NetworkMeeting10

Network Meeting 10: Blogging a Book on Bio-ontologies

Contents:

  1. Background and Introduction
    1. Motivation
    2. Solution
  2. Meeting Details
    1. Meeting Dates/Time
    2. Meeting Location
  3. Computers and Software
  4. Blog
  5. Ontogenesis Book Topics
      1. Internet Connectivity
    1. Accommodation (in Manchester)
    2. Evening Meal (12th May 2009)
    3. Costs
  6. Attendees
  7. Outcome
  8. References
  9. Organisers

1. Background and Introduction

1.1. Motivation

"How do you build an ontology? Is there are book or tutorial that describes how to do it?" are often the two most common questions that ontologists here. Despite this, there are only fragments of tutorials on the web, or some detailed books; neither of which provide a clear answer to the question. Both are often highly detailed and very technological.

If ontologies are to continue in their growth in biomedicine, this knowledge gap needs to be addressed. The current process of gathering knowledge from snippets on the web, wikis, mailing lists and contacting experts in the field is wholly inadequate. It is often too slow, too expensive and too difficult; more so, as the ontology community is itself evolving, old knowledge is often not current practice, something which the newcomer is hard-pressed to judge.

We believe, therefore, there is a need for a single resource to which people can be pointed, that is populated with short, succinct articles describing different aspects of ontologies, ontology technology, and the custom and practice of building ontologies.

1.2. Solution

The obvious solution would be to write a book, but due to (1) the time-consuming process; (2) the representation of a narrow spectrum on opinions (usually of the authors) from the h; (3) the content does not frequently change; and (4) the lack of instant gratification for authors, this does not offer that up-to-date, community-based practice reference point that we strongly feel is needed.

The actual solution would be to use the web!

2. Meeting Details

2.1. Meeting Dates/Time

2.2. Meeting Location

School of Computer Science

Atlas Room 1 Kilburn Building Oxford Road Manchester M13 9PL

Building 39 on the campus map found at: [WWW] http://www.manchester.ac.uk/visitors/travel/maps/az/

3. Computers and Software

4. Blog

The main Knowledge Blog ([WWW] http://knowledgeblog.org) details the overall problem, the more specific Ontogenesis Blog ([WWW] http://ontogenesis.knowledgeblog.org) outlines our specific aims and objectives.

The resulting contents of our blogged book, entitled The Ontogenesis KnowledgeBlog, are to be found at [WWW] http://ontogenesis.knowledgeblog.org/table-of-contents/.

5. Ontogenesis Book Topics

Here is a list of potential topics for the book, proposed in advance of the meeting.

1. Motivation for ontology in life sciences
2. What is an ontology
3. Knowledge representation
4. OWL
5. RDF
6. OBOF
7. Protege
8. The OWL API
9. OBO-Edit
10. OBO-Edit API
11. Using ontologies in software; applications of ontologies [BR] 12. Ontological annotation of data
13. Knowledge representation
14. Components of an ontology
15. Classes and instances
16. Syntax, semantics, expressivity and reasoning
17. OWL syntaxes
18. Relationship of OWL and RDF
19. Automaed reasoners
20. Decideability: what is it and why is it a good thing
21. Formal and informal ontologies
22. Upper level ontologies
23. Ontology normalisation
24. Naming conventions; Labels and identifiers
25. OBO Foundary
26. Semantic Publishing
27. Linked data
28. First order logic
29. Reasoning with time
30. Describing species in an ontology
31. The process of building GO
32. Definitions: Natural language and logical
33. Semantic integration
34. Anatomies

5.0.1. Internet Connectivity

During the meeting you will require internet connection. Should you wish to use your own computer, it is a requirement for it to be registered with the University. Please could you send me the MAC address.

5.1. Accommodation (in Manchester)

5.2. Evening Meal (12th May 2009)

5.3. Costs

The Ontogenesis Network will cover the costs of both workshop days, two nights accommodation and reasonable travel for Ontogenesis Network Members and speakers.

6. Attendees

7. Outcome

8. References

9. Organisers

For general enquires please contact: Robert Stevens ([MAILTO] robert.stevens@manchester.ac.uk) and Georgina Moulton ([MAILTO] georgina.moulton@manchester.ac.uk)

-- GeorginaMoulton 2009-03-03 16:27:51

last edited 2010-01-27 21:49:03 by DavidShotton