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