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 |