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-Date
: The date on which the file was saved in storage (YYYY-MM-DD).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