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
Contents:
This page provides a list of the FHIR artifacts defined as part of this implementation guide.
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 |
These define constraints on FHIR data types for systems conforming to this implementation guide
| DRS Attachment |
A FHIR Attachment with a DRS url. |
These define constraints on FHIR data types for systems conforming to this implementation guide
| Supporting Information |
Additional information relevant to interpreting/understanding the report. |
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 |
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. |
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| Dataset CodeSystem (lists all tables) |
Example Dataset with 1 table and 4 variables |
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| Datatable CodeSystem (lists all variables) |
Example Data Table with 4 variables |
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| 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 |
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| Human Genome Variation Society nomenclature |
HGVS nomenclatures are the guidelines for mutation nomenclature made by the Human Genome Variation Society.
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. |
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| LOINC Answers |
LOINC ANSWERS used by NCPI resources |
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| 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.’ |
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| 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. |
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| NCPI FHIR Codes |
Codes that would apply to NCPI projects |
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| Data Types for NCPI Research |
Data Types for NCPI Research |
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| Online Mendelian Inheritance in Man |
An online database that describes the function and phenotypes associated with human genes |
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| ToBeDeterminedCodes ('TbdCodes') |
These codes are currently ‘TBD-LOINC’ codes. The CG WG is requesting formal LOINC codes. |
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 |