RDFIO Extension for Semantic MediaWiki

Updates

Sep 4, 2017: Our paper on RDFIO was just published! If you use RDFIO in scientific work, please cite:
Lampa S, Willighagen E, Kohonen P, King A, Vrandečić D, Grafström R, Spjuth O
RDFIO: extending Semantic MediaWiki for interoperable biomedical data management
Journal of Biomedical Semantics. 8:35 (2017). DOI: 10.1186/s13326-017-0136-y.

Introduction

This extension extends the RDF import and export functionality in Semantic MediaWiki by providing import of arbitrary RDF triples (not only OWL ontologies, as before (see about Ontology import, and a SPARQL endpoint that allows write operations.

Technically, RDFIO implements the PHP/MySQL based triple store (and its accompanying SPARQL Endpoint) provided by the ARC2 library. For updating wiki pages with new triples on import/sparql update, the WOM extension is used.

The RDF import stores the original URI of all imported RDF entities (in a special property), which can later be used by the SPARQL endpoint, instead of SMW's internal URIs, which thus allows to expose the imported RDF data "in its original formats", with its original URIs. This allows to use SMW as a collaborative RDF editor, in workflows together with other semantic tools, from which it is then possible to "export, collaboratively edit, and import again", to/from SMW.

This extensions was initially developed as part of a Google Summer of Code 2010 project, and further extended as part of a FOSS OPW 2014 project.

Installation

Easiest: Use the ready-made Virtual Machine

The absolute easiest way to try out RDFIO is to import the Ready-made Virtual Machine with RDFIO 3.0.2 (with MW 1.29 and SMW 2.5) into VirtualBox or VMWare, and just start browsing the local wiki installation.

Steps:

1. Download the .ova file from doi.org/10.6084/m9.figshare.5383966.v1
2. In VirtualBox (should be similar in VMWare), select "File > Import appliance"
3. Click the folder icon
4. Locate the .ova file you downloaded
5. Click "Next", "Agree" to the license, and finally "Import", to start the import
6. Start the virtual machine
7. Click log in (No password required)
8. Click the icon on the desktop
9. You will now see a local wiki installation with an RDFIO enabled wiki, in a browser!
10. Enjoy!

Easy: Vagrant box

Another quite easy way, is to use the RDFIO Vagrant box, which will automatically set up MediaWiki, SemanticMediaWiki and RDFIO in a virtual machine in under 20 minutes.

Medium-hard: Install semi-manually using composer

Install dependencies

• Composer
  • See this page for installation instructions.
• MediaWiki
  • See this page for installation instructions.
• Semantic MediaWiki
  • See this page for installation instructions.
  • To show the "Semantic factbox" on all pages, make sure to include this in your LocalSettings.php file:

$smwgShowFactbox = SMW_FACTBOX_NONEMPTY;

Installation steps

Assuming you have followed the steps above to install the dependencies for RDFIO:

1. Install RDFIO by executing the following commands in a terminal:

   cd <wiki_folder>
   composer require rdfio/rdfio --update-no-dev
   

2. Log in to your wiki as a super user

3. Browse to http://[your-domain]/wiki/Special:RDFIOAdmin

4. Click the "Setup" button to set up ARC2 database tables.

5. If you already have semantic annotations in your wiki, you need to go to the article "Special:SMWAdmin" in your wiki, and click "Start updating data", and let it complete, in order for the data to be available in the SPARQL endpoint.

Optional but recommended steps

• Edit the MediaWiki:Sidebar page and add the following wiki snippet, as an extra menu (I use to place it before just the "* SEARCH" line), which will give you links to the main functionality with RDFIO from the main links in the left sidebar on the wiki:

  * Semantic Tools
  ** Special:RDFIOAdmin|RDFIO Admin
  ** Special:RDFImport|RDF Import
  ** Special:SPARQLEndpoint|SPARQL Endpoint
  ** Special:SPARQLImport|SPARQL Import
  

• Create the article "MediaWiki:Smw_uri_blacklist" and make sure it is empty (you might need to add some nonsense content like {{{<!--empty-->}}}).

Test that it works

• Access the SPARQL endpoint at http://[url-to-your-wiki]/Special:SPARQLEndpoint
• Access the RDF Import page at http://[url-to-your-wiki]/Special:RDFImport
• Access the SPARQL Import page at http://[url-to-your-wiki]/Special:SPARQLImport
• Optionally, if you want to really see that it works, try adding some semantic data to wiki pages, and then check the database (using phpMyAdmin e.g.) to see if you get some triples in the table named arc2store_triple.

Additional configuration

These are some configuration options that you might want to adjust to your specific use case. That goes into your LocalSettings.php file. Find below a template with the default options, which you can start from, add to your LocalSettings.php file and modify to your liking:

# ---------------------------------------------------------------
#  RDFIO Configuration
# ---------------------------------------------------------------
# An associative array with base uris as keys and corresponding 
# prefixes as the items. Example:
# array( 
#       "http://example.org/someOntology#" => "ont1",
#       "http://example.org/anotherOntology#" => "ont2"
#      );
# $rdfiogBaseURIs = array();
# ---------------------------------------------------------------
# Query by /Output Equivalent URIs SPARQL Endpoint 
# (overrides settings in HTML Form)
# 
# $rdfiogQueryByEquivURI = false;
# $rdfiogOutputEquivURIs = false;
#
# $rdfiogTitleProperties = array(
#  'http://semantic-mediawiki.org/swivt/1.0#page',
#  'http://www.w3.org/2000/01/rdf-schema#label',
#  'http://purl.org/dc/elements/1.1/title',
#  'http://www.w3.org/2004/02/skos/core#preferredLabel',
#  'http://xmlns.com/foaf/0.1/name',
#  'http://www.nmrshiftdb.org/onto#spectrumId'
# );
# ---------------------------------------------------------------
# Allow edit operations via SPARQL from remote services
#
# $rdfiogAllowRemoteEdit = false;
# ---------------------------------------------------------------

Dependencies

• PHP 5.3 - latest (SMW might have more strict deps)
• MySQL (MariaDB unfortunatly not supported yet. See #48)
• MediaWiki - Tested with 1.27 - 1.29
• Semantic MediaWiki Extension - Tested with 2.4 - 3.0-alpha
• The ARC2 RDF library for PHP - Latest version on github should work

Known limitations

• RDFIO does not yet support all the features of SMW's vocabulary import.

Bugs, new feature request and contact information

Please reports bugs and feature requests in the issue tracker here on Github.

Links

• RDFIO's page on MediaWiki.org
• RDFIO project page on pharmb.io (where it is partly developed)

Related work

• FresnelForms
• KnowledgeWiki
• LinkedData Extension