INTRODUCTION

LIPID MAPS Ontology Tools package provides a command line Perl script to
generate ontology data using structure data in SD file(s). 

The current release of ontology data generation script generates the count of
following 26 molecular descriptors:

    Abbreviation    Description

    CARBONS         # of carbons
    DOUBLEBONDS     # of double bonds
    TRIPLEBONDS     # of triple bonds
    RINGS           # of rings
    NH2             # of amino groups
    OH              # of hydroxy groups
    OOH             # of hydroperoxy groups
    KETONES         # of keto groups
    EPOXIDES        # of of epoxy groups
    COOH            # of carboxy groups
    METHYLS         # of methyl groups
    SH              # of thio groups
    BR              # of bromo groups
    CL              # of chloro groups
    F               # of fluoro groups
    METHYLENES      # of methylene groups
    CHO             # of aldehyde groups
    OME             # of methoxy groups
    OAC             # of acetoxy groups
    ET              # of ethyl groups
    PR              # of propyl groups
    COOME           # methyl ester groups
    NO2             # of nitro groups
    ESTER           # of ester groups
    ETHER           # of ether groups
    AMIDES          # of amide groups

Additionally, a  52 character FINGERPRINT string, with two characters
corresponding to value of each ontology data type, can also be generated.

INSTALLATION

1. Add <YOUR LIPID MAPS ONTOLOGY TOOLS DIR>/bin to your PATH environment
   variable.

      C shell example:

          set path = "$path <YOUR LIPID MAPS ONTOLOGY TOOLS DIR>/bin"

      Bourne shell example:

          PATH = "$PATH:<YOUR LIPID MAPS ONTOLOGY TOOLS DIR>/bin"

      Windows:

          o Right click on "My Computer" icon and select properties. And
             Select "Environment Variables" button under Advanced tab.

          o Select path under "System Variables" and click on Edit button. And 
             system variable "path" to include <LIPID MAPS ONTOLOGY TOOLS> bin
             directory.

2. And you're all set to try out the command line script.

RUN TIME DEPENDENCIES

The LIPID MAPS ontology data generation script uses Perl modules from an external
open source package named MayaChemTools to generate ontology data. The
latest release of MayaChemTools package must be available on your system through
MAYACHEMTOOLS environment variable:

1. Download and install MayaChemTools package available at: www.MayaChemTools.org

2. Set MAYACHEMTOOLS environment variable point to <YOUR MAYACHEMTOOLS ROOT DIR>

CAVEATS

On some systems, command line scripts may need to be invoked using
"perl -S <ScriptName.pl>" instead of "<ScriptName.pl>". Example:

      % perl -S GenerateLMOntologyData.pl

FEEDBACK

webmaster@lipidmaps.org

AUTHOR

Manish Sud

CONTRIBUTOR(S)

Eoin Fahy

COPYRIGHT & LICENSE

Copyright (C) 2006-2012. The Regents of the University of California. All Rights Reserved.

LICENSE

Modified BSD License
