######## 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_ .. _MetaboCloud Web Portal: https://metabocloud.mesocentre.uca.fr/ .. _Chemical Entities of Biological Interest (ChEBI): https://www.ebi.ac.uk/chebi/ .. _CHEBI:27732: https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:27732 .. note:: All examples described below are using `GET` type request. !!!! 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. .. _/compounds/{inchiKey}.{format}: https://metabocloud.mesocentre.uca.fr/index/api/swagger-ui/index.html#/InDex/getFile 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 .. code-block:: 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 .. code-block:: 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 ---------------------------------- .. tabs:: .. tab:: ChEBI .. tabs:: .. tab:: Small .. tabs:: .. tab:: As Resource *Example of the retrieval of the Caffeine small PNG image from ChEBI using its InChI Key* **Request URL :** .. code-block:: https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.png?community=chebi&size=small&outputType=resource **Output :** *Body :* .. image:: https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.png?community=chebi&size=small&outputType=resource :alt: PNG representation of the Caffeine :align: center *Headers :* .. code-block:: 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 ... .. tab:: As URL *Example of the retrieval of the Caffeine small PNG image from ChEBI using its InChI Key as an URL* **Request URL :** .. code-block:: https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.png?community=chebi&size=small&outputType=url **Output :** *Body :* .. code-block:: https://unh-metabocloud-resources.s3.mesocentre.uca.fr/png/chebi/small/RYYVLZVUVIJVGH-UHFFFAOYSA-N_50.png *Headers :* .. code-block:: 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 ... .. tab:: Medium .. tabs:: .. tab:: As Resource *Example of the retrieval of the Caffeine medium PNG image from ChEBI using its InChI Key* **Request URL :** .. code-block:: https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.png?community=chebi&size=medium&outputType=resource **Output :** *Body :* .. image:: https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.png?community=chebi&size=medium&outputType=resource :alt: PNG representation of the Caffeine :align: center *Headers :* .. code-block:: HTTP/1.1 200 # Standard response headers ... ### Start custom headers with metadata related to the requested file X-Metadata-Image-Size: 350 x 350 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 ... .. tab:: As URL *Example of the retrieval of the Caffeine medium PNG image from ChEBI using its InChI Key as an URL* **Request URL :** .. code-block:: https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.png?community=chebi&size=medium&outputType=url **Output :** *Body :* .. code-block:: https://unh-metabocloud-resources.s3.mesocentre.uca.fr/png/chebi/medium/RYYVLZVUVIJVGH-UHFFFAOYSA-N_350.png *Headers :* .. code-block:: HTTP/1.1 200 # Standard response headers ... ### Start custom headers with metadata related to the requested file X-Metadata-Image-Size: 350 x 350 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 ... .. tab:: Large .. tabs:: .. tab:: As Resource *Example of the retrieval of the Caffeine large PNG image from ChEBI using its InChI Key* **Request URL :** .. code-block:: https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.png?community=chebi&size=large&outputType=resource **Output :** *Body :* .. image:: https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.png?community=chebi&size=large&outputType=resource :alt: PNG representation of the Caffeine :align: center *Headers :* .. code-block:: HTTP/1.1 200 # Standard response headers ... ### Start custom headers with metadata related to the requested file X-Metadata-Image-Size: 700 x 700 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 ... .. tab:: As URL *Example of the retrieval of the Caffeine large PNG image from ChEBI using its InChI Key as an URL* **Request URL :** .. code-block:: https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.png?community=chebi&size=large&outputType=url **Output :** *Body :* .. code-block:: https://unh-metabocloud-resources.s3.mesocentre.uca.fr/png/chebi/large/RYYVLZVUVIJVGH-UHFFFAOYSA-N_700.png *Headers :* .. code-block:: HTTP/1.1 200 # Standard response headers ... ### Start custom headers with metadata related to the requested file X-Metadata-Image-Size: 700 x 700 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 ---------------------------------- .. tabs:: .. tab:: ChEBI .. tabs:: .. tab:: As Resource *Example of the retrieval of the Caffeine MOL file from ChEBI using its InChI Key* **Request URL :** .. code-block:: https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.mol?community=chebi&outputType=resource **Output :** *Body :* .. code-block:: 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 :* .. code-block:: 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 ... .. tab:: As URL *Example of the retrieval of the Caffeine MOL file from ChEBI using its InChI Key as an URL* **Request URL :** .. code-block:: https://metabocloud.mesocentre.uca.fr/index/compounds/RYYVLZVUVIJVGH-UHFFFAOYSA-N.mol?community=chebi&outputType=url **Output :** *Body :* .. code-block:: https://unh-metabocloud-resources.s3.mesocentre.uca.fr/mol/chebi/RYYVLZVUVIJVGH-UHFFFAOYSA-N.mol *Headers :* .. code-block:: 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 ...