[KF] Identify FHIR DocumentReferences for Gene Expression Summary files

[RobertJCarroll]

Save JSON containing all DocumentReferences for KF Gene Expression Summary files into this bucket: https://console.cloud.google.com/storage/browser/fc-be286b9f-3acf-4168-af6e-592df509391d/DocumentReference
gs://fc-be286b9f-3acf-4168-af6e-592df509391d/DocumentReference

[RobertJCarroll]

This query grabs the relevant files: https://kf-api-fhir-service.kidsfirstdrc.org/DocumentReference?type:text=Gene%20Expression&security-label=U

The lack of a vocabulary means it might not be capturing everything, though. There are some Gene Expression Quantification results also, but they look to be restricted access only.

[liberaliscomputing]

Here is the number of breakdowns by study of the above resources:

• Total: 2,920
• _tag=SD_8Y99QZJJ (PBTA-PNOC): 64
• _tag=SD_DYPMEHHF (KF-NBL): 672

[ianfore]

For Kids First Study - (PBTA-PNOC
ResearchStudy/48656
SD_8Y99QZJJ
Pediatric Brain Tumor Atlas: PNOC
For a single example patient Patient/48592 there are 61 files
Accessible file count by type
{'tbi': 5, 'maf': 5, 'vcf': 5}
Inaccessible file count by type
{'tbi': 12, 'vcf': 11, 'maf': 10, 'bam': 7, 'cram': 2, 'crai': 2, 'bai': 1, 'gvcf': 1})

[RobertJCarroll]

I believe rsem.genes.results.gz files are the files we need for this.

[liberaliscomputing]

Use these:

• 64: https://kf-api-fhir-service.kidsfirstdrc.org/DocumentReference?type:text=Gene%20Expression&security-label=U&_tag=SD_8Y99QZJJ
• 672: https://kf-api-fhir-service.kidsfirstdrc.org/DocumentReference?type:text=Gene%20Expression&security-label=U&_tag=SD_DYPMEHHF

[RobertJCarroll]

EG: https://kf-api-fhir-service.kidsfirstdrc.org/DocumentReference/378682