Tutorial: Generating Ontology Alignments with LogMap

This tutorial shows how to generate ontology alignments using the LogMap tool.
LogMap is a state-of-the-art ontology matching system that combines lexical and structural matching strategies and includes logical reasoning to ensure that the resulting ontology network is consistent.

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Clone this projet

$ git clone git@github.com:LiUSemWeb/Onto-DESIDE-AlignmentTutorial.git
$ cd Onto-DESIDE-AlignmentTutorial

Clone the LogMap repository or download a release

$ git clone https://github.com/ernestojimenezruiz/logmap-matcher.git
$ cd logmap-matcher

Compile using maven:

$ mvn clean package

This creates an executable JAR in the target directory

Alternatively, download a precompiled distribution from the relase page.

Running LogMap

Java 11+ (required to run LogMap)
Verify with:

$ java -version

$ java -jar logmap-matcher-<version>.jar MATCHER \
  http://w3id.org/CEON/ontology/product/ \
  http://w3id.org/dppo/ontology/dpp-core/ \
  /absolute_path_of_output/

• MATCHER tells LogMap to perform ontology matching.
• ontologyA.owl and ontologyB.owl are the input ontologies.
• /absolute_path_of_output/ is the absolute path of the location where you want to save the output alignments.

Understanding the Output

After running LogMap, the absolute_path_of_output/ folder will contain: logmap2_mappings.rdf – The alignment in RDF format (recommended for interoperability). logmap2_mappings.txt – The alignment in a simple tabular text format. A typical mapping in RDF format looks like:

<map>
	<Cell>
		<entity1 rdf:resource="http://w3id.org/CEON/ontology/product/Product"/>
		<entity2 rdf:resource="http://w3id.org/dppo/ontology/dpp-odp/Product"/>
		<measure rdf:datatype="xsd:float">0.5</measure>
		<relation>=</relation>
	</Cell>
</map>

Optional: Converting to SSSOM

For richer metadata, you can convert RDF mappings into the SSSOM tabular format (tSV). We provide a small converter script in this project:

$ python3 -m venv matching-venv
$ source matching-venv/bin/activate
$ pip3 install -r requirements.txt
$ python rdf2sssom.py --config config.yaml

The config.yaml looks like this:

input_file: /absolute_path_of_output/logmap2_mappings.rdf
output_file: ./aligments.tsv
tool: LogMap 

# optional
verbose: true