Pr4 UG mi Colophon

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Protege 4 User's Guide
Page List
Page Report

Wikipedia describes a colophon as a "brief description, usually located at the end of a book, describing production notes relevant to the edition". Although wikis are far more dynamic than books, the current page serves a corresponding purpose. That is, it describes the approach used in "producing" the guide, credits major contributors and infrastructure providers, etc.


The Protege 4 User's Guide is composed of a set of wiki pages. This should allow the Protege 4 staff and user community to improve the content, keep it up to date, etc. In short, it is intended (and designed) to be an evolving document.

More to the point, the initial version of the guide is not intended to be comprehensive, let alone definitive. However, it should be a well-organized framework and a good starting point for long-term growth.

Much like an artificial reef, the initial skeleton for this guide provides lots of structure, but little in the way of content. Thus, the intent is for Protege 4 users to "colonize" the guide, adding content as the package is used, extended, etc.

The guide is constructed as a set of background chapters (eg, Examples, Concepts, HowTos, Overviews), supplemented by (and cross-linked to) the Glossary and a comprehensive set of reference chapters. For more information, see the Outline.


Additions to the guide may take the form of new content (eg, images, text) for existing pages, new pages, or even new sections and/or chapters. Obviously, the more fundamental the addition, the more need there will be for coordination.

New Content

Protege 4 users are encouraged to add new content to pages, following the prevailing structure of the page and similar pages. For more information, see Conventions.

Background Pages

We are going to need lots of background pages, so feel free to try your hand at writing one. Even a "stub" page can be useful, if it causes other contributors to add their own content. Background pages could take the form of:

  • documenting an example
  • defining a concept
  • writing up a HowTo

Reference Pages

Reference pages should only be added to document (or follow changes in) the underlying program. So, for example, if a new menu item, plugin, tab, or view is added, a corresponding page should be created.



The initial skeleton for this guide was developed by Rich Morin, with help from:


This wiki is based on Semantic MediaWiki:

Semantic MediaWiki (SMW) is an extension to MediaWiki (the wiki software implementation that Wikipedia and other sites run), that allows for annotating semantic data within wiki pages, thus turning a wiki that incorporates the extension into a semantic wiki. Data that has been encoded can be used in semantic searches, used for aggregation of pages, displayed in formats like maps, calendars and graphs, and exported to the outside world via formats like RDF and CSV.

The official version of this guide is served by the Stanford Center for Biomedical Informatics Research (BMIR).

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