From 15bc2b865bf97e5272a8f3437fc69d37ff41c055 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Thu, 20 Sep 2012 08:56:33 +0200 Subject: Improved PC descriptor page --- ...-chemical-descriptors-with-opentox-algorithm.md | 31 +++++++++------------ images/pc.png | Bin 0 -> 71887 bytes 2 files changed, 13 insertions(+), 18 deletions(-) create mode 100644 images/pc.png diff --git a/_posts/2012-05-02-calculating-physico-chemical-descriptors-with-opentox-algorithm.md b/_posts/2012-05-02-calculating-physico-chemical-descriptors-with-opentox-algorithm.md index 11995e6..74737f7 100644 --- a/_posts/2012-05-02-calculating-physico-chemical-descriptors-with-opentox-algorithm.md +++ b/_posts/2012-05-02-calculating-physico-chemical-descriptors-with-opentox-algorithm.md @@ -12,7 +12,7 @@ tags: [Feature Generation, Feature Selection, Tutorials] Three libraries are employed for descriptor calculation: -* [Chemistry Development Kit](http://cdk.sf.net), developed by Chris Steinbeck, Egon Willighagen, and others. +* [Chemistry Development Kit](http://cdk.sf.net) (CDK), developed by Chris Steinbeck, Egon Willighagen, and others. * [OpenBabel](http://openbabel.sf.net), developed by Noel O'Boyle and others. @@ -21,7 +21,7 @@ Three libraries are employed for descriptor calculation: * [Joelib2](http://sourceforge.net/projects/joelib/), developed by Jörg Wegener. -CDK and OpenBabel are actively maintained packages with a large community, while Joelib seems to be a one-man effort that has reached its final state. +CDK and OpenBabel are actively maintained packages with a large community, while Joelib seems is more or less a single man's work. Descriptors have been categorized across libraries. It is possible to calculate descriptors individually, or calculate groups of descriptors according to categories and/or libraries. @@ -29,7 +29,7 @@ Descriptors have been categorized across libraries. It is possible to calculate # Categories -Descriptors were categorized based on work by [Guha](http://www.rguha.net/code/java/cdkdesc.html). The list gives code names and number of descriptors in braces: +Descriptors were categorized based on work by [R. Guha](http://www.rguha.net/code/java/cdkdesc.html). The list gives code names and number of descriptors in braces: * _geometrical (20)_ @@ -60,25 +60,23 @@ Three libraries are employed. The list gives code names and number of descriptor * _joelib (32)_ -**Note:** CDK descriptors are calculated via REST calls to [Ambit](http://ambit.sf.net), while the others are derived locally on the server. - # Creating a Feature Dataset -The deployment on ot-test.in-silico.ch is used to demonstrate the usage: +![Descriptor Calculation](/images/pc.png) +The deployment on `ot-test.in-silico.ch` is used to demonstrate the usage: - -* Get a list of all descriptors: Query the pc descriptor service without parameters. + +Get a list of all descriptors: Query the pc descriptor service without parameters. curl "http://ot-test.in-silico.ch/algorithm/pc" - -* Calculate all descriptors (using _AllDescriptors_ from the above list) by POSTing a dataset uri. +Calculate all descriptors (using *AllDescriptors* from the above list) by POSTing a dataset uri. curl -X POST \ @@ -87,7 +85,7 @@ The deployment on ot-test.in-silico.ch is used to demonstrate the usage: pc/AllDescriptors" -Pass arguments _pc_type_ and/or _lib_  to constrain the query to certain categories and/or libraries. Use code names from above as argument values. E.g., to calculate constitutional and electronic descriptors from CDK, use pc_type=constitutional,electronic and lib=cdk. +Pass arguments *pc_type* and/or *lib* to constrain the query to certain categories and/or libraries. Use code names from above as argument values. E.g., to calculate constitutional and electronic descriptors from CDK, use `pc_type=constitutional,electronic` and `lib=cdk`. curl -X POST \ @@ -97,7 +95,7 @@ Pass arguments _pc_type_ and/or _lib_  to constrain the query to certain catego "http://ot-test.in-silico.ch/algorithm/pc/AllDescriptors" -Clearly, it is possible to combine values by appending them in a comma-separated list. +It is possible to combine values by appending them in a comma-separated list. Moreover, * Calculate individual descriptors by POSTing to one of the other URIs from the list. @@ -107,17 +105,14 @@ Clearly, it is possible to combine values by appending them in a comma-separated That's it! The resulting feature dataset contains extensive [OWL feature metadata](http://opentox.org/data/documents/development/RDF%20files): -* OT.hasSource: The dataset passed as _dataset_uri_ argument - -* DC.creator: The webservice used to calculate the feature - -* DC.description: Free text with a human readable description, library, and category of the feature +* `OT.hasSource`: The dataset passed as *dataset_uri* argument +* `DC.creator`: The webservice used to calculate the feature +* `DC.description`: Free text with a human readable description, library, and category of the feature # Notes - * As with any dataset, resulting feature datasets may also be requested in CSV or YAML formats by specifying appropriate accept-Headers. diff --git a/images/pc.png b/images/pc.png new file mode 100644 index 0000000..ebd73ce Binary files /dev/null and b/images/pc.png differ -- cgit v1.2.3