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 Pythons RDF manipulation module, rdflib. An ontology to be documented is parsed and inspected using rdflib and HTML is generated using basic Python scripting and Python's Jinja2 templating.

The tool can be run either via command line or as-a-service. The latter is implemented via the popular Falcon framework.

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

Examples

pyLODE has been tested with all of the ontologies in 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 HTML.

Ontologies online using pyLODE:

• Geological Survey of Queensland's Boreholes Profile - http://linked.data.gov.au/def/borehole
• Geoscience Australia's Place Names Profile - http://linked.data.gov.au/def/placenames
• Epimorphic's Registry Ontology - https://epimorphics.com/public/vocabulary/Registry.html
• Semantic Web for Earth and Environmental Terminology (SWEET)

See pairs of RDF & HTML files in the pylode/examples/ directory for other, preprocessed examples.

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

Currently 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.

An online version of it will be available soon too, just as LODE is (was) available online.

Server arguments

` gunicorn server:api ` Then, in another terminal: ` curl localhost:8000/lode?url=http://sweetontology.net/sweetAll.ttl `

Command line arguments

For the command line running of pyLODE, these are the command line argument options:

• -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. If not specified, the name of the input file or last segment of RDF URI will be used, + .html.

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

Annotations

pyLODE understands the following ontology annotations:

• ontology metadata
  • imports - owl:imports
  • title - rdfs:label or skos:prefLabel or dct:title
  • version URI - owl:versionIRI as a URI
  • version info - owl:versionInfo as a string
  • publishers, creators, contributors
    • 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" .
    • if using the DCT form, range should be a foaf:Agent or schema:Person Blank Node with the following properties: foaf:name/sdo:name, foaf:mbox/sdo:email or foaf:homepage/schema:identifier properties
    • see the pylode/examples/ directory for examples!
  • created, modified, issued - dct:created etc., all as xsd:date or xsd:dateTime datatype properties
  • description - rdf:comment or skos:definition or dct:description
  • 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 using 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!

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.

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.

Online use

Soon (July 2019?) an online, hosted, version of this tool will be implemented so you can use it live, online.

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.

Suggestions

If you have suggestions, please email the contacts below or leave Issues in this repositories 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

nicholas.car@surround.com