Wizard for documenting ontologies. WIDOCO is a step by step generator of HTML templates with the documentation of your ontology. It uses the LODE environment to create part of the template.
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README.md

WIzard for DOCumenting Ontologies (WIDOCO)

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Author: Daniel Garijo Verdejo

Contributors: María Poveda, Idafen Santana, Almudena Ruiz, Miguel Angel García, Oscar Corcho, Daniel Vila, Sergio Barrio, Martin Scharm, Maxime Lefrancois.

Citing WIDOCO: Please cite the latest version of WIDOCO in Zenodo: https://zenodo.org/badge/latestdoi/11427075. Also see our ISWC 2017 paper: https://iswc2017.semanticweb.org/paper-138

Downloading the executable

To download WIDOCO, you need to download a JAR executable file. Check the latest release for more details: (https://github.com/dgarijo/WIDOCO/releases/latest).

Description

WIDOCO helps you to publish and create an enriched and customized documentation of your ontology, by following a series of steps in a wizard. We extend the LODE framework by Silvio Peroni to describe the classes, properties and data properties of the ontology, the OOPS! webservice by María Poveda to print an evaluation and the Licensius service by Victor Rodriguez Doncel to determine the license URI and title being used. In addition, we use WebVowl to visualize the ontology and have extended Bubastis to show a complete changelog between different versions of your ontology.

Features of WIDOCO:

  • Automatic documentation of the terms in your ontology (based on LODE)
  • Automatic annotation in JSON-LD snippets of the html produced.
  • Association of a provenance page which includes the history of your vocabulary (W3C PROV-O compliant).
  • Metadata extraction from the ontology plus the means to complete it on the fly when generating your ontology. Check the best practice document to know more about the terms recognized by WIDOCO.
  • Guidelines on the main sections that your document should have and how to complete them.
  • Integration with diagram creators (WebVOWL).
  • Automatic changelog of differences between the actual and the previous version of the ontology (based on Bubastis).
  • Separation of the sections of your html page so you can write them independently and replace only those needed.
  • Content negotiation and serialization of your ontology according to W3C best practices

Examples

Examples of the features of WIDOCO can be seen on the gallery

How to use WIDOCO

Download all the files of the "JAR" folder into the same folder. Then just double click the .jar file.

Now you can execute WIDOCO through the console. Usage:

java -jar widoco-VERSION-jar-with-dependencies.jar [-ontFile file] or [-ontURI uri] [-outFolder folderName] [-confFile propertiesFile] or [-getOntologyMetadata] [-oops] [-rewriteAll] [-crossRef] [-saveConfig configOutFile] [-useCustomStyle] [-lang lang1-lang2] [-includeImportedOntologies] [-htaccess] [-webVowl] [-licensius] [-ignoreIndividuals]

The ontFile and ontURI options allow you to choose the ontology file or ontology URI of your ontology.

The -outFolder option specifies where you want to place the output.

The -confFile allows you to choose your own configuration file for the ontology metadata. However you can tell WIDOCO to try to extract some of the metadata from the ontology with getOntologyMetadata.

The -oops flag creates an html page with the evaluation from the OOPS service (http://oops.linkeddata.es/)

The -rewriteAll option will tell WIDOCO to rewrite files if the new generate files are replacing existing files. Otherwise the tool will promt a window asking the user.

The -crossRef option will ONLY generate the overview and cross reference sections. The index document will NOT be generated. The htaccess, provenance page, etc., will not be generated unless requested by other flags. This flag in intended to be used only after a first version of the documentation exists.

The -saveConfig option allows you to save a configuration file on the "configOutFile" route with the properties of a given ontology.

The -useCustomStyle option allows exporting the documentation using alternate css files (thanks to Daniel Vila).

The -lang option allows showing the languages in which the documentation will be published (separated by "-"). Note that if the language is not supported, the system will load the labels in english. For example: en-pt-es

The -includeImportedOntologies flag indicates whether the terms of the imported ontologies of the current ontology should be documented as well or not.

The -htaccess flag creates a bundle for publication ready to be deployed on your apache server.

The -webVowl flag provides a link to a visualization based on WebVowl (http://vowl.visualdataweb.org/webvowl/index.html#).

The -licensius flag uses the Licensius web services (http://licensius.com/apidoc/index.html) to retrieve license metadata. Only works if the -getOntologyMetadata flag is enabled.

The -ignoreIndividuals allows you to ignore the named individuals in the ontology.

The -includeAnnotationProperties will include annotation properties defined in your ontology (by default they are not included)

How can I make WIDOCO automatically recognize my vocabulary annotations?

There are two ways for making WIDOCO get your vocabulary metadata annotations and use them automatically to document the ontology.

  • Add them in your OWL file. For guidelines on which ones to include, follow our Best Practices document, which indicates which ones we recommend.
  • Edit the project properties of /config/config.properties. This is a key-value pair file with metadata properties. Some people consider it easier than adding the property annotations to the OWL file, although I recommmend doing the former option. Note that the character ";" is used for lists (for instance first author; second author; third author).

Browser issues

The result of executing WIDOCO is an HTML file. We have successfully tested it in Mozilla, IE, Safari and Chrome. When the page is stored in a server, WIDOCO's HTML works correctly in all browsers. If you view the file on your local browser, we recommend you to use Mozilla Firefox, Safari or Internet Explorer. Google Chrome will not show the contents correctly, as it doesn't allow XMLHttpRequest without HTTP. If you want to view the page locally with Google Chrome you have two possibilities:

a) Place the file in a server and access it via its URL (for example, put it in dropbox and access through its public url, or on a Github page).

b) Execute Chrome with the following commands (Thanks to Alejandro Fernandez Carrera):

(WIN) chrome.exe --allow-file-access-from-files,

(OSX) open /Applications/Google\ Chrome.app/ --args --allow-file-access-from-files

(UNX) /usr/bin/google-chrome --allow-file-access-from-files

Current improvements

We are working on the following features:

  • Means to add examples to your ontology terms.
  • Previsualization of the terms that will be generated.

For a complete list, check the project open issues.

Requirements

You will need Java 1.8 or higher (SDK 1.8 or JRE 8) for WIDOCO to work Otherwise, you will probably experience an "Unsupported major.minor version 52.0" exception when executing the JAR file.