Provides access to OpenTox algorithms. There are several algorithm services, developed by different OpenTox partners. List of algorithms can be retrieved by HTTP GET operation at http://host:port/algorithm.

Documentation, Representation, Examples

An OpenTox Algorithm resource is an instance of class ot:Algorithm, a subclass of ot:OpentoxResource.

As it can be notices, there are multiple kinds of algorithms, some are descriptor calculation algorithms, and others provide access to different machine learning procedures or data preprocessing. The representation of algorithms is again defined by Opentox ontology, where all algorithms are subclass of ot:Algorithm.

Algorithm name is defined by dc:title (Dublin Core namespace). Parameters, supported by the algorithm are specified via object property ot:parameters and should be of class ot:Parameter (as defined in opentox.owl). These entries serve as a information what parameters are required in order to run the algorithm, the values itself should be provided by the client when initiating the calculations via POST. Algorithm types are distinguished by means of Algorithm types ontology.

Algorithm types ontology is available at http://opentox.org/data/documents/development/RDF%20files/AlgorithmTypes and provides a hierarchical classification of algorithm types. Algorithm type in RDF representation is set by direct subclassing (rdf:type) of a class from the algorithm types ontology (ota:http://www.opentox.org/algorithms.owl ) , e.g. myalgorithm rdf:type ota:Classification, Example 21.

Algorithm types ontology can be used to query algorithms of specific type, via OpenTox Ontology service

Descriptor calculation Classification Regression Expert rules Applicability domain

  • Example 1. Retrieve list of all algorithm URIs at IdeaConsult algorithm service :
    curl -H "Accept:text/uri-list" https://apps.ideaconsult.net/ambit2/algorithm
    https://apps.ideaconsult.net/ambit2/algorithm/SimpleKMeans
    https://apps.ideaconsult.net/ambit2/algorithm/J48
    https://apps.ideaconsult.net/ambit2/algorithm/RandomForest
    https://apps.ideaconsult.net/ambit2/algorithm/Functional+tree
    https://apps.ideaconsult.net/ambit2/algorithm/LibLINEAR
    https://apps.ideaconsult.net/ambit2/algorithm/IB1
    https://apps.ideaconsult.net/ambit2/algorithm/LR
    https://apps.ideaconsult.net/ambit2/algorithm/GaussianProcesses
    https://apps.ideaconsult.net/ambit2/algorithm/IsotonicRegression
    https://apps.ideaconsult.net/ambit2/algorithm/LMSLR
    https://apps.ideaconsult.net/ambit2/algorithm/LogisticRegression
    https://apps.ideaconsult.net/ambit2/algorithm/MLP
    https://apps.ideaconsult.net/ambit2/algorithm/PaceRegresion
    https://apps.ideaconsult.net/ambit2/algorithm/RBFNetwork
    https://apps.ideaconsult.net/ambit2/algorithm/SMO
    https://apps.ideaconsult.net/ambit2/algorithm/SMOreg
    https://apps.ideaconsult.net/ambit2/algorithm/VotedPerceptron
    https://apps.ideaconsult.net/ambit2/algorithm/Winnow
    https://apps.ideaconsult.net/ambit2/algorithm/Bayesian+Logistic+Regression
    https://apps.ideaconsult.net/ambit2/algorithm/DMNBtext
    https://apps.ideaconsult.net/ambit2/algorithm/NaiveBayes
    https://apps.ideaconsult.net/ambit2/algorithm/NBM
    https://apps.ideaconsult.net/ambit2/algorithm/BayesianLogisticRegression
    https://apps.ideaconsult.net/ambit2/algorithm/AODE
    https://apps.ideaconsult.net/ambit2/algorithm/HNB
    https://apps.ideaconsult.net/ambit2/algorithm/pka
    https://apps.ideaconsult.net/ambit2/algorithm/categories
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreecramer
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreecramer2
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreeverhaar
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreeverhaar2
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreeeye
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreeskinirritation
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreemic
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreeskinsens
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreesmartcyp
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreemichaelacceptors
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreecarc
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreebiodeg
    https://apps.ideaconsult.net/ambit2/algorithm/toxtreekroes
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MannholdLogPDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/ambit2.descriptors.MolecularWeight
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.CPSADescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AromaticAtomsCountDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AromaticBondsCountDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BondCountDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.RotatableBondsCountDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ChiPathDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LargestPiSystemDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.HBondAcceptorCountDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.HBondDonorCountDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.ZagrebIndexDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.APolDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorCharge
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMass
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorPolarizability
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.CarbonTypesDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.EccentricConnectivityIndexDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.FragmentComplexityDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.IPMolecularDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.KierHallSmartsDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MDEDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.PetitjeanNumberDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.PetitjeanShapeIndexDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.VAdjMaDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.WienerNumbersDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/ambit2.mopac.MopacOriginalStructure
    https://apps.ideaconsult.net/ambit2/algorithm/ambit2.dragon.DescriptorDragonShell
    https://apps.ideaconsult.net/ambit2/algorithm/ambit2.some.DescriptorSOMEShell
    https://apps.ideaconsult.net/ambit2/algorithm/ambit2.descriptors.InChI
    https://apps.ideaconsult.net/ambit2/algorithm/ambit2.descriptors.AtomTypeVerifierDescriptor
    https://apps.ideaconsult.net/ambit2/algorithm/ambit2.descriptors.KekulizationVerifier
    https://apps.ideaconsult.net/ambit2/algorithm/ambit2.mopac.MopacShell
    https://apps.ideaconsult.net/ambit2/algorithm/finder
    https://apps.ideaconsult.net/ambit2/algorithm/pcaRanges
    https://apps.ideaconsult.net/ambit2/algorithm/distanceEuclidean
    https://apps.ideaconsult.net/ambit2/algorithm/distanceCityBlock
    https://apps.ideaconsult.net/ambit2/algorithm/distanceMahalanobis
    https://apps.ideaconsult.net/ambit2/algorithm/nparamdensity
    https://apps.ideaconsult.net/ambit2/algorithm/leverage
    https://apps.ideaconsult.net/ambit2/algorithm/fptanimoto
    https://apps.ideaconsult.net/ambit2/algorithm/fpmissingfragments
    https://apps.ideaconsult.net/ambit2/algorithm/fingerprints
    https://apps.ideaconsult.net/ambit2/algorithm/atomenvironments
    https://apps.ideaconsult.net/ambit2/algorithm/structurequality
    https://apps.ideaconsult.net/ambit2/algorithm/struckeys
    https://apps.ideaconsult.net/ambit2/algorithm/smartsprop
    https://apps.ideaconsult.net/ambit2/algorithm/inchi
    https://apps.ideaconsult.net/ambit2/algorithm/mcss
    https://apps.ideaconsult.net/ambit2/algorithm/superservice
    https://apps.ideaconsult.net/ambit2/algorithm/superbuilder
    https://apps.ideaconsult.net/ambit2/algorithm/mockup
    https://apps.ideaconsult.net/ambit2/algorithm/expert
    
  • Example 3. Retrieve list of all algorithm URIs at NTUA algorithm service http://opentox.ntua.gr:8080/algorithm
    curl -H "Accept:text/uri-list" http://opentox.ntua.gr:8080/algorithm
    http://opentox.ntua.gr:8080/algorithm/fastRbfNn
    http://opentox.ntua.gr:8080/algorithm/pls
    http://opentox.ntua.gr:8080/algorithm/scaling
    http://opentox.ntua.gr:8080/algorithm/svm
    http://opentox.ntua.gr:8080/algorithm/mvh
    http://opentox.ntua.gr:8080/algorithm/leverages
    http://opentox.ntua.gr:8080/algorithm/modelBundler
    http://opentox.ntua.gr:8080/algorithm/mlr
    http://opentox.ntua.gr:8080/algorithm/consensus
    http://opentox.ntua.gr:8080/algorithm/cleanup
    
    • Example4. Retrieve a representation of a descriptor calculation algorithm https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
      curl -H "Accept:text/uri-list" https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor
      @prefix ot:      <http://www.opentox.org/api/1.1#> .
      @prefix dc:      <http://purl.org/dc/elements/1.1/> .
      @prefix ota:     <http://www.opentox.org/algorithmTypes.owl#> .
      @prefix otee:    <http://www.opentox.org/echaEndpoints.owl#> .
      @prefix bx:      <http://purl.org/net/nknouf/ns/bibtex#> .
      @prefix dcterms:  <http://purl.org/dc/terms/> .
      @prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
      @prefix bo:      <http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#> .
      @prefix bo1:     <http://ambit.sourceforge.net/descriptors.owl#> .
      @prefix owl:     <http://www.w3.org/2002/07/owl#> .
      @prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .
      @prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
      
      ot:Algorithm
            a       owl:Class .
      
      dc:description
            a       owl:AnnotationProperty .
      
      dc:date
            a       owl:AnnotationProperty .
      
      dc:publisher
            a       owl:AnnotationProperty .
      
      dc:format
            a       owl:AnnotationProperty .
      
      <https://apps.ideaconsult.net/ambit2/algorithm/org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor>
            a       ot:Algorithm , ota:DescriptorCalculation ;
            dc:publisher "https://apps.ideaconsult.net/ambit2/algorithm/"^^xsd:anyURI ;
            dc:title "XLogP"^^xsd:string ;
            bo:instanceOf bo:xlogP .
      
      dc:type
            a       owl:AnnotationProperty .
      
      ot:Parameter
            a       owl:Class .
      
      dc:title
            a       owl:AnnotationProperty .
      
      ota:DescriptorCalculation
            a       owl:Class .
      

    The algorithm resource is declared as an instance of bo:instanceOf a xlogP algorithm, declared in the BlueObelisk ontology http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#xlogP. The BlueObelisk ontology provides details of the algorithm itself, e.g. publication reference.

    The BlueObelisk ontology can be queried via Ontology service.

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Last Published: 2017-06-11.