NCPI FHIR Implementation Guide v2
0.1.0 - ci-build

NCPI FHIR Implementation Guide v2 - Local Development build (v0.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Table of Contents

.. 0 Table of Contents
... 1 Home
... 2 Authors
... 3 Conformance
... 4 Contact
... 5 Contributing
... 6 Downloads
... 7 Example Cbtn
... 8 Example Gregor
... 9 FHIR Basics
... 10 Fhir Version
... 11 IG Versioning
... 12 Module Assays
... 13 Module Family
... 14 Module Filemetadata
... 15 Module Files
... 16 Module Overview
... 17 Module Participant
... 18 Module Phenotype Condition
... 19 Module Research Study
... 20 Module Specimen
... 21 Must Support
... 22 Ncpi
... 23 Research Study Example Cbtn
... 24 Use Case Tbd
... 25 Artifacts Summary
.... 25.1 Shared Data Model for Aliquot
.... 25.2 Shared Data Model for Biospecimen Collection
.... 25.3 Shared Data Model for Condition
.... 25.4 Shared Data Model for Family Relationship
.... 25.5 Shared Data Model for Family Role
.... 25.6 Shared Data Model for File
.... 25.7 Shared Data Model for Research Collection
.... 25.8 Shared Data Model for Research Data Access Policy
.... 25.9 Shared Data Model for Research Participant and Study Mapping
.... 25.10 Shared Data Model for Research Participants
.... 25.11 Shared Data Model for Research Persons
.... 25.12 Shared Data Model for Research Study
.... 25.13 Shared Data Model for Sample
.... 25.14 Shared Data Model for Study Family
.... 25.15 BAM or CRAM file profile
.... 25.16 Family Relationship
.... 25.17 FHIR Profile for NCPI Sample
.... 25.18 Gene fusion or gene expression file profile
.... 25.19 Linkage for related samples
.... 25.20 MAF (Somatic Mutation) file profile
.... 25.21 NCPI biospecimen definition for collected samples
.... 25.22 NCPI biospecimen definition for non-collected samples
.... 25.23 NCPI Conditon
.... 25.24 NCPI FASTQ File
.... 25.25 NCPI File
.... 25.26 NCPI File Meta Data
.... 25.27 NCPI Participant
.... 25.28 NCPI Person
.... 25.29 NCPI Research Access Policy
.... 25.30 NCPI Research Collection
.... 25.31 NCPI Research Study
.... 25.32 NCPI Research Study Group
.... 25.33 NCPI Study Family
.... 25.34 NCPI Study Participant
.... 25.35 Proteomics file profile
.... 25.36 VCF or gVCF file profile
.... 25.37 Access policy
.... 25.38 Access Policy Description
.... 25.39 Access Type
.... 25.40 Age at Assertion
.... 25.41 Age at Last Vital Status Extension
.... 25.42 Algorithm used to calculate the hash (and size, where applicable)
.... 25.43 Availability Status of Aliquot
.... 25.44 Concentration of the Aliquot
.... 25.45 Consanguinity Extension
.... 25.46 Family Type Extension
.... 25.47 If present, only those under the specific Access Policy can access the file in this location.
.... 25.48 Label
.... 25.49 Laterality Information
.... 25.50 Laterality Information
.... 25.51 Linkage for related samples
.... 25.52 Location Information
.... 25.53 Person who recorded assertion about participant
.... 25.54 Provides a list of hashes for confirming file transfers
.... 25.55 Research Date of Birth Method
.... 25.56 Research Population
.... 25.57 Research Study Acknowledgement
.... 25.58 Research Study Associated Party
.... 25.59 Research Study Design
.... 25.60 Research Study Result
.... 25.61 Research Usage Limitation Disease Code
.... 25.62 Research Web Link
.... 25.63 Spatial Information
.... 25.64 Study Family Description
.... 25.65 Study Family Focus
.... 25.66 Study Family Focus Extension
.... 25.67 The file format used
.... 25.68 The size of the file, e.g., in bytes.
.... 25.69 Value of hashing the file
.... 25.70 Version of the contents of the file
.... 25.71 Assertion of Condition Codes
.... 25.72 Collection Type
.... 25.73 Conditon Codes
.... 25.74 Consanguinity Value Codes
.... 25.75 Enumerations for how DOB was constructed
.... 25.76 Enumerations for the EDAM ontology
.... 25.77 Family Types Codes
.... 25.78 Laterality Information
.... 25.79 Location Information
.... 25.80 MeSH Terms
.... 25.81 Research Data Access Codes
.... 25.82 Research Data Access Type Codes
.... 25.83 Study Name Type
.... 25.84 Study Personnel Role
.... 25.85 Type of Condition
.... 25.86 Adaptor trimmed options
.... 25.87 Assay strategy options
.... 25.88 Assertion of Condition Codes
.... 25.89 Collection Type
.... 25.90 Elements of Component
.... 25.91 Enumerations for how DOB was constructed
.... 25.92 Hash Types Code System
.... 25.93 Library prep options
.... 25.94 Library selection options
.... 25.95 NCPI Family Types CodeSystem
.... 25.96 NCPI FHIR Codes
.... 25.97 NCPI Metadata slices
.... 25.98 Platform instrument options
.... 25.99 Reference genome examples
.... 25.100 Related File Type Code System
.... 25.101 Research Data Access Codes
.... 25.102 Research Data Access Type Codes
.... 25.103 Sample availability for Sample and Aliquot modules
.... 25.104 Strandedness options
.... 25.105 Study Name Type
.... 25.106 Study Personnel Role
.... 25.107 Type of Condition
.... 25.108 Workflow tool options
.... 25.109 Workflow type options
.... 25.110 An example family relationship based on data from CBTN
.... 25.111 An example family relationship based on data from CBTN
.... 25.112 An example family relationship based on data from CBTN
.... 25.113 CBTN General Research Use (GRU) Consent DAC
.... 25.114 CBTN General Research Use (GRU) Consent dbGaP
.... 25.115 CBTN Operations Lead
.... 25.116 Children's Brain Tumor Network (CBTN)
.... 25.117 Children's Hospital of Philadelphia
.... 25.118 dbGaP PI
.... 25.119 dbGaP PI, X01 FY 2021
.... 25.120 Example biospecimen based on data from CBTN
.... 25.121 Example biospecimen based on data from GREGoR
.... 25.122 Example condition using data from CBTN
.... 25.123 Example condition using data from GREGoR
.... 25.124 Example family member based on data from GREGoR
.... 25.125 Example file based on CBTN
.... 25.126 Example file based on CBTN
.... 25.127 Example file metadata for a BAM-CRAM file from GREGoR
.... 25.128 Example file metadata for a FASTQ file
.... 25.129 Example mappings based on data from GREGoR
.... 25.130 Example patients based on data from CBTN
.... 25.131 Example patients based on data from CBTN
.... 25.132 Example patients based on data from GREGoR
.... 25.133 Example patients based on data from GREGoR
.... 25.134 Example patients based on data from GREGoR
.... 25.135 Example patients based on data from PCGC
.... 25.136 Example patients based on data from PCGC
.... 25.137 Example study from GREGoR
.... 25.138 Genomic Summary Results (GSR) Allowed Access
.... 25.139 GREGoR General Research Use (GRU) Consent
.... 25.140 Kids First X01s
.... 25.141 Participants from the CBTN research study
.... 25.142 Participants from the CBTN research study
.... 25.143 Pediatric Brain Tumor Atlas
.... 25.144 Registered Tier Access