Interactive predictive toxicology with Bioclipse and OpenTox - Open Source Software in Life Science Research - page 30

Bioclipse-OpenTox functionality from the Graphical
User Interface is also available from the scripting
environment ( Continued )

Table 2.1

Data exchange ( Continued )
addMolecules(dataset, molecules) Adds a list of molecules to an existing

data set.

deleteDataset(dataset) Deletes a data set.

downloadCompoundAsMDLMolfi le
(service, dataset, molecule)

Downloads a molecule from a data set
as a MDL molfi le.

downloadDataSetAsMDLSDfi le
(service, dataset, fi lename)

Downloads a complete data set as MDL
SD fi le and save it to a local fi le in the
Bioclipse workspace.

listCompounds(service, dataset) Lists the molecules in a data set.

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.