Alignment API: Command line interface
The implementation offers various command line tools available in
the fr.inrialpes.exmo.align.cli package:
- Procalign
- Runs a matcher on a pair of ontologies
- ParserPrinter
- Parses and alignment and displays it in
various formats.
- EvalAlign
- Evaluates and alignment with respect to a
reference alignment.
- TestGen
- Generates tests for evaluating matchers.
- GroupAlign
- Runs a matcher against several different test cases.
- GroupEval
- Evaluates several matcher results in several different test cases.
- ExtGroupEval
- Same as above with extended evaluators
- WGroupEval
- Same as above with weighted evaluators.
- GenPlot
- Generates various pliots from matcher resulst
(ROC curves or precision/recall graphs).
- GroupOutput
- Generates other representations of matcher results.
These command line operations usually share switch conventions:
- displaying help (-h);
- displaying debug information (-d);
- directing the output to a file (-o);
Displaying alignments
Another such utility (ParserPrinter) allows to read an
alignment, to manipulate it and to output it without processing
the align method.
Matching
The implementation offers a stand-alone program (fr.inrialpes.exmo.align.util.Procalign) which:
- Reads two OWL/RDF ontologies;
- Creates an alignment object;
- Computes the alignment between these ontologies;
- Eventually cut the alignment under a threhold:
- Displays the result.
Additional options are available:
- controlling the way of rendering the output (-r);
- deciding the implementation of the matching method (-i);
- providing an input alignment (-a).
Running the program is achieved through:
$ java -jar lib/procalign.jar
Two URIs required
usage: Procalign [options] URI1 URI2
options are:
--impl=className -i classname Use the given alignment implementation.
--renderer=className -r className Specifies the alignment renderer
--output=filename -o filename Output the alignment in filename
--params=filename -p filename Reads parameters from filename
--alignment=filename -a filename Start from an XML alignment file
--threshold=double -t double Filters the similarities under threshold
--cutmethod=hard|perc|prop|best|span -T hard|perc|prop|best|span method for computing the threshold
--debug[=n] -d [n] Report debug info at level n
-Dparam=value Set parameter
--help -h Print this message
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Parameters can be passed to all the command line interfaces through the "-Dname=value" scheme. These parameters are either used by the command line utility or transmitted to the called programs, e.g., align(). Parameters can also be passed through an XML file through the "-P filename" option.
Batch matching
There is a small utility (GroupAlign) which allows to implement batch matching. It starts with a directory containing a set of subdirectories. Each subdirectory contains an ontology to align (usually called onto.rdf) and there exist an ontology to be aligned againts these (-n argument, e.g., named ./onto.rdf).
Invoking GroupAlign with some implementation (-i argument), some set of parameters (-p argument), the name of the output file (-o argument) and optionally a renderer (-r argument) will output the resulting alignment in each of these directories:
$ java -cp $CWD/../lib/procalign.jar fr.inrialpes.exmo.align.util.GroupAlign
-o edna -n file://$CWD/101/onto.rdf
-i fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment
This will compare each onto.rdf file in each of the subdirectory to the file://$CWD/101/onto.rdf with the EditDistNameAlignment method and output the result in a edna.rdf file in each directory.
The output is ready to be evaluated by GroupEval.
Generating tests
Tools for generating matching tests (TestGen) are described
in the test generation page.
Evaluating alignments
Tools for evaluating (EvalAlign) and batch evaluating
alignments (GroupEval, ExtGroupEval, WGroupEval) and displaying
results (GenPlot, GroupOutput) are described in the evaluation page.
http://alignapi.gforge.inria.fr/builtin.html
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