NCPI FHIR Implementation Guide v2
0.2.0 - ci-build

NCPI FHIR Implementation Guide v2 - Local Development build (v0.2.0) 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 Fshgenidx
... 12 IG Versioning
... 13 Module Assays
... 14 Module Family
... 15 Module Filemetadata
... 16 Module Files
... 17 Module Overview
... 18 Module Participant
... 19 Module Phenotype Condition
... 20 Module Research Study
... 21 Module Specimen
... 22 Must Support
... 23 Ncpi
... 24 Research Study Example Cbtn
... 25 Use Case Tbd
... 26 Artifacts Summary
.... 26.1 Shared Data Model for Aliquot
.... 26.2 Shared Data Model for Biospecimen Collection
.... 26.3 Shared Data Model for Condition Assertions
.... 26.4 Shared Data Model for Family Relationship
.... 26.5 Shared Data Model for Family Role
.... 26.6 Shared Data Model for File
.... 26.7 Shared data model for File Metadata
.... 26.8 Shared Data Model for Participant Assertion
.... 26.9 Shared Data Model for Research Collection
.... 26.10 Shared Data Model for Research Data Access Policy
.... 26.11 Shared Data Model for Research Participant and Study Mapping
.... 26.12 Shared Data Model for Research Participants
.... 26.13 Shared Data Model for Research Persons
.... 26.14 Shared Data Model for Research Study
.... 26.15 Shared Data Model for Sample
.... 26.16 Shared Data Model for Study Family
.... 26.17 BAM or CRAM file profile
.... 26.18 Family Relationship
.... 26.19 Gene fusion or gene expression file profile
.... 26.20 Linkage for related samples
.... 26.21 MAF (Somatic Mutation) file profile
.... 26.22 NCPI Conditon Summary
.... 26.23 NCPI DRS File
.... 26.24 NCPI FASTQ File
.... 26.25 NCPI File
.... 26.26 NCPI File Meta Data
.... 26.27 NCPI Participant
.... 26.28 NCPI Participant Assertion
.... 26.29 NCPI Person
.... 26.30 NCPI Phenotypic Feature Assertion
.... 26.31 NCPI Research Access Policy
.... 26.32 NCPI Research Collection
.... 26.33 NCPI Research Study
.... 26.34 NCPI Research Study Group
.... 26.35 NCPI Sample
.... 26.36 NCPI Study Family
.... 26.37 NCPI Study Participant
.... 26.38 Proteomics file profile
.... 26.39 VCF or gVCF file profile
.... 26.40 DRS Attachment
.... 26.41 Access policy
.... 26.42 Access Policy Description
.... 26.43 Access Type
.... 26.44 Age at Assertion
.... 26.45 Age at Event
.... 26.46 Age at Last Vital Status Extension
.... 26.47 Algorithm used to calculate the hash (and size, where applicable)
.... 26.48 Any additional modifiers for this condition, such as severity.
.... 26.49 Availability Status of Aliquot
.... 26.50 Concentration of the Aliquot
.... 26.51 Consanguinity Extension
.... 26.52 Description
.... 26.53 Family Role
.... 26.54 Family Type Extension
.... 26.55 If present, only those under the specific Access Policy can access the file in this location.
.... 26.56 Label
.... 26.57 Laterality Information
.... 26.58 Linkage for related samples
.... 26.59 Part of Study
.... 26.60 Patient Knowledge Source
.... 26.61 Person who recorded assertion about participant
.... 26.62 Provides a list of hashes for confirming file transfers
.... 26.63 Research Date of Birth Method
.... 26.64 Research Population
.... 26.65 Research Study Acknowledgement
.... 26.66 Research Study Associated Party
.... 26.67 Research Study Design
.... 26.68 Research Usage Limitation Disease Code
.... 26.69 Research Web Link
.... 26.70 Spatial Information
.... 26.71 Study Family Focus Extension
.... 26.72 The file format used
.... 26.73 The size of the file, e.g., in bytes.
.... 26.74 Value of hashing the file
.... 26.75 Version of the contents of the file
.... 26.76 Assay strategy options
.... 26.77 Assertion of Phenotypic Feature Codes
.... 26.78 Biological Relationship Codes
.... 26.79 Collection Type
.... 26.80 Condition Codes
.... 26.81 Consanguinity Value Codes
.... 26.82 Enumerations for how DOB was constructed
.... 26.83 Enumerations for the EDAM ontology
.... 26.84 Family Types Codes
.... 26.85 Family Types Codes
.... 26.86 MeSH Terms
.... 26.87 Patient Knowledge Source
.... 26.88 Phenotypic Feature Codes
.... 26.89 Platform instrument options
.... 26.90 Research Data Access Codes
.... 26.91 Research Data Access Type Codes
.... 26.92 Study Name Type
.... 26.93 Study Personnel Role
.... 26.94 Title Type
.... 26.95 Type of Condition
.... 26.96 Adaptor trimmed options
.... 26.97 Collection Type
.... 26.98 Elements of Component
.... 26.99 Enumerations for how DOB was constructed
.... 26.100 Hash Types Code System
.... 26.101 Library prep options
.... 26.102 Library selection options
.... 26.103 NCPI Family Types CodeSystem
.... 26.104 NCPI FHIR Codes
.... 26.105 NCPI Metadata slices
.... 26.106 Patient Knowledge Source
.... 26.107 Reference genome examples
.... 26.108 Related File Type Code System
.... 26.109 Research Data Access Codes
.... 26.110 Research Data Access Type Codes
.... 26.111 Research Study Party Role
.... 26.112 Sample availability for Sample and Aliquot modules
.... 26.113 Strandedness options
.... 26.114 Study Name Type
.... 26.115 Study Personnel Role
.... 26.116 TitleType
.... 26.117 Type of Condition
.... 26.118 Workflow tool options
.... 26.119 Workflow type options
.... 26.120 An example family relationship (child to parent) based on data from CBTN
.... 26.121 An example family relationship (child-to-parent) based on data from GREGoR
.... 26.122 An example family relationship (parent to child) based on data from CBTN
.... 26.123 CBTN General Research Use (GRU) Consent DAC
.... 26.124 CBTN General Research Use (GRU) Consent dbGaP
.... 26.125 CBTN Operations Lead
.... 26.126 Children's Brain Tumor Network (CBTN)
.... 26.127 Children's Hospital of Philadelphia
.... 26.128 dbGaP PI
.... 26.129 dbGaP PI, X01 FY 2021
.... 26.130 Example assertion using data from GREGoR
.... 26.131 Example biospecimen based on data from CBTN
.... 26.132 Example biospecimen based on data from GREGoR
.... 26.133 Example biospecimen based on data from GREGoR
.... 26.134 Example biospecimen based on data from GREGoR, intentionally breaking the no parent and collection together rule. This should generate a warning.
.... 26.135 Example condition assertion using data from CBTN
.... 26.136 Example condition assertion using data from GREGoR
.... 26.137 Example condition summary using data from GREGoR
.... 26.138 Example family member based on data from GREGoR
.... 26.139 Example file based on CBTN
.... 26.140 Example file based on GREGoR
.... 26.141 Example file metadata for a BAM-CRAM file from GREGoR
.... 26.142 Example file metadata from CBTN
.... 26.143 Example mappings based on data from GREGoR
.... 26.144 Example patients based on data from CBTN
.... 26.145 Example patients based on data from CBTN
.... 26.146 Example patients based on data from GREGoR
.... 26.147 Example patients based on data from GREGoR
.... 26.148 Example patients based on data from GREGoR
.... 26.149 Example patients based on data from PCGC
.... 26.150 Example patients based on data from PCGC
.... 26.151 Example study from GREGoR
.... 26.152 Genomic Summary Results (GSR) Allowed Access
.... 26.153 GREGoR General Research Use (GRU) Consent
.... 26.154 Kids First X01s
.... 26.155 Participants from the CBTN research study
.... 26.156 Participants from the GREGoR research study
.... 26.157 Pediatric Brain Tumor Atlas
.... 26.158 Registered Tier Access