[tdwg-content] Semantics of Biodiversity Workshop
jdeck at berkeley.edu
Fri Apr 6 23:49:46 CEST 2012
Following is a workshop of broad interest to many of you. If you are
interested in attending or have further questions, please contact John Deck
(jdeck at berkeley.edu). Note that there is a limited time in which to make
your guaranteed hotel reservations at the The Oread hotel in Lawrence,
under the "Biodiversity Semantics Workshop", which must be done before
April 15th to get the reserved rate.
Feel free to forward or post.
Google Doc link describing workshop and agenda:
Text Description of above google doc link:
Semantics of Biodiversity Workshop May 16 - 18, 2012
University of Kansas Biodiversity Institute -- Lawrence, Kansas
Sponsored by RCN4GSC, Morphbank, Kansas University Biodiversity Informatics
and BiSciCol in collaboration with the National Center for Biomedical
ABOUT THE SPEAKER
Barry Smith is a prominent contributor to ontology research in biomedical
and other domains. He is one of the principal scientists of the NIH
National Center for Biomedical Ontology, a Scientific Advisor to the Gene
Ontology Consortium, a PI on the Protein Ontology and Infectious Disease
Ontology projects, and one of the founders of the Open Biomedical
Ontologies (OBO) Foundry initiative.
The Semantics of Biodiversity Workshop will explore terms used to describe
biological collection objects and their derivatives using the Darwin Core
standard as a starting point. The goal is to enable linking data across
domains and to produce a deeper understanding of our planet’s biodiversity.
For example, by linking information about the ecosystem (both gross and
micro-habitat) and the geospatial environment to tissue samples and derived
sequences, we can better understand population dynamics, ecosystem gene
expression, and the significance of biodiversity in different environments.
While the biodiversity informatics community has made much progress in
standardizing terms over the last 20 years, specific problem areas are
encountered both within and between relevant standards domains. Drawing
on community discussions from the TDWG and GSC communities, and using the
experiences of OBO in integrating information, Smith will guide a
discussion of term clarification for the Darwin Core standard. Some example
discussion topics are:
- How do samples and occurrences relate to each other?
- How can we best distinguish between collection objects, observations,
- What is the nature of the relationship between habitats, environments,
and environmental materials?
- What is the difference between a set, a lot, and a collection?
- How to deal with taxonomic names associated with collection objects?
Much of the workshop will be devoted to these and other discussion topics
that will be introduced by attendees. Come prepared with your topics
and/or important darwin core terms and be able to introduce them. It will
be helpful to indicate before the workshop what topic you can introduce at
the meeting by emailing jdeck at berkeley.edu. **
Day 1 (Wednesday, May 16th)
9am - 5:30pm
Coffee & treats Wednesday and Thursday hosted by KU
Breakfast at Hotel all 3 days
Lunch and dinner on your own, with plenty of options within walking distance
Background and problem statement (Wednesday)
- Review successful examples from other communities
- Getting clear on the distinctions between objects, data, and metadata
- Contrasting annotation with metadata
- Relationship expressions.
- Tracking Identifiers to refer to objects or classes uniquely.
Applying ontological principles to our subject domain (Wednesday and
- Interactive review of 10 or so of the most important Darwin core terms
from the ground up. Participants will be describing terms and the
intention behind their original formation. Come prepared to discuss your
term(s) of interest.
6pm- 7:30pm Reception hosted by Kansas University’s Biodiversity Institute
Day 2 (Thursday, May 17th)
9am - 5:30pm
Solutions for the future (Thursday)
- Enabling linked data
- Pitfalls, traps, and planning
- Creating a sociology so people can re-use ontologies
Planning the 3rd Day discussions (4-5:30pm on Thursday)
- Barry will be departing at 4pm on Thursday and so we will use the
remainder of day to plan our discussion for Friday.
Day 3 (Friday, May 19th)
9am - Noon
We will be collecting discussion topics on Thursday afternoon for our
Friday discussion. Some possible topics include:
- Develop concrete proposals for Darwin Core term clarification
- Do we need a new namespace for Darwin Core (for enforcing URIs)?
- Implications for MIxS Standard
- Implications for the Darwin Core Archive Format
- Recommendations to the TDWG-RDF Group
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