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
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 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 FHIR ResearchStudy resource and shall act as the umbrella under which all study resources can ultimately be found. For the purposes of interoperability, some restrictions have been made to enforce a common mechanism for describing enrollment and provide a simple means for summarizing subject count and consent group membership. |
| 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 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. |
| 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. |
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.
| 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 |
| NCPI FHIR Codes |
Codes that would apply to NCPI projects |
| Phenotype Codes |
This value set includes all codes from Human Phenotype Ontology. |
| Table ValueSet |
Example Data Table with 4 variables |
| 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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| Data Types for NCPI Research |
Data Types for NCPI Research |
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| Dataset CodeSystem (lists all tables) |
Example CodeSystem for a data-dictionary dataset with only 1 table. |
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| Datatable CodeSystem (lists all variables) |
Example CodeSystem for a data-dictionary table with 4 variables represented as codes. |
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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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| 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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| 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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| 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.
| Baylor Hopkins Center for Mendelian Genomics (BH CMG) |
Baylor Hopkins Center for Mendelian Genomics (BH CMG) |
| 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 |
| NCPI Research Study 01 Specimen 01 |
An example Specimen used to indicate which sample a row of raw data is associated with. |
| Summary detail for Center for Mendelian Genomics |
Summary detail for Center for Mendelian Genomics |
| 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. |
| 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. |
| ncpi-research-study-01 |
An example research study |
| 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 |
| 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 |