Updated README

1 files changed, 123 insertions, 85 deletions

diff --git a/README.md b/README.md
index df16dce..043f001 100644
--- a/README.md
+++ b/README.md
@@ -7,82 +7,100 @@ OpenTox Algorithm
     - subgraph descriptor calculation (fminer)
     - physico-chemical descriptor calculation (pc) for more than 300 descriptors
     - feature selection (fs) using recursive feature elimination (rfe)
-- See http://opentox-ruby.maunz.de for high-level workflow documentation
+- See [opentox-ruby on maunz.de](http://opentox-ruby.maunz.de) for high-level workflow documentation
 
 REST operations
 ---------------
 
-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]
+    DESCRIPTION                  TYPE  ADDRESS           ARGUMENTS                      RETURN TYPE               RETURN CODE
+    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               -                              URIs of algorithms        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 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].
-- del_missing: one of true, false
+- *del_missing*: one of 
+    - *true*
+    - *false*
+
+- *feature\_type*: Type of subgraphs when no feature dataset is supplied, one of
+    - *trees*
+    - *paths*
+
+- *lib*: Mandatory for feature datasets that do not contain appropriate feature metadata, one of 
+    - *cdk*
+    - *openbabel*
+    - *joelib*
+
+- *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].
+
+- *nr_hits*: Whether nominal features should be instantiated with their occurrence counts in the instances. One of 
+    - *true*
+    - *false*
+
+- *pc_type*: Mandatory for feature datasets that do not contain appropriate feature metadata, one of 
+    - *geometrical*
+    - *topological* 
+    - *electronic*
+    - *constitutional*
+    - *hybrid*
+    - *cpsa*
+
+- *prediction\_algorithm*: One of 
+    - *weighted\_majority\_vote* (default for classification, n.a. for regression)
+    - *local\_svm\_classification*
+    - *local\_svm\_regression* (default for regression). 
 
 
 Supported MIME formats
@@ -96,17 +114,39 @@ Examples
 
 NOTE: http://webservices.in-silico.ch hosts the stable version that might not have complete functionality yet. **Please try http://ot-test.in-silico.ch** for latest versions.
 
+### Get the OWL-DL representation of lazar
+
+    curl http://webservices.in-silico.ch/algorithm/lazar
+
 ### Get the OWL-DL representation of fminer
 
     curl http://webservices.in-silico.ch/algorithm/fminer
 
-### Get the OWL-DL representation of lazar
+### Get the OWL-DL representation of pc
 
-    curl http://webservices.in-silico.ch/algorithm/lazar
+    curl http://webservices.in-silico.ch/algorithm/pc
+
+### Get the OWL-DL representation of fs
+
+    curl http://webservices.in-silico.ch/algorithm/fs
 
 * * * 
 
-The following creates datasets with backbone refinement class representatives or latent structure patterns, using supervised graph mining, see http://cs.maunz.de. These features can be used e.g. as structural alerts, as descriptors (fingerprints) for prediction models or for similarity calculations.
+### Create lazar model
+
+Creates a standard Lazar model with subgraph descriptors.
+
+    curl -X POST -d dataset_uri={datset_uri} -d prediction_feature={feature_uri} -d feature_generation_uri=http://webservices.in-silico.ch/algorithm/fminer/bbrc http://webservices.in-silico.ch/test/algorithm/lazar 
+
+Creates a Lazar model with physico-chemical descriptors.
+
+    curl -X POST -d dataset_uri={datset_uri} -d prediction_feature={feature_uri} -d feature_dataset_uri={feature_dataset_uri} http://webservices.in-silico.ch/test/algorithm/lazar 
+
+feature_uri specifies the dependent variable from the dataset.
+
+* * *
+
+Creates subgraph descriptors with backbone refinement class representatives or latent structure patterns, using supervised graph mining, see http://cs.maunz.de. These features can be used e.g. as structural alerts, as descriptors (fingerprints) for prediction models or for similarity calculations.
 
 ### Create the full set of frequent and significant subtrees
 
@@ -121,7 +161,7 @@ backbone=false reduces BBRC mining to frequent and correlated subtree mining (mu
 
 feature_uri specifies the dependent variable from the dataset.   
 Adding -d nr_hits=true produces frequency counts per pattern and molecule.
-Please click [here](http://bbrc.maunz.de#usage) for more guidance on usage.
+Click [here](http://bbrc.maunz.de#usage) for more guidance on usage.
 
 ### Create [LAST-PM](http://last-pm.maunz.de) descriptors, recommended for small to medium-sized datasets.
 
@@ -129,28 +169,26 @@ Please click [here](http://bbrc.maunz.de#usage) for more guidance on usage.
 
 feature_uri specifies the dependent variable from the dataset.   
 Adding -d nr_hits=true produces frequency counts per pattern and molecule.
-Please click [here](http://last-pm.maunz.de#usage) for guidance for more guidance on usage.
+Click [here](http://last-pm.maunz.de#usage) for guidance for more guidance on usage.
 
-* * * 
 
-### Create lazar model
+* * * 
 
-Creates a standard Lazar model.
+### Create a feature dataset of physico-chemical descriptors with CDK
 
-    curl -X POST -d dataset_uri={datset_uri} -d prediction_feature={feature_uri} -d feature_generation_uri=http://webservices.in-silico.ch/algorithm/fminer/bbrc http://webservices.in-silico.ch/test/algorithm/lazar 
+    curl -X POST -d dataset_uri={dataset_uri} -d lib=cdk http://webservices.in-silico.ch/test/algorithm/pc/AllDescriptors
 
-[API documentation](http://rdoc.info/github/opentox/algorithm)
---------------------------------------------------------------
+lib specifies the library to use.
 
 * * *
 
-### 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={feature_uri} -d feature_dataset_uri={feature_dataset_uri} http://webservices.in-silico.ch/test/algorithm/fs/rfe
 
-### 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
+feature_uri specifies the dependent variable from the dataset.   
 
+* * *
 
 Copyright (c) 2009-2011 Christoph Helma, Martin Guetlein, Micha Rautenberg, Andreas Maunz, David Vorgrimmler, Denis Gebele. See LICENSE for details.
+