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Reasoning mechanisms to produce harmonized provenance graphs, that can be more easily linked together and shared as Linked Data.
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SharpProvToolbox
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sample-data
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LICENCE.txt
README.md
SHARP-1.0-SNAPSHOT-launcher.jar

README.md

SHARP provenance toolbox Build Status

Synopsis

SHARP is a reasearch prototype aimed at harmonizing heterogeneous provenance graphs through reasoning (PROV inferences). PROV Constraints inferences rules have been implemented through the JENA forward chaining inference engine.

Motivations

Several ontologies have been proposed to extend the multi-purpose PROV-O ontology, such as prov-one, wfprov. The mutiplication of PROV-extended vocabularies makes it diffcult to link and cross-exploit multi-systems provenance graphs. In addition, even if workflow management systems produce strictly PROV-O entities, there is no guaranty that the same classes and properties are used, which possibly leads to non joinable graphs.

With SHARP, our goal is to propose reasoning mechanisms to produce harmonized provenance graphs, that can be more easily linked together and shared.

Contributors

Usage in command line

SHARP is available as a standalone command line interface. Here is the description of the command line parameters :

usage: SharpTB [-h] [-i <input_file_1> ... <input_file_n>] [-s] [-v]
SharpTB is a tool to maturate provenance based on PROV inferences
     -h,--help                                            print the help
     -i,--input_files <input_file_1> ... <input_file_n>   The list of PROV
                                                          input files, in RDF
                                                          Turtle.
     -s,--summary                                         Materialization of
                                                          wasInfluencedBy
                                                          relations.
     -v,--version                                         print the version
                                                          information and exit

It can be used to infer PROV statements for a single provenance trace :

java -jar SHARP-1.0-SNAPSHOT-launcher.jar -i sample-data/provstore-114819.ttl -s

Or it can be used to interlink and harmonize cross workflow provenance traces, as demonstrated here :

java -jar SHARP-1.0-SNAPSHOT-launcher.jar -i sample-data/galaxy.prov.ttl sample-data/taverna.prov.ttl sample-data/sameas.ttl -s

Finally, the -s option generates a visualization of the resulting provenance graph, based on inferred prov:wasInfluencedBy predicates.

Sample results are available in the sample-results directory.

In the following screenshot, a workflow partly enacted on Galaxy and Taverna is depicted. While the left part of the graph, disconnected, represents hidden data from the user Galaxy history, the right part represents influence chain from an initial Galaxy bioinformatics worklfow to a Taverna post-processing workflow.

Harmonized provenance graphs

Usage as an API

The project can be compiled as follows :

cd SharpProvToolbox
mvn clean install -Dmaven.test.skip=true

Then, when this jar is in your classpath, you can benefit from PROV inferences as follows.

An RDF PROV graph can be loaded with the JENA API :

String inputGraph = "Your PROV graph in TTL syntax";
Model data = ModelFactory.createDefaultModel();
InputStream stream = new ByteArrayInputStream(inputGraph.getBytes(StandardCharsets.UTF_8));
RDFDataMgr.read(data, stream, Lang.TTL);

Then, the inferences and blank node unification is performed as follows :

Model res = Harmonization.harmonizeProv(data);
Util.dumpPredStats(res); // prints the main predicates in the graph

Finally, we povides a basic visualization of the resulting PROV graph, based on the D3.js framework :

Util.writeHtmlViz(data);
Util.writeHtmlViz(res);

Maven dependencies

This software is built on top of the following Java dependencies :

More details can be found in the pom.xml file.

License

MIT License

Copyright (c) 2017 albangaignard

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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