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An OWL ontology documentation tool using Python and templating, based on LODE.

Project description

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pyLODE

An OWL ontology documentation tool using Python and templating, based on LODE.

The Live OWL Documentation Environment tool (LODE) is a well-known (in Semantic Web circles) Java & XSLT-based tool used to generate human-readable HTML documents for OWL and RDF ontologies. That tool is now a bit dated (old-style HTML, use of older technologies like XSLT) and it’s (online version) is not always online.

This tool is a complete re-implementation of LODE’s functionality using Python and Python’s RDF manipulation module, rdflib. An ontology to be documented is parsed and inspected using rdflib and HTML or Markdown is generated using basic Python scripting and Python’s Jinja2 templating.

The tool can be run as in these ways:

Examples

pyLODE has been tested with all of the 30+ ontologies in src/pylode/examples/ and we are trying to ensure it captures all of their annotations. For each example, there is the original RDF file and the corresponding output, either HTML, Markdown or both.

For example, Epimorphic’s’s Registry Ontology is:

Installation

This tool can be used either as a command line utility (see below) or as a Python module in other Python code.

This tool is available on PyPI, the Python Package Index, at https://pypi.org/project/pyLODE/ and can be installed for use as a Python module via pip:

pip install pylode

For desktop command line use, just clone this repository and either use Python or the provided BASH scrip (see below).

Use

pyLODE presents as a Python & BASH command-line utility, pylode/cli.py & pylode/bin/pylode respectively as well as a server implementation powered by the Falcon framework. Windows scripts may appear soon. All use the same command line arguments.

Online API

An online API to access pyLODE is now available in test mode at https://kurrawong.net/pylode-online.

Local server

You can run pyLODE using your own, local, HTTP server like this: ` gunicorn server:api ` Then, in another terminal: ` curl localhost:8000/lode?url=http://sweetontology.net/sweetAll.ttl `

Command line

These are the command line arguments to run pyLODE as a BASH or Python script:

  • -i or --inputfile, required if -u not used
    • The RDF ontology file you wish to generate HTML for Must be in either Turtle, RDF/XML, JSON-LD or N-Triples formats indicated by the file type extensions .rdf, .owl, .ttl, .n3, .nt, .json respectively
  • -u or --url, required if -i not used
    • The RDF ontology you wish to generate HTML for, online. Must be an absolute URL that can be resolved to RDF, preferably via Content Negotiation.
  • -c or --css, optional, default ‘false’
    • Whether (true) or not (false) to copy the default CSS file to the output directory.
  • -o or --outputfile, optional
    • A name you wish to assign to the output file. Will be postfixed with .html or .md. If not specified, the name of the input file or last segment of RDF URI will be used, + .html/.md.
  • -f or --outputformat, optional, default ‘html’
    • The output format of the documentation. ‘html’ or ‘markdown’ accepted.

Example call

This call to the BASH script in pylode/bin/ will create an HTML document for an ontology called placenames.html and save it with a basic CSS file into pylode/output_files/:

$ ./pylode -i ../example/prof.ttl --css true

HTML results

Annotations

pyLODE understands the following ontology annotations:

  • ontology metadata
    • imports - owl:imports
    • title - rdfs:label or skos:prefLabel or dct:title or dc:title
    • description - rdfs:comment or skos:definition or dct:description or dc:description
      • Markdown is supported
    • historyNote - skos:historyNote
      • Markdown is supported
    • version URI - owl:versionIRI as a URI
    • version info - owl:versionInfo as a string
      • preferred namespace prefix - vann:preferredNamespacePrefix as a token
      • preferred namespace URI - vann:preferredNamespaceUri as a URI
    • agents: publishers, creators, contributors
      • see Agent Formatting below for details
      • see the pylode/examples/ directory for examples!
    • dates: created, modified, issued - dct:created etc., all as xsd:date or xsd:dateTime datatype properties
    • rights: license - dct:license as a URI & rights - dct:rights as a string
  • classes
    • per rdfs:Class or owl:Class
    • title - rdfs:label or skos:prefLabel or dct:title
    • description - rdf:comment or skos:definition or dct:description as a string or usingc`Markdown <https://daringfireball.net/projects/markdown/>`__ or HTML
    • usage note - a skos:scopeNote string
    • super classes - by declaring a class to be owl:subClassOf something
    • sub classes - pyLODE will work these out itself
    • restrictions - by declaring a class to be owl:subClassOf of an owl:Restriction with any of the normal cardinality or property existence etc. restrictions
    • in domain/range of - pyLODE will auto-calculate these
  • properties
    • per owl:ObjectProperty, owl:DatatypeProperty or owl:AnnotationProperty
    • title - rdfs:label or skos:prefLabel or dct:title
    • description - rdf:comment or skos:definition or dct:description
    • usage note - a skos:scopeNote string
    • super properties - by declaring a class to be owl:subPropertyOf something
    • sub properties - pyLODE will work these out itself
    • domains - rdfs:domain or schema:domainIncludes
    • ranges - rdfs:range or schema:rangeIncludes
  • namespaces
    • pyLODE will honour any namespace prefixes you set and look up others in http://prefix.cc
    • it will either read your ontology’s default/base URI in annotations or guess it using a number of methods
  • named individuals
    • coming!
Agent Formatting
  • Use either the DC versions of properties (dc:publisher etc.) or the DCT versions (dct:publisher etc.)
  • if using the DC form, the range should just be a string, e.g. dc:publisher "Geoscience Australia" . or dc:creator "Nicholas J. Car" .
  • if using the DCT form, the range should be a foaf:Agent or schema:Person Blank Node or URI (if details are given elsewhere in the ontology) with the following properties:
    • foaf:name/sdo:name
    • foaf:mbox/sdo:email
    • foaf:homepage/schema:identifier / sdo:url
  • Affiliation of people to organisation can be made if schem.aorg is used using sdo:member or sdo:affiliation (latter preferred)
    • e.g.
<ontology_x>
    dct:creator [
        sdo:name "Nicholas J. Car" ;
        sdo:identifier <http://orcid.org/0000-0002-8742-7730> ;
        sdo:affiliation [
            sdo:name "SURROUND Australia Pty Ltd" ;
            sdo:url <https://surroundaustralia.com> ;
        ] ;
    ] ;
Additions

To help pyLODE understand more annotations, see Suggestions below.

Styling

This tool generates HTML that is shamelessly similar to LODE’s styling. That’s because we want things to look familiar and LODE’s outputs look great. The Markdown’s pretty vanilla.

Also, pyLODE generates and uses only static HTML + CSS, no JavaScript, live loading Google Fonts etc. This is to ensure that all you nned for nice display is within a couple of static, easy to use and maintain, files. Prevents documentation breaking over time.

Feel free to extend your styling with your own CSS.

Differences from LODE

  • command line access
    • you can use this on your own desktop so you don’t need me to maintain a live service for use
  • use of more modern & simpler HTML
  • catering for a wider range of ontology options such as:
    • schema.org domainIncludes & rangeIncludes for properties
  • better Agent linking
    • foaf:Agent or schema:Person objects for creators, contributors & publishers
    • you can still use simple string peoperties like dc:contributor "Nicholas J. Car" too if you really must!
<ontology_x>
    dct:creator [
        sdo:name "Nicholas J. Car" ;
        sdo:identifier <http://orcid.org/0000-0002-8742-7730> ;
    ] ;
  • smarter CURIES
    • pyLODE caches and looks up well-known prefixes to make more/better CURIES
    • it tries to be smart with CURIE presentation by CURIE-ising all URIs it finds, rather than printing them
  • active development
    • this software is in use and will be improved for the foreseeable future so we will cater for more and more things
    • recent ontology documentation initiatives such as the MOD Ontology will be handled, if requested

License

This code is licensed using the GPL v3 licence. See the LICENSE file for the deed. Note Citation below though for attribution.

Citation

If you use pyLODE, please leave the pyLODE logo with a hyperlink back here in the top left of published HTML pages.

Collaboration

The maintainers welcome any collaboration.

If you have suggestions, please email the contacts below or leave Issues in this repository’s Issue tracker.

But the very best thing you could do is create a Pull Request for us to action!

Contacts

Author:
Nicholas Car
Data System Architect
SURROUND Australia Pty Ltd

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