SHACL validation of evolving RDF graphs

Implementation of a transformation that takes a set of SHACL constraints and a sequence of actions and transforms them into a modified set of constraints.

See all released versions in the Releases Overview or download the executable and the related data (excluding MeSH data) directly.

Get the MeSH data from https://nlmpubs.nlm.nih.gov/projects/mesh/rdf/2022/mesh2022.nt (Courtesy of the U.S. National Library of Medicine).

Usage

Each experiment requires multiple command-line arguments

1. either the world `local` or `remote`
2. the path to a file with the shapes graph
3. the path to a file with the actions
4. for the data graph
• either the path to a file with the data graph
• or a number as LIMIT for a SPARQL query to the Yago experiment

Optional: To build the project, install Maven and run

mvn package

which will place the results in the subfolder target

For the Medical Subject Headings (MeSH) experiment, first download the data graph from https://nlmpubs.nlm.nih.gov/projects/mesh/rdf/2022/mesh2022.nt (Courtesy of the U.S. National Library of Medicine), then use

java -jar -Xmx9g .\validatingevolvingrdf-0.5-jar-with-dependencies.jar local <pathToShapes> <pathToActions> <pathToDataGraph>

For the Yago experiment, use

java -jar -Xmx9g .\validatingevolvingrdf-0.5-jar-with-dependencies.jar remote <pathToShapes> <pathToActions> 1000

Main algorithms

The algorithms are in the directory src/main/java/com/validatingevolvingrdf. In this folder,

• Transformer.java contains the main transformation algorithm
• ActionUtil.java contains the parser for the action files as well as the algorithm to apply actions to a data graph
• Main.java contains the code that performs local experiments (MeSH) and remote experiments (using the Yago SPARQL endpoint).

Resources

The directory src/main/resources contains the resources that were used during the experiments.

The shapes graph for the Yago experiment is a copy of the SHACL constraints available at the Yago project page. The shapes graph for the MeSH experiment and the actions are custom made.

The data graphs are not included due to the large file sizes. The data graph for the MeSH experiment can be downloaded as single file at https://www.nlm.nih.gov/databases/download/mesh.html courtesy of the U.S. National Library of Medicine. We query the Yago data graph using the SPARQL endpoint https://yago-knowledge.org/sparql/query.

Test cases

The directory src/test/resources/main contains the most important test cases. They display how the transformation works and check that G validates (C,T) if and only if G^α validates (C^α,T). The folders contain four files:

1. actions a sequence of updates
2. shapes.ttl the original shapes graph
3. shapesGoal.ttl the expected result of the transformation
4. data.ttl the data graph for the test case

The unit tests for these test cases are located in src/test/java. The most important test cases start with TestMain.... They test

• if the transformation algorithm correctly transforms the graph from shapes.ttl into the expected shapesGoal.ttl
• if the validation report is the same for the original data graph with the updated shapes graph as for the updated data graph with the original shapes graph
• some additional smaller tests, like if some triples are contained in the updated data graph

Tests are automatically executed whenever a push to the repository happens. The results can be seen in the GitHub Actions.