Genome-to-FHIR

GTF-to-FHIR

In this functionality, the gene marker data is read from the GTF files and ingested in to the FHIR server.

The root tag for this functionality is run_config_gtf_to_fhir in the configuration file.

There can be multiple configuration blocks under the parent tag. An outline of a configuration block for migrating GTF file is given below;

## Migrating ``GTF`` files
{
    'type': 'migrate',
    'index_file': '<Index File Path>',
    'jsonTemplatePath': '<FHIR Reource JSON Template File Path>',
    'save': <True/False>,
    'savePath': '<Save Path>',
},

Please refer the table below for information on the configuration fields.

Configuration Field	Field Details
type	Type of operation performed (migrate for migration configuration)
index_file	Path to the index file (csv) containing specimen_id, person_id, episode_id, annotation_file (GTF File)
jsonTemplatePath	Path to the file containing FHIR resource JSON template
save	A Boolean value indicating if the intermediate files data needs to be saved to a directory (<True/False>)
savePath	Path to the directory where the intermediate files are saved

An example configuration block for migrate functionality is given below;

# Migrating "patient" entity
{
    'type': 'migrate',
    'index_file': os.environ['GENOMIC_DATA_LOCATION'] + '/index.csv',
    'jsonTemplatePath': os.environ['GENOMIC_DATA_LOCATION'] + '/templates/Measurement.json',
    'save': True,
    'savePath': os.environ['INTERMEDIATE_DATA_LOCATION'] + '/data/gtf_to_fhir/measurement',
},

Note

In this functionality, the gene markers present in the GTF file are read and perisisted in the FHIR resource as provided in the jsonTemplatePath. In this example. we are using Measurement FHIR resource for representing the gene markers, but the utility offers flexibility to persist this information in any desired FHIR resource.

FASTA-to-FHIR

In this functionality, the data is read from the FASTA files and ingested in to the FHIR server.

Note

FASTA file is a custom format designed to represent the tokensised genomic sequences that are obtained using LLM models.

The root tag for this functionality is run_config_fasta_to_fhir in the configuration file.

There can be multiple configuration blocks under the parent tag. An outline of a configuration block for migrating FASTA file is given below;

## Migrating ``FASTA`` files
{
    'type': 'migrate',
    'index_file': '<Index File Path>',
    'jsonTemplatePath': '<FHIR Reource JSON Template File Path>',
    'save': <True/False>,
    'savePath': '<Save Path>',
},

Please refer the table below for information on the configuration fields.

Configuration Field	Field Details
type	Type of operation performed (migrate for migration configuration)
index_file	Path to the index file (csv) containing specimen_id, person_id, episode_id, annotation_file (GTF File)
jsonTemplatePath	Path to the file containing FHIR resource JSON template
save	A Boolean value indicating if the intermediate files data needs to be saved to a directory (<True/False>)
savePath	Path to the directory where the intermediate files are saved

An example configuration block for migrate functionality is given below;

# Migrating "patient" entity
{
    'type': 'migrate',
    'index_file': os.environ['GENOMIC_DATA_LOCATION'] + '/index.csv',
    'jsonTemplatePath': os.environ['GENOMIC_DATA_LOCATION'] + '/templates/MolecularSequence.json',
    'save': True,
    'savePath': os.environ['INTERMEDIATE_DATA_LOCATION'] + '/data/gtf_to_fhir/molecular_sequence',
},

Note

In this functionality, the FASTA file is read and perisisted in the FHIR resource as provided in the jsonTemplatePath. In this example. we are using MolecularSequence FHIR resource for representing the FASTA file, but the utility offers flexibility to persist this information in any desired FHIR resource.