NCPI FHIR Implementation Guide
0.2.0 - ci-build

NCPI FHIR Implementation Guide - Local Development build (v0.2.0). See the Directory of published versions

Artifacts Summary

This page provides a list of the FHIR artifacts defined as part of this implementation guide.

Structures: Logical Models

These define data models that represent the domain covered by this implementation guide in more business-friendly terms than the underlying FHIR resources.

Study information model

This is an example to see how the logical models might be used for describing the information model

Structures: Resource Profiles

These define constraints on FHIR resources for systems conforming to this implementation guide.

DRS Document Reference

A FHIR Document Reference with an embedded DRS URI. See https://github.com/ga4gh/data-repository-service-schemas.

NCPI Data Dictionary Harmony

Based on the FHIR resource type, ConceptMap, the StudyDataDictionaryHarmony resource provides insight into the transformations made during the ETL from source data into FHIR allowing clients to use the $translate function to discover all of the public codes that were mapped from one of the study’s actual vocabulary.

NCPI Disease

Representation for a disease under study for a given research dataset.

NCPI Family Relationship

Representation of a family relationship.

NCPI Phenotype

Representation of phenotypic observations (present or absent)

NCPI Research Study

The NCPI Research Study is based upon the core HL7 FHIR ResearchStudy resource (R4) and shall act as the umbrella under which all study resources can ultimately be found.

NCPI Study Data Dictionary Data Table

Aggregates Variable Details associated with a single dataset table that are represented in FHIR as as list of references to StudyDataDictionaryVariables in the observationResultRequirement property.

NCPI Study Data Dictionary Data Variable

FHIR profile used to describe single variable from the dataset. This resource should be as complete as possible including details such as description, data-type, permitted enumerations, quantity units, etc.

NCPI Study Group

Grouping subject participation within a research study is helpful to provide definitive lists of participants that fit a specific criteria such as All Participants or Participants From a Particular Consent Group, etc.

Raw Data Observation

Representation for a row of data from one of the dataset’s tables.

Research Consortium

A FHIR Organization representing a single consortium of which one or more NCPI Research Studies is a member.

Research Document Reference

A FHIR Document Reference created by an analysis task. Context.related = Task

Research Study Consent

A ResearchStudyConsent represents the core NIH Consent properties as they apply when consenting subjects to a research study.

Research Study Subject

A ResearchStudySubject is representative of a group of participants whose consent and data use is governed by the same restrictions. This profile is an R4 proxy for the more flexible R5 ResearchSubject.

Research Task

A FHIR analysis task that takes at least one specimen as input and produces at least one document.

Study Summary

An observation containing summary information about a study in it’s entirety or one of it’s subpopulations.

Study Variable Summary

An observation containing summary data associated with research data from FHIR.

Structures: Data Type Profiles

These define constraints on FHIR data types for systems conforming to this implementation guide.

DRS Attachment

A FHIR Attachment with a DRS url.

Structures: Extension Definitions

These define constraints on FHIR data types for systems conforming to this implementation guide.

Research Consent Disease Abbreviation

Full code string for disease specific consent abbreviations

Research Study Design

Codes categorizing the type of study such as investigational vs. observational, type of blinding, type of randomization, safety vs. efficacy, etc.

Research Study Subject Consent

ResearchStudySubjectConsent provides link to a consent through which participants were enrolled.

Research Usage Limitation Disease Code

Coding associated with limitation on what research can be performed this data.

Supporting Information

Additional information relevant to interpreting/understanding the report.

Terminology: Value Sets

These define sets of codes used by systems conforming to this implementation guide.

Case/Control Vars for 'status' categoricals

Example ValueSet listing all possible ‘values’ from the Case/Control variable.

Condition Inheritance Pattern

Value Set for specific ttransmission patterns of a condition in a pedigree

Disease Codes

This value set includes all codes from this FHIR server’s representation of OMIM, Mondo and NICt CodeSystems.

Harmonized ValueSet for data table

Public codes mapped from example dataset

The codes used below were chosen purely for example’s sake and are in no way an endorsement or suggestion for terms that should be used in a real data-dictionary.

LOINC Answers

LOINC ANSWERS used by NCPI resources

MeSH Terms

Example terms from Medical Subject Headings (MeSH) Ontology

NCPI FHIR Codes

Codes that would apply to NCPI projects

NIH Consent Code ValueSet

List of Abbreviations and titles associated with core NIH Consent types

Phenotype Codes

This value set includes all codes from Human Phenotype Ontology.

Study Design

This is a set of terms for study design characteristics.

Table ValueSet

Example Data Table with 4 variables

tbd-codes

This value set includes all TBD Codes

Terminology: Code Systems

These define new code systems used by systems conforming to this implementation guide.

Condition Inheritance Pattern

A set of terms that describe the transmission pattern of a condition in a pedigree.

Data Types for NCPI Research

Data Types for NCPI Research

Dataset CodeSystem (lists all tables)

Example CodeSystem for a data-dictionary dataset with only 1 table.

Datatable CodeSystem (lists all variables)

Example CodeSystem for a data-dictionary table with 4 variables represented as codes.

Human Genome Variation Society nomenclature

HGVS nomenclatures are the guidelines for mutation nomenclature made by the Human Genome Variation Society.

HGVS nomenclature can be used with the HL7 coded data type (code data type that accepts expression data, or a coded expression data type). This coded data type should be able to distinguish expressions in HGVS nomenclature from coded concepts. For example, in the HL7 messages specified according to the HL7 V2 Clinical Genomics Fully LOINC-Qualified Genetic Variation Model, HGVS nomenclature can be used to as the observation values for DNA sequence variations. For example, OBX 1 CWE 48004-6^DNA Sequence Variation^LN   c.1129C>T^^HGVS

Versioning information: The HGVS nomenclature for the description of sequence variants was last modified Feb 20, 2008. The HGVS nomenclature for the description of protein sequence variants was last modified May 12, 2007. The HGVS nomenclature for the description of DNA sequence variants was last modified June 15, 2007 The HGVS nomenclature for the description of RNA sequence variants was last modified May 12, 2007

HGVS nomenclatures can be used freely by the public.

Human Phenotype Ontology

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Please see license of HPO at http://www.human-phenotype-ontology.org

LOINC Answers

LOINC ANSWERS used by NCPI resources

Mondo Disease Ontology

The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. The name Mondo comes from the latin word ‘mundus’ and means ‘for the world.’

NCI Thesaurus

NCI Thesaurus (NCIt) provides reference terminology for many NCI and other systems. It covers vocabulary for clinical care, translational and basic research, and public information and administrative activities.

NCPI FHIR Codes

Codes that would apply to NCPI projects

NCPI Study Type

Enumerated List of Research Study Types used in NCPI Funded studies.

NIH Consent Codes

A set of terms describing the data use limitations associated with a given consent group.

Online Mendelian Inheritance in Man

An online database that describes the function and phenotypes associated with human genes

ToBeDeterminedCodes ('TbdCodes')

These codes are currently ‘TBD-LOINC’ codes. The CG WG is requesting formal LOINC codes.

dbGaP Study Design

StudyDesign codes from dbGaP FHIR Service pulled Aug 2023.

Example: Example Instances

These are example instances that show what data produced and consumed by systems conforming with this implementation guide might look like.

BH CMG Study Participants

BH-CMG study’s entire population

Baylor Hopkins Center for Mendelian Genomics (BH CMG)

Baylor Hopkins Center for Mendelian Genomics (BH CMG)

Baylor Hopkins Center for Mendelian Genomics (BH CMG)

The Centers for Mendelian Genomics project uses next-generation sequencing and computational approaches to discover the genes and variants that underlie Mendelian conditions. By discovering genes that cause Mendelian conditions, we will expand our understanding of their biology to facilitate diagnosis and new treatments.

Concept Map showing representing harmonization mappings

Data Harmonization for example dataset

Data Dictionary Variable status

Subject’s Case/Control Status

Data-Dictionary Table

Example Study Data Dictionary Data Table definition

Example Encounter Study 01 Patient 01

Example encounter for use with raw data to help tie different rows associated with the same event together.

Example Group used for Summary Results

Just an example group for demonstrational purposes

Example Study Data Dictionary Variable age_at_enrollment

Subject’s Age at Enrollment (Example with a range of 30-40 years of age)

Example Study Data Dictionary Variable bmi

Subject’s BMI at Enrollment

Example Study Data Dictionary Variable gender

Subject’s gender

Example Study Data Dictionary Variable subjectid

Participant’s Unique Identifier (example of simple variable)

Example Variable Summary with categories (gender)

Simple example of a VariableSummary using components to capture counts of different categories (male, female and missing)

Example of Raw Data

Example Observation representing a single row of raw data from an single data table.

Example of a Questionnaire to Represent Raw Data

An example Questionnaire that is used to describe the individual rows of data that are to be stored as QuestionnaireResponses

Example of a QuestionnaireResponse to Represent Raw Data

A Single row of data represented in FHIR as a QuestionnaireResponse

HMB-IRB-NPU Consent

Consented with Health/Medical/Biomedical + IRB Required + Not for profit use

HMB-NPU Consent

Consented with Health/Medical/Biomedical + Not for profit use

NCPI Research Study 01 Specimen 01

An example Specimen used to indicate which sample a row of raw data is associated with.

Participants consented under HMB-IRB-NPU

BH-CMG study’s population consented under Health/Medical/Biomedical + IRB Approval Required + Not for profit use

Participants consented under HMB-IRB-NPU

CMG Consent Group, HMB-IRB-NPU

Participants consented under HMB-NPU

BH-CMG study’s population consented under Health/Medical/Biomedical + Not for profit use

Participants consented under HMB-NPU

CMG Consent Group, Health/Medical/Biomedical + Not for profit use

Summary detail for Center for Mendelian Genomics

Summary detail for Center for Mendelian Genomics

The Center for Mendelian Genomics Consortium (CMG) Consortium

The Center for Mendelian Genomics Consortium.

diagnostic-implication-1

Example representation of a known variant found during genetic testing

diagnostic-report-1

Example of a DiagnosticReport which aggregates genetic findings for a given test or run

disease-example-1

Example of the representation of Disease.

drs-document-reference-example-1

Example of the representation of DRS Document Reference.

ds-bav-consent

Example of Disease Specific Consent resource

family-relationship-example-1

Example of the representation of Family Relationship.

family-relationship-example-2

Example of the representation of Family Relationship.

family-relationship-example-3

Example of the representation of Family Relationship.

family-relationship-example-4

Example of the representation of Family Relationship.

gru-consent

Example Consent resource

ncpi-research-consortium-01

Example Consortium

ncpi-research-study-01

An example research study

ncpi-research-study-01-conset-group-01-main

Study 01’s Group consented under GRU

ncpi-research-study-01-group-01-main

Study 01’s complete enrollment

ncpi-research-study-01-patient-01

Example of a patient from study 01

ncpi-research-study-01-patient-02

Example of a patient from study 02

ncpi-research-study-subject-01

An example of an R4 Research Study Subject which connects subjects to a research study and their consent

organization-example-1

Example of the representation of Organization.

patient-example-1

Example of the representation of Patient.

patient-example-2

Example of the representation of Patient.

patient-example-3

Example of the representation of Patient.

phenotype-example-1

Example of the representation of observed Phenotype.

practitioner-example-1

Example of the representation of Practitioner.

practitioner-role-example-1

Example of the representation of Practitioner Role.

research-document-reference-example-1

Example of the representation of Research Document Reference.

research-study-cmg

Center for Mendelian Genomics

research-study-example-1

Example of the representation of Research Study.

research-study-phs000711

Baylor Hopkins Center for Mendelian Genomics (BH CMG)

research-subject-example-1

Example of the representation of Research Subject.

research-subject-example-2

Example of the representation of Research Subject.

research-subject-example-3

Example of the representation of Research Subject.

research-subject-study-01-patient-01

Example representation of a research subject

research-subject-study-01-patient-02

Example representation of a research subject

specimen-example-1

Example of the representation of Specimen.

task-example-1

Example of the representation of Task.

task-example-2

Example of the representation of Task that points to a ResearchDocumentReference.

variant-example-1

Example of a fhir representation of a variant