Shared Data Model for Aliquot

Shared Data Model for Biospecimen Collection

The Shared Data Model for Condition

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 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

FHIR Profile for NCPI Sample

Family Relationship

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

Person

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.

Study Family

Research Study

NCPI biospecimen definition for collected samples

NCPI biospecimen definition for non-collected samples

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 Last Vital Status Extension

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

Availability Status of Aliquot

Concentration of the Aliquot

Extension containing Consanguinity

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

Laterality Information

Linkage for related samples

Location Information

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.

Link to citations associated with the study's publications.

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

Free text describing the study family, such as potential inheritance or details about consanguinity

Extension containing Family Role

Extension containing Study Family Focus

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

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.

Laterality Information

Location Information

Example terms from Medical Subject Headings (MeSH) Ontology

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.

Adaptor trimmed options

Assay strategy options

Code System for assertion of condition presence

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

Platform instrument options

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'

Sample availability for Sample and Aliquot modules

Strandedness options

Some common types of study 'names'.

Roles associated with study personnel.

Code System for type of condition

Workflow tool options

Workflow type options

An example family relationship based on data from CBTN.

An example family relationship based on data from CBTN.

An example family relationship based on data from GREGoR.

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 biospecimen based on data from CBTN

Example biospecimen based on data from GREGoR

Example condition using data from CBTN.

Example condition 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