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Table 1 Summary of the OpenTox API, implemented by AMBIT REST services. {service} defaults to "ambit2".

From: AMBIT RESTful web services: an implementation of the OpenTox application programming interface

1. Chemical compound http(s)://host:port/{service}/compound/{id}

GET

Retrieves a representation of the chemical compound (in Chemical MIME [32] formats or image/* formats)

PUT

Updates the chemical compound

POST

Creates a new chemical compound, returns the URI of the new chemical compound

DELETE

Deletes the chemical compound

2. Features (or properties) of chemical compounds http(s)://host:port/{service}/feature/{id}

GET

Retrieves a representation of the property (RDF representation of the ot:Feature class)

PUT

Updates the property representation

POST

Creates a new property, returns a URI of the new property

DELETE

Deletes the property

3. Datasets of chemical compounds http(s)://host:port/{service}/dataset/{id}

GET

Retrieves a representation of the dataset (RDF representation of the ot:Dataset class, or Chemical MIME formats)

PUT

Updates the dataset (adds new compounds and/or properties)

POST

Creates a new dataset (e.g. uploads a file, which is transformed into a dataset). Returns the new dataset URI, or a Task URI for long running jobs. Parameters are expected in the body of the POST command, several formats are supported via the "Content-type" HTTP header, including RDF and chemical MIME formats.

DELETE

Deletes the dataset

4. Algorithms http(s)://host:port/{service}/algorithm/{id}

GET

Retrieves a representation of the algorithm (RDF representation of the ot:Algorithm class)

POST

• Given a compound URI, or a dataset URI as input parameter, launches the processing algorithm and returns the URI of the dataset, containing the results, or returns a Task URI for long running jobs.

 

• If the algorithm is a machine learning one, given a dataset URI as input parameter, builds a new predictive model and returns the Model URI, or the Task URI.

 

• Parameters are expected in the body of the POST command, in "application/x-www-form-urlencoded" MIME format.

 

• A common required parameter is dataset_uri = http://host:port/{service}/dataset/{datasetid}, which specifies the data set to be operated on.

5. Models http(s)://host:port/{service}/model/{id}

GET

Retrieves a representation of the model (RDF representation of the ot:Model class)

POST

• Given a compound URI, or a dataset URI as input parameter, applies the predictive model, and returns the URI of the dataset, containing the predictions, or a Task URI for long running jobs.

 

• Parameters are expected in the body of POST command, in "application/x- www-form-urlencoded" MIME format.

 

• A common required parameter (in the body of the POST command is dataset_uri = http://host:port/{service}/dataset/{datasetid}, which specifies the data set to be operated on.

DELETE

Deletes the model

6. Task http(s)://host:port/{service}/task/{id}

GET

Retrieves a representation of the task (RDF representation of the ot:Task class). The task status can be one of Queued, Running, Cancelled, Error or Completed.

DELETE

Cancels the task

7.Query for compounds http(s)://host:port/{service}/query/compound/{identifier}/{results}

GET

Returns compounds, features and feature values, matching the submitted search criteria, in supported formats (dataset representation in RDF, SDF, MOL or SMILES format), according to the mime type requested by the corresponding Accept header:

 

identifier - any name, formula, registry identifier, InChI , SMILES, or predefined string "url"; if the string "url" is used, a query parameter is expected ?search=<compound url>

 

results - predefined strings: 'names', 'stdinchi', 'all', 'smiles', 'stdinchikey'

8. Ontology http(s)://host:port/ontology

GET

Submits a SPARQL query and retrieves the result in "application/sparql-results+xml" format. Requires an input parameter query = "SPARQL"

POST

Submits a SPARQL query and retrieves the result in "application/sparql-results+xml" format. Requires an input parameter query = "SPARQL" in the message body in "application/x-www-form- urlencoded" MIME format. Useful for submitting long queries that might exceed the supported URI length.

POST

Reads the RDF representation of an OpenTox object and adds it into the triple storage. Requires input parameter uri="OpenTox resource URI"

DELETE

Deletes all RDF triples that refer to a given URI. Requires an input parameter uri="OpenTox resource URI"