FHIR Standards

Profiles Used

Resource

Profile URL

Patient

https://fhir.kemkes.go.id/r4/StructureDefinition/Patient

Specimen

https://fhir.kemkes.go.id/r4/StructureDefinition/Specimen

Organization

https://fhir.kemkes.go.id/r4/StructureDefinition/Organization

Practitioner

https://fhir.kemkes.go.id/r4/StructureDefinition/Practitioner

DiagnosticReport

http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report

Observation (Laboratory)

http://terminology.hl7.org/CodeSystem/observation-category

Observation (Genetics)

http://terminology.hl7.org/CodeSystem/v2-0074

Variant

http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant

Standard Terminologies

LOINC Codes (Sputum & Genomics)

Code

Display Name

Usage

69548-6

Genetic variant assessment

Observation (Variant)

89486-5

Mycobacterial susceptibility panel

Observation (Panel)

81247-9

Master HL7 genetic variant reporting panel

DiagnosticReport

81290-9

Genomic DNA change (gHGVS)

Variant Component

48005-3

Amino acid change (pHGVS)

Variant Component

48018-6

Gene studied [ID]

Variant Component

48019-4

DNA change type

Variant Component (SO terms)

53037-8

Genetic variation clinical significance [Imp]

Variant Component (WHO Class)

81254-5

Variant exact start-end

Variant Component

82121-5

Allelic read depth

Variant Component

614-8

Mycobacterial strain [Type]

Lineage Observation

LOINC Codes (Drug Susceptibility)

Used within the Susceptibility Panel Observation.

Code

Display Name

89489-9

Rifampin [Susceptibility] by Genotype method

89488-1

Isoniazid [Susceptibility] by Genotype method

92242-7

Pyrazinamide [Susceptibility] by Genotype method

89491-5

Ethambutol [Susceptibility] by Genotype method

96112-8

Moxifloxacin [Susceptibility] by Genotype method

20629-2

levoFLOXacin [Susceptibility]

96107-8

Bedaquiline [Susceptibility] by Genotype method

96111-0

Linezolid [Susceptibility] by Genotype method

96114-4

Streptomycin [Susceptibility] by Genotype method

89484-0

Amikacin [Susceptibility] by Genotype method

Sequence Ontology (SO)

Used for 48019-4 (DNA change type).

Code

Display Name

SO:0001583

missense_variant

SO:0001819

synonymous_variant

SO:0001587

stop_gained

SO:0001578

stop_lost

SO:0001589

frameshift_variant

SO:0001821

inframe_insertion

SO:0001822

inframe_deletion

SO:0001629

splice_site_variant

SO:0001631

upstream_gene_variant

SO:0001632

downstream_gene_variant

SO:0001628

intergenic_variant

SO:0001627

intron_variant

SO:0001623

5_prime_UTR_variant

SO:0001624

3_prime_UTR_variant

SO:0002012

start_lost

SO:0001567

stop_retained_variant

SO:0001818

protein_altering_variant

SO:0001580

coding_sequence_variant

SO:0001619

non_coding_transcript_variant

SO:0001566

regulatory_region_variant

WHO Classification

Code

Display Name

Usage

LA26333-7

http://loinc.org

Uncertain significance

SP000478

http://terminology.kemkes.go.id/sp

Assoc w R

SP000479

http://terminology.kemkes.go.id/sp

Assoc w R - Interim

SP000481

http://terminology.kemkes.go.id/sp

Not assoc w R

SP000480

http://terminology.kemkes.go.id/sp

Not assoc w R - Interim

Clinical Conclusion Codes

Used in DiagnosticReport.conclusionCode.

Diagnosis

Code

System

Sensitive

TB-SO

https://terminology.kemkes.go.id/CodeSystem/episodeofcare-type

RR-TB

415345001

http://snomed.info/sct

HR-TB

414546009

http://snomed.info/sct

MDR-TB

423092005

http://snomed.info/sct

Pre-XDR-TB

OV000435

http://terminology.kemkes.go.id/CodeSystem/clinical-term

XDR-TB

710106005

http://snomed.info/sct

Streptomycin mono-resistant

415622003

http://snomed.info/sct

Ethionamide mono-resistant

414149006

http://snomed.info/sct

Pyrazinamide mono-resistant

415222009

http://snomed.info/sct

Ciprofloxacin mono-resistant

413852006

http://snomed.info/sct

Ethambutol mono-resistant

414146004

http://snomed.info/sct

Drug-resistant (Other)

413556004

http://snomed.info/sct