Skip to main content
Version: v0.2.3

Transform a lab result

An ORU^R01 carries lab results: an OBR per report and an OBX per result. toFhir turns each OBR into a DiagnosticReport and each OBX under it into an Observation the report references. This guide shows the result and the decisions that matter when you read it.

Transform the message​

import { parseHL7 } from "@cosyte/hl7";
import { serializeResource } from "@cosyte/fhir";
import { createNamingSystem, toFhir } from "@cosyte/transform";

const raw = [
  "MSH|^~\\&|LAB|LABFAC|EHR|HOSP|20260721150000-0500||ORU^R01^ORU_R01|MSG0002|P|2.5.1",
  "PID|1||MRN12345^^^HOSP^MR||Public^Jane^Q||19800115|F",
  "OBR|1|PLACER1|FILLER1|24331-1^Lipid Panel^LN|||20260721143000-0500|||||||||||||||20260721150000-0500||LAB|F",
  "OBX|1|NM|2093-3^Cholesterol^LN||210.50|mg/dL^mg/dL^UCUM|<200|H|||F|||20260721143000-0500",
  "NTE|1||Fasting sample",
  "OBX|2|CWE|32207-3^Appearance^LN||NORMAL^Normal^L||||||C",
].join("\r");

const { bundle } = toFhir(parseHL7(raw), {
  namingSystem: createNamingSystem({ authorities: { HOSP: "urn:oid:2.16.840.1.113883.19" } }),
});
const json = JSON.parse(serializeResource(bundle)) as {
  entry: { fullUrl: string; resource: Record<string, unknown> & { resourceType: string } }[];
};

json.entry.map((e) => e.resource.resourceType); // => ["MessageHeader", "Patient", "DiagnosticReport", "Observation", "Observation"]

const report = json.entry[2]?.resource;
report?.["status"]; // => "final"
(report?.["result"] as { reference: string }[]).map((r) => r.reference); // => [json.entry[3]?.fullUrl, json.entry[4]?.fullUrl]

The report's status comes from OBR-25 and each observation's from OBX-11, each through the guide's status map.

Read each result's status​

The status maps are exported, so you can see exactly what each v2 code becomes. A corrected result is corrected and a cancelled one cancelled; neither is ever reported as final. A code the map has no target for leaves status absent, and because status is required, that resource is withheld from the bundle with TRANSFORM_RESOURCE_INVALID rather than sent with a guessed status.

import { DIAGNOSTIC_REPORT_STATUS_MAP, OBSERVATION_STATUS_MAP } from "@cosyte/transform";

OBSERVATION_STATUS_MAP["F"]; // => "final"
OBSERVATION_STATUS_MAP["C"]; // => "corrected"
OBSERVATION_STATUS_MAP["X"]; // => "cancelled"
DIAGNOSTIC_REPORT_STATUS_MAP["F"]; // => "final"

Read each result's value​

OBX-2 says what kind of value OBX-5 holds, and it picks the value[x] element. A result is never forced into a Quantity it is not. When a value cannot be carried faithfully in its element (a TM with a UTC offset, an NA with a magnitude a FHIR decimal cannot hold unchanged, an NR neither of whose bounds a decimal can hold unchanged, an ED in any encoding but Base64), it falls back to the raw text in valueString with TRANSFORM_ELEMENT_DROPPED; the NA and NR cases also raise TRANSFORM_QUANTITY_VALUE_INVALID for each magnitude refused. An NM or SN magnitude a decimal cannot hold unchanged, such as +210, also falls back to the raw text in valueString, but it raises TRANSFORM_QUANTITY_VALUE_INVALID and no TRANSFORM_ELEMENT_DROPPED.

import { parseHL7 } from "@cosyte/hl7";
import { serializeResource } from "@cosyte/fhir";
import { toFhir } from "@cosyte/transform";

const raw = [
  "MSH|^~\\&|LAB|LABFAC|EHR|HOSP|20260721150000-0500||ORU^R01^ORU_R01|MSG0003|P|2.5.1",
  "PID|1||MRN12345^^^HOSP^MR||Public^Jane^Q||19800115|F",
  "OBR|1|PLACER1|FILLER1|24331-1^Lipid Panel^LN|||20260721143000-0500|||||||||||||||20260721150000-0500||LAB|F",
  "OBX|1|NM|2093-3^Cholesterol^LN||+210|mg/dL^mg/dL^UCUM|||||F",
].join("\r");

const { bundle, issues } = toFhir(parseHL7(raw));
serializeResource(bundle).includes('"valueString":"+210"'); // => true
issues.some((i) => i.code === "TRANSFORM_QUANTITY_VALUE_INVALID"); // => true
issues.some((i) => i.code === "TRANSFORM_ELEMENT_DROPPED"); // => false
OBX-2FHIR element
NMvalueQuantity
CWE, CE, CF, CNE, ISvalueCodeableConcept
DT, DTM, TSvalueDateTime
SNa valueQuantity with a comparator, a valueRange or a valueRatio
DRvaluePeriod
NRvalueRange
TMvalueTime
NAvalueSampledData
ED with Base64 encodingthe guide's valueAttachment extension, the payload carried as sent
ST, TX, FTvalueString
any other, such as RPthe raw text in valueString, with TRANSFORM_ELEMENT_DROPPED

A numeric value keeps its digits exactly as sent: 210.50 stays 210.50 in the serialized JSON, never the number 210.5. The unit becomes Quantity.code only when it is declared UCUM and looks like UCUM; otherwise it stays in Quantity.unit alone with TRANSFORM_UNIT_NOT_UCUM. Magnitudes are never converted between units.

import { parseHL7 } from "@cosyte/hl7";
import { serializeResource } from "@cosyte/fhir";
import { createNamingSystem, toFhir } from "@cosyte/transform";

const raw = [
  "MSH|^~\\&|LAB|LABFAC|EHR|HOSP|20260721150000-0500||ORU^R01^ORU_R01|MSG0002|P|2.5.1",
  "PID|1||MRN12345^^^HOSP^MR||Public^Jane^Q||19800115|F",
  "OBR|1|PLACER1|FILLER1|24331-1^Lipid Panel^LN|||20260721143000-0500|||||||||||||||20260721150000-0500||LAB|F",
  "OBX|1|NM|2093-3^Cholesterol^LN||210.50|mg/dL^mg/dL^UCUM|<200|H|||F|||20260721143000-0500",
  "NTE|1||Fasting sample",
].join("\r");

const { bundle } = toFhir(parseHL7(raw), {
  namingSystem: createNamingSystem({ authorities: { HOSP: "urn:oid:2.16.840.1.113883.19" } }),
});
const text = serializeResource(bundle);

text.includes('"valueQuantity":{"value":210.50,"unit":"mg/dL","system":"http://unitsofmeasure.org","code":"mg/dL"}'); // => true
text.includes('"note":[{"text":"Fasting sample"}]'); // => true
text.includes('"referenceRange":[{"text":"<200"}]'); // => true

Read the result from the serialized JSON when the exact digits matter: JSON.parse turns 210.50 into the number 210.5.

Notes and specimens​

  • An NTE right after an OBX becomes that observation's note. An NTE at the patient or order level has no published target and reaches nothing.
  • An SPM becomes a Specimen the report references. If the report is withheld, its specimen is withheld with it rather than left on its own. Specimen.status is never set.

What is not mapped​

DiagnosticReport.category comes from OBR-24 when it is valued and is never defaulted. Only the first PID and PV1 are read, so a message with several patient result groups is not handled. OBR performers, the specimen OBR names, and basedOn are not built. Mapping scope has the full list.

Reference​