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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 121 |
1 files changed, 74 insertions, 47 deletions
@@ -3,60 +3,81 @@ OpenTox Algorithm - An [OpenTox](http://www.opentox.org) REST Webservice - Implements the OpenTox algorithm API for - - fminer - lazar + - subgraph descriptor calculation (fminer) + - physico-chemical descriptor calculation (pc) for more than 300 descriptors + - feature selection (fs) using recursive feature elimination (rfe) REST operations --------------- - Get a list of all algorithms GET / - URIs of algorithms 200 - Get a representation of the GET /fminer/ - fminer representation 200,404 - fminer algorithms - Get a representation of the GET /fminer/bbrc - bbrc representation 200,404 - bbrc algorithm - Get a representation of the GET /fminer/last - last representation 200,404 - last algorithm - Get a representation of the GET /lazar - lazar representation 200,404 - lazar algorithm - Get a representation of the GET /feature_selection - feature selection representation 200,404 - feature selection algorithms - Get a representation of the GET /feature_selection/rfe - rfe representation 200,404 - rfe algorithm - - - Create bbrc features POST /fminer/bbrc dataset_uri, URI for feature dataset 200,400,404,500 - feature_uri, - [min_frequency=5 per-mil], - [feature_type=trees], - [backbone=true], - [min_chisq_significance=0.95], - [nr_hits=false] - Create last features POST /fminer/last dataset_uri, URI for feature dataset 200,400,404,500 - feature_uri, - [min_frequency=8 %], - [feature_type=trees], - [nr_hits=false] - Create lazar model POST /lazar dataset_uri, URI for lazar model 200,400,404,500 - [prediction_feature], - [feature_generation_uri], - [prediction_algorithm], - [feature_dataset_uri], - [pc_type=null], - [nr_hits=false (class. using wt. maj. vote), true (else)], - [min_sim=0.3 (nominal), 0.4 (numeric features)] - [min_train_performance=0.1] - - Create selected features POST /feature_selection/rfe dataset_uri, URI for dataset 200,400,404,500 - prediction_feature, - feature_dataset_uri, - [del_missing=false] - - +DESCRIPTION REST ADDRESS ARGUMENTS RETURN CODES + +Get a representation of the GET /lazar - lazar representation 200,404 +lazar algorithm + +Get a list of all algorithms GET / - URIs of algorithms 200 +Get a representation of the GET /fminer/ - fminer representation 200,404 +fminer algorithms +Get a representation of the GET /fminer/bbrc - bbrc representation 200,404 +bbrc algorithm +Get a representation of the GET /fminer/last - last representation 200,404 +last algorithm + +Get a representation of the GET /pc - URIs of algorithms 200,404 +pc algorithms +Get a representation of the GET /pc/<name> - descriptor representation 200,404 +pc algorithm <name> + +Get a representation of the GET /fs - fs representation 200,404 +fs algorithms +Get a representation of the GET /fs/rfe - rfe representation 200,404 +rfe algorithm + +Create lazar model POST /lazar dataset_uri, URI for lazar model 200,400,404,500 + [prediction_feature], + [feature_generation_uri], + [feature_dataset_uri], + [prediction_algorithm], + [pc_type=null], + [lib=null], + [nr_hits=false (cl.wmv), + true (else)], + [min_sim=0.3 (nominal), 0.4 + (numeric features)], + [min_train_performance=0.1] + +Create bbrc features POST /fminer/bbrc dataset_uri, URI for feature dataset 200,400,404,500 + prediction_feature, + [min_frequency=5 per-mil], + [feature_type=trees], + [backbone=true], + [min_chisq_significance=0.95], + [nr_hits=false] +Create last features POST /fminer/last dataset_uri, URI for feature dataset 200,400,404,500 + prediction_feature, + [min_frequency=8 %], + [feature_type=trees], + [nr_hits=false] + +Create features POST /pc/AllDescriptors dataset_uri, URI for dataset 200,400,404,500 + [pc_type=constitutional, + topological,geometrical, + electronic,cpsa,hybrid], + [lib=cdk,joelib,openbabel] + +Create feature POST /pc/<name> dataset_uri URI for dataset 200,400,404,500 + +Select features POST /fs/rfe dataset_uri, URI for dataset 200,400,404,500 + prediction_feature, + feature_dataset_uri, + [del_missing=false] Synopsis -------- - prediction\_algorithm: One of "weighted\_majority\_vote" (default for classification), "local\_svm\_classification", "local\_svm\_regression" (default for regression). "weighted\_majority\_vote" is not applicable for regression. -- pc_type: Mandatory for feature dataset, one of [geometrical, topological, electronic, constitutional, hybrid, cpsa]. +- pc_type: Mandatory for feature datasets that do not contain appropriate feature metadata, one of [geometrical, topological, electronic, constitutional, hybrid, cpsa]. +- lib: Mandatory for feature datasets that do not contain appropriate feature metadata, one of [cdk, openbabel, joelib]. - nr_hits: Whether nominal features should be instantiated with their occurrence counts in the instances. One of "true", "false". - min_sim: The minimum similarity threshold for neighbors. Numeric value in [0,1]. - min_train_performance. The minimum training performance for "local\_svm\_classification" (Accuracy) and "local\_svm\_regression" (R-squared). Numeric value in [0,1]. @@ -124,7 +145,13 @@ Creates a standard Lazar model. * * * -### Create a feature dataset of selected features - curl -X POST -d dataset_uri={dataset_uri} -d prediction_feature_uri={prediction_feature_uri} -d feature_dataset_uri={feature_dataset_uri} -d del_missing=true http://webservices.in-silico.ch/test/algorithm/feature_selection/rfe +### Create a feature dataset of physico-chemical descriptors with CDK + curl -X POST -d dataset_uri={dataset_uri} -d lib=cdk http://webservices.in-silico.ch/test/algorithm/pc/AllDescriptors + +* * * + +### Select features from a feature dataset + curl -X POST -d dataset_uri={dataset_uri} -d prediction_feature_uri={prediction_feature_uri} -d feature_dataset_uri={feature_dataset_uri} http://webservices.in-silico.ch/test/algorithm/fs/rfe + Copyright (c) 2009-2011 Christoph Helma, Martin Guetlein, Micha Rautenberg, Andreas Maunz, David Vorgrimmler, Denis Gebele. See LICENSE for details. |