Shared Data Model for Aliquot

Shared Data Model for Biospecimen Collection

The Shared Data Model for Condition Assertions

The Shared Data Model for Family Relationship

The Shared Data Model for Family Role

The Shared Data Model for File

The Shared Data Model for Participant Assertion

The Shared Data Model for Research Collection represent various collections of research data including, but not limited, to Consortia, Programs, adhoc collections of Studies and datasets among other types of collections.

The Shared Data Model for Research Data Access Policy represent the various Data Use Agreements that govern a researcher's access and use of research data.

The Shared data model for StudyParticipant

The Shared Data Model for Research Participants

The Shared data model for Person

The Shared Data Model for Research Study represents the understanding of what a Research Study is from the context of users and authors of the NCPI FHIR IG.

Shared Data Model for Sample

The Shared Data Model for Study Family

The Shared Data Model for File Metadata

BAM or CRAM file profile

A relationship between individuals in a pedigree or family.

Gene fusion or gene expression file profile

Linkage for related samples

MAF (Somatic Mutation) file profile

Information about a condition related to a research participant

Information about a DRS file related to a research participant

NCPI FASTQ File

Information about a file related to a research participant

Representation of file metadata for NCPI

Research oriented patient

Assertion about a particular Participant. May include Conditions, Measurements, etc.

Person

Assertion about a phenotypic feature's presence or absence given a particular participant.

Limitations and/or requirements that define how a user may gain access to a particular set of data.

Collections of research data including, but not limited, to Consortia, Programs, adhoc collections of Studies and datasets among other types of collections.

The NCPI Research Study FHIR resource represents an individual research effort and acts as a grouper or “container” for that effort’s study participants and their related data files.

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.

FHIR Profile for NCPI Sample

Study Family

Research Study

Proteomics file profile

VCF or gVCF file profile

A FHIR Attachment with a DRS url.

Descriptive text summarizing the policy restrictions and other details associated with this access provision.

Access Policy Extension

Age at Assertion Extension

Age at Event Extension

Age at Last Vital Status Extension

Algorithm used to calculate the hash (and size, where applicable)

Any additional modifiers for this condition, such as severity.

Availability Status of Aliquot

Concentration of the Aliquot

Extension containing a consanguinity assertion

Free text describing containing resource.

Extension containing Family Role

Extension containing Family Type

If present, only those under the specific Access Policy can access the file in this location.

A text label accompanied by a code indicating the label type (such as Acronym, subtitle, etc)

Laterality Information

Linkage for related samples

Link study related sources back to the relevant study.

An extension to record the source of the knowledge in a particular Patient resource.

The primary use case is to identify those Patient resources created via inference in order to support indirect pedigree relationships.

Person who recorded assertion about participant

Provides a list of hashes for confirming file transfers

Code indicating method of the DOB construction

Code describing the population (CDC)

Provides an informative description of acknowledgement expectations for those using data from the research study.

Sponsors, collaborators, and other parties affiliated with a research study.

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

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

A URL pointing to a either a research study's website, an online document or other research related site or document.

Spatial Information

Extension containing a study family focus assertion

The file format used

The size of the file, e.g., in bytes.

Value of hashing the file

Version of the contents of the file

Assay strategy options

Assertion of Phenotypic Feature Codes

List of codes indicating the biological relationship between two individuals in a family. It is restrictive to encourage a standardized representation.

Code Selection Rationale

Parent Codes

We use the NCI Thesaurus here for the mother and father because its definitions are more precise.

• C96572 ("Biological Father"): A male who contributes to the genetic makeup of his offspring through the fertilization of an ovum by his sperm.
• C96580 ("Biological Mother"): A female who contributes to the genetic makeup of her offspring from the fertilization of her ovum.

In contrast, the parental family-role's codes are less refined:

• NMTH ("natural mother"): The player of the role is a female who conceives or gives birth to the scoping entity (child).
• NFTH ("natural father"): The player of the role is a male who begets the scoping entity (child).

In particular, "Biological Mother" excludes surrogates but NMTH is ambiguous. "Biological Father" specifies fertilization of an ovum by sperm, whereas NFTH uses the ambiguous term "begets," which could include other mechanisms.

Twin Codes

For twins, we use the RoleCode ITWIN code rather than the NCI C73429.

• C73429 ("Identical Twin"): Either of the two offspring resulting from a shared ovum.
• ITWIN ("Identical Twin"): The scoper and player are offspring of the same egg-sperm pair.

Though being "offspring" of the same fertilized egg is questionable wording, we use ITWIN because it also allows other multiples (triplets, quadruplets, etc.) to be represented with the same code whereas C73429 is only for twins.

Note for upgrading to FHIR R5

When we add support for R5 to the IG, we should add the rest of the codes from <http://terminology.hl7.org/ValueSet/v3-FamilyMember> as additional bindings to guide users when not using one of the main bindings.

We intend that when users need to use a code that is not in the main bindings, they should default to the FamilyMember ValueSet. However, in R4, there is no way to express this in the ValueSet itself.

Enumerated list of Collection types

Includes all codes from HPO and MONDO

List of codes indicates the level of known consanguinity (blood relation) within a study family.

Enumerations for how DOB was constructed

Enumerations for the EDAM ontology

A value set with all codes used for the expected family types.

A value set with all codes used for the expected family types.

Example terms from Medical Subject Headings (MeSH) Ontology

The source of the knowledge represented in a Patient resource.

Includes all codes from HPO

Platform instrument options

Enumerated list of access codes such as dbGaP consent codes among others.

Enumerated list of access type codes such as 'Open Access', 'Registered Access' and 'Controlled Access'

Some common types of study 'names'.

Roles associated with study personnel.

Used to express the reason and specific aspect for the variant title, such as language and specific language.

Type of Condition

Adaptor trimmed options

Enumerated list of collection types

Slicing for elements of component

Enumerations for how DOB was constructed

Algorithm used to calculate the hash (and size, where applicable)

Library prep options

Library selection options

Codes that would apply to NCPI projects

CodeSystem for Types of Families

NCPI Metadata slices

The source of the knowledge represented in a Patient resource.

Reference genome examples

Explains the relationship of this file to the file of reference

Enumerated list of access codes such as dbGaP consent codes among others.

Enumerated list of access type codes such as 'Open Access', 'Registered Access' and 'Controlled Access'

This is a ResearchStudy's party role.

Sample availability for Sample and Aliquot modules

Strandedness options

Some common types of study 'names'.

Roles associated with study personnel.

Used to express the reason and specific aspect for the variant title, such as language and specific language.

Code System for type of condition

Workflow tool options

Workflow type options

An example family relationship based on data from CBTN.

PT-006SP675 (the patient) is female and 5 years old PT-006SP660 (the relative) is female and 17 years old This is the "mother" relationship. The relative is the mother of the patient.

This instance instantiates the minimum relationship direction to reproduce a PED file.

An example family relationship based on data from GREGoR.

GSS123456 (the patient) is male and >= 64 years old GSS654321 (the relative) has no information in the patient record This is the "mother" relationship. The relative is the mother of the patient.

This instance instantiates the minimum relationship direction to reproduce a PED file.

An example family relationship based on data from CBTN.

• extension[+]
  • url = "https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/part-of-study"
  • valueReference = Reference(kf-research-study-cbtn)

PT-006SP675 (the relative) is female and 5 years old PT-006SP660 (the patient) is female and 17 years old This is the "daughter" relationship. The relative is the daughter of the patient.

This demonstrates using extensibility to express the reverse of the minimum relationship convention.

General Research Use (GRU)

General Research Use (GRU)

CBTN Operations Lead

Brain tumors are the most common form of cancer in children aged 0-19 in the United States, and are the largest cause of cancer-related deaths. The estimated number of new cases in 2019 is nearly 3,800 and thus brain tumors are a rare disease. Despite their relative rarity, the years of potential life lost due to brain tumors in 2009 was estimated at 47,631 years for children and adolescents aged 0-19 in the United States; this is a disproportionate amount of life lost compared to adult cancers and represents an unrecognized societal threat. There is an urgent need to improve therapies for these children. Most of the high-grade glial and embryonal brain cancers still remain largely incurable despite decades of clinical and laboratory research. Existing non-targeted chemotherapies and radiation, while at times effective, often represent pyrrhic victories, leaving behind life-long health burdens and causing a significant risk of secondary malignancies. NIH funded pediatric brain tumor cohort-based genomic dataset generation efforts have lagged behind other histologies and have yet to be included as part of large-scale sequencing efforts. However, consortia-based initiatives like those supported by the Children's Brain Tumor Network (CBTN) have demonstrated the early potential for clinically annotated genomic cohorts and their utility and interest by both the pediatric cancer and structural birth defect community with more than 130 data access requests for a non-embargoed cohort of tumor/normal whole genomes and paired tumor RNAseq. Indeed more than one quarter of this 800-subject initial sequencing cohort were identified to have birth-defect-associated clinical annotations in their clinical records, however, to our knowledge limited to no trio-based genomics cohort studies exist for any one pediatric brain tumor histology. The project's proposed sequencing cohort defines the largest, clinically annotated pediatric brain tumor cohort study to date and seeks to define the intersection of germline and somatic underpinnings of pediatric brain tumors across a shared developmental context of cancer and structural birth defects.

Represents the Organization for which CHOP PIs are affiliated

Example assertion using data from GREGoR

Example biospecimen based on data from CBTN

Example biospecimen based on data from GREGoR

Example biospecimen based on data from GREGoR

Example biospecimen based on data from GREGoR that will generate a warning

Example condition assertion using data from CBTN.

Example condition assertion using data from GREGoR

Example condition summary using data from GREGoR

Example family member based on data from GREGoR.

Use case of file information from CBTN

Use case of file information from GREGor

Example file metadata for a BAM-CRAM file from GREGoR

Example file metadata from CBTN

Example mappings based on data from GREGoR

Example patients based on data from CBTN.

Example patients based on data from CBTN.

Example patients based on data from GREGoR.

Example patients based on data from GREGoR.

Example patients based on data from GREGoR

Example patients based on data from PCGC.

Example patients based on data from PCGC

Example study from GREGoR

General Research Use (GRU)

Genomic Summary Results (GSR) Allowed Access

Kids First X01s

Participants from the CBTN research study

Participants from the GREGoR research study

Pediatric Brain Tumor Atlas

Registered Tier Access

dbGaP PI

dbGaP PI, X01 FY 2021