The AMBIT Project

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

http://opentox.org/dev/apis/api-1.1/structure

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.

OpenTox API : Algorithm