Examples

The examples below were obtained using the InDex REST API on MetaboCloud Web Portal. The InChI Key used as input were obtained from Chemical Entities of Biological Interest (ChEBI).

• Caffeine : CHEBI:27732

Note

All examples described below are using GET type request.

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Get a file associated with a molecule

This application offers the functionality of retrieving a structure/representation file associated with a molecule in a specific community from an InChI Key of a compound, along with associated metadata returned in the HTTP response headers. It is provided by the /compounds/{inchiKey}.{format} endpoint.

Currently, only one community is available, which is chebi containing files coming from the ChEBI database.

Two types of format are available in the chebi community :

• png : to retrieve a PNG image along with its associated metadata

  X-Metadata-Chebi-Id : XXXX # The ChEBI ID
  X-Metadata-Creation-Date : YYYY-MM-DD # The date on which the MOL file was stored in the S3
  X-Metadata-Data-License : Creative Commons License (CC BY 4.0) # The MOL file license
  X-Metadata-Data-Source : Chemical Entities of Biological Interest (ChEBI) Database # The MOL file provenance
  X-Metadata-Image-Size : XXX x XXX px # The image size (in pixels)
  

• mol : to retrieve a MOL file along with its associated metadata

  X-Metadata-Chebi-Id : XXXX # The ChEBI ID
  X-Metadata-Creation-Date : YYYY-MM-DD # The date on which the MOL file was stored in the S3
  X-Metadata-Data-License : Creative Commons License (CC BY 4.0) # The MOL file license
  X-Metadata-Data-Source : Chemical Entities of Biological Interest (ChEBI) Database # The MOL file provenance
  

In addition of the two mandatory parameters inchiKey and format, three optional parameters are available :

• community (“chebi” by default) : to indicate from which community the file must be retrieved (currently, only chebi is available)

• outputType (“url” by default) : to choose the type of output wanted, either as a URL or as the resource directly (url or resource)

• size (“medium” by default) : when retrieving a PNG image only, it is for choosing the size of the image among three available. (small : 50 x 50 px, medium : 350 x 350 px or large : 700 x 700 px)

Here are some examples of output obtained after querying the /compounds/{inchiKey}.{format} application endpoint.

Retrieve a PNG image of a molecule

ChEBI

SmallMediumLarge

As ResourceAs URL

Example of the retrieval of the Caffeine small PNG image from ChEBI using its InChI Key

Request URL :

https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.png?community=chebi&size=small&outputType=resource

Output :

Body :

Headers :

HTTP/1.1 200
# Standard response headers
...

### Start custom headers with metadata related to the requested file
X-Metadata-Image-Size: 50 x 50 px
X-Metadata-Data-Source: Chemical Entities of Biological Interest (ChEBI) Database
X-Metadata-Chebi-Id: 27732
X-Metadata-Creation-Date: 2024-04-20
X-Metadata-Data-License: Creative Commons License (CC BY 4.0)
### End custom headers with metadata related to the requested file

# Standard response headers
...

Retrieve a MOL file of a molecule

ChEBI

As ResourceAs URL

Example of the retrieval of the Caffeine MOL file from ChEBI using its InChI Key

Request URL :

https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.mol?community=chebi&outputType=resource

Output :

Body :

 Marvin  02080816422D

14 15  0  0  0  0            999 V2000
  -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -0.7145    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   0.0000   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   1.4992    0.6674    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   1.4992   -0.6675    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   1.9841    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -1.4289   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   0.0001    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   0.0001   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   1.7541    1.4520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 10  1  2  0  0  0  0
  1  2  1  0  0  0  0
 14  2  1  0  0  0  0
  8  3  1  0  0  0  0
  4  3  2  0  0  0  0
  7  4  1  0  0  0  0
  1  5  1  0  0  0  0
  5  3  1  0  0  0  0
 12  5  1  0  0  0  0
  6  2  1  0  0  0  0
  6  4  1  0  0  0  0
 11  6  2  0  0  0  0
  9  7  1  0  0  0  0
 13  7  1  0  0  0  0
  9  8  2  0  0  0  0
M  END

Headers :

HTTP/1.1 200
# Standard response headers
...

### Start custom headers with metadata related to the requested file
X-Metadata-Data-Source: Chemical Entities of Biological Interest (ChEBI) Database
X-Metadata-Chebi-Id: 27732
X-Metadata-Creation-Date: 2024-04-20
X-Metadata-Data-License: Creative Commons License (CC BY 4.0)
### End custom headers with metadata related to the requested file

# Standard response headers
...