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

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

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.

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

Representation of a family relationship.

Representation of phenotypic observations (present or absent)

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.

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.

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.

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.

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

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

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

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

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.

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

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

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

A FHIR Attachment with a DRS url.

Full code string for disease specific consent abbreviations

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

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

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

Additional information relevant to interpreting/understanding the report.

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

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

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

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 used by NCPI resources

Example terms from Medical Subject Headings (MeSH) Ontology

Codes that would apply to NCPI projects

List of Abbreviations and titles associated with core NIH Consent types

This value set includes all codes from Human Phenotype Ontology.

This is a set of terms for study design characteristics.

Example Data Table with 4 variables

This value set includes all TBD Codes

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

Data Types for NCPI Research

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

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

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.

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 used by NCPI resources

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 (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.

Codes that would apply to NCPI projects

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

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

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

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

StudyDesign codes from dbGaP FHIR Service pulled Aug 2023.

BH-CMG study’s entire population

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.

Data Harmonization for example dataset

Subject’s Case/Control Status

Example Study Data Dictionary Data Table definition

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

Just an example group for demonstrational purposes

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

Subject’s BMI at Enrollment

Subject’s gender

Participant’s Unique Identifier (example of simple variable)

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

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

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

A Single row of data represented in FHIR as a QuestionnaireResponse

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

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

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

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

CMG Consent Group, HMB-IRB-NPU

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

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

Summary detail for Center for Mendelian Genomics

The Center for Mendelian Genomics Consortium.

Example representation of a known variant found during genetic testing

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

Example of the representation of Disease.

Example of the representation of DRS Document Reference.

Example of Disease Specific Consent resource

Example of the representation of Family Relationship.

Example of the representation of Family Relationship.

Example of the representation of Family Relationship.

Example of the representation of Family Relationship.

Example Consent resource

Example Consortium

An example research study

Study 01’s Group consented under GRU

Study 01’s complete enrollment

Example of a patient from study 01

Example of a patient from study 02

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

Example of the representation of Organization.

Example of the representation of Patient.

Example of the representation of Patient.

Example of the representation of Patient.

Example of the representation of observed Phenotype.

Example of the representation of Practitioner.

Example of the representation of Practitioner Role.

Example of the representation of Research Document Reference.

Center for Mendelian Genomics

Example of the representation of Research Study.

Baylor Hopkins Center for Mendelian Genomics (BH CMG)

Example of the representation of Research Subject.

Example of the representation of Research Subject.

Example of the representation of Research Subject.

Example representation of a research subject

Example representation of a research subject

Example of the representation of Specimen.

Example of the representation of Task.

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

Example of a fhir representation of a variant