Representation and Use of Clinical Data in Immport

HLA Genetics Consortium Meeting, December 14-15, 2010

HLA region genomics consortium

David Karp, M.D., Ph.D.Richard Scheuermann, Ph.D.

General Thoughts Regarding Clinical Data

Please make sure any prospectively collected data used consent forms that take data sharing into account. Other researchers NIH De-identified

No Protected Healthcare Information is displayed. E.g., dates are converted to study times

Genetic data such as SNP haplotypes or frequencies are not part of the Semi-Public Workspace.

Levels of Clinical Data

Simple – Subject demographics and phenotype Can use built-in data submission templates (Excel)

Complex – Clinical measurements, time course Vital signs CBC Chemistry Serologies Response to vaccination Pulmonary function tests BASDI, BASFI, Rodnan Skin Score, etc.

Submitting Clinical Data

Investigator controls data during loading Give BISC team (Meagan Kong, Ph.D.) a data dictionary,

protocol, and database schema We create map from your data to our data model You generate the load file More time-consuming on your part

Investigator gives data to BISC for loading BISC team creates data maps and load files Investigator can then validate the data integrity

Neither method is easy to do incrementally – best to have all data loaded at once

Standard Subject Templates

ImmPort Data Templates

Content of Study Design Workbook

StudyInterventional ParametersObservational ParametersInclusion Exclusion

Arm or CohortPeriodEvent PlanVisit PlanVisit to ArmEvent PanelEvent Panel components

SiteStudy Personnel

Subject Measure DefinitionsOutcome Measure Definitions

Glossary

Cartoon Representation of ImmPort Study Schema

StudyTitleObjectivesDescription…

ARM_or_COHORTArm_NameNameDescription…

PLANNED_VISITVisit_Order_NumberVisit_Name…

PLANNED_EVENTEvent_Name_Reported…

PERIODTitleOrder_number…

VISIT_2_ARM

PLANNED_EVENT_2_EVENT_PANEL

EVENT_PANELUser_Def_Event_Panel_IDEvent_Panel_Desc…

EVENT_PANEL_COMPONENTSComponent_Order_NumComponent_Desc…

INTERVENTIONAL_PARAMETERSPrimary_PurposeStudy_Phase…

OUTCOME_MEASURE_DEFINTIONAnalysisPopDescOutcomeType…

OBSERVATIONAL_PARAMETERSObservation_ModelTime_perspective…

SUBJECT_MEASURE_DEFINTIONOutcomeTypeMeasureType…

POPULATION_SELECTION_RULEPopulation_NameDesc…

SITESite_Name…

STUDY_PERSONNELLast_NameFirst_Name…

STUDY_PERSONNEL_2_SITE

GLOSSARYTermDefinition…

INclUSION_EXCLUSIONCriterion_NameCriterion_Category…

Nov 2009

Study Design Workbook

Arm or Cohort

Period

Event Plan

Visit Plan

Study Design Workbook

Observational parameters

Interventional Parameters

Subject Measure Definitions

Dropdown Menus

Comments

Case Report Form Data Templates Content

Biosampling (e.g., Blood draw)Substance Merge (e.g., Medication)Assessment (e.g., Medical History)Lab test Reference RangeAdverse EventEarly TerminationProtocol DeviationActual Visit

Subject Measure ResultsLab Test (panel ) Derived Results

Arm or Cohort to SubjectBiosampling to Biological SamplesStudy to Protocol

Case Report Form Data Templates

Assessment (e.g., Medical History, Family History, Vital Signs)

Biosampling

Lab Test

Case Report Form Data Submission

Mapping File Generation

Experiment (Mechanistic Assay)

SUBJECTNameDescription…

BIOLOGICAL SAMPLENameDescription…

EXPERIMENT_SAMPLENameDescription…

EXPERIMENTNameDescription…

PROTOCOLNameDescription…

Assay ResultsNameDescription…

REAGENTNameDescription…

Tube 33 Population 2

Lymphocyte Region

ImmPort Clinical Data

ImmPort currently has a wealth of experimental data in the personal workspaces of investigators

Use of data in the Semi-Public Workspaces offers an exciting ability to collaborate, generate hypotheses, and share data

Structured data models are necessary to use complex clinical research data

Mapping data to make it useful for translational and clinical studies is time-consuming – work with us early!

Representation and Use of Clinical Data in Immport

Documents

Mining electronic health records: towards better research applications and clinical care Standardising the representation of clinical information: for

Toward Clinical Excellencevi Toward Clinical Excellence: A toolkit to develop consumer participation in credentialling Figures and Tables Table 1: The three types of consumer representation

PRO and the NIF / ImmPort Antibody Registries Alexander Diehl Protein Ontology Workshop 6/18/14

A Semantic-Web Representation of Clinical Element Models

FCM Data Management and Analysis in ImmPort Richard H. Scheuermann, Ph.D. Department of Pathology and Division of Biomedical Informatics U.T. Southwestern

Immunology Database and Analysis Portal ( ImmPort )

Catalogue, synthesise Templates, forms, data sets used in real, diverse health settings Formal representation of clinical business object REQUIREMENTS

Representing clinical information using SNOMED Clinical ... · composition, openEHR reference model, CDA documents, HL7 messages. Representation of constraints on use of particular

Knowledge Representation in Practice: SNOMED CT · Knowledge Representation in Practice: SNOMED CT Kent A. Spackman, MD, PhD Chief Terminologist, IHTSDO. Clinical Professor, Oregon

Enhancing the Quality of ImmPort Data Barry Smith ImmPort Science Meeting, February 27, 2014 With thanks to Anna Maria Masci

HLA Allelic and Genotypic Ambiguity Reduction in ImmPort

Computable Declarative Representation of Clinical ...ceur-ws.org/Vol-1114/Session1_Casteleiro.pdf · Computable Declarative Representation of Clinical Assessment Scales in EHRs

Strategies to Enhance the Utility of Data in ImmPort

Clinical Flowsheets€¦ · Web viewThe Clinical Flowsheets patch of the Clinical Procedures (CP) package provides an electronic representation of the traditional paper flowsheet

Semantic Representation of Evidence-based Clinical Guidelinesannette/papers-pdf/2014KR4HC-Huang.pdf · semantic representation of evidence-based clinical guidelines. Section 6 discusses

Clinical Flowsheets - U.S. Department of Veterans Affairs Web viewThe Clinical Flowsheets patch of the CP package provides an electronic representation of the traditional paper flowsheet

Knowledge Representation, Ontologies and Logicedshare.soton.ac.uk/4983/1/2_-_Ontologies_and_Logic.pdf · • 004.8 - artificial intelligence • 616 - clinical medicine • 004.8=20

ImmPort strategies to enhance discoverability of clinical trial data

Medical informatics Lecture 2 Formalising clinical data and medical knowledge, Clinical coding systems, Formal knowledge representation … if time … formalising

2007 CDISC International Interchange Ontologies in Clinical Research: Representation of clinical research data in the framework of formal biomedical ontologies