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https://rawcdn.githack.com/RDFLib/pyLODE/b1ff1b1e19262cdc21ee28c7362b1690ca18e30b/img/pyLODE-250.png

pyLODE.md

An OWL ontology Markdown documentation tool forked from pyLODE v2.13.3 (https://github.com/RDFLib/pyLODE/releases/tag/2.13.3).

In addition to making human-readable forms of ontologies/taxonomies, pyLODE encourages ontology annotation best practice by only producing good results for well documented inputs! pyLODe defines what it considers w'well documented' in sections below, such as Profiles & What pyLODE understands.

Contents

  1. Quick Intro
  2. Examples
  3. Installation
  4. Use
  5. What pyLODE understands
  6. Profiles
  7. Differences from LODE
  8. Releases
  9. License
  10. Citation
  11. Collaboration
  12. Contacts

Quick Intro

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 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, in HTML & Markdown. There are some examples of ADOC too.

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

  • reg.ttl - source file
  • reg.html - HTML output
  • reg.md - Markdown output

Another, the Australian Government's Records Interoperability Framework (AGRIF) Ontology:

You can build all of the example outputs locally by running pylode/examples/_make_examples.py which also serves as a good demonstration of calling pyLODE from a Python file.

Ontologies online using pyLODE:

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 (Linux, Mac or Windows, see below) or as a Python module in other Python code. It can also be used via a hosted, online, service or even as a local web server that you can run. This repo contains executable files for Mac & Windows (soon Linux!) that you can use without any installation too.

The most important dependency to get correct when using this as a Python script of a command line program is the package rdflib which must be v5.0.0 or greater (see requirements.txt).

Python

Do this to use pyLODE as a Python command line program.

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

To use pyLODE within Python, try something like this:

import pylode

html = pylode.MakeDocco(
    input_data_file=input_file_path,
    outputformat="html",
    profile="ontdoc"
).document()

You will now have the HTML content within the variable html.

For desktop command line use, just clone this repository and either use cli.py as per the command line instructions below or use makedocco.py as a Python script directly.

Use

pyLODE presents natively as a Python command-line utility, pylode/cli.py and there are also a BASH, Windows & Mac OS options available for command line use:

All use the same command line arguments.

Additionally, there is a Falcon framework local HTTP server option.

Also, a web UI for pyLODE is available at <https://pylode.surroundaustralia.com>.

Command line arguments

These are the command line arguments to run pyLODE as a BASH or Python script on Linux, Mac etc. or via the Windows executable:

  • -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 'true'
    • Whether (true) or not (false) to include CSS in an HTML output.
  • -o or --outputfile, optional
    • A name you wish to assign to the output file. Will be postfixed with .html, .md or .adoc. If not specified, the name of the input file or last segment of RDF URI will be used, + .html/.md/.adoc.
  • -f or --outputformat, optional, default 'html'
    • The output format of the documentation. 'html', 'md' or 'adoc' accepted.
  • -p or --profile, optional, default 'ontdoc'
  • -lp or --listprofiles, optional, no arguments
    • Lists all the profiles (specifications) for ontology documentation supported by pyLODE

Example call

This basic call to the BASH script in pylode/bin/ will print to standard out an HTML document for an ontology called placenames.html.

./pylode -i ../example/prof.ttl

An output file could be specified by using -o, rather than printing to standard out.

Online Service

An online version of pyLODE is now available at https://pylode.surroundaustralia.com/.

Docker

Install locally by first building the container

docker build -t pylode:latest --build-arg PYTHON_VERSION=3.8-slim .

Then run the container

docker run -it -d -p 8000:8000 -e GTAGID=${Google TagID} pylode

N.B. The Google TagID is NOT required unless Google Analytics is required. It looks as follows GTAGID=UA-168806395-1.

You can now access the service on localhost

curl localhost:8000/lode?url=http://sweetontology.net/sweetAll.ttl

Local server - Falcon

You can run pyLODE using your own, local, HTTP server like this:

gunicorn --chdir /path/to/pyLODE/pylode server:api

The server is then available at localhost:8000 and localhost:8000/pylode for the active endpoint. Note that the server must be fed a URL to an ontology to document supplied by a server capable of responding to Content Negotiation, i.e. it must supply RDF according to an HTTP Accept request for text/turtle, application/rdf+xml etc.

curl localhost:8000/pylode?url=http://sweetontology.net/sweetAll.ttl

Windows

In pylode/bin/, a Windows executable, pylode.exe is available for command line use.

Be sure to add pylode.exe to your Windows user's PATH variable so you can run pylode.exe from any folder. Just run the Registry Editor (search for "Regedit" in the Start menu) and then navicate to HKEY_CURRENT_USER > Environment > Path. Adding the full path of the folder pylode/bin/ to Path will ensure you can run pylode.exe within the Windows command prompt, regardless of what folder you are in.

You can rebuild the pylode.exe file from the source code, if you like. Use the Python program Pyinstaller as per its instructions. The created pylode.exe will have the same characteristics as the Linux/Mac CLI program.

Pyinstaller uses a .spec file to make the binary and that is included in this repository: pylode-cli.spec.

See the PyInstaller installation guide for info on how to install PyInstaller for Windows.

Once you have PyInstaller, use pyinstaller to generate the pyLODE.exe CLI file like so:

cd pylode
pyinstaller pylode-cli.spec

This will output pylode.exe in the dist directory in pylode. The .exe file in bin/ is just the latest copy of this.

You can now run the pyLODE Command Line utility via pylode.exe. See above for the pyLODE command line util usage instructions.

Mac OS

In pylode/bin/, there is a Mac executable, pylode.app.

As per instructions for PyInstaller use on Windows, you can rebuild the file pylode.app using pylode.spec, if you wish.

Linux

In pylode/bin/, there is a shell script pylode.sh. You can run this on the command line. It just pushes queries to the Python command line cli.py.

What pyLODE understands

pyLODE understands Ontologies, Taxonomies & Profiles and handles them based on the Ontology Document, Vocabulary Publication and PROF profiles that it contains. These three profiles share understanding of basic annotation properties.

Annotations

pyLODE understands the following ontology constructs:

  • ontology/taxonomy/profile metadata
    • imports - owl:imports
    • title - rdfs:label, skos:prefLabel, dct:title or dc:title
    • description - rdfs:comment, skos:definition, dct:description or dc:description
      • inline HTML & Markdown are supported
    • historyNote - skos:historyNote
      • inline HTML & Markdown are 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
    • code respository - schema:codeRepository as a literal of type xsd:anyURI
    • source - dcterms:source as a literal of type xsd:anyURI or text
  • ontology classes
    • per rdfs:Class or owl:Class
    • title - rdfs:label or skos:prefLabel or dct:title
    • description - rdf:comment, skos:definition, dct:description as a string or using inline HTML or Markdown
    • scope note - a skos:scopeNote as a literal
      • inline HTML & Markdown are supported
    • example - a skos:example
      • see Example Handling below
    • 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
  • ontology properties
    • per owl:ObjectProperty, owl:DatatypeProperty or owl:AnnotationProperty
    • title - rdfs:label or skos:prefLabel or dct:title string literal
    • description - rdf:comment, skos:definition, dct:description string literal
      • inline HTML & Markdown are supported
    • scope note - a skos:scopeNote string literal
      • inline HTML & Markdown are supported
    • example - a skos:example
      • see Example Handling below
    • super properties - by declaring a class to be owl:subPropertyOf something
    • sub properties - pyLODE will work these out itself
    • equivalent properties - by declaring a class to be owl:equivalentProperty something
    • inverse of - by declaring a class to be owl:inverseOf something
    • 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
    • as per class but also owl:sameAs
Example Handling

pyLODE can handle many forms of examples for Classes & Properties and can handle multiple examples per class/property. In all cases, the example value is indicated with a skos:example property like this:

<x>
    a owl:Class ;
    skos:example {Literal, Blank Node or URI}
.

Simple Literals

The most basic form is an example that is a literal with no format type indicated. This will be printed out in monospaced text, e.g. the Class Fish in the Examples Ontology has a plain Turtle example like this:

<x> a eggs:Fish ;
    skos:prefLabel "Fish X"@en ;
    eggs:livesInFreshWater true ;
    ...
.

If you indicate one of the RDF built-in formats (rdf:HTML, rdf:XMLLiteral or rdf:JSON), it will be interpreted in the markup form specified, which means, in practice, that HTML will be rendered where as XML or JSON will be monospaced. The Examples Ontology has this HTML example for the property has scale colour:

scale colour:

  • blue
  • orange
  • white

You can use Markdown in example literals too, but to do so, you must set the format to text/markdown so see the Resource Descriptor method below.

URIs

If you put a URI in the example field like this: <x> skos:example <...> ; or like this <x> skos:example "..."^^xsd:anyURI ; then pyLODE will render it as a clickable hyperlink in HTML, Markdown or ASCIIDOC, as per your chose output format.

Images

You can use images in the example field. To do so, either use a URI to an image on the web or a relative URI to a local image file. pyLODE will render either form as an inline image. See the Fish Food class example that looks like this:

examples/examples-ont/fish-food.png

"Resource Descriptor" Examples

To do more you can use a Profiles Vocabulary (PROF) ResourceDescriptor to define multiple properties for an example resource. This involves defining a ResourceDescriptor either as a Blank Node or a URI node like this, the Examples Ont 'eats' property:

:eats skos:example :eats-example .

:eats-example
    a prof:ResourceDescriptor ;
    dcterms:format "text/turtle" ;
    dcterms:conformsTo <https://example.com> ;
    prof:hasArtifact """<x> a :Creature ;
    :eats <y> ;
.
<y> a :Food .""" ;
.

Here the ResourceDescriptor says that this example is in the text/turtle format, has an inline artifact (the actual example text) and conforms to something, in this case the profile defined by <https://example.com>.

You can use this ResourceDescriptor method to create multiple examples for a class or property that conform to different things (perhaps profiles of your ontology).

Agents

Agents, individual persons or organisations, should be associated with ontologies/taxonomies/profiles to indicate authors, creators, publishers etc. There are 2 ways to do this that pyLODE understands: datatype & object type.

Datatype - not preferred

A simple literal value for an agent that a human can read but not a machine can't understand:

  • <ONTOLOGY_URI> dc:creator "AGENT NAME" .
    • the range value is a string literal, either string typed (^^xsd:string) or language typed (@en or @de)
    • the following Dublin Core Elements 1.1 properties may be used:
      • dc:contributor
      • dc:creator
      • dc:publisher
    • the following schema.org properties may be used:
      • schema:author
      • schema:contributor
      • schema:creator
      • schema:editor
      • schema:funder
      • schema:publisher
      • schema:translator
<ontology_x>
    dc:creator "Nicholas J. Car" ;
Object type - preferred

An RDF object is used for the agent and can contain multiple details. A Blank Node or a URI can be used. Best case, a persistent agent URI!

img/contributor-object.png
  • <ONTOLOGY_URI> dct:creator [...] .

or

  • <ONTOLOGY_URI> dct:creator <SOME_URI> .
    • the range value is a Blank Node or a URI of type:
      • schema:Person
      • schema:Organization
      • foaf:Person
      • foaf:Organization
    • the properties of the Blank Node or the URI are as below
    • the following Dublin Core Terms properties may be used:
      • dct:contributor
      • dct:creator
      • dct:publisher
      • dct:rightsHolder
    • the following schema.org properties may be used:
      • schema:author
      • schema:contributor
      • schema:creator
      • schema:editor
      • schema:funder
      • schema:publisher
      • schema:translator
    • the following FOAF properties may be used:
      • foaf:maker

e.g. (Blank Node):

<ontology_x>
    schema:editor [
        a schema:Organization ;
        ...
    ] ;

or (URI):

<ontology_x>
    schema:editor <https://orcid.org/0000-0002-8742-7730> ;
    ...

<https://orcid.org/0000-0002-8742-7730>
    a foaf:Person ;
    ...
Agent datatype properties
  • foaf:name / schema:name
  • foaf:mbox / schema:email
  • foaf:homepage / schema:url
  • schema:identifier

e.g.:

<ontology_x>
    dct:creator [
        schema:name "Nicholas J. Car" ;
        schema:identifier <http://orcid.org/0000-0002-8742-7730> ;
        schema:email <mailto:nicholas.car@surroundaustralia.com> ;
    ] ;
Linking a Person to an Organization

Use schema:member, schema:affiliation (there is no FOAF Person -> Group/Org property):

e.g.:

<ontology_x>
    dct:creator [
        schema:name "Nicholas J. Car" ;
        schema:identifier <http://orcid.org/0000-0002-8742-7730> ;
        schema:email <mailto:nicholas.car@surroundaustralia.com> ;
        schema:affiliation [
            schema:name "SURROUND Australia Pty Ltd" ;
            schema:url <https://surroundaustralia.com> ;
        ] ;
    ] ;

Provenance

Ontology/Taxonomy Source

The ontology's HTML representation linking back to the RDF: generated automatically

img/source.png
Code Repositories

Indicating to readers where the 'live' version of the ontology/taxonomy is managed:

img/code-repository.png

This should not be done for profiles, instread, create a prof:ResourceDescriptor instance with role:repository to indicate a profile's repository.

Code repositories that house an ontology can be indicated either using schema.org's codeRepository property or a combination of the Description of a Project and PROV:

@prefix schema: <https://schema.org/> .

<ONTOLOGY_URI>
    schema:codeRepository <REPO_URI> ;
    ...

or

@prefix doap: <http://usefulinc.com/ns/doap#> .
@prefix prov: <http://www.w3.org/ns/prov#> .

<ONTOLOGY_URI>
    prov:wasGeneratedBy [
        a doap:Project , prov:Activity ;
        doap:repository <REPO_URI>
    ]
    ...

e.g., for the ontology version on ISO 19160-1:

<http://linked.data.gov.au/def/iso19160-1-address>
    prov:wasGeneratedBy [
        a doap:Project , prov:Activity ;
        doap:repository <https://github.com/AGLDWG/iso19160-1-address-ont>
    ] ;
    ...

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 need 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.

Profiles

pyLODE can document ontologies, taxonomies and profiles according to different profiles which are specifications. The basic, default, profile is pyLODE's so-called Ontology Documentation profile, which is a profile of OWL and a few other bits and pieces. See What pyLODE understands section.

pyLODE can tell you what profiles it supports: just run ~$ pylode -lp ("list profiles") or, if calling from Python:

m = MakeDocco(input_data_file="examples/data-access-rights.ttl", profile="vocpub")
print(m.list_profiles())

Supported Profiles

Currently pyLODE supports its OWL profile, as described above, and a profile of SKOS. For full details of what the profiles include, see the profiles' definitions at:

Token URI
prof https://www.w3.org/TR/dx-prof/
ontdoc https://w3id.org/profile/ontdoc
vocpub https://w3id.org/profile/vocpub

Creating New Profiles

In the folder pylode/profiles/, you will see an __init__.py file containing the BaseProfile class which all profiles must inherit from. The existing OntDoc, Prof & VocPub profile classes are in files ontdoc.py, prof.py & vocpub.py respectively. They do all the things profiles need to do and are listed in pylode/profiles/__init__.py for pyLODE to know about with both a profile declaration and an entry in the PROFILES list. The profile declaration for PROF is:

PROF_PROFILE = Profile(
    "https://www.w3.org/TR/dx-prof/",
    "The Profiles Vocabulary",
    "The Profiles Vocabulary is an RDF vocabulary created to allow the machine-readable description of profiles of "
    "specifications for information resources.",
    [HTML_MEDIA_TYPE, "text/markdown"],
    HTML_MEDIA_TYPE,
    languages=["en"],
    default_language="en"
)

See the Profile class in pylode/profiles/__init__.py for mor details.

The PROFILES object currently contains:

PROFILES = {
    "prof": PROF_PROFILE,
    "ontdoc": ONT_DOC_PROFILE,
    "vocpub": VOC_PUB_PROFILE,
}

Profiles also contain templates in pylode/templates/FOLDER and need to be imported into pylode/__init.py and added to that file's document() finction to be made accessible.

So, to create your own profile:

  1. create a class to inherit from BaseProfile
  2. do the work of profileing in your class, following the prof, ontdoc & vocpub examples
  3. list your profile with a profile declaration and an entry in PROFILES in pylode/profiles/__init__.py
  4. place your templates in pylode/templates/FOLDER (FOLDER being your profile's folder name)
  5. make your profile work with pyLODE by importing it into pylode/__init.py and adding a call to its constructor in document()

We hope to simplify this with profile auto-discovery soon!

Transformation by Profile

You can, of course, document an OWL ontology using the owldoc profile or a SKOS taxonomy using the vocpub profile however, you can also document an OWL ontology using the vocpub profile! This is because SKOS is conceptually a subset of OWL - whatever you can express in SKOS you can express in OWL.

pyLODE performs an OWL > SKOS transformation on OWL ontologies to produce a taxonomy document. The following conversions are made:

  • owl:Ontology > skos:ConceptScheme
    • and all the ontology metadata is used with the ConceptScheme
  • owl:Class > skos:Concept
    • and other class annotation properties used with Concept
  • owl:subClassOf > skos:broader
    • and the inverses, skos:narrower

To see the full list of transformations, see the function _expand_graph_for_skos() in makedocco.py.

Examples of a small taxonomies documented using the vocpub profile are:

An example of a large one:

An example of a vocpub-documented OWL ontology and the corresponding owldoc original is AGRIF:

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

Releases

pyLODE is under continual and constant development. The current developers have a roadmap for enhancements in mind, which is given here, however, since this is an open source project, new developers may join the pyLODE dev community and change/add development priorities.

Current Release

The current release, as of December, 2021, is 2.13.2.

Release Schedule

pyLODE Release Schedule
Version Date Description
3.0 ? Will include pre-testing inputs with SHACL
2.13.2 21 December 2021 Updated RDFlib to 6.1.1, improved test to properly use pytest
2.10.0 24 May 2021 Update Windows EXE build process, simplified versioning
2.9.1 28 Apr 2021 Support for ASCIIDOC format (OntDoc profile only)
2.8.11 28 Apr 2021 Further changes for PyPI only
2.8.10 27 Apr 2021 Further changes for PyPI only
2.8.9 27 Apr 2021 PyPI enhancements only
2.8.8 27 Apr 2021 Several small bugs fixed, auto-generation of version no. from Git tag
2.8.6 23 Feb 20201 Fixing char encoding issues, updated examples, new test files style - per issue
2.8.5 5 Jan 20201 Small enhancements to the Falcon server deployment option
2.8.3 3 July 2020 Packaging bugfixes only
2.7 1 July 2020 Much refactoring for new profile creation ease
2.6 June 2020 Supports PROF profiles as well as taxonomies & ontologies
2.4 27 May 2020 Small improvements over 2.0
2.0 18 Apr 2020 Includes multiple profiles - OWP & vocpub
1.0 15 Dec 2019 Initial working release

Release Notes

3.0 - expected

Expected to handle

  • pre-documentation graph shape testing using SHACL
    • you will be able to see what pyLODE-recommended annotation and design patterns your inputs do/don't handle
  • "modp", a documentation profile based on the MOD Ontology
2.0 - current
  • handles complex Examples (skos:example)
  • can export to ASCIIDOC format
  • includes 3rd-party-created profile: NMPF
  • handles Named Individuals in OWL ontologies
  • implements "owldoc" & "vocpub" documentation profiles for OWL, SKOS and OWL-as-SKOS results
  • implements "prof" profile for documentation of Profiles Vocabulary profiles
  • has a more modular structure than 1.0 to assist with the creation or more profiles
1.0 - previous

Initial pyLODE release. Generated HTML documentation for OWL ontologies, missed quite a few expected ontology elements, such as Named Individuals.

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

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