OpenTox API 1.2 Compound

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Contents

Chemical compound

Component description

Provides different representations for chemical compounds with a unique and defined chemical structure.

REST operations

Description Method URI Parameters Result Status codes
Search for compounds
GET
/compound
[subjectid]
?search=value&sameas=URI_FROM_AN_ONTOLOGY
List of compounds, matching the query
200,404,503
Get the representation of a compound GET /compound/{id} [subjectid]
(optional)
?feature_uris[]="URI to features"
Compound representation in one of the supported MIME formats, if feature_uris[] provided includes features and values 200,404,503
Create a new compound POST /compound [subjectid]
Compound representation in a supported MIME format
URIs for new compounds 200,400,503
Update a compound (optional)
PUT /compound/{id} [subjectid]
Compound representation in a supported MIME format
200,400,404,503
Delete a compound (optional)
DELETE /compound/{id} [subjectid]
Delete all feature values per compound recursively?
200,400,404,503</tbody>

 

Features per Compound

Description
Method
URI
Parameter
Result
Status codes
Get available feature URIs for a compound
GET
 /compound/{cid}/feature
[subjectid]
?feature_uris[]="URI to features" (optional)
Returns representation of the features as uri-list or RDF
All available features are returned, if no parameter is specified
200,404,503
Create a new feature value
POST
/compound/{cid}/feature [subjectid]
?feature_uri="URI to feature" (mandatory, single feature)&value=the_value
URI of the compound with the new feature, e.g.
/compound/{id}?feature_uris[]=the-new-feature
200,400,503
Update a new feature value PUT
/compound/{cid}/feature [subjectid]
?feature_uri="URI to feature" (mandatory, single feature)&value=the_value


200,400,404,503
Delete specified features from the compound DELETE
/compound/{cid}/feature [subjectid]
?feature_uris[]="URI to features" (optional)

200,400,404,503</tbody>

HTTP status codes

Interpretation Nr Name
Success 200 OK
Compound not found 404 Not Found
Incorrect MIME type 400 Bad request
Service not available 503 Service unavailable</tbody>

Compound representation

Supported MIME formats

http://chemical-mime.sourceforge.net/

Mandatory:

  • chemical/x-daylight-smiles (default)
  • chemical/x-inchi
  • chemical/x-mdl-sdfile
  • chemical/x-mdl-molfile

Optional:

  • chemical/x-mol2
  • chemical/x-cml
  • other chemical formats
  • image/png
  • other image formats
  • text/plain (chemical names)
  • application/rdf+xml

Conformers (optional)

Component description

[Optional] support for multiple (e.g. 3D) structures per chemical compound (single structure by default)

REST operations

Description Method URI Parameters Result Status codes
Get available structures of a compound GET /compound/{id1}/conformer/ [subjectid] List of structure URIs
200,404,503
Create a new structure POST /compound/{id1}/conformer [subjectid]
Representation in a supported MIME format
New URI /compound/{id1}/conformer/{id2} 200,400,503
Remove all structures DELETE /compound/{id1}/conformer/ [subjectid] 200,400,404,503
Get the representation of a structure
GET /compound/{id1}/conformer/{id2} [subjectid]
?feature_uris[]="URI to features"
Representation in a supported MIME format , with feature values , if feature_uris[] provided
200,404,503
Update the representation of a structure PUT /compound/{id1}/conformer/{id2} [subjectid]
Representation in a supported MIME format
URI /compound/{id1}/conformer/{id2} 200,400,404,503
Remove a structure DELETE /compound/{id1}/conformer/{id2} 200,400,404,503</tbody>

Features per Conformer

 

Description
Method
URI
Parameter
Result
Status codes
Get available feature URIs for a compound
GET
 /compound/{cid}/conformer/{cid}/feature
[subjectid]
?feature_uris[]="URIto features" (optional)
Returns representation of the features as uri-list or RDF
All available features are returned, if no parameter is specified
200,404,503
Create a new feature value
POST
/compound/{cid}/conformer/{cid}/feature [subjectid]
?feature_uri="URIto feature" (mandatory, single feature)&value=the_value
URI of the compound with the new feature, e.g.

/compound/{id}/conformer/{cid}?feature_uris[]=the-new-feature

200,400,503
Update a new feature value PUT
/compound/{cid}/conformer/{cid}/feature [subjectid]
?feature_uri="URIto feature" (mandatory, single feature)&value=the_value


200,400,404,503
Delete specified features from the compound DELETE
/compound/{cid}/conformer/{cid}/feature [subjectid]
?feature_uris[]="URIto features" (optional)

200,400,404,503</tbody>
  • subjectid (optional) parameter that contains the OpenSSO A&A token needed to access protected services.

 

HTTP status codes

same as for Compounds

Structure representation

same as for Compounds

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