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API-Definition =================================================================== see http://opentox.org/dev/apis/api-1.1/Validation API-Examples Validation =================================================================== how to ------------------------------------------------------------------- the examples listed below can be performed with the command line tool curl get list of available validations ------------------------------------------------------------------- >>> curl http://opentox.informatik.uni-freiburg.de/validation result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/1 <<< http://opentox.informatik.uni-freiburg.de/validation/validation_id_i <<< http://opentox.informatik.uni-freiburg.de/validation/validation_id_j get validation ------------------------------------------------------------------- >>> curl http://opentox.informatik.uni-freiburg.de/validation/1 supported accept-headers: "text/x-yaml" and "application/rdf+xml" validate model on test-dateset ------------------------------------------------------------------- >>> curl -X POST -d model_uri="http://opentox.informatik.uni-freiburg.de/model/1" \ -d test_dataset_uri="http://opentox.informatik.uni-freiburg.de/dataset/3" \ -d test_target_dataset_uri="http://opentox.informatik.uni-freiburg.de/dataset/1" \ http://opentox.informatik.uni-freiburg.de/validation/test_set_validation optional params: test_target_dataset_uri, default is test_dataset_uri result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/id_i validate an algorithm on a training- and test-dataset ------------------------------------------------------------------- >>> curl -X POST -d algorithm_uri="http://opentox.informatik.uni-freiburg.de/algorithm/lazar" \ -d training_dataset_uri="http://opentox.informatik.uni-freiburg.de/dataset/2" \ -d test_dataset_uri="http://opentox.informatik.uni-freiburg.de/dataset/3" \ -d test_target_dataset_uri="http://opentox.informatik.uni-freiburg.de/dataset/1" \ -d prediction_feature="http://opentox.informatik.uni-freiburg.de/dataset/1/feature/Hamster%2520Carcinogenicity" \ -d algorithm_params="feature_generation_uri=http://opentox.informatik.uni-freiburg.de/algorithm/fminer/bbrc" \ http://opentox.informatik.uni-freiburg.de/validation/training_test_validation optional params: algorithm_params, default is empty test_target_dataset_uri, default is test_dataset_uri result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/id_i validate an algorithm on a dataset via training-test-split ------------------------------------------------------------------- >>> curl -X POST -d algorithm_uri="http://opentox.informatik.uni-freiburg.de/algorithm/lazar" \ -d dataset_uri="http://opentox.informatik.uni-freiburg.de/dataset/1" \ -d prediction_feature="http://opentox.informatik.uni-freiburg.de/dataset/1/feature/Hamster%2520Carcinogenicity" \ -d algorithm_params="feature_generation_uri=http://opentox.informatik.uni-freiburg.de/algorithm/fminer/bbrc" \ -d split_ratio=0.9 \ -d random_seed=2 \ http://opentox.informatik.uni-freiburg.de/validation/training_test_split optional params: algorithm_params, default is empty split_ratio, default is 0.67 random_seed, default is 1 result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/id_i validate an algorithm on a dataset via bootstrapping ------------------------------------------------------------------- >>> curl -X POST -d algorithm_uri="http://opentox.informatik.uni-freiburg.de/algorithm/lazar" \ -d dataset_uri="http://opentox.informatik.uni-freiburg.de/dataset/1" \ -d prediction_feature="http://opentox.informatik.uni-freiburg.de/dataset/1/feature/Hamster%2520Carcinogenicity" \ -d algorithm_params="feature_generation_uri=http://opentox.informatik.uni-freiburg.de/algorithm/fminer/bbrc" \ -d random_seed=2 \ http://opentox.informatik.uni-freiburg.de/validation/bootstrapping optional params: algorithm_params, default is empty random_seed, default is 1 result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/id_i get list of available crossvalidations ------------------------------------------------------------------- >>> curl http://opentox.informatik.uni-freiburg.de/validation/crossvalidation result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/crossvalidation/1 <<< http://opentox.informatik.uni-freiburg.de/validation/crossvalidation/crossvalidation_id_i <<< http://opentox.informatik.uni-freiburg.de/validation/crossvalidation/crossvalidation_id_j get crossvalidation ------------------------------------------------------------------- >>> curl http://opentox.informatik.uni-freiburg.de/validation/crossvalidation/1 supported accept-headers: "text/x-yaml" and "application/rdf+xml" validate an algorithm on a dataset via crossvalidation (may take a couple of minutes) ------------------------------------------------------------------- >>> curl -X POST -d algorithm_uri="http://opentox.informatik.uni-freiburg.de/algorithm/lazar" \ -d dataset_uri="http://opentox.informatik.uni-freiburg.de/dataset/1" \ -d prediction_feature="http://opentox.informatik.uni-freiburg.de/dataset/1/feature/Hamster%2520Carcinogenicity" \ -d algorithm_params="feature_generation_uri=http://opentox.informatik.uni-freiburg.de/algorithm/fminer/bbrc" \ -d num_folds=5 \ -d random_seed=2 \ -d stratified=false \ http://opentox.informatik.uni-freiburg.de/validation/crossvalidation optional params: algorithm_params, default is empty num_folds, default is 10 random_seed, default is 1 stratified, default is false result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/crossvalidation/id_i API-Examples Reports =================================================================== get list of available report types ------------------------------------------------------------------- >>> curl http://opentox.informatik.uni-freiburg.de/validation/report result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/report/validation <<< http://opentox.informatik.uni-freiburg.de/validation/report/crossvalidation <<< http://opentox.informatik.uni-freiburg.de/validation/report/algorithm_comparison get list of available reports of type validation ------------------------------------------------------------------- >>> curl http://opentox.informatik.uni-freiburg.de/validation/report/validation result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/report/validation/1 <<< http://opentox.informatik.uni-freiburg.de/validation/report/validation/id_i <<< http://opentox.informatik.uni-freiburg.de/validation/report/validation/id_j get validation report ------------------------------------------------------------------- >>> curl http://opentox.informatik.uni-freiburg.de/validation/report/validation/1 Supported formats (accept-headers): * "text/xml" content of report in docbook-article format * "text/html" report formated with default docbook-article-xsl * "text/x-yaml" returns report object with meta-info (without the actual report content) * "application/rdf+xml" returns report object with meta-info (without the actual report content) Hint: Visit http://opentox.informatik.uni-freiburg.de/validation/report/validation/1 with a browser to see the report in html format create validation report from validation ------------------------------------------------------------------- >>> curl -X POST -d validation_uris="http://opentox.informatik.uni-freiburg.de/validation/1" \ http://opentox.informatik.uni-freiburg.de/validation/report/validation result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/report/validation/id_i get list of available reports of type crossvalidation ------------------------------------------------------------------- >>> curl http://opentox.informatik.uni-freiburg.de/validation/report/crossvalidation result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/report/crossvalidation/2 <<< http://opentox.informatik.uni-freiburg.de/validation/report/crossvalidation/id_i <<< http://opentox.informatik.uni-freiburg.de/validation/report/crossvalidation/id_j get crossvalidation report ------------------------------------------------------------------- >>> curl http://opentox.informatik.uni-freiburg.de/validation/report/crossvalidation/2 Supported formats (accept-headers): * "text/xml" content of report in docbook-article format * "text/html" report formated with default docbook-article-xsl * "text/x-yaml" returns report object with meta-info (without the actual report content) * "application/rdf+xml" returns report object with meta-info (without the actual report content) Hint: Visit http://opentox.informatik.uni-freiburg.de/validation/report/crossvalidation/2 with a browser to see the report in html format create crossvalidation report from crossvalidation ------------------------------------------------------------------- >>> curl -X POST -d validation_uris="http://opentox.informatik.uni-freiburg.de/validation/crossvalidation/1" \ http://opentox.informatik.uni-freiburg.de/validation/report/crossvalidation result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/report/crossvalidation/id_i manually format html report ------------------------------------------------------------------- >>> curl -X POST -d css_style_sheet=http://apps.ideaconsult.net:8080/ToxPredict/style/global.css \ http://opentox.informatik.uni-freiburg.de/validation/report/crossvalidation/2/format_html This explicity invokes the report convertion to html, with css-style-sheet as parameter. result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/report/crossvalidation/id_i Filter resources =================================================================== It is possible to filter the list of available resources (i.e. validations, crossvalidation, reports) according to property-values. filter available validations for a particular training dataset and model ------------------------------------------------------------------- >>> curl http://opentox.informatik.uni-freiburg.de/validation?trainingDataset=http://opentox.informatik.uni-freiburg.de/dataset/2\&model=http://opentox.informatik.uni-freiburg.de/model/1 alternatively, use property names in (internal) yaml format: >>> curl http://opentox.informatik.uni-freiburg.de/validation?training_dataset_uri=http://opentox.informatik.uni-freiburg.de/dataset/2\&model_uri=http://opentox.informatik.uni-freiburg.de/model/1 search available validation report for a particular algorithm ------------------------------------------------------------------- >>> curl http://opentox.informatik.uni-freiburg.de/validation/report/validation?algorithm=lazar alternatively, use property names in (internal) yaml format: >>> curl http://opentox.informatik.uni-freiburg.de/validation/report/validation?algorithm_uris=lazar Reach reporting =================================================================== get list of available qmrf report ------------------------------------------------------------------- >>> curl http://opentox.informatik.uni-freiburg.de/validation/reach_report/qmrf result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/reach_report/qmrf/1 <<< http://opentox.informatik.uni-freiburg.de/validation/reach_report/qmrf/report_id_i <<< http://opentox.informatik.uni-freiburg.de/validation/reach_report/qmrf/report_id_j create a QMRF from a model ------------------------------------------------------------------- >>> curl -X POST -d model_uri="http://opentox.informatik.uni-freiburg.de/model/1" \ http://opentox.informatik.uni-freiburg.de/validation/reach_report/qmrf result example (accept-header: application/rdf+xml) <<< not yet supported result example (accept-header: text/uri-list) <<< http://opentox.informatik.uni-freiburg.de/validation/reach_report/qmrf/id