Gryphon Framework - Preliminary Results Feb-2014

ADRIEL CAFÉ[email protected]

* Preliminary Results - February, 2014

ADRIEL CAFÉ <[email protected]>

Gryphon Framework Our goal is to simplify the integration process of

ontologies and relational databases Virtual mediation of SPARQL queries

Based on GAV (Global As View) approach

Developed with Java


Features (work in progress)

Supports multiple connections from ontologies and relational databases

Designed for large data sources

Align ontologies and map databases automatically

Rewrites SPARQL queries made for global ontology in:◦ SPARQL queries for local ontologies◦ SQL queries for local databases


Why Gryphon? Gryphon, griffin or griffon (Greek: γρύφων, grýphōn, or γρύπων, grýpōn; Latin: gryphus).

Is a legendary creature with:◦ The body, tail, and back legs of a lion; ◦ The head and wings of an eagle, and an eagle's talons as its front feet

Because the lion was traditionally considered the king of the beasts and the eagle the king of birds, the gryphon was thought to be an especially powerful and majestic creature.

The gryphon creature represents a perfectunion between two distinct races. Bringing to our context, the Gryphon Framework proposes a harmonious integration between ontologies and relational databases.


Gryphon Architecture

SPARQL Query

Alignment and MappingQuery Rewriting

3rd Party Frameworks

SPARQL QuerySQL Query


3rd party frameworks used

Jenahttp://jena.apache.org

OWL APIhttp://owlapi.sourceforge.net

D2RQhttp://d2rq.org

Alignment APIhttp://alignapi.gforge.inria.fr


Gryphon integration process

1. Maps the local databases using D2RQ (creates TTL files)

2. Aligns the global ontology with the database mappings using Alignment API (creates OWL files)

3. Aligns the global ontology with the local ontologies using Alignment API (creates OWL files)

4. Uses the alignment files to rewrite SPARQL queries

5. Queries the local sources:1. Uses Jena to query the local ontologies2. Uses D2RQ to rewrite SPARQL queries in SQL queries

6. Get the queries' results and convert them to global ontology components (classes, attributes, instances, axioms)

PracticalExample

Sources used in this

example

Bibtex OWL Ontologyhttp://zeitkunst.org/bibtex/0.1/bibtex.owl

PublicationOWL Ontologyhttp://ebiquity.umbc.edu/v2.1/ontology/publication.owl

Bibsql MySQL Databasehttp://ftp.math.utah.edu/pub/bibsql/

Global Bibtex OWL Ontology



example







example







example





* We’ll focus in only one domain partADRIEL CAFÉ <[email protected]>


The 4 steps to integration1. Set up the Gryphon Framework

2. Set the global ontology and the local ontologies and databases

3. Align the ontologies and map the databases

4. Query the global ontology using SPARQL


Step 1: Set up the framework

GryphonConfig.setWorkingDirectory(Paths.get("alignments"));

GryphonConfig.setAlignmentThreshold(0.3);

GryphonConfig.setAlignmentFunctions(new AlignmentFunctions[] { AlignmentFunctions.EQUAL_DISTANCE, AlignmentFunctions.HAMMING_DISTANCE,

AlignmentFunctions.JARO_MEASURE, AlignmentFunctions.JARO_WINKLER_MEASURE, AlignmentFunctions.LEVENSHTEIN_DISTANCE, AlignmentFunctions.NEEDLEMAN_WUNSCH_2_DISTANCE, AlignmentFunctions.NEEDLEMAN_WUNSCH_DISTANCE, AlignmentFunctions.NGRAM_DISTANCE, AlignmentFunctions.SMOA_DISTANCE, AlignmentFunctions.SUBSTRING_DISTANCE });


Step 2: Set the sources

OWLOntology globalOnt = new OWLOntology(uriToGlobalOnt); OWLOntology localOntBibtex = new OWLOntology(uriToBibtex); OWLOntology localOntPublication = new OWLOntology(uriToPublication);MySQLDatabase localDBBibsql = new MySQLDatabase("localhost", 3306, "root", “root", "bibsql");

Gryphon.setGlobalOntology(globalOnt);

Gryphon.getLocalOWLOntologies().put("bibtex", localOntBibtex);Gryphon.getLocalOWLOntologies().put("publication", localOntPublication);Gryphon.getLocalDatabases().put("bibsql", localDBBibsql);


Step 3: Align and map

Gryphon.alignAndMap();


Step 4: Use SPARQL to query

String queryGlobal = "PREFIX owl: <http://www.w3.org/2002/07/owl#> \n" + "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n“ + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" + "PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> \n" + "PREFIX global_bibtex: <http://aac3.cin.ufpe.br/ns/global_bibtex#> \n" + "SELECT DISTINCT ?x ?y \n" + "WHERE { global_bibtex:author ?x ?y . }";

Gryphon.query(queryGlobal);


Putting it all together GryphonConfig.setWorkingDirectory(Paths.get("alignments")); GryphonConfig.setAlignmentThreshold(0.3); GryphonConfig.setAlignmentFunctions(new AlignmentFunctions[] {

// Alignment Functions });

OWLOntology globalOnt = new OWLOntology(uriToGlobalOnt); OWLOntology localOntBibtex = new OWLOntology(uriToBibtex); OWLOntology localOntPublication = new OWLOntology(uriToPublication);MySQLDatabase localDBBibsql = new MySQLDatabase("localhost", 3306, "root", “root", "bibsql");

Gryphon.setGlobalOntology(globalOnt);

Gryphon.getLocalOWLOntologies().put("bibtex", localOntBibtex); Gryphon.getLocalOWLOntologies().put("publication", localOntPublication); Gryphon.getLocalDatabases().put("bibsql", localDBBibsql); Gryphon.alignAndMap();

String queryGlobal = "PREFIX owl: <http://www.w3.org/2002/07/owl#> \n"

+ "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n" + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n" + "PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> \n" + "PREFIX global_bibtex: <http://aac3.cin.ufpe.br/ns/global_bibtex#> \n" + "SELECT DISTINCT ?x ?y \n" + "WHERE { global_bibtex:author ?x ?y . }";

Gryphon.query(queryGlobal);


Rewritten queries Global Ontology (Original query) SELECT DISTINCT ?x ?yWHERE { global_bibtex:author ?x ?y . }

Local Ontologies and Databases (Rewritten queries) Bibtex Ontology

SELECT DISTINCT ?x ?yWHERE { <http://purl.org/net/nknouf/ns/bibtex#hasAuthor> ?x ?y}

Publication Ontology

SELECT DISTINCT ?x ?yWHERE { <http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#author> ?x ?y }

Bibsql Database

SELECT DISTINCT ?x ?yWHERE { <alignments/dbPublication.ttl#author> ?x ?y }


Query results Bibtex Ontology

X Y

<http://purl.org/dc/elements/1.1/description> "This is tricky due to the fact that order is not (generally) preserved in RDF documents. The problem arises when you want to have an author list where the order is _extremely_ important. How shall we do that? Perhaps we want to define \"hasPrimaryAuthor\", \"hasSecondaryAuthor\", \"hasTertiaryAuthor\", and \"hasRemainingAuthors\", or something of that sort. This will be have to given more thought."

<http://www.w3.org/2000/01/rdf-schema#comment> "The name(s) of the author(s), in the format described in the LaTeX book."@en

<http://www.w3.org/2000/01/rdf-schema#label> "has author"@en

<http://www.w3.org/2000/01/rdf-schema#subPropertyOf> <http://purl.org/net/nknouf/ns/bibtex#humanCreator>

<http://www.w3.org/2000/01/rdf-schema#range> <http://www.w3.org/2001/XMLSchema#string>

<http://www.w3.org/2000/01/rdf-schema#domain> <http://purl.org/net/nknouf/ns/bibtex#Entry>

<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#DatatypeProperty>


Query results Publication Ontology

Bibsql Database

Working on it

X Y

<http://www.w3.org/2000/01/rdf-schema#label> "Resource Author"

<http://www.w3.org/2000/01/rdf-schema#range> <http://ebiquity.umbc.edu/v2.1/ontology/person.owl#Person>

<http://www.w3.org/2000/01/rdf-schema#domain> <http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#Resource>

<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#ObjectProperty>


Next development steps1. Query the local databases using D2RQ

2. Unify the results (convert to components of global ontology)

3. Improve the alignment and mapping process

4. Improve the query rewrite algorithm

5. Test on more biggest and complex sources

That's all folks!

Adriel Café [email protected]

Technology

Gryphon Framework - Preliminary Results Feb-2014