pgxlod-reconciliation-rules

Python scripts applying reconciliation rules on a triplestore.

Execution modes

batch mode

Executes reconciliation rules on every relationship in the triplestore.

Execution (without Docker)

python main.py --configuration conf.json --integration-ontology pgxo.owl --max-rows ResultSetsMaxRows --threads 4 batch --output output.ttl

where:

• conf.json: is the configuration file needed to configure the scripts -- see below
• pgxo.owl: is the ontology used to integrate and represent relationships
• ResultSetMaxRows: corresponds to the parameter ResultSetMaxRows of the virtuoso.ini file used to configure the virtuoso instance
• threads: number of threads
• output.ttl: is the path to the output TTL file where the generated links between relationships will be stored

Execution (in Docker)

You can use the target run of the provided Makefile that calls the Docker image with:

docker run --rm $(MAPUSER) -v ${PWD}/data:/data $(INAME):$(VERSION) --configuration /data/conf.json.example --integration-ontology data/pgxo.owl --max-rows 10000 --threads 4 batch --output /data/output.ttl

The data subdirectory of the current directory is shared with the Docker container as /data. It is expected that the JSON configuration file and the integration ontology file are in this directory. /data is also the directory where the output TTL file will be stored. max-rows is set to 10000.

explain mode

Execution (without Docker)

python main.py --configuration conf.json --integration-ontology pgxo.owl --max-rows ResultSetsMaxRows --threads 4 explain --uri1 URI1 --uri2 URI2

where:

• conf.json: is the configuration file needed to configure the scripts -- see below
• pgxo.owl: is the ontology used to integrate and represent relationships
• ResultSetMaxRows: corresponds to the parameter ResultSetMaxRows of the virtuoso.ini file used to configure the virtuoso instance
• threads: number of threads
• URI1 and URI2: URIs of relationships to reconcile. The result will be explained for each dimension.

Execution (in Docker)

Not available.

Input

Configuration JSON file

A configuration JSON file is needed to configure the scripts. An example is provided. It should contains:

{
    "server-address": "http://127.0.0.1:8890/sparql",
    "url-json-conf-attribute": "format",
    "url-json-conf-value": "application/sparql-results+json",
    "url-default-graph-attribute": "default-graph-uri",
    "url-default-graph-value": "http://pgxlod.loria.fr/",
    "url-query-attribute": "query",
    "timeout": 10000000,
    "part-of-predicates": [
        "http://purl.obolibrary.org/obo/BFO_0000050"
    ],
    "has-part-predicates": [
        "http://purl.obolibrary.org/obo/BFO_0000051"
    ],
    "depends-on-predicates": [
        "http://purl.obolibrary.org/obo/RO_0002502"
    ],
    "integration-ontology-relationships-classes": [
        "http://pgxo.loria.fr/PharmacogenomicRelationship"
    ],
    "dimensions": [
        {
            "name": "GeneticFactor",
            "integration-ontology-top-classes": [
                "http://pgxo.loria.fr/GeneticFactor"
            ],
            "integration-ontology-top-linking-predicates": [
                "http://pgxo.loria.fr/isAssociatedWith",
                "http://pgxo.loria.fr/isNotAssociatedWith"
            ],
            "preorder": "PartOfPreorder",
            "comparison-ontology-base-uris": [
            ],
            "depends-on-similarity": false
        },
        {
            "name": "Drug",
            "integration-ontology-top-classes": [
                "http://pgxo.loria.fr/Drug"
            ],
            "integration-ontology-top-linking-predicates": [
                "http://pgxo.loria.fr/isAssociatedWith",
                "http://pgxo.loria.fr/isNotAssociatedWith"
            ],
            "preorder": "MsciPreorder",
            "comparison-ontology-base-uris": [
                "http://purl.obolibrary.org/obo/CHEBI_",
                "http://bio2rdf.org/chebi:",
                "http://identifiers.org/chebi/",
                "http://purl.bioontology.org/ontology/UATC/",
                "http://bio2rdf.org/atc:",
                "http://identifiers.org/atc/"
            ],
            "depends-on-similarity": false
        },
        {
            "name": "Phenotype",
            "integration-ontology-top-classes": [
                "http://pgxo.loria.fr/Phenotype"
            ],
            "integration-ontology-top-linking-predicates": [
                "http://pgxo.loria.fr/isAssociatedWith",
                "http://pgxo.loria.fr/isNotAssociatedWith"
            ],
            "preorder": "MsciPreorder",
            "comparison-ontology-base-uris": [
                "http://purl.bioontology.org/ontology/MESH/",
                "http://bio2rdf.org/mesh:",
                "http://identifiers.org/mesh/"
            ],
            "depends-on-similarity": true
        }
    ],
    "output-equal-predicate": "http://www.w3.org/2002/07/owl#sameAs",
    "output-equiv-predicate": "http://www.w3.org/2004/02/skos/core#closeMatch",
    "output-leq-predicate": "http://www.w3.org/2004/02/skos/core#broadMatch",
    "output-geq-predicate": "http://www.w3.org/2004/02/skos/core#narrowMatch",
    "output-do-related-predicate": "http://www.w3.org/2004/02/skos/core#relatedMatch"
}

with:

• server-address: address of the SPARQL endpoint to query
• url-json-conf-attribute: URL attribute to use to get JSON results
• url-json-conf-value: value of the url-json-conf-attribute to get JSON results
• url-default-graph-attribute: URL attribute to use to define the default graph
• url-default-graph-value: value of url-default-graph-attribute to define the default graph
• url-query-attribute: URL attribute to use to define the query
• timeout: timeout value for HTTP requests
• part-of-predicates: URIs of predicates corresponding to a partOf relationship
• has-part-predicates: URIs of predicates corresponding to the inverse of a partOf relationship
• depends-on-predicates: URIs of predicates corresponding to a dependsOn relationship
• integration-ontology-relationships-classes: URIs of classes from the integration ontology that are used to identify relationships
• dimensions: array of dimensions. Each dimension should contain:
  • name: name identifying the dimension
  • integration-ontology-top-classes: classes of the integration ontology that are instantiated by elements of this dimension. Subclasses will be considered as well.
  • integration-ontology-top-linking-predicates: predicates of the integration ontology that are used to connect elements of this dimension with relationships. Subproperties will be considered as well
  • preorder: preorder to use for comparisons on this dimension. Value should be PartOfPreorder or MsciPreorder.
  • comparison-ontology-base-uris: base URIs of the ontologies to use for the MsciPreorder
  • depends-on-similarity: boolean enabling dependsOn similarity comparison on this dimension
• output-equal-predicate: URI of a predicate to use to identify equal relationships
• output-equiv-predicate: URI of a predicate to use to identify equivalent relationships
• output-leq-predicate: URI of a predicate to use to identify lower or equal relationships
• output-geq-predicate: URI of a predicate to use to identify greater or equal relationships
• output-do-related-predicate: URI of a predicate to use to identify relationships that are related through dependsOn

Tests

A test/pgxo+test.owl file is available to test the scripts. It should be imported in a triplestore instance that will then be queried. After the import, start the tests with make test. The description of the test cases and their results can be found in test/documentation-tests.pdf

Dependencies

• Python3.6
• requests Python module
• rdflib Python module
• tqdm Python module

References

• [1] Monnin, P., Jonquet, C., Legrand, J., Napoli, A., & Coulet, A. (2017). PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units. In PeerJ Preprints 5:e3140v1 https://doi.org/10.7287/peerj.preprints.3140v1
• [2] Monnin, P., Legrand, J., Husson, G., Ringot, P., Tchechmedjiev, A., Jonquet, C., Napoli, A., & Coulet, A. (2018). PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison. bioRxiv, 390971.