http://opentox.org/dev/apis/api-1.1 2009-11-22 martin.guetlein@gmail.com jeliazkova.nina@gmail.com OpenTox resource ontology OpenTox API OpenTox http://opentox.org/dev/apis/api-1.1/dataset /dataset/{datasetid} Original source of the dataset Provides access to chemical compounds and their features (e.g. structural, physical-chemical, biological, toxicological properties) A generic OpenTox resource name of the resource URI of the resource 1.1 TODO: Specify allowed values for model content The native format of the model content (e.g. PMML, Weka model, etc.) TODO: Introduce a link to User resource /model/{modelid} The model creator (perhaps a link to User resource) The date of model creation A validation corresponds to the validation of a model on a test dataset. The results are stored in another dataset. Parameters with default values are optional. Datetime http://opentox.org/dev/apis/api-1.1/Validation http://opentox.org/dev/apis/api-1.1/Validation#validation-report TODO: AlgorithmType, or link to Algorithm ontology 1.1 Reference TODO: statistics supported - is it possible to reuse ValidationInfo classes? /algorithm/{algorithmid} http://opentox.org/dev/apis/api-1.1/Algorithm Name of the algorithm Provides access to OpenTox algorithms encapsulates validation information /compound/{compoundid} http://opentox.org/dev/apis/api-1.1/structure 1.1 API for OpenTox compound webservices true [Optional] support for multiple (e.g. 3D) structures per chemical compound (single structure by default) /compound/{compoundid}/conformer/{conformerid} 1.1 /feature/{featureid} /dataset/{datasetid}/compound/{compoundid}?feature_uri[]=featureuris 1.1 Encapsulates a dataset entry - defined by a single Compound (or conformer) and multiple FeatureValues. Could be regarded as "Compound with features" PredictionDatasetURI A model can have one or more dependent variables, described as multiple features, specified by this relationship. Algorithms and Models can have multiple parameters http://opentox.org/api/1.1 Test dataset , used in a validation exercise http://opentox.org/api/1.1 Variables, holding the predicted values, generated by the model http://opentox.org/api/1.1 A Dataset contains multiple DataEntries. This property specifies the relationship between Dataset and DataEntry. a link to UnscrambledDataset UnscrambledDatasetURI http://opentox.org/api/1.1 A model can have multiple independent variables, described as multiple features, specified by this relationship. Links Validation with Validation Info. One validation exercise may have multiple types of validation informaton A DataEntry is defined with a single compound and multiple feature values. This property sets the relationship between a DataEntry and multiple FeatureValues http://opentox.org/api/1.1 Cancelled Running Completed Parameter value The value of a Parameter Units Units for a feature value TODO: make use of units ontology Allows to define "is a" relationships outside of particular class hierarchy Model used in a validation exercise Number incorrect Percent Correct RootMeanSquaredError YScramblingEnabled YScramblingEnabled YScramblingSeed YScramblingSeed Has 3D structure True, if the compound has 3D structure Literal Feature value A model is derived by applying an Algorithm on a training Dataset. http://opentox.org/api/1.1 http://opentox.org/api/1.1 The algorithm, used to create the Model Number correct specifies if a parameter is optional or mandatory optional mandatory Parameter scope Percentage completed http://opentox.org/api/1.1 A DataEntry is defined with a single compound and multiple feature values. This property sets the relationship between a DataEntry and a Compound Percent Incorrect MeanAbsolutError FeatureValue contains a value for specific Feature, specified by this relationship. http://opentox.org/api/1.1