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COCONUT API Documentation ​

COCONUT API provides a variety of end points to extensively query the database and get the required details. The API documentation can be found here

  • Current Version: 2.0.0 (Open API Standard 3.1)

General Notes ​

  • All endpoints return data in application/json format
  • Authentication is required for accessing the API
  • The API uses standard HTTP response codes

Base Information ​

Authentication Endpoints ​

Login ​

POST /api/auth/login

Request Body (application/json):

json
{
  "email": "john@example.com",
  "password": "password"
}

Response:

json
{
  "access_token": "string",
  "token_type": "string"
}

INFO

The token is of Bearer type. This has to be supplied in the headers of the requests. In case you are using the swagger UI of the API, click on the Authorize button and provide the token as per the instruction.

Logout ​

GET /api/auth/logout

Response:

json
{
  "logout": "string"
}

Register ​

POST /api/auth/register

Request Body (application/json):

json
{
  "first_name": "John",
  "last_name": "Doe",
  "username": "JDoe",
  "affiliation": "JD",
  "email": "john@example.com",
  "password": "password",
  "password_confirmation": "password"
}

Response:

json
{
  "success": true,
  "message": "string",
  "token": "string"
}

Molecules Endpoints ​

Get Molecules ​

GET /api/molecules

Get every detail about the molecule at hand.

Search Molecules ​

POST /api/molecules/search

Search Molecules using various attributes. There are two tables invovled in this: molecules and properties.

Searchable fields ​

molecules

'standard_inchi', 'standard_inchi_key', 'canonical_smiles', 'sugar_free_smiles', 'identifier', 'name', 'cas', 'iupac_name', 'murko_framework', 'structural_comments', 'name_trust_level', 'annotation_level', 'variants_count', 'status', 'active', 'has_variants', 'has_stereo', 'is_tautomer', 'is_parent', 'is_placeholder'

properties

'total_atom_count', 'heavy_atom_count', 'molecular_weight', 'exact_molecular_weight', 'molecular_formula', 'alogp', 'topological_polar_surface_area', 'rotatable_bond_count', 'hydrogen_bond_acceptors', 'hydrogen_bond_donors', 'hydrogen_bond_acceptors_lipinski', 'hydrogen_bond_donors_lipinski', 'lipinski_rule_of_five_violations', 'aromatic_rings_count', 'qed_drug_likeliness', 'formal_charge', 'fractioncsp3', 'number_of_minimal_rings', 'van_der_walls_volume', 'contains_sugar', 'contains_ring_sugars', 'contains_linear_sugars', 'murcko_framework', 'np_likeness', 'chemical_class', 'chemical_sub_class', 'chemical_super_class', 'direct_parent_classification', 'np_classifier_pathway', 'np_classifier_superclass', 'np_classifier_class', 'np_classifier_is_glycoside'

Note

The fields in the molecules table can be accessed directly with their column names. The fields in the properties table are to be accessed prefixing them with the table name. Ex: properties.field-name.

Request Body Example (application/json):

json
{
  "search": {
    "scopes": [],
    "filters": [
      {
        "field": "standard_inchi",
        "operator": "=",
        "value": ""
      },
      {
        "field": "standard_inchi_key",
        "operator": "=",
        "value": ""
      },
      {
        "field": "canonical_smiles",
        "operator": "=",
        "value": ""
      },
      {
        "field": "sugar_free_smiles",
        "operator": "=",
        "value": ""
      }
    ]
  }
}

Mutate Molecules ​

POST /api/molecules/mutate

Update the molecule properties.

Note

General users cannot perform this. Special access privileges and vetting are done by the Scientific Advisory Board before anyone can be granted permission to perform this operation. For any queries, please contact: info.COCONUT@uni-jena.de

Request Body Example (application/json):

json
{
  "mutate": [
    {
      "operation": "create",
      "attributes": {
        "standard_inchi": "",
        "standard_inchi_key": "",
        "canonical_smiles": "",
        "sugar_free_smiles": "",
        "identifier": "",
        "name": "",
        "cas": "",
        "iupac_name": "",
        "murko_framework": "",
        "structural_comments": "",
        "name_trust_level": "",
        "annotation_level": "",
        "variants_count": "",
        "status": "",
        "active": "",
        "has_variants": "",
        "has_stereo": "",
        "is_tautomer": "",
        "is_parent": ""
      }
    }
  ]
}

Molecule Actions ​

POST /api/molecules/actions/{action}

Launch actions.

Collections Endpoints ​

Get Collections ​

GET /api/collections

Get details about the collections hosted on COCONUT.

Search Collections ​

POST /api/collections/search

Search Collections using various attributes.

Request Body Fields:

  • title
  • description
  • identifier
  • url

Mutate Collections ​

POST /api/collections/mutate

Update the collection details.

Note

General users cannot perform this. Special access privileges and vetting are done by the Scientific Advisory Board before anyone can be granted permission to perform this operation. For any queries, please contact: info.COCONUT@uni-jena.de

Citations Endpoints ​

Get Citations ​

GET /api/citations

Get details about the citations connected to various resources on COCONUT.

Search Citations ​

POST /api/citations/search

Search Citations using various attributes.

Search Fields:

  • doi
  • title
  • authors
  • citation_text

Mutate Citations ​

POST /api/citations/mutate

Update citation details.

Note

General users cannot perform this. Special access privileges and vetting are done by the Scientific Advisory Board before anyone can be granted permission to perform this operation. For any queries, please contact: info.COCONUT@uni-jena.de

Organisms Endpoints ​

Get Organisms ​

GET /api/organisms

Get the detials of organisms where the molecules are reported to be found in.

Search Organisms ​

POST /api/organisms/search

Search Organisms using various attributes.

Search Fields:

  • name
  • iri
  • rank
  • molecule_count

Mutate Organisms ​

POST /api/organisms/mutate

Update organism details.

Note

General users cannot perform this. Special access privileges and vetting are done by the Scientific Advisory Board before anyone can be granted permission to perform this operation. For any queries, please contact: info.COCONUT@uni-jena.de

Properties Endpoints ​

Get Properties ​

GET /api/properties

Exclusively search for molecule properties.

Search Properties ​

POST /api/properties/search

Search properties based on various attributes.

Available Fields:

  • total_atom_count
  • heavy_atom_count
  • molecular_weight
  • exact_molecular_weight
  • molecular_formula
  • alogp
  • topological_polar_surface_area
  • rotatable_bond_count
  • hydrogen_bond_acceptors
  • hydrogen_bond_donors
  • hydrogen_bond_acceptors_lipinski
  • hydrogen_bond_donors_lipinski
  • lipinski_rule_of_five_violations
  • aromatic_rings_count
  • qed_drug_likeliness
  • formal_charge
  • fractioncsp3
  • number_of_minimal_rings
  • van_der_walls_volume

Mutate Properties ​

POST /api/properties/mutate

Update molecule properties.

Note

General users cannot perform this. Special access privileges and vetting are done by the Scientific Advisory Board before anyone can be granted permission to perform this operation. For any queries, please contact: info.COCONUT@uni-jena.de