Overview

InDex is a REST API developed from scratch, meaning that it is not based on a pre-existing tool. It enables the retrieval of molecule structure/representation files from a custom S3 storage containing data from different communities. It was developed to be used as a microservice.

Currently, there is only one community available :

  • chebi : which provides two types of files from the Chemical Entities of Biological Interest (ChEBI) database.

    • PNG image : a visual representation of the molecule.

    • MOL file : a chemical structure file format used to describe the structure of a molecule.

Additionally, this application returns metadata in the response headers for each retrieved file :

  • Common metadata :

    • X-Metadata-Creation-DateThe date on which the file was saved in storage (YYYY-MM-DD).

      It enables to know when the file becomes outdated. A file is consider as expired if it is older than 1 month from its creation date.

    • X-Metadata-Data-License : The license of the file.

    • X-Metadata-Data-Source : The source of the file.

  • For the chebi community only :

    • X-Metadata-Chebi-Id : The ChEBI ID associated with the file.

  • For the png format only :

    • X-Metadata-Image-Size : The image size in pixels (XXX x XXX px).

This allows to get additional information about the retrieved file.

Example

To fetch the PNG image of the Caffeine molecule with its InChI Key RYYVLZVUVIJVGH-UHFFFAOYSA-N from the chebi community in medium size as a resource :

Request :

GET /compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.png?community=chebi&size=medium&outputType=resource

Response :

  • If the file is found, the response will contain the PNG image as a resource with metadata in the response headers.

  • If not found, a 404 Not Found error will be returned.

Metadata in Response Headers :

X-Metadata-Chebi-Id: 90
X-Metadata-Creation-Date: 2024-08-26
X-Metadata-Data-License: Creative Commons License (CC BY 4.0)
X-Metadata-Data-Source: Chemical Entities of Biological Interest (ChEBI) Database
X-Metadata-Image-Size: 350 x 350 px

Other examples are available in the Examples page.

Installation

This application cannot be run locally on a machine as private configurations are required to set up the S3 Storage linked to this REST API. It can only be used via the MetaboCloud Portal. See the section below for more information.

Web usage

You can use it directly from the MetaboCloud Web Portal by querying it at the following domain : https://metabocloud.mesocentre.uca.fr/index/

See the Swagger documentation below for details of the endpoints available.

Documentation

You can find information on the use of this REST API :

  • Here on this documentation, for generic information about the API and some examples of use.

  • On the Swagger documentation, for the information about the different endpoints available, such as accepted requests, required parameters, possible responses, as well as examples.

References

N/A