OpenTox API
type: Ontology
date: 2009-11-22
comment: OpenTox resource ontology
creator: OpenTox

Dataset
type: Class
source: Original source of the dataset
comment: Provides access to chemical compounds and their features (e.g. structural, physical-chemical, biological, toxicological properties)
disjoint with: Feature
disjoint with: Parameter
subclass of: name of the resource
disjoint with: Model
disjoint with: FeatureValuePair

Feature
type: Class
disjoint with: Model
version info: 1.1
subclass of: name of the resource
disjoint with: FeatureValuePair
disjoint with: Parameter

name of the resource
type: Class
comment: A generic OpenTox resource
identifier: URI of the resource
version info: 1.1

Model
type: Class
version info: TODO: Specify allowed values for model content
format: The native format of the model content (e.g. PMML, Weka model, etc.)
disjoint with: Parameter
version info: TODO: Introduce a link to User resource
creator: The model creator (perhaps a link to User resource)
subclass of: name of the resource
date: The date of model creation

Validation
type: Class
comment: 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.
date: Datetime
subclass of: name of the resource

Name of the algorithm
type: Class
version info: TODO: AlgorithmType, or link to Algorithm ontology
version info: 1.1
source: Reference
version info: TODO: statistics supported - is it possible to reuse ValidationInfo classes?
disjoint with: Feature
disjoint with: Model
disjoint with: Compound
disjoint with: Dataset
subclass of: name of the resource
disjoint with: Parameter
comment: Provides access to OpenTox algorithms
disjoint with: FeatureValuePair
disjoint with: DataEntry

Compound
type: Class
disjoint with: Model
disjoint with: FeatureValuePair
subclass of: name of the resource
disjoint with: Feature
version info: 1.1
disjoint with: DataEntry
disjoint with: Parameter
disjoint with: Dataset
comment: API for OpenTox compound webservices

DataEntry
type: Class
disjoint with: Feature
disjoint with: Model
version info: 1.1
disjoint with: Parameter
comment: Encapsulates a dataset entry - defined by a single Compound (or conformer) and multiple FeatureValues. Could be regarded as "Compound with features"
disjoint with: FeatureValuePair
subclass of: name of the resource
disjoint with: Dataset

ValidationInfo
type: Class
comment: encapsulates validation information
subclass of: Validation

Conformer
type: Class
subclass of: Restriction
  on property: Has 3D structure
  has value: true
subclass of: Compound
comment: [Optional] support for multiple (e.g. 3D) structures per chemical compound (single structure by default)

Has 3D structure
type: FunctionalProperty
range: boolean
comment: True, if the compound has 3D structure
domain: Compound
type: DatatypeProperty

validationPredictionDataset
type: ObjectProperty
comment: PredictionDatasetURI
sub property of: validation
domain: Validation
range: Dataset

dependentVariables
type: ObjectProperty
comment: A model can have one or more dependent variables, described as multiple features, specified by this relationship.
domain: Model
sub property of: model
range: Feature

parameters
type: ObjectProperty
sub property of: model
range: Parameter
comment: Algorithms and Models can have multiple parameters
domain: Class
  union of: Name of the algorithm
  union of: Model

validationTestDataset
type: ObjectProperty
range: Dataset
sub property of: validation
comment: Test dataset , used in a validation exercise
domain: Validation

predictedVariables
type: ObjectProperty
range: Feature
sub property of: model
domain: Model
comment: Variables, holding the predicted values, generated by the model

dataEntry
type: ObjectProperty
range: DataEntry
domain: Dataset
comment: A Dataset contains multiple DataEntries. This property specifies the relationship between Dataset and DataEntry.

a link to UnscrambledDataset
type: ObjectProperty
domain: YScrambling
sub property of: validation
range: Dataset
comment: UnscrambledDatasetURI

independentVariables
type: ObjectProperty
domain: Model
comment: A model can have multiple independent variables, described as multiple features, specified by this relationship.
sub property of: model
range: Feature

hasValidationInfo
type: ObjectProperty
sub property of: validation
comment: Links Validation with Validation Info. One validation exercise may have multiple types of validation informaton
domain: Validation
range: ValidationInfo

values
type: ObjectProperty
range: FeatureValuePair
comment: A DataEntry is defined with a single compound and multiple feature values. This property sets the relationship between a DataEntry and multiple FeatureValues
domain: DataEntry

hasStatus
type: DatatypeProperty
range: DataRange
  one of: Cancelled
  one of: Completed
  one of: Running
domain: Task

Parameter value
type: DatatypeProperty
domain: Parameter
comment: The value of a Parameter

Units
type: DatatypeProperty
comment: Units for a feature value
version info: TODO: make use of units ontology

isA
type: TransitiveProperty
comment: Allows to define "is a" relationships outside of particular class hierarchy
type: ObjectProperty

validationModel
type: FunctionalProperty
comment: Model used in a validation exercise
sub property of: validation
range: Model
domain: Validation
type: ObjectProperty

Number incorrect
type: FunctionalProperty
domain: ClassificationStatistics
range: int
sub property of: classificationStatistics
type: DatatypeProperty

Percent Correct
type: FunctionalProperty
range: float
domain: ClassificationStatistics
sub property of: classificationStatistics
type: DatatypeProperty

rootMeanSquaredError
type: FunctionalProperty
range: float
comment: RootMeanSquaredError
type: DatatypeProperty
sub property of: regressionStatistics

YScramblingEnabled
type: FunctionalProperty
sub property of: yScramblingInfo
type: DatatypeProperty
domain: YScrambling
range: boolean
comment: YScramblingEnabled

YScramblingSeed
type: FunctionalProperty
sub property of: yScramblingInfo
range: int
comment: YScramblingSeed
type: DatatypeProperty
domain: YScrambling

Feature value
type: FunctionalProperty
type: DatatypeProperty
comment: Literal
domain: FeatureValue

trainingDataset
type: FunctionalProperty
type: ObjectProperty
domain: Model
sub property of: model
comment: A model is derived by applying an Algorithm on a training Dataset.
range: Dataset

algorithm
type: FunctionalProperty
comment: The algorithm, used to create the Model
range: Name of the algorithm
sub property of: model
domain: Model
type: ObjectProperty

Number correct
type: FunctionalProperty
range: int
sub property of: classificationStatistics
domain: ClassificationStatistics
type: DatatypeProperty

Parameter scope
type: FunctionalProperty
type: DatatypeProperty
comment: specifies if a parameter is optional or mandatory
domain: Parameter
range: DataRange
  one of: mandatory
  one of: optional

Percentage completed
type: FunctionalProperty
domain: Task
range: float
sub property of: classificationStatistics
type: DatatypeProperty

compound
type: FunctionalProperty
range: Compound
domain: DataEntry
type: ObjectProperty
comment: 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
type: FunctionalProperty
sub property of: classificationStatistics
type: DatatypeProperty
domain: ClassificationStatistics
range: float

meanAbsolutError
type: FunctionalProperty
sub property of: regressionStatistics
comment: MeanAbsolutError
range: float
type: DatatypeProperty

feature
type: FunctionalProperty
range: Feature
comment: FeatureValue contains a value for specific Feature, specified by this relationship.
domain: FeatureValuePair
type: ObjectProperty

ActivityOutcome_CPDBAS_Hamster
type: Feature
source: http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: false

DataEntry
compound: Compound
values: FeatureValue
  feature: ActivityOutcome_CPDBAS_Hamster
  Feature value: true

Hamster Carcinogenicity
type: Dataset
type: Ontology
source: http://www.epa.gov/NCCT/dsstox/sdf_cpdbas.html