Table 1

BSL script commands for interacting with the OpenTox platform

Command(parameters)

Description

Querying

listModels(service)

Lists the predictive models available from the given service.

getFeatureInfo(ontologyServer, feature)

Returns information about a particular molecular feature (property).

getFeatureInfo(ontologyServer, features)

Returns information about a set of molecular features.

getModelInfo(ontologyServer, model)

Returns information for a computational model.

getModelInfo(ontologyServer, models)

Returns information for a list of computational models.

getAlgorithmInfo(ontologyServer, algorithm)

Returns information for a computational algorithm.

getAlgorithmInfo(ontologyServer, algorithms)

Returns information for a list of computational algorithms.

listAlgorithms(ontologyServer)

Returns a list of algorithms.

listDescriptors(ontologyServer)

Returns a list of descriptor algorithms.

listDataSets(service)

Returns the data sets available at the given OpenTox server.

searchDataSets(ontologyServer, query)

Returns matching data sets using a free text search.

search(service, inchi)

Returns matching structures based on the InChI given.

search(service, molecule)

Returns matching structures based on the molecule given.

Computation

calculateDescriptor(service, descriptor, molecules)

Calculates a descriptor value for a set of molecules.

calculateDescriptor(service, descriptor, molecule)

Calculates a descriptor value for a single molecule.

predictWithModel(service, model, molecules)

Predicts modeled properties for the given list of molecules.

predictWithModel(service, model, molecule)

Predicts modeled properties for the given molecule.

Data exchange

createDataset(service)

Creates a new data set on an OpenTox server.

createDataset(service, molecules)

Creates a new data set on an OpenTox server and adds the given molecules.

createDataset(service, molecule)

Creates a new data set on an OpenTox server and adds a single molecule.

addMolecule(dataset, mol)

Adds a molecule to an existing data set.

addMolecules(dataset, molecules)

Adds a list of molecules to an existing data set.

deleteDataset(dataset)

Deletes a data set.

downloadCompoundAsMDLMolfile(service, dataset, molecule)

Downloads a molecule from a data set as a MDL molfile.

downloadDataSetAsMDLSDfile(service, dataset, file-name)

Download a complete data set as MDL SD file and saves it to a local file in the Bioclipse workspace.

listCompounds(service, dataset)

Lists the molecules in a data set.

Authentication

login(accountname, password)

Authenticate the user with OpenSSO and login on the OpenTox network.

logout()

Logout from the OpenTox network.

getToken()

Returns a security token when Bioclipse is logged in on the OpenTox network.

Willighagen et al. BMC Research Notes 2011 4:487   doi:10.1186/1756-0500-4-487