OWL-Simple
This package contains a set of modules to parse
an OWL ontology into a hash.
SCRIPTS
The similarity_match.pl compares a list of annotations to
another ontology and suggests the best match based on a
similarity metric (n-grams).
Usage:
similarity_match.pl (-w owlfile || -o obofile || -m meshfile)
-t targetfile -r resultfile
[--obotarget || --owltarget]
Optional '--obotarget' setting specifies that the target file is an OBO ontology
Optional '--owltarget' setting specifies that the target file is an OWL ontology
The script expects the first column in the tab delimited input
flat file to contain the values to be matched. Other columns
are preserved in the output.
It is also possible to align one ontology to another and the
accepted formats are: OWL, OBO, MeSH ASCII (see the optional obotarget
and owltarget parameters).
INSTALLATION
Use:
perl Build.PL
./Build
./Build test
./Build install
DEPENDENCIES
IO::File
IO::Handle
GO::Parser
Getopt::Long
Moose
Log::Log4perl
List::Util
XML::Parser
Benchmark
DOCUMENTATION
After installing, you can find documentation modules and scripts with the perldoc
command, e.g.:
perldoc OWL::Simple::Parser
perldoc similarity_match.pl
KNOWN ISSUES
COPYRIGHT AND LICENSE
Copyright (c) 2010 European Bioinformatics Institute. All Rights Reserved.
This module is free software; you can redistribute it and/or modify it
under GPLv3.
This software is provided "as is" without warranty of any kind.