Science Environment for Ecological Knowledge
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Science Environment for Ecological Knowledge




KR Meeting Jan 06


Where: San Antonio, Texas
Hotel: La Mansion del Rio Hotel
When: Jan. 23-26, 2006

The meeting will begin promptly at 8:00 am in the El Conde/La Condessa Meeting Room located on the 3rd floor of the hotel. The hotel does not provide shuttle service from San Antonio International Airport to La Mansion del Rio Hotel. You may book SATrans shuttle or take a cab. SATrans is $14 one way, $24 round trip. A cab is $18-$20 one way.

Agenda items

1. Observation ontology (ObsOnt) Tuesday

  • Objective: to provide a rigorous framework for annotating ecological data with sufficient resolution for data merging and suggesting potential statistical analysis.
  • Three sub-model framework (critical evaluation):
  • 1. Observation
    • Spatial component
    • Temporal component
    • Material component
    • How should taxonomy be integrated? (add a provisional component)
  • 2. Abstraction
    • Value
    • Units
  • 3. Context
    • Association
    • Mereology
    • OLAP?
  • Agree upon basic OO framework before end of meeting

2. Textbook parsing project (PP) Wednesday afternoon

  • Objective: to generate an objective graph of relationship among ecological concept (including observation). To be used as a comparative model to aid in ontology building.
  • Begon et al project
    • Show various analysis done so far
    • Ideas for interesting future analyses
  • Wikipedia project
  • Developing a glossary (set of terms defined in natural language, including synonyms)
  • Controlled vocabulary (list of agreed-upon terms)

3. Publications Thursday afternoon

  • Objective: to disseminate what we done so far, focusing on ecological aspects of ontology building.
    • Come up with three (partially overlapping) ideas for papers and divide among participants.
  • Potential journals:
    • Ecological Applications, Bioscience (others): Ontology guide for ecologists.
    • TREE: brief overview of the important role ontologies will play in ecological research (Use boxes for definitions and examples)
    • Ecol. Lett.: a more detailed review of the constructs that ecologists use subconsciously.
    • Computer Science Journals(?): More technical details of ecological constructs using description logic
    • Ontology Journals(?): Comparison and elaboration of an ecological ontology with other types of ontologies; pros, cons and difficulties.

4. Bibliography Throughout meeting

  • Objective: to build a bibliography of must-read items current and fundamental to ontologies, and a brief description of why they are important.
    • The bibliography will form the basis for published literature reviews (above).
    • Also helps define our view-points/who we agree with as far as ontology building

5. Technology surrounding Ontologies (in Kepler)

  • What functionality do we need?
    • External ontologies / ontology repository
    • Uploading
    • Editing
    • Naming Conventions
    • Organizing Ontologies (file based? clusters?)
    • Versioning
    • Navigation/access/searching/interacting ontologies
  • How to "publish" ontologies
  • Annotation mechanisms and grain (dataset, attribute or cell level)

6. Units ontology

  • Objective: Evaluate how to approach unit identification and conversion; extending derived units; relating units ontology to material ontology; how to add new units
    • Unit.xml in EML and STMML approaches relative to OWL

7. Statistical ontology

  • Potential statistical analysis inferred from OO
  • Linkage to actors

8. Spatial-Temporal Ontology

  • Discuss

9. Ecological concepts ontology

10. Community effort

11. Actor ontology and Kepler customization

12. Taxonomy

  • Possible to use OWL for taxonomies?
  • How to use taxonomies in Kepler?
  • Define some of the most compelling use cases...
  • Review of Dave's work

Meeting Notes

Monday, January 22rd

  • Arrivals

Tuesday, January 23rd

  • 8:00 am Coffee/Breakfast
  • 9:00 - 11:00 Fleshed out agenda items
  • 11:15 - ... Josh on observation ontology
    • Some notes
    • More work on basic observation ontology
    • See draft

Wednesday, January 24th

  • 8:00 Coffee/Breakfast
  • More on observation ontology; focus on units, dimensions, traits, measurements, etc.

Thursday, January 26th

  • 8:00 am Coffee/Breakfast
  • 8:30
  • 12:00 Lunch

Friday, January 27th

  • 8:00 Coffee/Breakfast
  • 8:30
  • 12:00 Meeting Ends
  • Departures



  • Shawn Bowers
  • Serguei Krivov
  • Josh Madin
  • Deana Pennington
  • Mark Schildhauer
  • Ferdinando Villa

Meeting Summary

Go here for a summary of the meeting and task deligation.

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This page last changed on 30-Jan-2006 16:50:20 PST by NCEAS.madin.