Value Set Specification ISO 21090?
Local Metadata Repository
OBI
LSDAM
Local Library
Knowledge Acquisition Data
Concepts Structure
Content
Configuration Specification
Study Data Set