Runtime: Browser + Node.js

Why

PubMed XML has dozens of structural edge cases — structured abstracts with labeled sections, collective author names, MedlineDate fallback formats, multiple article IDs across different schemes. Writing a one-off parser means rediscovering these pitfalls. This package handles them all and returns clean typed objects.

• PubmedArticleSet XML — full parse of the standard PubMed efetch XML format
• Streaming parser — process large XML responses article-by-article via AsyncIterableIterator
• MEDLINE plain-text — parse the tagged MEDLINE format (PMID- ..., TI - ...)
• Complete field coverage — abstract (structured/unstructured), authors, journal, MeSH, grants, keywords, data banks, comments/corrections, article IDs, publication types

Install

npm install @ncbijs/pubmed-xml

Quick start

Parse XML

import { parsePubmedXml } from '@ncbijs/pubmed-xml';

const xml = await fetch(
  'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=12345678&rettype=xml',
).then((r) => r.text());

const articles = parsePubmedXml(xml);

for (const article of articles) {
  console.log(article.pmid, article.title);
  console.log(article.journal.title, article.publicationDate.year);
}

Stream large responses

import { createPubmedXmlStream } from '@ncbijs/pubmed-xml';

const response = await fetch(
  'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=1,2,3&rettype=xml',
);
const textStream = response.body!.pipeThrough(new TextDecoderStream());

for await (const article of createPubmedXmlStream(textStream)) {
  console.log(article.pmid, article.title);
}

Parse MEDLINE text

import { parseMedlineText } from '@ncbijs/pubmed-xml';

const medline = `
PMID- 12345678
TI  - A novel approach to cancer treatment
AU  - Smith J
AU  - Jones M
DP  - 2024 Mar 15
AB  - This study demonstrates...
MH  - Neoplasms/*therapy
`;

const articles = parseMedlineText(medline);
console.log(articles[0].title); // 'A novel approach to cancer treatment'

API

parsePubmedXml(xml)

Parse a PubmedArticleSet XML string into an array of typed article objects.

const articles = parsePubmedXml(xmlString);

| Parameter | Type | Description | | --------- | -------- | ---------------------------- | | xml | string | PubmedArticleSet XML string. |

Returns ReadonlyArray<PubmedArticle>.

createPubmedXmlStream(input)

Create a streaming parser that yields PubmedArticle objects as complete <PubmedArticle> elements arrive. Useful for large responses that should not be buffered entirely in memory.

for await (const article of createPubmedXmlStream(textStream)) {
  // process each article as it arrives
}

| Parameter | Type | Description | | --------- | ------------------------ | ---------------------------- | | input | ReadableStream<string> | Readable stream of XML text. |

Returns AsyncIterableIterator<PubmedArticle>.

Throws if the stream ends with an incomplete <PubmedArticle> element.

parseMedlineText(text)

Parse MEDLINE plain-text format (tagged format with PMID-, TI -, etc.) into typed article objects.

const articles = parseMedlineText(medlineString);

| Parameter | Type | Description | | --------- | -------- | ----------------------------- | | text | string | MEDLINE tagged-format string. |

Returns ReadonlyArray<PubmedArticle>.

PubmedArticle

Every parser returns PubmedArticle objects with the following fields:

| Field | Type | Description | | --------------------- | ---------------------------------- | ------------------------------------------------------------------ | | pmid | string | PubMed ID. | | title | string | Article title (tags stripped). | | vernacularTitle | string (optional) | Title in original language. | | abstract | AbstractContent | Abstract text, with structured sections if available. | | authors | ReadonlyArray<Author> | Author list. | | journal | JournalInfo | Journal title, abbreviation, ISSN, volume, issue. | | publicationDate | PartialDate | Year, month, day, or season/raw fallback. | | mesh | ReadonlyArray<MeshHeading> | MeSH headings with descriptors, qualifiers, and major topic flags. | | articleIds | ArticleIds | PMID, DOI, PMC, PII, MID identifiers. | | publicationTypes | ReadonlyArray<string> | Publication type list (e.g., "Journal Article", "Review"). | | grants | ReadonlyArray<Grant> | Funding grants. | | keywords | ReadonlyArray<Keyword> | Author and NLM keywords. | | commentsCorrections | ReadonlyArray<CommentCorrection> | Errata, retractions, comments. | | dataBanks | ReadonlyArray<DataBank> | Data bank accession numbers (e.g., GenBank). | | language | string | Language code (e.g., "eng"). | | dateRevised | PartialDate (optional) | Date last revised. | | dateCompleted | PartialDate (optional) | Date citation completed. |

Types

All types are exported for use in your own interfaces:

import type {
  PubmedArticle,
  Author,
  MeshHeading,
  MeshQualifier,
  AbstractSection,
  AbstractContent,
  CommentCorrection,
  DataBank,
  Grant,
  JournalInfo,
  Keyword,
  ArticleIds,
  PartialDate,
} from '@ncbijs/pubmed-xml';