[seek-taxon] FW: [seek-kr] next steps for KR/SMS

Beach, James H beach at ku.edu
Wed Jul 16 14:03:31 PDT 2003


SEEK Taxon -- this message is FYI.  The attached preprint looks very
interesting wrt mediating concepts.  Jim

 
--------------------------------
James H. Beach
Biodiversity Research Center
University of Kansas
1345 Jayhawk Boulevard
Lawrence, KS 66045, USA
Tel: 785 864-4645, Fax: 785 864-5335
Televideocon: (H.323): 129.237.201.102



-----Original Message-----
From: Mark Schildhauer [mailto:schild at nceas.ucsb.edu] 
Sent: 16 July, 2003 2:55 PM
To: Deana Pennington; seek-kr at ecoinformatics.org
Cc: Rich Williams; Bertram Ludaescher
Subject: [seek-kr] next steps for KR/SMS


Hi Deanna and KR folks,

Here's a shot at a summary of some recent discussion among Bertram, Rich 
and myself relative to what we might be able to accomplish in the 
short-term relative to KR/SMS, and specifically --what Deanna could 
possibly do at the upcoming meeting with the BEAM ENM (ecological niche 
modeling) group in a couple of weeks, and what we can present at the 
AMS/KR tutorial/workshop in Albuquerque at the end of next month. 
Comments welcomed!

For upcoming BEAM meeting in Mexico--
1) It will indeed be valuable (as Deanna suggested) to identify and 
clarify common terms and concepts used by ENM scientists.  This can be 
done in two distinct areas--
    a) clarifying the specific types of data that go into parameterizing 
ENM models, and their outputs--relative to themes, attributes, formats, 
sources, etc.  This will be particularly relevant for parameter 
ontologies that inform the AMS.  Should specifically think about how to 
describe data needs in general terms sufficient to clarify how 
*additional* data sources might be incorporated or assimilated by the 
models.
    b) identifying higher-level conceptual issues related to reifying 
"ecological niches"-- formal definitions, algorithms, etc.  This will be 
relevant not only for heuristic value to scientists (if we can find good 
ways to visualize and reconcile these belief/concept maps), but also for 
enhanced querying (e.g., via term expansion) on EcoGRID, and what 
Bertram calls "concept-based indices" for identifying tools within an 
AMS library.

Ideally we'd want to capture these thoughts in a formal framework, e.g. 
using an RDF or OWL plugin to some tool like Protege.  Unfortunately, 
based on Rich's experience, while Protege is an excellent tool, it is 
NOT suitable for a casual end-user.  A current best-fit model would 
involve a "knowledge engineer" working closely with domain scientists to 
clarify and formalize an ontology.  But luckily, we feel that a 
whiteboard style capturing of directed graphs, lists of terms with 
definitions, etc. can be accomplished at the BEAM meeting, and later 
formalized through discussion, e.g., between Deanna and Rich.  So, 
Visio, Illustrator, graphVIZ-- whatever-- can be used to capture 
concepts, relationships, definitions, etc.  And we can hopefully 
formalize these later through dialogue among e.g., Deanna, and Rich.
 
2) Bertram is going to attempt to get out (within the next several days) 
a working copy of his Prolog application that could do simple unit 
conversions (based on the EML unit dictionary) using an ontology and 
inferencing approach.  This would be a simple "proof of concept" of the 
utility of KR/SMS technology.  We thought this might be useful for 
Deanna to carry down to Mexico, that displays some of the potential 
utility of  this approach.  Deanna-- when is the latest that you might 
be able to receive/download some application prior to departing for Mexico?

3) Rich is actively thinking about niche theory, and hopes to begin work 
on some ontology creation for this subject area soon.  He has recently 
checked in to the SEEK CVS repository a Protege-compliant ontology for 
Food Webs, that could serve as good exemplar for ecologists wanting to 
build ontologies.  Rich feels that there are some good visualization 
capabilities for ontologies within Protege using the graphVIZ or 
touchGraph plug-ins, so you might want to give these a try.

For AMS/KR workshop at end of August--
We are still thinking Protege is a good tool for working with 
ontologies.  Very strong and diverse developer community, lots of 
momentum, mature code, etc.  Need to work on simplifying it (according 
to Rich, can highly customize the appearance of Protege for different 
audiences), testing plug-ins for visualization, choice of OWL, RDF, etc.

Have a couple of example ontologies (Food Web, Ecological Niche) in hand 
to walk-thru with scientists

Have working application for unit conversions (Bertram's prolog app). 
 Might want to investigate other Protege plug-ins for this purpose, 
including Algernon.

Some of these tasks can be moved forward by Rich, and Sean, Bertram's 
new full-time SMS programmer, who started work yesterday!

Need some work on How-To: create/edit ontologies, visualize these, reason.

Bertram and I are going to be on vacation for most of August.  Rich is 
getting married this weekend (congratulations!) and his life is hectic 
this week, but settling into blissful tranquility the week after.  Sean 
is jumping onboard this week, and will be able to actively pursue some 
of these issues (right, Bertram?) along with Rich.  Chad is also working 
on the AMS, and will be keeping in mind linkages with the KR/SMS component.

Finally, I am attaching a preprint that Deanna received from Mark 
Gahegan during her recent visit with the Geovista project.  This is an 
interesting document with a lot of apparent overlap with our goals and 
interests in KR/SMS.  Mark Gahegan said we were welcome to share this 
with the SEEK KR participants.

Any comments, corrections or additions to this note are welcomed!

Cheers,
Mark

-- 
Mark P. Schildhauer, Ph.D. --  Director of Computing 
NCEAS --  National Center for Ecological Analysis and Synthesis
735 State St., Suite 300       Santa Barbara, CA   93101-3351	
Email: schild at nceas.ucsb.edu   WEB: http://www.nceas.ucsb.edu
Phone: 805-892-2509            FAX: 805-892-2510


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