Kansas:
Semantics of Biodiversity Workshop
May 16 - 18, 2012
University of Kansas Biodiversity Institute
Lawrence, Kansas
Sponsored by RCN4GSC, Morphbank, Kansas University Biodiversity Informatics Center, and BiSciCol in
collaboration with the National Center for Biomedical Ontology
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.
TOPICS
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, and individuals?
•
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@berkeley.edu.
AGENDA
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 Thursday)
•
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