Medplum

// SPDX-FileCopyrightText: Copyright Orangebot, Inc. and Medplum contributors // SPDX-License-Identifier: Apache-2.0 import { createReadStream, createWriteStream, existsSync, mkdirSync } from 'node:fs'; import { createInterface } from 'node:readline'; /** * This utilitity generates data for ValueSet and ConceptMap resources from the UMLS Metathesaurus. * * The source files provided by UMLS are quite large (GB+) and are not included in this repository. * * The objective of this utility is to generate a subset of the UMLS that is useful for the Medplum FHIR server. * * Output format is a tab-delimited file with the following columns: * * - code * - display * * Outputs: * * - output/icd10.txt (23MB) - ICD-10-CM and ICD-10-PCS codes * - output/loinc.txt (12MB) - LOINC codes * - output/rxnorm.txt (9MB) - RxNorm codes * - output/snomed.txt (14MB) - SNOMED CT codes * * Requirements: * * - Download the UMLS Metathesaurus from https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html * - For terminology alone, only MRCONSO.RRF is required * - For terminology and concept maps, both MRCONSO.RRF and MRMAP.RRF are required * * Most recently tested with the 2022AB release. * * References: * * UMLS Metathesaurus Vocabulary Documentation * https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html * * 2022AB Release Documentation * https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/index.html * * Columns and Data Elements - 2022AB * https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/columns_data_elements.html * * Abbreviations Used in Data Elements - 2022AB Release * https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/abbreviations.html */ async function main(): Promise<void> { if (!existsSync('./output')) { mkdirSync('./output'); } await processMrconso(); } async function processMrconso(): Promise<void> { const inStream = createReadStream('MRCONSO.RRF'); const rl = createInterface(inStream); const snomedStream = createWriteStream('./output/snomed.txt'); const loincStream = createWriteStream('./output/loinc.txt'); const rxnormStream = createWriteStream('./output/rxnorm.txt'); const icd10Stream = createWriteStream('./output/icd10.txt'); for await (const line of rl) { // Columns: // 0 CUI Unique identifier for concept // 1 LAT Language of Term(s) // 2 TS Term status // 3 LUI Unique identifier for term // 4 STT String type // 5 SUI Unique identifier for string // 6 ISPREF Indicates whether AUI is preferred // 7 AUI Atom Unique Identifiers (AUI) // 8 SAUI Source asserted atom identifier // 9 SCUI Source asserted concept identifier // 10 SDUI Source asserted descriptor identifier // 11 SAB Source abbreviation // 12 TTY Term type in source // 13 CODE Unique Identifier or code for string in source // 14 STR String // 15 SRL Source Restriction Level // 16 SUPPRESS Suppressible flag const columns = line.split('|'); // Language of Term(s) if (columns[1] !== 'ENG') { // Ignore non-english continue; } // TS Term status // P = Preferred LUI of the CUI // S = Non-Preferred LUI of the CUI if (columns[2] !== 'P') { // Ignore non-preferred terms continue; } // STT String type // PF = Preferred form of term // VCW = Case and word-order variant of the preferred form // VC = Case variant of the preferred form // VO = Variant of the preferred form // VW = Word-order variant of the preferred form if (columns[4] !== 'PF') { // Ignore non-preferred terms continue; } // ISPREF Indicates whether AUI is preferred if (columns[6] !== 'Y') { // Ignore non-preferred terms continue; } // TTY Term type in source if (columns[12] === 'ET') { // Ignore "Entry Term" continue; } // SUPPRESS Suppressible flag if (columns[16] === 'Y') { // Ignore suppressed terms continue; } const source = columns[11]; let outStream = undefined; switch (source) { case 'SNOMEDCT_US': outStream = snomedStream; break; case 'LNC': outStream = loincStream; break; case 'RXNORM': outStream = rxnormStream; break; case 'ICD10CM': case 'ICD10PCS': outStream = icd10Stream; break; } if (!outStream) { continue; } const code = columns[9] || columns[10] || columns[7]; const display = columns[14]; outStream.write(`${code}\t${display}\n`); } snomedStream.end(); loincStream.end(); rxnormStream.end(); icd10Stream.end(); } if (import.meta.main) { main() .then(() => console.log('Done')) .catch(console.error); }