OntoViewer Toolkit

Goals

OntoViewer Toolkit can be run with a few different goals that are described below. For each goal, there are a few relevant arguments that can be passed to control the way a goal is run. Some of these arguments are required, some of them are optional.

Name	Description	Relevant argument
consistency-check	Check whether provided ontologies are consistent. The result of this goal is written to an output file with one of two values: true, false.	data (required), output (required)
extract-data	Create a CSV file with data from provided ontologies. This is the default goal. filter-pattern is used to filter out all entities that doesn't contain the given pattern within their IRIs. ontology-mapping is a file created in the standard XML Catalogs format.	data (required), output (required), filter-pattern (optional), ontology-mapping (optional)
merge-imports	Merge ontologies with their imports and save them in RDF/XML format. ontology-iri will be used as a new IRI for the merged ontology. When ontology-version-iri option is provided, it is used as the new version IRI. If it is not provided, the ontology-iri is used as the version IRI.	data (required), output (required), ontology-iri (required), ontology-version-iri (optional), ontology-mapping (optional)

Options

Name	Description	Example
data	Path to the input ontology	ontology/example.rdf
extract-data-column	Used for specifying property IRI for specific column in extract-data output. Supported values: definition, example, explanatoryNote, synonym, usageNote	synonym=http://example.com/synonym
filter-pattern	String that should be within entity's IRI to include it	test
goal	Specify which goal should be executed by the toolkit	extract-data
maturity-level	Override default maturity levels; should have format 'maturityLevelIri=label'	https://example.com/Provisional=Provisional
maturity-level-property	Override default maturity level property	https://example.com/hasMaturityLevel
ontology-iri	New IRI for merged ontology	http://example.com/ontology
ontology-mapping	Path to the catalog file with ontology mapping	catalog-v001.xml
ontology-version-iri	New version IRI for merged ontology	http://example.com/ontology1/v1
output	Path where the result will be saved	output.rdf

Examples

consistency-check

java -jar onto-viewer-toolkit.jar \
    --goal consistency-check \
    --data my-ontology.rdf \
    --output consitency-check-result.txt

extract-data

java -jar onto-viewer-toolkit.jar \
    --goal extract-data \
    --data my-ontology1.rdf \
    --data my-ontology2.rdf \
    --filter-pattern foo \
    --ontology-mapping catalog-v001.xml \
    --output extracted-data.csv

extract-data with maturity-level

java -jar onto-viewer-toolkit.jar \
    --goal extract-data \
    --data my-ontology.rdf \
    --maturity-level https://spec.industrialontologies.org/ontology/core/meta/AnnotationVocabulary/Provisional=Provisional \
    --output extracted-data.csv

extract-data with maturity-level and maturity-level-property

java -jar onto-viewer-toolkit.jar \
    --goal extract-data \
    --data my-ontology.rdf \
    --maturity-level https://spec.industrialontologies.org/ontology/core/meta/AnnotationVocabulary/Provisional=Provisional \
    --maturity-level-property https://spec.edmcouncil.org/fibo/ontology/FND/Utilities/AnnotationVocabulary/hasMaturityLevel \
    --output extracted-data.csv

extract-data with extract-data-column

java -jar onto-viewer-toolkit.jar \
    --goal extract-data \
    --data my-ontology.rdf \
    --extract-data-column synonym=https://spec.industrialontologies.org/ontology/core/meta/AnnotationVocabulary/synonym,https://www.omg.org/spec/Commons/AnnotationVocabulary/synonym,https://spec.edmcouncil.org/fibo/ontology/FND/Utilities/AnnotationVocabulary/synonym \
    --extract-data-column definition=https://spec.industrialontologies.org/ontology/core/meta/AnnotationVocabulary/naturalLanguageDefinition \
    --extract-data-column example=http://www.w3.org/2004/02/skos/core#example \
    --extract-data-column explanatoryNote=https://spec.industrialontologies.org/ontology/core/meta/AnnotationVocabulary/explanatoryNote \
    --extract-data-column usageNote=https://spec.industrialontologies.org/ontology/core/meta/AnnotationVocabulary/usageNote \
    --output extracted-data.csv

merge-imports

Without new version IRI:

java -jar onto-viewer-toolkit.jar \
    --goal merge-imports \
    --data my-ontology.rdf \
    --ontology-iri http://example.com/my-merged-ontology/ \
    --ontology-mapping catalog-v001.xml \
    --output my-merged-ontology.rdf

With new version IRI:

java -jar onto-viewer-toolkit.jar \
    --goal merge-imports \
    --data my-ontology.rdf \
    --ontology-iri http://example.com/my-merged-ontology/ \
    --ontology-version-iri http://example.com/my-merged-ontology/version1/ \
    --ontology-mapping catalog-v001.xml \
    --output my-merged-ontology.rdf