We use a simple alignment format example of which can be found in the alignments of the benchmark dataset.
This format is described in the API documentation.
These formats can be manipulated through the Alignment API (see below).
The instructions here work with version 2.3 of the alignment API
See the instructions on http://alignapi.gforge.inria.fr or download directly now at: http://gforge.inria.fr/frs/?group_id=117
All required libraries are included.
Please, always download the last version.
$ mkdir test $ cd test $ curl http://co4.inrialpes.fr/align/align.zip -o align.zip $ unzip align.zip
First here is a simple test that it works:
$ setenv CWD `pwd` $ java -jar lib/procalign.jar --help $ java -jar lib/procalign.jar file://localhost$CWD/rdf/onto1.owl file://localhost$CWD/rdf/onto2.owlThe last instruction should output some XML.
You can run all the tests at once by using the GroupAlign class
$ curl http://oaei.ontologymatching.org/2006/benchmarks/bench.zip -o bench.zip $ unzip bench.zip $ cd benchmarks $ java -cp $CWD/lib/procalign.jar fr.inrialpes.exmo.align.util.GroupAlign -o stringeq -n http://oaei.inrialpes.fr/2006/benchmarks/101/onto.rdf -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -Dnoinst=1This will output the results of the test in the Alignment format, required by the organizers, in one file named stringeq.rdf in each test directory.
Note for using ISO-Latin: For using the ISO-Latin files it is first necessary to replace the onto.rdf by their onto-iso8859.rdf counterpart.
$ mkdir directory $ cd directory $ curl http://dit.unitn.it/~accord/ev_subs.zip -o ev_subs.zip $ unzip ev_subs.zip $ java -Xmx100000k -cp $CWD/lib/procalign.jar fr.inrialpes.exmo.align.util.GroupAlign -o stringeq -s source.owl -t target.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignmentThis will output the results of the test in the Alignment format, required by the organizers, in one file named stringeq.rdf in each test directory.
Currently this test breaks after having dealt with most of the tests (it breaks at 97 in alphabetical order with the standard 64Kb of heap). We are currently working towards spotting memory leaks; a temporary fix is the one given above: expanding memory size with -Xmx100000k.
Currently the anatomy test breaks on loading ontologies.
In the case of the benchmark tests, the reference ontologies are available so you can directly get the performance of the used method by using the GroupEval class:
$ java -cp $CWD/lib/procalign.jar fr.inrialpes.exmo.align.util.GroupEval -c -l "edna" > result.htmlwhich will output the precision and recall results in the results.html file which looks like this:
| algo | edna | |
|---|---|---|
| test | Prec. | Rec. |
| 101 | 0.90 | 0.99 |
| 103 | 0.90 | 0.99 |
| 104 | 0.90 | 0.99 |
| ... | ||
Note for using ISO-Latin: For using the ISO-Latin files it is first necessary to replace the onto.rdf by their onto-iso8859.rdf counterpart.
It is not possible to use this for the directory and anatomy tests because reference alignments are not available (but you can create yours and check your performances in the same way).
In order for your method to be used in this way you have to implement the Alignment API (or rather to extend our implementation of the Alignment API).
Instructions for implementing the API can be found in the API documentation.
This basically amounts to define a subclass of BasicAlignment, getting its parameters from a Parameters structure and to fill the alignment with the results of the algorithm.
If you use the Procalign or GroupAlign class, it is very convenient to pass them parameters stored in a file (e.g., param.xml) by:
$ java -cp ... -p param.xmlSuch a parameter file can be sent to the organizers of the evaluation.
Parameter file are in a simple XML format:
<Whatever> <param name="name1">value1</param> ... <param name="namen">valuen</param> </Whatever>