Stream: hapi
Topic: modeling component (Observation) in HAPI
Peter Robinson (Mar 25 2022 at 17:42):
Hi everybody, I am working on a Java class to model a profiled resource of the GA4GH Phenopacket (http://phenopackets.org/core-ig/StructureDefinition-phenopackets-variant.html). The resource extends Observation and makes use of the components list. I would like to know how to model each of these components in a Java HAPI FHIR class. Is there a good example?
Here is the signature of the class
@ResourceDef(
profile="https://github.com/phenopackets/core-ig/StructureDefinition/PhenopacketsVariant")
public class PhenopacketsVariant extends Observation
// ???
}
Here is the corresponding FSH code:
Profile: PhenopacketsVariant
Parent: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant // Genomics Reporting Variant profile
Id: phenopackets-variant
Title: "Phenopackets Variant"
Description: "A profile of Genomics Reporting Variant profile that represents relevant phenopackets building blocks."
- ^status = #draft // This would be changed later to active
- ^version = "0.1.0"
- ^date = "2021-10-18T06:00:00-04:00"
- ^publisher = "GA4GH Phenopacket Working Group"
-
^contact.name = "Aly Khalifa"
//* ^short = "A phenopackets profile of the genomics reporting Variant profile. It represents
//phenopackets GeneDescriptor, VariationDescriptor, VcfRecord, and VariantInterpretation building blocks."
//This is a placeholder for all Must-support elements (MS). Based on a team discussion, all elements should be MS. -
component[gene-studied] and
component[ref-sequence-assembly] and
component[cytogenetic-location] and
Peter Robinson (Mar 26 2022 at 15:38):
I think I figured this out. It needs to be like this
/**
* We want have something like this:
* Note that 48001-2 Cytogenetic (chromosome) location
* <component>
* <code>
* <coding>
* <system value="http://loinc.org"/>
* <code value="48001-2"/>
* </coding>
* </code>
* <valueCodeableConcept>
* <coding>
* <system value="http://loinc.org"/>
* <code value="LA21263-1"/>
* <display value="10"/>
* </coding>
* </valueCodeableConcept>
* </component>
* @param loincCode the LOINC code to represent a chromosome, e.g., "LA21263-1" for chromosome 10
* @param display The display value, e.g., "10" for chromosome 10
*/
public void setCytogeneticLocation(String loincCode, String display) {
Coding loincCytogeneticCoding = new Coding();
loincCytogeneticCoding.setSystem(LOINC_SYSTEM)
.setCode(LOINC_CYTOGENETIC_CHROMOSOME_LOCATION_ID)
.setDisplay(LOINC_CYTOGENETIC_CHROMOSOME_LOCATION_DISPLAY);
CodeableConcept cytogeneticCodeableConcept = new CodeableConcept().addCoding(loincCytogeneticCoding);
Coding chromosomeCoding = new Coding();
chromosomeCoding.setSystem(LOINC_SYSTEM)
.setCode(loincCode)
.setDisplay(display);
CodeableConcept cc = new CodeableConcept();
cc.addCoding(chromosomeCoding);
ObservationComponentComponent occ = new ObservationComponentComponent();
occ.setCode(cytogeneticCodeableConcept);
occ.setValue(chromosomeCoding);
this.addComponent(occ);
}
Last updated: Apr 12 2022 at 19:14 UTC
