From 2c25251eabd876610335e534aa084f34be88e36c Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 11 Mar 2011 13:27:34 +0100 Subject: .yardopts added to include *rb, README converted to markdown --- .yardopts | 4 ++++ README | 53 ----------------------------------------------------- README.md | 60 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 64 insertions(+), 53 deletions(-) create mode 100644 .yardopts delete mode 100644 README create mode 100644 README.md 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..ae3f24d --- /dev/null +++ b/README.md @@ -0,0 +1,60 @@ +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 +- 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. + -- cgit v1.2.3 From d78cda250030776580d69e902d5b17d64350075c Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 11 Mar 2011 13:30:00 +0100 Subject: README.md indents fixed --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index ae3f24d..a10553c 100644 --- a/README.md +++ b/README.md @@ -41,15 +41,15 @@ Examples 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) +(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. +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) +(feaure_uri specifies the dependent variable, e.g. http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster) API documentation ----------------- -- cgit v1.2.3 From 3d6cc268f7f26188f384066cdfb23f7aa4d480f3 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 11 Mar 2011 13:33:10 +0100 Subject: README.md links fixed --- README.md | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index a10553c..cf1f519 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ OpenTox Algorithm ================= -- An OpenTox REST Webservice (http://www.opentox.org) +- An [OpenTox](http://www.opentox.org) REST Webservice - Implements the OpenTox algorithm API for - fminer - lazar @@ -20,8 +20,8 @@ REST operations prediction_feature, feature_generation_uri -Supported MIME formats (http://chemical-mime.sourceforge.net/) --------------------------------------------------------------- +Supported MIME formats +---------------------- - application/rdf+xml (default): read/write OWL-DL - application/x-yaml: read/write YAML @@ -51,10 +51,8 @@ Creates a dataset with fminer features (backbone refinement class representative (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 +[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. -- cgit v1.2.3