Converters¶

converters.resources.age_to_fhir(obj, mapping, field)¶

Generic function to convert Phenopackets Age or AgeRange to FHIR Age.

Parameters

obj – object to which field Age or AgeRange belongs to
mapping – mapping from PHENOPACKETS_ON_FHIR
field – name of the field that stores age

Returns

age extension object

converters.resources.biosample_to_fhir(obj)¶

Converts Biosample to FHIR Specimen.

Parameters: obj – Biosample json
Returns: FHIR Specimen json

converters.resources.check_disease_onset(disease)¶

Phenopackets schema allows age to be represented by ISO8601 string, whereis Pheno-FHIR guide requires it to be represented by CodeableConcept. This function checks how age is represented in data.

Parameters: disease – disease json object
Returns: True/False

converters.resources.codeable_concepts_fields(field_list, profile, obj)¶

Converts a list of fields to FHIR CodeableConcepts and returns a list of extensions.

Parameters

field_list – fields to convert to codeable concepts
profile – name of an object in phenopackets mappings
obj – object to which fields belong to

Returns

list of extensions

converters.resources.disease_to_fhir(obj)¶

Converts Disease to FHIR Condition.

Parameters: obj – Disease json
Returns: FHIR Condition json

converters.resources.fhir_codeable_concept(obj)¶: Generic function to convert object to FHIR CodeableConcept.

converters.resources.fhir_coding_util(obj)¶: Genenric function to convert object to FHIR Coding.

converters.resources.gene_to_fhir(obj)¶

Convert Gene to Observation.component:gene property. GA4GH Phenopackets Implementation Guide provides a link to Genomics Reporting Implementation Guide (STU1) mapping http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/region-studied .

Parameters: obj – gene json
Returns: Observation.component:gene json

converters.resources.hts_file_to_fhir(obj)¶

Converts HTS file to FHIR DocumentReference.

Parameters: obj – HTS file json
Returns: FHIR DocumentReference json

converters.resources.individual_to_fhir(obj)¶

Converts Individual to FHIR Patient.

Parameters: obj – Individual json
Returns: FHIR Patient json

converters.resources.phenopacket_to_fhir(obj)¶

Converts Phenopacket to FHIR Composition.

Parameters: obj – Phenopacket json
Returns: FHIR Composition json

converters.resources.phenotypic_feature_to_fhir(obj)¶

Converts Phenotypic feature to FHIR Observation.

Parameters: obj – PhenotypicFeature json
Returns: FHIR Observation json

converters.resources.procedure_to_fhir(obj)¶: Converts Procedure to FHIR Specimen collection.

converters.resources.variant_to_fhir(obj)¶

Variant corresponds to Observation.component:variant. GA4GH Phenopackets Implementation Guide provides a link to Genomics Reporting Implementation Guide (STU1) mapping http://hl7.org/fhir/uv/genomics-reporting/STU1/variant.html.

Parameters: obj – Variant json
Returns: Observation.component:variant json