Merge branch 'release/v1.0.1' into development

3 files changed, 58 insertions, 52 deletions

diff --git a/.yardopts b/.yardopts
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--- /dev/null
+++ b/.yardopts
@@ -0,0 +1 @@
+application.rb
diff --git a/README b/README
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--- a/README
+++ /dev/null
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-OpenTox Compound
-================
-
-* An OpenTox REST Webservice (http://www.opentox.org)
-* Implements the OpenTox compound API 1.1 (http://opentox.org/dev/apis/api-1.1/structure)
-
-REST operations
----------------
-
-Get the representation of a compound 	GET 	/compound/{id} 	- 												Compound representation		200,404,500
-Create a new compound 							 	POST 	/compound 			Compound representation		URIs for new compounds 		200,400,500
-
-Supported MIME formats (http://chemical-mime.sourceforge.net/)
---------------------------------------------------------------
-
-	* chemical/x-daylight-smiles (default)
-	* chemical/x-inchi
-	* chemical/x-mdl-sdfile
-	* text/plain (chemical names)
-	* image/gif (returns image uri, output only)
-
-Examples
---------
-
-	Create a compound_uri from smiles:
-		curl -X POST  -H "Content-Type:chemical/x-daylight-smiles" --data-binary "c1ccccc1" http://webservices.in-silico.ch/compound
-
-	Create a compound_uri from a SD file:
-		curl -X POST -H "Content-Type:chemical/x-mdl-sdfile" --data-binary @my.sdf http://webservices.in-silico.ch/compound
-
-	Create a compound_uri from name (or any other identifier that can be resolved with the Cactus service):
-		curl -X POST  -H "Content-Type:text/plain" --data-binary "Benzene" http://webservices.in-silico.ch/compound
-
-	Create a compound_uri from CAS:
-		curl -X POST  -H "Content-Type:text/plain" --data-binary "71-43-2" http://webservices.in-silico.ch/compound
-
-	Get SMILES for a compound_uri:
-		curl http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
-
-	Get a SD file for a compound_uri:
-		curl -H "Accept:chemical/x-mdl-sdfile" http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
-
-	Get all names for a compound_uri:
-		curl -H "Accept:text/plain" http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
-
-API documentation
------------------
-
-http://rdoc.info/github/opentox/compound
-
-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
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+++ b/README.md
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+epenTox Compound
+================
+
+- An [OpenTox](http://www.opentox.org) REST Webservice 
+- Implements the [OpenTox compound API 1.2](http://opentox.org/dev/apis/api-1.2/structure)
+
+REST operations
+---------------
+
+    Get the representation of a compound  GET   /compound/{id}  -                         Compound representation   200,404,500
+    Create a new compound                 POST  /compound       Compound representation   URIs for new compounds    200,400,500
+
+Supported MIME formats (http://chemical-mime.sourceforge.net/)[http://chemical-mime.sourceforge.net/]
+--------------------------------------------------------------
+
+- chemical/x-daylight-smiles (default)
+- chemical/x-inchi
+- chemical/x-mdl-sdfile
+- text/plain (chemical names)
+- image/gif (returns image uri, output only)
+
+Examples
+--------
+
+### Create a compound_uri from smiles
+
+    curl -X POST  -H "Content-Type:chemical/x-daylight-smiles" --data-binary "c1ccccc1" http://webservices.in-silico.ch/compound
+
+### Create a compound_uri from a SD file
+
+    curl -X POST -H "Content-Type:chemical/x-mdl-sdfile" --data-binary @my.sdf http://webservices.in-silico.ch/compound
+
+### Create a compound_uri from name (or any other identifier that can be resolved with the Cactus service)
+
+    curl -X POST  -H "Content-Type:text/plain" --data-binary "Benzene" http://webservices.in-silico.ch/compound
+
+### Create a compound_uri from CAS
+
+    curl -X POST  -H "Content-Type:text/plain" --data-binary "71-43-2" http://webservices.in-silico.ch/compound
+
+### Get SMILES for a compound_uri
+
+    curl http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
+
+### Get a SD file for a compound_uri:
+
+    curl -H "Accept:chemical/x-mdl-sdfile" http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
+
+### Get all names for a compound_uri
+
+    curl -H "Accept:text/plain" http://webservices.in-silico.ch/compound/InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
+
+[API documentation](http://rdoc.info/github/opentox/compound)
+-------------------------------------------------------------
+
+Copyright (c) 2009-2011 Christoph Helma, Martin Guetlein, Micha Rautenberg, Andreas Maunz, David Vorgrimmler, Denis Gebele. See LICENSE for details.
+