The NCBI Entrez API is a powerful resource for scientists, researchers, and engineers. The api allows consistent access patterns to over 40 databases. This module is a wrapper that allows calls to be made to the NCBI Entrez API.
npm install ncbi-entrez-api
import {DB, dbFactory} from 'ncbi-entrez-api'
let gene = dbFactory(DB.GENE) //DB.GENE is the mapping for 'gene'
gene.einfo({ format: 'json' }, function(err, response, data) {
console.log(data)
})
var NcbiApi = require('ncbi-entrez-api')
var gene = NcbiApi.dbFactory(NcbiApi.DB.GENE)
gene.einfo({ format: 'json' }, function(err, response, data) {
console.log(data)
})
We use request - which provides both callback and streaming style api calls.
import fs from 'fs'
import {DB, dbFactory} from 'ncbi-entrez-api'
let gene = dbFactory(DB.GENE)
gene.info({ format: 'json'}).pipe(fs.createWriteStream('myFile.json'))
var NcbiApi = require('ncbi-entrez-api')
//Constants mapping to available databases
//console.log to see your options
console.log(NcbiApi.DB)
//Create an instance of a db fetcher
var gene = NcbiApi.dbFactory(NcbiApi.DB.GENE)
//Call any of the following endpoints
//options - Required for each endpoint
//callback - optional. Without a callback will receive a stream
gene.einfo(options, callback)
gene.epost(options, callback)
gene.elink(options, callback)
gene.espell(options, callback)
gene.esearch(options, callback)
gene.esummary(options, callback)
gene.efetch(options, callback)
For a list of all api specific options, see http://www.ncbi.nlm.nih.gov/books/NBK25499/
einfo, esummary, and efetch are the only 3 endpoints that currently return JSON. The rest return XML by default.
options = {retmode: 'json'}
var NcbiApi = require('ncbi-entrez-api')
var protein = NcbiApi.dbFactory(NcbiApi.DB.PROTEIN)
var callback = function(err, response, data) {
console.log(data)
}
protein.einfo({
retmode: 'json'
}, callback)
protein.epost({
ids: ['id_1', 'id_2']
}, callback)
protein.elink({
dbFrom: 'homologene',
ids: ['id_1', 'id_2']
}, callback)
protein.espell({
term: 'organism[homo]'
}, callback)
protein.esearch({
term: 'organism[homo]',
retmode: 'json'
}, callback)
protein.esummary({
ids: ['id_1', 'id_2'],
retmode: 'json'
}, callback)
protein.efetch({
ids: ['id_1', 'id_2'],
rettype: 'fasta',
retmode: 'text'
}, callback)
efetch pulls down full records in various formats. Each database supports different data formats.
Use options.retmode and options.rettype to control the format.
See more options here.
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