Class PubMedClient

PubMed/PMC API client

Constructors

constructor

new PubMedClient(): PubMedClient
Create a new PubMed client with default configuration

Returns PubMedClient
- Defined in index.d.ts:6

Methods

checkPmcAvailability

checkPmcAvailability(pmid: string): Promise<string | null>
Check if a PubMed article has full-text available in PMC
Parameters
- pmid: string
  PubMed ID
Returns Promise<string | null>
PMC ID if available, null otherwise
- Defined in index.d.ts:81

downloadFiles

downloadFiles(pmcid: string, outputDir: string): Promise<string[]>
Download a PMC article's Open Access files to a directory

Downloads each of the article's files individually from the PMC OA Cloud (AWS S3) service for the given PMC ID, returning the list of downloaded file paths.
Parameters
- pmcid: string
  PMC ID (e.g., "PMC7906746")
- outputDir: string
  Directory to download files into
Returns Promise<string[]>
Array of downloaded file paths
- Defined in index.d.ts:256

epost

epost(pmids: string[]): Promise<EPostResult>
Upload a list of PMIDs to the NCBI History server using EPost

Stores UIDs on the server and returns WebEnv/query_key identifiers that can be used with subsequent API calls.
Parameters
- pmids: string[]
  Array of PubMed IDs as strings
Returns Promise<EPostResult>
EPostResult containing webenv and query_key
Example
```
const client = new PubMedClient();
const result = await client.epost(["31978945", "33515491", "25760099"]);
console.log(`WebEnv: ${result.webenv}, Query Key: ${result.queryKey}`);
```
- Defined in index.d.ts:149

europePmcDownloadSupplementaryFiles

europePmcDownloadSupplementaryFiles(
    id: string,
    outputPath: string,
    source?: string | null,
): Promise<string>
Download a Europe PMC record's supplementary-files ZIP archive

Europe PMC returns supplementary materials as a single ZIP; unpacking is left to the caller.
Parameters
- id: string
  Record id, bare or fully qualified
- outputPath: string
  Full path of the ZIP file to write
- Optionalsource: string | null
  Source database (MED, PMC, PPR, AGR, CBA, PAT)
Returns Promise<string>
The written path
- Defined in index.d.ts:349

europePmcFetchFullText

europePmcFetchFullText(
id: string,
source?: string | null,
): Promise<FullTextArticle>
Fetch and parse the full text of a Europe PMC record

Parsing into an article requires a PMC id, so this supports PMC-sourced records only; use europePmcFetchFullTextXml for other sources.
Parameters
- id: string
  Record id, bare or fully qualified
- Optionalsource: string | null
  Source database (MED, PMC, PPR, AGR, CBA, PAT)
Returns Promise<FullTextArticle>
Structured full-text article
- Defined in index.d.ts:302

europePmcFetchFullTextXml

europePmcFetchFullTextXml(id: string, source?: string | null): Promise<string>
Fetch the raw JATS XML full text of a Europe PMC record
Parameters
- id: string
  Record id, bare or fully qualified
- Optionalsource: string | null
  Source database (MED, PMC, PPR, AGR, CBA, PAT)
Returns Promise<string>
JATS XML
- Defined in index.d.ts:310

europePmcGetCitations

europePmcGetCitations(
id: string,
source?: string | null,
): Promise<EuropePmcCitationEntry[]>
List the articles citing a Europe PMC record

Broader coverage than getCitations, which is PubMed-only: includes preprints and other non-PubMed sources.
Parameters
- id: string
  Record id, bare or fully qualified
- Optionalsource: string | null
  Source database (MED, PMC, PPR, AGR, CBA, PAT)
Returns Promise<EuropePmcCitationEntry[]>
Array of citing articles
- Defined in index.d.ts:329

europePmcGetDatabaseLinks

europePmcGetDatabaseLinks(
id: string,
source?: string | null,
): Promise<EuropePmcDatabaseLinkEntry[]>
List cross-references from a Europe PMC record to external databases
Parameters
- id: string
  Record id, bare or fully qualified
- Optionalsource: string | null
  Source database (MED, PMC, PPR, AGR, CBA, PAT)
Returns Promise<EuropePmcDatabaseLinkEntry[]>
Array of per-database cross-reference groups
- Defined in index.d.ts:337

europePmcGetReferences

europePmcGetReferences(
id: string,
source?: string | null,
): Promise<EuropePmcReferenceEntry[]>
List the works cited by a Europe PMC record
Parameters
- id: string
  Record id, bare or fully qualified
- Optionalsource: string | null
  Source database (MED, PMC, PPR, AGR, CBA, PAT)
Returns Promise<EuropePmcReferenceEntry[]>
Array of cited works
- Defined in index.d.ts:318

europePmcSearch

europePmcSearch(
    query: string,
    limit?: number | null,
    resultType?: string | null,
    sort?: string | null,
): Promise<EuropePmcSearchResult[]>
Search Europe PMC across every source it indexes
Parameters
- query: string
  Europe PMC query (e.g., "TITLE:CRISPR AND SRC:PPR")
- Optionallimit: number | null
  Maximum number of records to return (default: 10)
- OptionalresultType: string | null
  "idlist", "lite" (default) or "core"
- Optionalsort: string | null
  Europe PMC sort expression (e.g., "CITED desc")
Returns Promise<EuropePmcSearchResult[]>
Array of Europe PMC records
- Defined in index.d.ts:277

europePmcSearchPage

europePmcSearchPage(
    query: string,
    resultType?: string | null,
    pageSize?: number | null,
    cursorMark?: string | null,
    sort?: string | null,
): Promise<EuropePmcSearchPage>
Fetch a single page of Europe PMC search results

Pass the returned nextCursorMark back as cursorMark to page through a result set; Europe PMC signals the end by returning the same cursor.
Parameters
- query: string
  Europe PMC query
- OptionalresultType: string | null
  "idlist", "lite" (default) or "core"
- OptionalpageSize: number | null
  Records per page, 1-1000 (default: 25)
- OptionalcursorMark: string | null
  Cursor for the page to fetch; "*" (default) is the first page
- Optionalsort: string | null
  Europe PMC sort expression
Returns Promise<EuropePmcSearchPage>
One page of records, with the total hit count and next cursor
- Defined in index.d.ts:291

executeQuery

executeQuery(query: SearchQuery): Promise<Article[]>
Execute a search query and return articles
Parameters
- query: SearchQuery
  SearchQuery instance
Returns Promise<Article[]>
Array of article metadata
- Defined in index.d.ts:132

exportBibtex

exportBibtex(pmids: string[]): Promise<string>
Export articles as BibTeX

Fetches the given PMIDs and formats them as a BibTeX bibliography.
Parameters
- pmids: string[]
  Array of PubMed IDs as strings
Returns Promise<string>
BibTeX string
- Defined in index.d.ts:223

exportCslJson

exportCslJson(pmids: string[]): Promise<string>
Export articles as CSL-JSON
Parameters
- pmids: string[]
  Array of PubMed IDs as strings
Returns Promise<string>
CSL-JSON string (array of items)
- Defined in index.d.ts:237

exportNbib

exportNbib(pmids: string[]): Promise<string>
Export articles in MEDLINE/NBIB format
Parameters
- pmids: string[]
  Array of PubMed IDs as strings
Returns Promise<string>
NBIB string
- Defined in index.d.ts:244

exportRis

exportRis(pmids: string[]): Promise<string>
Export articles in RIS format
Parameters
- pmids: string[]
  Array of PubMed IDs as strings
Returns Promise<string>
RIS string
- Defined in index.d.ts:230

extractFiguresWithCaptions

extractFiguresWithCaptions(
pmcid: string,
outputDir: string,
): Promise<ExtractedFigure[]>
Extract figures with their captions from a PMC article

Downloads the Open Access package, extracts figure image files, and associates them with caption metadata from the article XML.
Parameters
- pmcid: string
  PMC ID (e.g., "PMC7906746")
- outputDir: string
  Directory to extract figure files into
Returns Promise<ExtractedFigure[]>
Array of extracted figures with file metadata
- Defined in index.d.ts:267

fetchAllByPmids

fetchAllByPmids(pmids: string[]): Promise<Article[]>
Fetch all articles for a list of PMIDs using EPost and the History server

Uploads the PMID list via EPost (HTTP POST), then fetches articles in paginated batches. Recommended for large PMID lists (hundreds or thousands).
Parameters
- pmids: string[]
  Array of PubMed IDs as strings
Returns Promise<Article[]>
Array of article metadata
Example
```
const client = new PubMedClient();
const articles = await client.fetchAllByPmids(["31978945", "33515491", "25760099"]);
articles.forEach(a => console.log(a.title));
```
- Defined in index.d.ts:166

fetchArticle

fetchArticle(pmid: string): Promise<Article>
Fetch a single article by PMID
Parameters
- pmid: string
  PubMed ID
Returns Promise<Article>
Article metadata
- Defined in index.d.ts:38

fetchArticles

fetchArticles(pmids: string[]): Promise<Article[]>
Fetch multiple articles by PMIDs in a single batch request

This is significantly more efficient than fetching articles one by one. For large numbers of PMIDs, requests are automatically batched (200 per request).
Parameters
- pmids: string[]
  Array of PubMed IDs
Returns Promise<Article[]>
Array of article metadata
- Defined in index.d.ts:31

fetchPmcArticle

fetchPmcArticle(pmcid: string): Promise<FullTextArticle>
Fetch full-text article from PMC
Parameters
- pmcid: string
  PMC ID (e.g., "PMC7906746")
Returns Promise<FullTextArticle>
Full-text article data
- Defined in index.d.ts:66

fetchPmcAsMarkdown

fetchPmcAsMarkdown(
pmcid: string,
options?: MarkdownOptions | null,
): Promise<string>
Fetch PMC article and convert to Markdown
Parameters
- pmcid: string
  PMC ID (e.g., "PMC7906746")
- Optionaloptions: MarkdownOptions | null
  Markdown conversion options
Returns Promise<string>
Markdown string
- Defined in index.d.ts:74

fetchSummaries

fetchSummaries(pmids: string[]): Promise<Summary[]>
Fetch lightweight article summaries by PMIDs using the ESummary API

Returns basic metadata (title, authors, journal, dates, DOI) without abstracts, MeSH terms, or chemical lists. Faster than fetchArticles().
Parameters
- pmids: string[]
  Array of PubMed IDs
Returns Promise<Summary[]>
Array of article summaries
- Defined in index.d.ts:48

getCitations

getCitations(pmids: number[]): Promise<Citations>
Get citing articles for the given PMIDs using the ELink API
Parameters
- pmids: number[]
  Array of PubMed IDs
Returns Promise<Citations>
Citing articles
- Defined in index.d.ts:187

getDatabaseInfo

getDatabaseInfo(database: string): Promise<DatabaseInfo>
Get detailed information about a specific NCBI database using the EInfo API
Parameters
- database: string
  Database name (e.g., "pubmed", "pmc")
Returns Promise<DatabaseInfo>
Database information
- Defined in index.d.ts:200

getDatabaseList

getDatabaseList(): Promise<string[]>
List all available NCBI databases using the EInfo API

Returns Promise<string[]>
Array of database names
- Defined in index.d.ts:193

getPmcLinks

getPmcLinks(pmids: number[]): Promise<PmcLinks>
Get PMC links for the given PMIDs (check full-text availability)
Parameters
- pmids: number[]
  Array of PubMed IDs
Returns Promise<PmcLinks>
PMC links
- Defined in index.d.ts:180

getRelatedArticles

getRelatedArticles(pmids: number[]): Promise<RelatedArticles>
Get related articles for the given PMIDs using the ELink API
Parameters
- pmids: number[]
  Array of PubMed IDs
Returns Promise<RelatedArticles>
Related articles
- Defined in index.d.ts:173

globalQuery

globalQuery(term: string): Promise<GlobalQueryResults>
Query all NCBI databases for record counts using the EGQuery API
Parameters
- term: string
  Search term
Returns Promise<GlobalQueryResults>
Per-database record counts
- Defined in index.d.ts:214

isOaSubset

isOaSubset(pmcid: string): Promise<OaSubsetInfo>
Check if a PMC article is in the OA (Open Access) subset

The OA subset contains articles with programmatic access to full-text XML. Some publishers restrict programmatic access even though the article may be viewable on the PMC website.
Parameters
- pmcid: string
  PMC ID (e.g., "PMC7906746")
Returns Promise<OaSubsetInfo>
OaSubsetInfo containing detailed information about OA availability
Example
```
const client = new PubMedClient();
const info = await client.isOaSubset("PMC7906746");

if (info.isOaSubset) {
    console.log("Article is in OA subset");
    console.log("Download:", info.downloadLink);
} else {
    console.log("Not in OA subset:", info.errorCode);
}
```
- Defined in index.d.ts:105

matchCitations

matchCitations(citations: CitationQuery[]): Promise<CitationMatch[]>
Match citations to PMIDs using the ECitMatch API
Parameters
- citations: CitationQuery[]
  Array of citation queries
Returns Promise<CitationMatch[]>
Array of citation match results
- Defined in index.d.ts:207

search

search(query: string, limit?: number | null): Promise<Article[]>
Search PubMed and fetch article metadata
Parameters
- query: string
  Search query string (PubMed syntax supported)
- Optionallimit: number | null
  Maximum number of results to return
Returns Promise<Article[]>
Array of article metadata
- Defined in index.d.ts:21

searchSummaries

searchSummaries(query: string, limit?: number | null): Promise<Summary[]>
Search PubMed and fetch lightweight summaries

Combines search and ESummary fetch. Faster than search() when you only need basic metadata.
Parameters
- query: string
  Search query string
- Optionallimit: number | null
  Maximum number of results
Returns Promise<Summary[]>
Array of article summaries
- Defined in index.d.ts:59

spellCheck

spellCheck(term: string): Promise<SpellCheckResult>
Check spelling of a search term using the ESpell API

Provides spelling suggestions for terms within a single text query. Uses the PubMed database by default.
Parameters
- term: string
  The search term to spell-check
Returns Promise<SpellCheckResult>
Spelling suggestions with corrected query
- Defined in index.d.ts:115

spellCheckDb

spellCheckDb(term: string, db: string): Promise<SpellCheckResult>
Check spelling of a search term against a specific database using the ESpell API

Spelling suggestions are database-specific, so use the same database you plan to search.
Parameters
- term: string
  The search term to spell-check
- db: string
  The NCBI database to check against (e.g., "pubmed", "pmc")
Returns Promise<SpellCheckResult>
Spelling suggestions with corrected query
- Defined in index.d.ts:125

`Static`withConfig

withConfig(config: Config): PubMedClient
Create a new PubMed client with custom configuration
Parameters
- config: Config
  Client configuration
Returns PubMedClient

Throws
Error if rateLimit is not a positive number
- Defined in index.d.ts:13

Class PubMedClient

Index

Constructors

Methods

Constructors

constructor

Returns PubMedClient

Methods

checkPmcAvailability

Parameters

Returns Promise<string | null>

downloadFiles

Parameters

Returns Promise<string[]>

epost

Parameters

Returns Promise<EPostResult>

Example

europePmcDownloadSupplementaryFiles

Parameters

Returns Promise<string>

europePmcFetchFullText

Parameters

Returns Promise<FullTextArticle>

europePmcFetchFullTextXml

Parameters

Returns Promise<string>

europePmcGetCitations

Parameters

Returns Promise<EuropePmcCitationEntry[]>

europePmcGetDatabaseLinks

Parameters

Returns Promise<EuropePmcDatabaseLinkEntry[]>

europePmcGetReferences

Parameters

Returns Promise<EuropePmcReferenceEntry[]>

europePmcSearch

Parameters

Returns Promise<EuropePmcSearchResult[]>

europePmcSearchPage

Parameters

Returns Promise<EuropePmcSearchPage>

executeQuery

Parameters

Returns Promise<Article[]>

exportBibtex

Parameters

Returns Promise<string>

exportCslJson

Parameters

Returns Promise<string>

exportNbib

Parameters

Returns Promise<string>

exportRis

Parameters

Returns Promise<string>

extractFiguresWithCaptions

Parameters

Returns Promise<ExtractedFigure[]>

fetchAllByPmids

Parameters

Returns Promise<Article[]>

Example

fetchArticle

Parameters

Returns Promise<Article>

fetchArticles

Parameters

Returns Promise<Article[]>

fetchPmcArticle

Parameters

Returns Promise<FullTextArticle>

fetchPmcAsMarkdown

Parameters

Returns Promise<string>

fetchSummaries

Parameters

Returns Promise<Summary[]>

getCitations

`Static`withConfig