FrontPage - Ontogenesis Network Wiki

The Ontogenesis Network Wiki

This Wiki contains shared notes relating to The Ontegenesis Network fostering the creation, ontogeny and evolution of biological ontologies. It provides an area where we can pool and develop our thoughts: if you have comments about any page, or corrections to make, please use the Wiki page-editing features to make them directly in the Wiki website. The Wiki software maintains a history for each page, and editing mistakes can be recovered by reverting to any previous version.

Contents

The Ontogenesis Network Information
Latest News
Upcoming Events
Network Events
Ontology (proto-) patterns
Associated Projects
Administrative pages
Links to Other Resources
1. Tutorials and workshops
Accessing this wiki
How to use this site

1. The Ontogenesis Network Information

2. Latest News

3. Upcoming Events

NetworkMeeting7 Building an Ontology with Collaborative Protege, December 15/16 at European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge

4. Network Events

Initial Meeting July 2006 at The University of Oxford
Introductory OWL Tutorial July 2006
NetworkMeeting1 Informal meets Formal Ontology Building, October 30/31 in Manchester
NetworkMeeting2 The Ontology Lifecycle and Tools, March 21/22 at the School of Computer Science, University of Manchester
NetworkMeeting3 Temporal and geospatial modelling, July 2/3 at Freshwater Biological Association, Cumbria
NetworkMeeting4 Ontology-building Tools, April 24/25 at Manchester Conference Centre, University of Manchester
NetworkMeeting5 Experiment in Collaborative Normalisation of the Cell Type Ontology, June 25/26 at Wolfson College, University of Oxford
NetworkMeeting6 Ontology Learning from Texts, September 15/16 at Department of Computer Science, Regent Court, 211 Portebello, Sheffield
NetworkMeeting7 Building an Ontology with Collaborative Protege (upcoming), December 15/16 at European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge

5. Ontology (proto-) patterns

At the third Ontogenesis meeting (Windermere, 2-3 July 2007), participants were asked to add possible ontology design patterns relating to temporal and spatial information modeling to this wiki. Even if no specific modelling solution is offered, a clear problem statement provides something that can focus future design efforts. An index page for these pattern statements is here:

OntologyDesignPatterns - design patterns and problems for which patterns are sought

6. Associated Projects

Animal behaviour ontology development

7. Administrative pages

To help get the Wiki up and running with minimum friction, it is currently configured to allow read access to any visitor, and read/write access to anyone who is logged in to a profile (which is created by self-registration as described above). Later, depending upon how our plans develop, the access can be restricted to designated people if that is felt necessary.

8. Links to Other Resources

Ontogenesis network mailing list: http://lists.ontonet.org/mailman/listinfo/ontogenesis
Public Weblog site for Ontogenesis Network: http://www.ontogenesisnetwork.blogspot.com/. You'll need an assigned username/password to access this - ask George for details.

8.1. Tutorials and workshops

Introductory OWL tutorial: http://www.co-ode.org/events/tutorials/
Advanced OWL Ontologies in the Biological Domain: http://www.co-ode.org/events/tutorials/bio/details.php

9. Accessing this wiki

The intended access policy for this wiki is this:

Most pages are publicly readable (this is the default for any new pages)
Most pages are editable by anyone who is logged in to an account on this wiki (this is the default for new pages)
Some pages may be restricted for editing and/or viewing to listed wiki users who are participants in the Ontogenesis Network. These users are listed in page UserGroup.

To create a wiki account, use the Login link on any page, and enter a username and password for your account. For your username, please use the form "FirstnameLastname". To be added to the list of recognized Ontogenesis Network participants, please contact the site administrator (GeorginaMoulton or GrahamKlyne). (For more details of user administration, please see UserConfiguration.)

For more information about using a Wiki, see the section How to use this site below.

10. How to use this site

A Wiki is a collaborative site, anyone can contribute and share:

Edit any page by using the "Edit" or "Edit Text" link at the top or the bottom of the page. You may need to create an account and/or login to see this link (see "Accessing this wiki" above).
Create a link to another page with joined capitalized words (like WikiSandBox) or with ["quoted words in brackets"]
Search for page titles or text within pages using the search box at the top of any page
See HelpForBeginners to get you going, HelpContents for all help pages.

To learn more about what a WikiWikiWeb is, read about WhyWikiWorks and the WikiNature. Also, consult the WikiWikiWebFaq.

To experiment with page editing to get a feel of how it works, please try editing WikiSandBox, rather than creating an empty page without any meaningful content.