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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.

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Contents

1. The Ontogenesis Network Information
2. Latest News
3. Publications
4. Network Events
5. Ontology (proto-) patterns
6. Associated Projects
7. Administrative pages
8. Links to Other Resources
   1. Tutorials and workshops
9. Accessing this wiki
10. How to use this site

1. The Ontogenesis Network Information

• About the OntogenesisNetwork

• Network Partners and Members

• Links to other Network resources

• Summary of Ontogenesis Network activities

2. Latest News

* Blogging the Book. Organisers: Phillip Lord, Newcastle University, Robert Stevens and George Moulton, University of Manchester.

In two days, 21-22 January 2010, we wrote, edited, peer reviewed and published the Ontogenesis KnowledgeBlog ( http://ontogenesis.knowledgeblog.org/2010/01/22/table-of-contents/), a new experiment in rapid open access publishing using blogging technology. By the end of our collaborative meeting, the Ontogenesis KnowledgeBlog contained twelve peer-reviewed encyclopaedia-style articles and tutorials describing ontologies, their creation and use. It is our intention to write more. This novel form of publishing is attracting considerable interest in the blogosphere.

* Ontogenesis Network Tutorial 2 (Invitation only) Family History Knowledge Base Tutorial, December 2/3 2009, The University of Manchester.

3. Publications

Directly arising from the work of the Ontogenesis Network

Malone, J. Badarinarayan, N. Ison, J. Stevens, R. and Parkinson, H. An Ontology of Bioinformatics Software. Bio-Ontologies 2010, a Special Interest Group meeting at ISMB 2010. Boston, MA. Available at http://www.cs.man.ac.uk/~stevensr/papers/softwareontologyismb2010.pdf

Phillip Lord, James Malone, Robert Stevens and David Shotton. Blogging the Word about Ontologies. Bio-Ontologies 2010, a Special Interest Group meeting at ISMB 2010. Boston, MA. http://www.cs.man.ac.uk/~stevensr/papers/knowledgeblog.pdf

Dave Randall, Wes Sharrock, Rob Procter, Yuwei Lin, Meik Poschen and Robert Stevens (2010). Distributed Ontology Building as Practical Work: Lessons from CSCW. Intl Journal of Human-Machine Studies. Accepted for publication.

Lord, P., Stevens, R., Shotton, D. et al. (2010) The Ontogenesis Knowledgeblog, a novel form of book publication. Available at http://ontogenesis.knowledgeblog.org/2010/01/22/table-of-contents/.

Randall, D., Sharrock, W., Procter, R., Lin, Y., Poschen, M., Griefenhagen, C., and Stevens, R. (2009) What about Sea Urchins?: Collaborative Ontology Building among Bioinformaticians. Fifth International eSocial Science Conference Proceedings 2009. Available at http://www.ncess.ac.uk/resources/content/papers/Randall.pdf.

Shotton, D. (2009). CiTO, the Citation Typing Ontology, and its use for annotation of reference lists and visualization of citation networks. Bio-Ontologies 2009, a Special Interest Group meeting at ISMB 2009. Stockholm. Preprint available at http://imageweb.zoo.ox.ac.uk/pub/2008/publications/Shotton_ISMB_BioOntology_CiTO_final_postprint.pdf.

Shotton, D. (2010). CiTO, the Citation Typing Ontology. J. Biomedical Semantics, 1:S6. http://www.jbiomedsem.com/content/1/S1/S6.

Schober D, Malone J, Stevens R, Practical Experiences in Concurrent, Collaborative Ontology Building Using Collaborative Protégé, Proceedings of the ICBO 2009, p.147-150, International Conference on Biomedical Ontology, July 24-26, 2009 , Buffalo, New York, USA. Available at, http://icbo.buffalo.edu/Proceedings.pdf

Brewster, C., Jupp, S., Luciano, J., Shotton, D., Stevens, R. and Zhang, Z. (2009). Issues in learning an ontology from text. BMC Bioinformatics 10: S1. http://dx.doi.org/10.1186/1471-2105-10-S5-S1.

Related papers

Shotton D, Portwin K, Klyne G, Miles A (2009) Adventures in semantic publishing: exemplar semantic enhancement of a research article PLoS Computational Biology 5: e1000361. http://dx.doi.org/10.1371/journal.pcbi.1000361. (Contains first description of CiTO, the Citation Typing Ontology.)

Kurtz D, Parker G, Shotton D, Klyne G, Schroff F, Zisserman A and Wilks Y (2009). CLAROS – bringing classical art to a global public. Proc. IEEE e-Science Coference, Oxford, 9-11 December 2009. Available at http://imageweb.zoo.ox.ac.uk/pub/2009/publications/ Kurtz_Parker_Shotton_et_al-IEEE_CLAROS_paper.pdf. (Involved ontology extensions to CIDOC CRM.)

Zhao J, Klyne G, Miles A, Benson E, Gudmannsdottir E, White-Cooper H, Shotton D (2009) FlyTED: the Drosophila Testis Gene Expression Database. Nucleic Acids Research (Database Issue). http://dx.doi.org/10.1093/nar/gkp1006. (Involved enhancements to and use of the Drosophila Anatomy Ontology.)

Miles A, Zhao J, Klyne G, White-Cooper H, Shotton D: OpenFlyData: An exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster. Journal of Biomedical Informatics 2010, (submitted). Preprint and supplementary files available at http://imageweb.zoo.ox.ac.uk/pub/2009/publications/Miles_et_al_OpenFlyData_paper/. (Involved the development of several ontologies based on the data models of the underlying databases.)

Papers in preparation

Simon Jupp, Robert Stevens, Johanna Völker and David Shotton. Evaluating an Ontology Learning Tool in Biology.

David Shotton, Doug Altman, Nigel Collier, Lindsay Cowell, Mark Forster, Lynn Schriml, Chris Taylor, David Tovey and the MIIDI Standardization Consortium. MIIDI: a Minimal Information Standard for reporting an Infectious Disease Investigations.

4. Network Events

• Ontogenesis Kickoff Meeting 11-12 July 2006 at Wolfson College, University of Oxford.

• Introductory OWL Tutorial 13 July 2006 at Wolfson College, University of Oxford.

• NetworkMeeting1: Informal meets Formal Ontology Building, 30-31 October 2006 at the University of Manchester.

• NetworkMeeting2 The Ontology Lifecycle and Tools, 21-22 March 2007 at the School of Computer Science, University of Manchester.

• NetworkMeeting3 Temporal and geospatial modelling, 2-3 July 2007 at Freshwater Biological Association, Cumbria.

• Review and planning meeting, 11-12 October 2007 at Wolfson College, University of Oxford.

• NetworkMeeting4 Ontology-building Tools, 24-25 April 2008 at the Manchester Conference Centre, University of Manchester.

• NetworkMeeting5 Experiment in Collaborative Normalisation of the Cell Type Ontology I, 25-26 June 2008 at Wolfson College, University of Oxford.

• NetworkMeeting6 Ontology Learning from Texts, 15-16 September 2008 at Department of Computer Science, University of Sheffield.

• NetworkMeeting7 Building an Ontology with Collaborative Protege, 15-16 December 2008 at the European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge.

• NetworkMeeting5b Experiment in Collaborative Normalisation of the Cell Type Ontology II, 14-15 January 2009 at Wolfson College, University of Oxford.

• NetworkMeeting8 Building an Ontology of Bioinformatics Software with Collaborative Protege, 12-13 May 2009 at Smith Building Training Room, Smith Building, University of Manchester.

• NetworkMeeting9 (Invitation only) Workshop to develop MIIDI, a Minimal Information standard for reporting an Infectious Disease Investigation, 1-3 September 2009 at Wolfson College, University of Oxford.

• Advanced OWL Tutorial 11-12 December 2009, at the University of Manchester.

• NetworkMeeting10 Blogging a Book on Bioontologies, 21-22 January 2010 at the University of Manchester.

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

• AccessingThisWiki

• AccessingTheMailingLists

• GeneralTemplate

• PatternTemplate

• Wiki user configuration

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.

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