NCPI FHIR Implementation Guide
0.1.0 - ci-build

NCPI FHIR Implementation Guide - Local Development build (v0.1.0). 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: 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 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)

Research Document Reference

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

Research Task

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

NCPI Study DD Data Table

Aggregates Variable Details associated with a single dataset table that are represented in FHIR

NCPI Study DD Data Variable

Describes a single variable from the dataset

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

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

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.

Case/Control Vars for 'status' categoricals

Example Case/Control values

LOINC Answers

LOINC ANSWERS used by NCPI resources

NCPI FHIR Codes

Codes that would apply to NCPI projects

Phenotype Codes

This value set includes all codes from Human Phenotype Ontology.

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.

Dataset CodeSystem (lists all tables)

Example Dataset with 1 table and 4 variables

Datatable CodeSystem (lists all variables)

Example Data Table with 4 variables

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

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.

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

Data Types for NCPI Research

Data Types for NCPI Research

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.

Example: Example Instances

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

Summary detail for Center for Mendelian Genomics

Summary detail for Center for Mendelian Genomics

Baylor Hopkins Center for Mendelian Genomics (BH CMG)

Baylor Hopkins Center for Mendelian Genomics (BH CMG)

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.

Data-Dictionary Table

Example Data Table definition

DD Variable subjectid

Participant’s Unique Identifier (example of simple variable)

DD Variable gender

Subject’s gender

DD Variable age_at_enrollment

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

DD Variable bmi

Subject’s BMI at Enrollment

DD Variable status

Subject’s Case/Control Status

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.

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.

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