Merge branch 'release/v1.0.1'v1.0.1

3 files changed, 62 insertions, 53 deletions

diff --git a/.yardopts b/.yardopts
new file mode 100644
index 0000000..3703872
--- /dev/null
+++ b/.yardopts
@@ -0,0 +1,4 @@
+application.rb
+lazar.rb
+fminer.rb
+openbabel.rb
diff --git a/README b/README
deleted file mode 100644
index 8d515d2..0000000
--- a/README
+++ /dev/null
@@ -1,53 +0,0 @@
-OpenTox Algorithm
-=================
-
-* An OpenTox REST Webservice (http://www.opentox.org)
-* Implements the OpenTox algorithm API for
-  - fminer
-  - lazar
-
-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 algorithm  
-Get a representation of the   GET   /lazar  -                       lazar representation      200,404
-lazar algorithm   
-Create fminer features        POST  /fminer dataset_uri,            URI for feature dataset   200,400,404,500
-                                            feature_uri   
-Create lazar model            POST  /lazar  dataset_uri,            URI for lazar model       200,400,404,500
-                                            prediction_feature, 
-                                            feature_generation_uri  
-
-Supported MIME formats (http://chemical-mime.sourceforge.net/)
---------------------------------------------------------------
-
-  * application/rdf+xml (default): read/write OWL-DL
-
-Examples
---------
-
-Get the OWL-DL representation of fminer 
-  curl http://webservices.in-silico.ch/algorithm/fminer
-
-Get the OWL-DL representation of lazar 
-  curl http://webservices.in-silico.ch/algorithm/lazar
-
-Create fminer features
-  curl -X POST -d dataset_uri={datset_uri} -d prediction_feature={feature_uri} http://webservices.in-silico.ch/algorithm/fminer
-  (feature_uri specifies the dependent variable, e.g. http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster)
-
-  Creates a dataset with fminer features (backbone refinement class representatives from supervised graph mining, see http://www.maunz.de/libfminer-doc/). These features can be used e.g. as structural alerts, as descriptors (fingerprints) for prediction models or for similarity calculations.
-
-Create lazar model
-  curl -X POST -d dataset_uri={datset_uri} -d prediction_feature={feature_uri} -d feature_generation_uri=http://webservices.in-silico.ch/algorithm/fminer http://webservices.in-silico.ch/test/algorithm/lazar
-  (feaure_uri specifies the dependent variable, e.g. http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster)
-
-API documentation
------------------
-
-http://rdoc.info/github/opentox/algorithm
-
-Copyright (c) 2009-2011 Christoph Helma, Martin Guetlein, Micha Rautenberg, Andreas Maunz, David Vorgrimmler, Denis Gebele. See LICENSE for details.
-
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..cf1f519
--- /dev/null
+++ b/README.md
@@ -0,0 +1,58 @@
+OpenTox Algorithm
+=================
+
+- An [OpenTox](http://www.opentox.org) REST Webservice 
+- Implements the OpenTox algorithm API for
+    - fminer
+    - lazar
+
+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 algorithm  
+    Get a representation of the   GET   /lazar  -                       lazar representation      200,404
+    lazar algorithm   
+    Create fminer features        POST  /fminer dataset_uri,            URI for feature dataset   200,400,404,500
+                                                feature_uri   
+    Create lazar model            POST  /lazar  dataset_uri,            URI for lazar model       200,400,404,500
+                                                prediction_feature, 
+                                                feature_generation_uri  
+
+Supported MIME formats 
+----------------------
+
+- application/rdf+xml (default): read/write OWL-DL
+- application/x-yaml: read/write YAML
+
+Examples
+--------
+
+### Get the OWL-DL representation of fminer 
+
+    curl http://webservices.in-silico.ch/algorithm/fminer
+
+### Get the OWL-DL representation of lazar 
+
+    curl http://webservices.in-silico.ch/algorithm/lazar
+
+### Create fminer features
+
+    curl -X POST -d dataset_uri={datset_uri} -d prediction_feature={feature_uri} http://webservices.in-silico.ch/algorithm/fminer
+
+(feature_uri specifies the dependent variable, e.g. http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster)
+
+Creates a dataset with fminer features (backbone refinement class representatives from supervised graph mining, see http://www.maunz.de/libfminer-doc/). These features can be used e.g. as structural alerts, as descriptors (fingerprints) for prediction models or for similarity calculations.
+
+### Create lazar model
+
+    curl -X POST -d dataset_uri={datset_uri} -d prediction_feature={feature_uri} -d feature_generation_uri=http://webservices.in-silico.ch/algorithm/fminer http://webservices.in-silico.ch/test/algorithm/lazar
+
+(feaure_uri specifies the dependent variable, e.g. http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster)
+
+[API documentation](http://rdoc.info/github/opentox/algorithm)
+--------------------------------------------------------------
+
+Copyright (c) 2009-2011 Christoph Helma, Martin Guetlein, Micha Rautenberg, Andreas Maunz, David Vorgrimmler, Denis Gebele. See LICENSE for details.
+