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

[Deana Pennington]

Mark,

Great feedback!  I was starting to wonder what happened to you and 
Bertram!  I already have visio installed, and was planning to use it.  
Current thinking is that we'll have 2 people (probably me and Ricardo) 
put things in visio while the rest draw on anything available 
(whiteboards, scrap paper, etc).  I'll be in the office on Sat, Aug 2, 
to do a final download of all relevant things to my laptop.

I saw the docs Rich put in CVS on measurement ontologies and semantics 
(these were helpful to me).  I didn't see anything on food webs.  Do I 
have to install Protege to be able to look at it?

Deana


Mark Schildhauer wrote:

> 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
>

-- 
********

Deana D. Pennington, PhD
Long-term Ecological Research Network Office

UNM Biology Department
MSC03  2020
1 University of New Mexico
Albuquerque, NM  87131-0001

505-272-7460 (office)
505 272-7080 (fax)