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Norine REST services

Description

Norine provides usefull REST[1] services to access the Norine database. Whereas classical web approaches are mainly dedicated to humans by providing rich and interactive interfaces (such as web forms or pie diagrams) for querying the database, RESTful service main objective is to allow integration with computers through software, applications or programs. This section describes such services that are provided by Norine and how to use them and finally integrate with your application. Most of the time, results are proposed in various output formats such as HTML, XML or Json.

Table of contents

  1. Peptides
  2. Monomers
  3. Links to external databases (PDB, PubChem, ...)
  4. Organisms
  5. Connect your software/database with Norine!
  6. Use the Smiles2Monomers tool as a web service

Peptides


Retrieve peptide details from a Norine ID

To retrieve details of a peptide (name, biological activity, family, structure...) from a Norine ID, simply request the following URI using a browser, an HTTP client tool (e.g. wget, curl, etc.) :

A typical Norine ID starts with "NOR", followed by five digits. Nevertheless, entering an ID without "NOR" or that not respect the five digits convention is also supported (in other words, 00123 is equivalent to 123)
Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/id/NOR00123

By default, the server returns HTML content, as illustrated on the following figure:



To get XML content, just add "/xml" to the path: Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/id/xml/NOR00123

For Json, use: Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/id/json/00123


Retrieve peptide details by name (general search)

The general resource URI is the following:
Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/name/cyclosporin

This example gets all the peptides which name match the word cyclosporin. By default, the server returns HTML content, as illustrated on the following figure:



To get XML content, just add /xml to the URI, before the name value: Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/name/xml/cyclosporin



For Json, use: Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/name/json/cyclosporin



Get all peptides with smiles (JSON)

The general resource URI is the following:


Monomers


Retrieve all monomers

The general resource URI is the following:
Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/monomers

This example gets all the monomers. By default, the server returns HTML content, as illustrated on the following figure:



To get XML content, just add /hierarchicall/xml to the URI: Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/monomers/hierarchical/xml

Alternatively, you can get flat list of all monomers by replacing hierarchical by flat in resource URI, e.g:
Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/monomers/flat/xml



For Json, use: Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/monomers/flat/json



Retrieve clusters tree

The general resource URI is the following:



Links to external databases (PDB, PubChem, ...)


The general resource URI is the following:
Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/link/code/all



Retrieve database name from access codes

The general resource URI is the following:
Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/link/code/2why returns "PDB"

Organisms


Retrieve organism details by name

The general resource URI is the following:
Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/organism/xml/fungi



For Json, use:

Connect your software/database with Norine!


General search using an HTML form

The general search using a form has the same goal of previous examples but allows to combine multiple criterias

Using your favorite programming language

There are differents ways to connect your software to Norine web services. For instance, you can programmatically access the provided rest services by writing your own code in any programming language. Indeed, most of them provides libraries to create HTTP requests.
The following example of code, written in Java language, simply request peptide details for ID#000123. This example use the standard Http client library provided by the Apache foundation.


Use the Smiles2Monomers tool as a web service


Getting monomeric composition and 2D graph from smiles

The general resource URI is the following:
Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/s2m/graph/COc2ccc(CCCC1NC(=O)C(OC(=O)C(C)NC(=O)C(=C)NC1(=O))C(C)C)cc2 will return the following result :

Amv,Hiv,D-Ala,dh-Ala@3,1@0,2@1,3@0,2



Retrieve all information on monomers

This allows to retrieve all information on monomers that compose the entered peptide such as the code, the complete name, the smiles of the monomer, the molecular formula and the molecular weight.The general resource URI is the following:
Example : http://bioinfo.cristal.univ-lille.fr/norine/rest/s2m/graph/json/COc2ccc(CCCC1NC(=O)C(OC(=O)C(C)NC(=O)C(=C)NC1(=O))C(C)C)cc2


[1] REST: Representational state transfer