OpenTox API 1.2 A&A

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(Created page with "<h2>Chemical compound</h2> <h3>Component description</h3> <p>Provides different representations for chemical compounds with a unique and defined chemical structure.</p> <h3>REST ...")
 
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<h2>Chemical compound</h2>
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<h3>Component description</h3>
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<p>Provides different representations for chemical compounds with a unique and defined chemical structure.</p>
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<h3>REST operations</h3>
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{|  class="plain"<tbody>
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| <strong>Description</strong>
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| <strong>Method</strong>
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| <strong>URI</strong>
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| <strong>Parameters</strong>
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| <strong>Result</strong>
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| <strong>Status codes</strong>
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|-
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| Search for compounds<br>
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| GET<br>
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| /compound<br>
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| <strong>[subjectid]</strong><br>?<strong>search</strong>=value&amp;<strong>sameas</strong>=URI_FROM_AN_ONTOLOGY<br>
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| List of compounds, matching the query<br>
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| 200,404,503
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|-
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|  Get the representation of a compound
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|  GET
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|  /compound/{id}
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| <strong>[subjectid]</strong><br>(optional)<br>?<strong>feature_uris[]</strong>="URI to features"
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|  Compound representation in one of the supported MIME formats, if <strong>feature_uris[]</strong> provided includes features and values
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| 200,404,503
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|-
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|  Create a new compound
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|  POST
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|  /compound
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| <strong>[subjectid]</strong><br>Compound representation in a supported MIME format<br>
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|  URIs for new compounds
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| 200,400,503
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|-
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|  Update a compound (optional)<br>
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|  PUT
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|  /compound/{id}
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| <strong>[subjectid]</strong><br>Compound representation in a supported MIME format
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|  –
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| 200,400,404,503
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|-
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|  Delete a compound (optional)<br>
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|  DELETE
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|  /compound/{id}
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| <strong>[subjectid]</strong>
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|  –<br>Delete all feature values per compound recursively?<br>
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| 200,400,404,503</tbody>
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|}<p>&nbsp;</p><h3>Features per Compound<br></h3>
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{|  class="plain"<tbody>
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| <strong>Description<br></strong>
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| <strong>Method<br></strong>
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| <strong>URI<br></strong>
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| <strong>Parameter<br></strong>
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| <strong>Result<br></strong>
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| <strong>Status codes<br></strong>
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|-
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| Get available feature URIs for a compound<br>
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| GET<br>
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| &nbsp;/compound/{cid}/feature<br>
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| <strong>[subjectid]</strong><br>?<strong>feature_uris[]</strong>="URIto features" (optional)<br>
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| Returns representation of the features as uri-list or RDF<br>All available features are returned, if no parameter is specified<br>
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| 200,404,503<br>
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|-
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| Create a new feature value<br>
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| POST<br>
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| /compound/{cid}/feature
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| <strong>[subjectid]</strong><br>?<strong>feature_uri</strong>="URIto feature" (mandatory, single feature)&amp;<strong>value</strong>=the_value
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| URI of the compound with the new feature, e.g.<br>/compound/{id}?feature_uris[]=the-new-feature<br>
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| 200,400,503
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|-
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| Update a new feature value
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| PUT<br>
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| /compound/{cid}/feature
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| <strong>[subjectid]</strong><br>?<strong>feature_uri</strong>="URIto feature" (mandatory, single feature)&amp;<strong>value</strong>=the_value<br><br>
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| <br>
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| 200,400,404,503
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|-
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| Delete specified features from the compound
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| DELETE<br>
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| /compound/{cid}/feature
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| <strong>[subjectid]</strong><br>?<strong>feature_uris[]</strong>="URIto features" (optional)
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| <br>
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| 200,400,404,503</tbody>
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|}<h3>HTTP status codes</h3>
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{|  class="plain"<tbody>
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| <strong>Interpretation</strong>
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| <strong>Nr</strong>
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| <strong>Name</strong>
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|-
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| Success
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| 200
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| OK
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|-
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| Compound not found
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| 404
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| Not Found
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|-
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| Incorrect MIME type
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| 400
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| Bad request
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|-
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| Service not available
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|  503
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|  Service unavailable</tbody>
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|}
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<h3>Compound representation</h3>
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<h4>Supported MIME formats</h4>http://chemical-mime.sourceforge.net/
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<p>Mandatory:</p><ul><li>
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chemical/x-daylight-smiles (default)<br></li><li>
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chemical/x-inchi</li><li>
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chemical/x-mdl-sdfile</li><li>
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chemical/x-mdl-molfile</li></ul><p>Optional:</p><ul><li>
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chemical/x-mol2</li><li>
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chemical/x-cml</li><li>other chemical formats</li><li>image/png</li><li>other image formats</li><li>text/plain (chemical names)</li><li>application/rdf+xml</li></ul><h2>Conformers (optional)<br></h2><h3>Component description</h3><p>[Optional] support for multiple (e.g. 3D) structures per chemical compound (single structure by default)</p><h3>REST operations <br></h3>
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{|  class="plain"<tbody>
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| <strong>Description</strong>
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| <strong>Method</strong>
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| <strong>URI</strong>
+
| <strong>Parameters</strong>
+
| <strong>Result</strong>
+
| <strong>Status codes</strong>
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|-
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|  Get available structures of a compound
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|  GET
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|  /compound/{id1}/conformer/
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| <strong>[subjectid]</strong>
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|  List of structure URIs<br>
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| 200,404,503
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|-
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|  Create a new structure
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|  POST
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|  /compound/{id1}/conformer
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| <strong>[subjectid]</strong><br>Representation in a supported MIME format
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|  New URI /compound/{id1}/conformer/{id2}
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| 200,400,503
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|-
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|  Remove all structures
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|  DELETE
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|  /compound/{id1}/conformer/
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| <strong>[subjectid]</strong>
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|  –
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| 200,400,404,503
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|-
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|  Get the representation of a structure<br>
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|  GET
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|  /compound/{id1}/conformer/{id2}
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| <strong>[subjectid]</strong><br>?<strong>feature_uris[]</strong>="URI to features"
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|  Representation in a supported MIME format , with feature values , if <strong>feature_uris</strong>[] provided<br>
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| 200,404,503
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|-
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|  Update the representation of a structure
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|  PUT
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|  /compound/{id1}/conformer/{id2}
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| <strong>[subjectid]</strong><br>Representation in a supported MIME format
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|  URI /compound/{id1}/conformer/{id2}
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| 200,400,404,503
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|-
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|  Remove a structure
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|  DELETE
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|  /compound/{id1}/conformer/{id2}
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|  –
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|  –
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| 200,400,404,503</tbody>
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|}<h3>Features per Conformer</h3><p>&nbsp;</p>
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{|  class="plain"<tbody>
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| <strong>Description<br></strong>
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| <strong>Method<br></strong>
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| <strong>URI<br></strong>
+
| <strong>Parameter<br></strong>
+
| <strong>Result<br></strong>
+
| <strong>Status codes<br></strong>
+
|-
+
| Get available feature URIs for a compound<br>
+
| GET<br>
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| &nbsp;/compound/{cid}/conformer/{cid}/feature<br>
+
| <strong>[subjectid]</strong><br>?<strong>feature_uris[]</strong>="URIto features" (optional)<br>
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| Returns representation of the features as uri-list or RDF<br>All available features are returned, if no parameter is specified<br>
+
| 200,404,503<br>
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|-
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| Create a new feature value<br>
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| POST<br>
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| /compound/{cid}/conformer/{cid}/feature
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| <strong>[subjectid]</strong><br>?<strong>feature_uri</strong>="URIto feature" (mandatory, single feature)&amp;<strong>value</strong>=the_value
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| URI of the compound with the new feature, e.g.<br>
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/compound/{id}/conformer/{cid}?feature_uris[]=the-new-feature<br>
+
| 200,400,503
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|-
+
| Update a new feature value
+
| PUT<br>
+
| /compound/{cid}/conformer/{cid}/feature
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| <strong>[subjectid]</strong><br>?<strong>feature_uri</strong>="URIto feature" (mandatory, single feature)&amp;<strong>value</strong>=the_value<br><br>
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| <br>
+
| 200,400,404,503
+
|-
+
| Delete specified features from the compound
+
| DELETE<br>
+
| /compound/{cid}/conformer/{cid}/feature
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| <strong>[subjectid]</strong><br>?<strong>feature_uris[]</strong>="URIto features" (optional)
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| <br>
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| 200,400,404,503</tbody>
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|}<ul><li><strong>subjectid</strong> (optional) parameter that contains the OpenSSO A&amp;A token needed to access protected services.</li></ul><p>&nbsp;</p><h3>HTTP status codes</h3><p>same as for Compounds</p><h3>Structure representation</h3><p>same as for Compounds</p>
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Revision as of 15:03, 29 August 2011

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