nextprot-cli

Javasript Client of neXtProt (https://search.nextprot.org).

neXtProt contains a comprehensive set of human proteins knwoledge.

This module contains methods to access the neXtProt API (https://api.nextprot.org) as well as the SPARQL endpoint (http://snorql.nextprot.org).

Getting Started

Install the module with:

npm install nextprot-cli

Create a file, for example test-nextprot.js and write some javascript code: Import the module in your code and provide some information about your application:

var NextProtClient = require("nextprot-cli");

//neXtProt is free to use but we appreciate some information about your application and who you are :)
var applicationName = "my test application";
var clientInformation = "Student at UNIGE";
var nx = new NextProtClient(applicationName, clientInformation);

Once you have initialized the object you can either request the API directly in the following manner:

//Refer to API (https://api.nextprot.org) to get an extensive list of possible protein blocks
nx.getProteinBlock('NX_P01308', 'isoform', function (data) {
    data.entry.isoforms.map(function (i) {
        console.log(i.sequence)
    })
});

//node test-nextprot.js
//Will print out the sequence of the protein P01308 (insulin)
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN

Or run a SPARQL query against the neXtProt SPARQL endpoint. See https://snorql.nextprot.org for more examples

var chromosome = 13;
//Refer to http://snorql.nextprot.org for more example queries
var sparqlQuery = 'select distinct ?entry where { ?entry :gene / :chromosome "'+ chromosome +'"^^xsd:string}'

nx.executeSPARQL(sparqlQuery, function(data) {
	console.log("Found " + data.results.bindings.length + " entries ");
});

//node test-nextprot.js
//Will print the number of entries that have a gene on chromosome 13
Found 328 entries

You can even combine both (API and SPARQL), look at the examples folder for working code.

Support

If you have any problem or suggestion please open an issue here.

License

This software is licensed under the GNU GPL v2 license, quoted below.

Copyright (c) 2015, SIB Swiss Institute of Bioinformatics