Content:
Tool for checking that ontologies conform to EMMO conventions.
emmocheck [options] iripositional arguments:
iri File name or URI to the ontology to test.
optional arguments:
-h, --help show this help message and exit
--database FILENAME, -d FILENAME
Load ontology from Owlready2 sqlite3 database. The
`iri` argument should in this case be the IRI of the
ontology you want to check.
--local, -l Load imported ontologies locally. Their paths are
specified in Protégé catalog files or via the --path
option. The IRI should be a file name.
--catalog-file CATALOG_FILE
Name of Protégé catalog file in the same folder as the
ontology. This option is used together with --local
and defaults to "catalog-v001.xml".
--path PATH Paths where imported ontologies can be found. May be
provided as a comma-separated string and/or with
multiple --path options.
--check-imported, -i Whether to check imported ontologies.
--verbose, -v Verbosity level.
--configfile CONFIGFILE, -c CONFIGFILE
A yaml file with additional test configurations.
--skip, -s ShellPattern
Shell pattern matching tests to skip. This option may be
provided multiple times.
--url-from-catalog, -u
Get url from catalog file.
--ignore-namespace, -n
Namespace to be ignored. Can be given multiple times emmocheck http://emmo.info/emmo/1.0.0-alpha2
emmocheck --database demo.sqlite3 http://www.emmc.info/emmc-csa/demo#
emmocheck -l emmo.owl (in folder to which emmo was downloaded locally)
emmocheck --check-imported --ignore-namespace=physicalistic --verbose --url-from-catalog emmo.owl (in folder with downloaded EMMO)
emmocheck --check-imported --local --url-from-catalog --skip test_namespace emmo.owlThe --configfile options expects a YAML configuration file that specifies what tests to skip or enable.
The following keywords are recognised in the YAML file:
skip: List of tests to skipenable: List of tests to enable<test_name>: A name of a test. Recognised nested keywords are:exceptions: List of entities in the ontology to skip. Should be written as<ns0>.<name>, where<ns0>is the last component of the base IRI and<name>is the name of the entity.skipmodules: List of module names to skip the test for. The module names may be written either as the full module IRI or as the last component of the module IRI.
Example configuration file:
test_description:
skipmodules:
- manufacturing
- conformityassessment
test_unit_dimensions:
exceptions:
- myunits.MyUnitCategory1
- myunits.MyUnitCategory2
skip:
- name_of_test_to_skip
enable:
- name_of_test_to_enablePrints version of an ontology to standard output.
This script uses RDFLib and the versionIRI tag of the ontology to infer the version.
ontoversion [options] irirdflib(Python package)
positional arguments:
IRI IRI/file to OWL source to extract the version from.
optional arguments:
-h, --help show this help message and exit
--format FORMAT, -f FORMAT
OWL format. Default is "xml".ontoversion http://emmo.info/emmo/1.0.0-alpha!!! warning Fails if ontology has no versionIRI tag.
Tool for visualizing ontologies.
ontograph [options] iri [output]- Graphviz
positional arguments:
IRI File name or URI of the ontology to visualise.
output name of output file.
optional arguments:
-h, --help show this help message and exit
--format FORMAT, -f FORMAT
Format of output file. By default it is inferred from
the output file extension.
--database FILENAME, -d FILENAME
Load ontology from Owlready2 sqlite3 database. The
`iri` argument should in this case be the IRI of the
ontology you want to visualise.
--local, -l Load imported ontologies locally. Their paths are
specified in Protégé catalog files or via the --path
option. The IRI should be a file name.
--catalog-file CATALOG_FILE
Name of Protégé catalog file in the same folder as the
ontology. This option is used together with --local
and defaults to "catalog-v001.xml".
--path PATH Paths where imported ontologies can be found. May be
provided as a comma-separated string and/or with
multiple --path options.
--reasoner [{FaCT++,HermiT,Pellet}]
Run given reasoner on the ontology. Valid reasoners
are "FaCT++" (default), "HermiT" and "Pellet".
Note: FaCT++ is preferred with EMMO.
--root ROOT, -r ROOT Name of root node in the graph. Defaults to all
classes.
--leaves LEAVES Leaf nodes for plotting sub-graphs. May be provided
as a comma-separated string and/or with multiple
--leaves options.
--exclude EXCLUDE, -E EXCLUDE
Nodes, including their subclasses, to exclude from
sub-graphs. May be provided as a comma-separated
string and/or with multiple --exclude options.
--parents N, -p N Adds N levels of parents to graph.
--relations RELATIONS, -R RELATIONS
Comma-separated string of relations to visualise.
Default is "isA". "all" means include all relations.
--edgelabels, -e Whether to add labels to edges.
--addnodes, -n Whether to add missing target nodes in relations.
--addconstructs, -c Whether to add nodes representing class constructs.
--rankdir {BT,TB,RL,LR}
Graph direction (from leaves to root). Possible values
are: "BT" (bottom-top, default), "TB" (top-bottom),
"RL" (right-left) and "LR" (left-right).
--style-file JSON_FILE, -s JSON_FILE
A json file with style definitions.
--legend, -L Whether to add a legend to the graph.
--generate-style-file JSON_FILE, -S JSON_FILE
Write default style file to a json file.
--plot-modules, -m Whether to plot module inter-dependencies instead of
their content.
--display, -D Whether to display graph.ontograph --relations=all --legend --format=pdf emmo-inferred emmo.pdf # complete ontology
ontograph --root=Holistic --relations=hasInput,hasOutput,hasTemporaryParticipant,hasAgent --parents=2 --legend --leaves=Measurement,Manufacturing,CompleteManufacturing,ManufacturedProduct,CommercialProduct,Manufacturer --format=png --exclude=Task,Workflow,Computation,MaterialTreatment emmo-inferred measurement.png
ontograph --root=Material --relations=all --legend --format=png emmo-inferred material.pngThe figure below is generated with the last command in the list above.
Tool for documenting ontologies.
ontodoc [options] iri outfile- pandoc
- pdflatex or xelatex
positional arguments:
IRI File name or URI of the ontology to document.
OUTFILE Output file.
optional arguments:
-h, --help show this help message and exit
--database FILENAME, -d FILENAME
Load ontology from Owlready2 sqlite3 database. The
`iri` argument should in this case be the IRI of the
ontology you want to document.
--local, -l Load imported ontologies locally. Their paths are
specified in Protégé catalog files or via the --path
option. The IRI should be a file name.
--imported, -i Include imported ontologies
--no-catalog, -n Do not read url from catalog even if it exists.
--catalog-file CATALOG_FILE
Name of Protégé catalog file in the same folder as the
ontology. This option is used together with --local
and defaults to "catalog-v001.xml".
--path PATH Paths where imported ontologies can be found. May be
provided as a comma-separated string and/or with
multiple --path options.
--reasoner [{FaCT++,HermiT,Pellet}]
Run given reasoner on the ontology. Valid reasoners
are "FaCT++" (default), "HermiT" and "Pellet".
Note: FaCT++ is preferred with EMMO.
--template FILE, -t FILE
ontodoc input template. If not provided, a simple
default template will be used. Don't confuse it with
the pandoc templates.
--format FORMAT, -f FORMAT
Output format. May be "md", "simple-html" or any other
format supported by pandoc. By default the format is
inferred from --output.
--figdir DIR, -D DIR Default directory to store generated figures. If a
relative path is given, it is relative to the template
(see --template), or the current directory, if
--template is not given. Default: "genfigs"
--figformat FIGFORMAT, -F FIGFORMAT
Format for generated figures. The default is inferred
from --format."
--max-figwidth MAX_FIGWIDTH, -w MAX_FIGWIDTH
Maximum figure width. The default is inferred from
--format.
--pandoc-option STRING, -p STRING
Additional pandoc long options overriding those read
from --pandoc-option-file. It is possible to remove
pandoc option --XXX with "--pandoc-option=no-XXX".
This option may be provided multiple times.
--pandoc-option-file FILE, -P FILE
YAML file with additional pandoc options. Note, that
default pandoc options are read from the files
"pandoc-options.yaml" and "pandoc-FORMAT-options.yaml"
(where FORMAT is format specified with --format). This
option allows to override the defaults and add
additional pandoc options. This option may be provided
multiple times.
--keep-generated FILE, -k FILE
Keep a copy of generated markdown input file for
pandoc (for debugging).Basic documentation of an ontology demo.owl can be generated with:
ontodoc --format=simple-html --local demo.owl demo.htmlSee examples/emmodoc/README.md for how this tool is used to generate the html and pdf documentation of EMMO itself.
Tool for converting between different ontology formats.
ontoconvert [options] inputfile outputfilerdflib(Python package)
positional arguments:
INPUTFILE Name of inputfile.
OUTPUTFILE Name og output file.
optional arguments:
-h, --help show this help message and exit
--input-format, -f INPUT_FORMAT
Inputformat. Default is to infer from input.
--output-format, -F OUTPUT_FORMAT
Default is to infer from output.
--no-catalog, -n Do not read catalog even if it exists.
--inferred, -i Add additional relations inferred by the FaCT++ reasoner to the converted ontology. Implies --squash.
--base-iri BASE_IRI, -b BASE_IRI
Base iri of inferred ontology. The default is the base
iri of the input ontology with "-inferred" appended to
it. Used together with --inferred.
--recursive, -r The output is written to the directories matching the input. This requires Protege catalog files to be present.
--squash, -s Squash imported ontologies into a single output file.ontoconvert --recursive emmo.ttl owl/emmo.owl
ontoconvert --inferred emmo.ttl emmo-inferred.owlNote, it is then required to add the argument only_local=True when loading the locally converted ontology in EMMOntoPy, e.g.:
from ontopy import get_ontology
emmo_ontology = get_ontology("emmo.owl").load(only_local=True)Since the catalog file will be overwritten in the above example writing output to a separate directory is useful.
ontoconvert --recursive emmo.ttl owl/emmo.owlSince parsing the results from the reasoner is currently broken in Owlready2 (v0.37), a workaround has been added to ontoconvert. This workaround only only supports FaCT++. Hence, HermiT and Pellet are currently not available.
Tool for converting EMMO-based ontologies from Excel to OWL, making it easy for non-ontologists to make EMMO-based domain ontologies.
The Excel file must be in the format provided by ontology_template.xlsx.
excel2onto [options] excelpathpandas(Python package)
positional arguments:
excelpath path to excel book
options:
-h, --help show this help message and exit
--output OUTPUT, -o OUTPUT
Name of output ontology, ´ontology.ttl´ is default
--force, -f Whether to force generation of ontology on non-fatal
error.See the documentation of the python api for a thorough description of the requirements on the Excel workbook.
Create a new_ontology.ttl turtle file from the Excel file new_ontology.xlsx:
excel2onto -o new_ontology.ttl new_ontology.xlsxequivalentTo is currently not supported.