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

 


 

Features per Compound

Description
Method
URI
Parameter
Result
Status codes
Get available feature URIs for a compound GET  /compound/{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}/feature [subjectid]
?feature_uri="URIto 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="URIto feature" (mandatory, single feature)&value=the_value
 _ 200,400,404,503
Delete specified features from the compound DELETE /compound/{cid}/feature [subjectid]
?feature_uris[]="URIto features" (optional)
 _ 200,400,404,503

 


 

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

 

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

 

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
  • 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