Research Assistant
Research Assistant · Actions GPT
PubMed E-utilities API
Unofficial OpenAPI schema for the PubMed E-utilities API
GET /esearch.fcgiESearch - Text SearchesResponds to a text query with the list of matching UIDs in a given database (for later use in ESummary, EFetch or ELink), along with the term translations of the query.
GET /epost.fcgiEPost - UID UploadsAccepts a list of UIDs from a given database, stores the set on the History Server, and responds with a query key and web environment for the uploaded dataset.
GET /esummary.fcgiESummary - Document Summary DownloadsResponds to a list of UIDs from a given database with the corresponding document summaries.
GET /efetch.fcgiEFetch - Data Record DownloadsResponds to a list of UIDs in a given database with the corresponding data records in a specified format.
GET /elink.fcgiELink - Entrez LinksResponds with related UIDs in the same or a different Entrez database, checks for specified links from UIDs, creates hyperlinks to primary LinkOut providers, or lists LinkOut URLs and attributes.
GET /egquery.fcgiEGQuery - Global QueryResponds to a text query with the number of records matching the query in each Entrez database.
GET /espell.fcgiESpell - Spelling SuggestionsRetrieves spelling suggestions for a text query in a given database.
GET /ecitmatch.cgiECitMatch - Batch Citation Searching in PubMedRetrieves PubMed IDs (PMIDs) corresponding to a set of input citation strings.
Schéma original API
{
"openapi": "3.0.0",
"info": {
"title": "PubMed E-utilities API",
"version": "1.0.0",
"description": "Unofficial OpenAPI schema for the PubMed E-utilities API"
},
"servers": [
{
"url": "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
}
],
"paths": {
"/esearch.fcgi": {
"get": {
"summary": "ESearch - Text Searches",
"description": "Responds to a text query with the list of matching UIDs in a given database (for later use in ESummary, EFetch or ELink), along with the term translations of the query.",
"parameters": [
{
"name": "db",
"in": "query",
"required": true,
"description": "Database to search. Example: 'pubmed', 'protein'.",
"schema": {
"type": "string"
}
},
{
"name": "term",
"in": "query",
"required": true,
"description": "Search query. Terms must be URL-encoded. Example: 'asthma[mesh]+AND+leukotrienes[mesh]'.",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Successful response",
"content": {
"application/xml": {
"schema": {
"type": "object",
"properties": {
"WebEnv": {
"type": "string"
},
"QueryKey": {
"type": "string"
},
"Count": {
"type": "integer"
},
"RetMax": {
"type": "integer"
},
"RetStart": {
"type": "integer"
},
"IdList": {
"type": "array",
"items": {
"type": "integer"
}
},
"TranslationSet": {
"type": "array",
"items": {
"type": "object",
"properties": {
"From": {
"type": "string"
},
"To": {
"type": "string"
}
}
}
},
"QueryTranslation": {
"type": "string"
}
}
}
}
}
}
},
"operationId": "pubmed_esearch_get"
}
},
"/epost.fcgi": {
"get": {
"summary": "EPost - UID Uploads",
"description": "Accepts a list of UIDs from a given database, stores the set on the History Server, and responds with a query key and web environment for the uploaded dataset.",
"parameters": [
{
"name": "db",
"in": "query",
"required": true,
"description": "Database where the UIDs are coming from. Example: 'pubmed'.",
"schema": {
"type": "string"
}
},
{
"name": "id",
"in": "query",
"required": true,
"description": "List of UIDs to post. UIDs should be comma-separated. Example: '19880808,19990999'.",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Successful response",
"content": {
"application/xml": {
"schema": {
"type": "object",
"properties": {}
}
}
}
}
},
"operationId": "pubmed_epost_get"
}
},
"/esummary.fcgi": {
"get": {
"summary": "ESummary - Document Summary Downloads",
"description": "Responds to a list of UIDs from a given database with the corresponding document summaries.",
"parameters": [
{
"name": "db",
"in": "query",
"required": true,
"description": "Database from which the document summaries are requested. Example: 'pubmed'.",
"schema": {
"type": "string"
}
},
{
"name": "id",
"in": "query",
"required": true,
"description": "List of UIDs for which summaries are requested. UIDs should be comma-separated. Example: '19880808,19990999'.",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Successful response",
"content": {
"application/xml": {
"schema": {
"type": "object",
"properties": {}
}
}
}
}
},
"operationId": "pubmed_esummary_get"
}
},
"/efetch.fcgi": {
"get": {
"summary": "EFetch - Data Record Downloads",
"description": "Responds to a list of UIDs in a given database with the corresponding data records in a specified format.",
"parameters": [
{
"name": "db",
"in": "query",
"required": true,
"description": "Database from which the data records are requested. Example: 'nuccore', 'protein'.",
"schema": {
"type": "string"
}
},
{
"name": "id",
"in": "query",
"required": true,
"description": "List of UIDs for which data records are requested. UIDs should be comma-separated. Example: '34577062,4885471'.",
"schema": {
"type": "string"
}
},
{
"name": "rettype",
"in": "query",
"required": false,
"description": "Type of data record to return. Example: 'fasta', 'abstract'.",
"schema": {
"type": "string"
}
},
{
"name": "retmode",
"in": "query",
"required": false,
"description": "Mode of data return. Example: 'xml', 'text'.",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Successful response",
"content": {
"application/xml": {
"schema": {
"type": "object",
"properties": {}
}
}
}
}
},
"operationId": "pubmed_efetch_get"
}
},
"/elink.fcgi": {
"get": {
"summary": "ELink - Entrez Links",
"description": "Responds with related UIDs in the same or a different Entrez database, checks for specified links from UIDs, creates hyperlinks to primary LinkOut providers, or lists LinkOut URLs and attributes.",
"parameters": [
{
"name": "dbfrom",
"in": "query",
"required": true,
"description": "Database containing the input UIDs. Example: 'protein'.",
"schema": {
"type": "string"
}
},
{
"name": "db",
"in": "query",
"required": true,
"description": "Database for which to retrieve linked UIDs. Example: 'gene'.",
"schema": {
"type": "string"
}
},
{
"name": "id",
"in": "query",
"required": true,
"description": "List of UIDs for which to retrieve links. UIDs should be comma-separated. Example: '194680922,50978626'.",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Successful response",
"content": {
"application/xml": {
"schema": {
"type": "object",
"properties": {}
}
}
}
}
},
"operationId": "pubmed_elink_get"
}
},
"/egquery.fcgi": {
"get": {
"summary": "EGQuery - Global Query",
"description": "Responds to a text query with the number of records matching the query in each Entrez database.",
"parameters": [
{
"name": "term",
"in": "query",
"required": true,
"description": "Text query for which the number of records is requested in each Entrez database. Terms must be URL-encoded. Example: 'asthma[mesh]+AND+leukotrienes[mesh]'.",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Successful response",
"content": {
"application/xml": {
"schema": {
"type": "object",
"properties": {}
}
}
}
}
},
"operationId": "pubmed_egquery_get"
}
},
"/espell.fcgi": {
"get": {
"summary": "ESpell - Spelling Suggestions",
"description": "Retrieves spelling suggestions for a text query in a given database.",
"parameters": [
{
"name": "db",
"in": "query",
"required": true,
"description": "Database for which spelling suggestions are requested. Example: 'pubmed'.",
"schema": {
"type": "string"
}
},
{
"name": "term",
"in": "query",
"required": true,
"description": "Text query for which spelling suggestions are requested. Terms must be URL-encoded. Example: 'leukemia'.",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Successful response",
"content": {
"application/xml": {
"schema": {
"type": "object",
"properties": {}
}
}
}
}
},
"operationId": "pubmed_espell_get"
}
},
"/ecitmatch.cgi": {
"get": {
"summary": "ECitMatch - Batch Citation Searching in PubMed",
"description": "Retrieves PubMed IDs (PMIDs) corresponding to a set of input citation strings.",
"parameters": [
{
"name": "db",
"in": "query",
"required": true,
"description": "Database to search for citations. Currently, only 'pubmed' is supported.",
"schema": {
"type": "string"
}
},
{
"name": "term",
"in": "query",
"required": true,
"description": "Citation strings for which PubMed IDs are requested. The format should match the PubMed citation format. Example: 'Proc Natl Acad Sci U S A. 2021 Jan 19;118(3):e2024857118.'",
"schema": {
"type": "string"
}
}
],
"responses": {
"200": {
"description": "Successful response",
"content": {
"application/xml": {
"schema": {
"type": "object",
"properties": {}
}
}
}
}
},
"operationId": "pubmed_ecitmatch_get"
}
}
}
}arXiv API
Unofficial OpenAPI schema for the arXiv API
GET /queryQuery the arXiv APIRetrieve articles and their metadata based on various search criteria.
Schéma original API
{
"openapi": "3.0.0",
"info": {
"title": "arXiv API",
"version": "1.0.0",
"description": "Unofficial OpenAPI schema for the arXiv API"
},
"servers": [
{
"url": "https://export.arxiv.org/api"
}
],
"paths": {
"/query": {
"get": {
"summary": "Query the arXiv API",
"description": "Retrieve articles and their metadata based on various search criteria.",
"operationId": "queryArxiv",
"parameters": [
{
"name": "search_query",
"in": "query",
"required": false,
"schema": {
"type": "string"
},
"description": "A string that represents a search query used to find articles. If only 'search_query' is provided (and 'id_list' is blank or not given), the API will return results for each article that matches the search query."
},
{
"name": "id_list",
"in": "query",
"required": false,
"schema": {
"type": "string"
},
"description": "A comma-delimited list of arXiv IDs. If only 'id_list' is provided (and 'search_query' is blank or not given), the API will return results for each article in 'id_list'. If both 'search_query' and 'id_list' are given, the API will return each article in 'id_list' that matches 'search_query'."
},
{
"name": "start",
"in": "query",
"required": false,
"schema": {
"type": "integer",
"default": 0
},
"description": "The index of the first returned result, using 0-based indexing. This parameter is used for paging through results."
},
{
"name": "max_results",
"in": "query",
"required": false,
"schema": {
"type": "integer",
"default": 10
},
"description": "The number of results returned by the query. The maximum number of results from a single call is limited to 30000 in slices of at most 2000 at a time. A request with 'max_results' > 30,000 will result in an HTTP 400 error."
},
{
"name": "sortBy",
"in": "query",
"required": false,
"schema": {
"type": "string"
},
"description": "Determines the sorting field of the results. Can be 'relevance', 'lastUpdatedDate', or 'submittedDate'."
},
{
"name": "sortOrder",
"in": "query",
"required": false,
"schema": {
"type": "string"
},
"description": "Determines the order of the results. Can be either 'ascending' or 'descending'."
}
],
"responses": {
"200": {
"description": "Successful response",
"content": {
"application/xml": {
"schema": {
"type": "string"
}
}
}
},
"default": {
"description": "Unexpected error",
"content": {
"application/xml": {
"schema": {
"type": "string"
}
}
}
}
}
}
}
}
}