OpenTox API 1.2

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Revision as of 11:07, 29 August 2011

API 1.2

Interface specifications for OpenTox services (Version 1.2).

Common specifications for all APIs

OpenTox components are webservices with a REST (http://en.wikipedia.org/wiki/Representational_State_Transfer) interface. Parameters

Parameters are posted with a "Content-Type:application/x-www-form-urlencoded" HTTP header. Parameter names are typed in bold letters in the API definitions. Square brackets (e.g. compound_uris[]) indicate that a list of arguments is expected.

Ampersands in URI attribute values (e.g. dataset_uri="/dataset/abc?feature_uri=/feature/x&feature_uri=/feature/z") should be escaped, as explained in http://www.w3.org/TR/html401/appendix/notes.html#ampersands-in-uris

For curl POST requests the -d/--data option should be used to ensure the content type. See [[1]] for more information on the -d parameter.

subjectid is a (optional) parameter that contains the OpenSSO A&A token needed to access protected services.

Examples:

curl -X GET http://{server}/dataset?compound_uris[]={compound_uri1}&compound_uris[]={compound_uri2})

curl -X POST -d 'dataset_uri=http://{server}/dataset/5' http://{server}/algorithm/xxx

Request and submit formats

The default OpenTox format is RDF/XML (with exception of the compound API), but service developers may support additional formats. You can request them, by specifying the MIME type in the "Accept" and "Content-Type" HTTP headers.

If the service cannot serve the requested format, the default format (usually RDF/XML) will be returned. Examples:

Request a compound in SDF format:

curl -X GET -H "Accept:chemical/x-mdl-sdfile" http://{server}/compound/{id}

Submit a compound in InChI format:

curl -X POST -H "Content-Type:chemical/x-inchi" --data-binary "InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2" http://{server}/compound

Create a new dataset:

curl -X POST -H "Content-Type:application/rdf+xml" --data-binary@my_data_file.rdf http://{server}/dataset

File uploads

Files can be uploaded by specifying "multipart/form-data" in the Content-Type header. Bug reports and feature requests

Please use our Issue tracker to report problems with the current API. You can also discuss the APIs on the developers mailing list.