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Table 1 BSL script commands for interacting with the OpenTox platform

From: Computational toxicology using the OpenTox application programming interface and Bioclipse

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.