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AlgorithmProvides access to OpenTox algorithms REST operations
Notes:
Algorithm representation
ParametersInput parameters:
Algorithm typesAlgorithm types are defined in algorithm types ontology http://www.opentox.org/algorithms.owlData cleanup algorithms. Algorithm, which is a subclass of http://www.opentox.org/algorithms.owl#DataCleanup
Feature selection algorithms , subclass of http://www.opentox.org/algorithmTypes.owl#FeatureSelection
Sample curl calls for descriptor selection: Select the 40 most informative descriptors (according to Information Gain) from dataset http://apps.ideaconsult.net:8080/ambit2/dataset/1037: curl -X POST -d "dataset_uri=http://apps.ideaconsult.net:8080/ambit2/dataset/1037" -d "prediction_feature=http://apps.ideaconsult.net:8080/ambit2/feature/26701" \ -d 'numToSelect=40' http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/InfoGainAttributeEval
Supervised learning algorithms , subclass of http://www.opentox.org/algorithmTypes.owl#Supervied
Sample curl calls for learning models: Learn a dicision tree model: curl -X POST -d 'dataset_uri=http://apps.ideaconsult.net:8080/ambit2/dataset/1037' -d 'prediction_feature=http://apps.ideaconsult.net:8080/ambit2/feature/26701' \ -d 'dataset_service=http://apps.ideaconsult.net:8080/ambit2/dataset' http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/J48 Available options of J48 can be found at: http://opentox.informatik.tu-muenchen.de/trac/TUMOpenTox/wiki/j48. Learn a model with the k nearest neighbor algorithm (k=5): curl -X POST -d 'dataset_uri=http://apps.ideaconsult.net:8080/ambit2/dataset/1037' -d 'prediction_feature=http://apps.ideaconsult.net:8080/ambit2/feature/26701' \ -d 'dataset_service=http://apps.ideaconsult.net:8080/ambit2/dataset' -d 'KNN=5' \ http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/kNNclassification
Descriptor calculation algorithms subclass of http://www.opentox.org/algorithmTypes.owl#DescriptorCalculation
Sample curl calls for calculating descriptors: Calculate all CDK feature: curl -X POST -d 'dataset_uri=http://apps.ideaconsult.net:8080/ambit2/dataset/662?feature_uris[]=http://apps.ideaconsult.net:8080/ambit2/feature/26701' \ -d 'dataset_service=http://apps.ideaconsult.net:8080/ambit2/dataset' http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/CDKPhysChem Calculate WienerNumbers using CDK: curl -X POST -d 'dataset_uri=http://apps.ideaconsult.net:8080/ambit2/dataset/662?feature_uris[]=http://apps.ideaconsult.net:8080/ambit2/feature/26701' \ -d 'WienerNumbersDescriptor=true' -d 'ALL=false' -d 'dataset_service=http://apps.ideaconsult.net:8080/ambit2/dataset' \ http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/CDKPhysChem Available descriptors can be found here: http://opentox.informatik.tu-muenchen.de/trac/TUMOpenTox/wiki/CDKPhysChem Calculate structural descriptors with FreeTreeMiner with a minimum support of 80%: curl -X POST -d 'dataset_uri=http://apps.ideaconsult.net:8080/ambit2/dataset/662?feature_uris[]=http://apps.ideaconsult.net:8080/ambit2/feature/26701' \ -d 'dataset_service=http://apps.ideaconsult.net:8080/ambit2/dataset' -d 'minSup=0.8' http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/FTM An Algorithm service shall provide separate URLs for algorithms with default (or without) parameters and for algorithms with specific parameter values. The second type of algorithm URLs are created on the fly, when an algorithm with specific parameters or a dataset is invoked. For example, when calculating descriptors, depending on the http://dataset.service.eu/dataset/6 and a set of parameters, the calculation service creates the following feature: <ot:feature> <ot:NumericFeature rdf:about="http://dataset.service.eu/feature/1"> <dc:creator>Name of creator</dc:creator> <ot:hasSource rdf:resource="http://algorithm.service.org/algorithm/FTM1/C"/> <owl:sameAs rdf:resource="http://www.opentox.org/api/1.2#TUM_FTM_C"/> <ot:units>count</ot:units> <dc:title>TUM_FTM_C</dc:title> <rdf:type rdf:resource="http://www.opentox.org/api/1.2#Feature"/> </ot:NumericFeature> </ot:feature>and internally the algorithm service creates a new algorithm entry: http://algorithm.service.org/algorithm/FTM1/Cwith a representation like below: <ot:Algorithm rdf:about="http://algorithm.service.org/algorithm/FTM1"> <ot:parameters> <ot:Parameter> <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">minSup</dc:title> <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string"> Specifies the min support for mining (fraction). Is to be between 0 and 1</dc:description> <ot:paramScope rdf:datatype="http://www.w3.org/2001/XMLSchema#string">optional</ot:paramScope> <ot:paramValue rdf:datatype="http://www.w3.org/2001/XMLSchema#int">0.8</ot:paramValue> </ot:Parameter> </ot:parameters> <owl:sameAs>http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#subtree</owl:sameAs> <dc:contributor>contributor.name@domain.org</dc:contributor> <ot:parameters> <ot:Parameter> <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dataset_service</dc:title> <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">URI to the dataset service to be used</dc:description> <ot:paramScope rdf:datatype="http://www.w3.org/2001/XMLSchema#string">optional</ot:paramScope> <ot:paramValue rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></ot:paramValue> </ot:Parameter> </ot:parameters> <ot:isA>http://www.opentox.org/algorithms.owl#DescriptorCalculation</ot:isA> <ot:parameters> <ot:Parameter> <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">dataset_uri</dc:title> <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">URI to the dataset to be used</dc:description> <ot:paramScope rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mandatory</ot:paramScope> <ot:paramValue rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://dataset.service.eu/dataset/6</ot:paramValue> </ot:Parameter> </ot:parameters> <ot:parameters> <ot:Parameter> <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">hydrogen</dc:title> <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Include hydrogen atoms. </dc:description> <ot:paramScope rdf:datatype="http://www.w3.org/2001/XMLSchema#string">optional</ot:paramScope> <ot:paramValue rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">false</ot:paramValue> </ot:Parameter> </ot:parameters> <ot:isA>http://www.opentox.org/algorithms.owl#PatternMining</ot:isA> <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OpenTox REST interface to the FTM algorithm implementation of TUM.</dc:description> <dc:contributor>contributor.name@domain.org</dc:contributor> <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FreeTreeMiner </dc:title> <dc:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://algorithm.service.org/algorithm/FTM1</dc:identifier> <dc:creator>creator.name@domain.org</dc:creator> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">Tue Jun 22 16:14:24 CEST 2010</dc:date> </ot:Algorithm>
Return results:
Supported MIME typesMandatory:
Optional:
HTTP status codes
Background:This is a generic interface for OpenTox algorithms. As algorithms can be used for a wide variety of purposes (e.g. model building, feature calculation, feature selection, similarity calculation, substructure matching), required and optional input parameters and algorithm results (e.g. model or dataset URIs, literal values) have to be specified in the algorithm representation together with a definition of the algorithm.
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