[seek-taxon] RE: some ideas
Beach, James H
beach at ku.edu
Fri Sep 19 06:20:22 PDT 2003
All --
Dave will be in Lisbon.
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: Kennedy, Jessie [mailto:J.Kennedy at napier.ac.uk]
> Sent: 18 September, 2003 10:17 AM
> To: Beach, James H; Robert K. Peet
> Cc: thau at learningsite.com; Kennedy, Jessie; Bertram
> Ludaescher; Gauch, Susan Evalyn; seek-taxon at ecoinformatics.org
> Subject: RE: [seek-taxon] RE: some ideas
>
>
> Hi Folks
>
> I had a look at Dave's ideas and "think" they seem
> appropriate but until we really sit down and get a common
> understanding it'd be hard to be sure - they are certainly
> possibilities - some I like more than others. for example
> idea 1. doesn't really fit with how I see things (at the
> moment - unless I'm convinced otheriwse), 2. would seem
> sensible but we'd need to look at how we interoperate between
> the SMS and TCS (taxonomic concept server) representations;
> 3. Is necessary and I have thought a bit about it but agree
> this would be another place where the SMS and TCS stuff
> should be epxlored; 4 agree with this too but have some views
> on where we do the cut-off of usable names to reason about.
>
> I think it would be very profitable to chat with Dave and
> think that would be best as a group rather than individual
> calls - but if that's the best we can do then so be it.
>
> I would like to say I'll come over and meet up but I don't
> think it'll be possible to meet up before Lisbon - will Dave
> be there? - I would hope so...
>
> ok speak to you all soon,
>
> Jessie
>
> > -----Original Message-----
> > From: Beach, James H [mailto:beach at ku.edu]
> > Sent: 15 September 2003 03:06
> > To: Robert K. Peet
> > Cc: thau at learningsite.com; Kennedy, Jessie; Bertram
> Ludaescher; Gauch,
> > Susan Evalyn; seek-taxon at ecoinformatics.org
> > Subject: RE: [seek-taxon] RE: some ideas
> >
> >
> > In the SEEK NSF proposal and budget we had included a slot
> > and funding for a
> > programmer who would work at the interface of the Taxon and
> > SMS groups. The
> > intent was that this person would start to develop connection
> > between the
> > intellectual modelling of the Taxon group and the semantic
> > architecture of
> > SMS.
> >
> > The thought behind hiring Dave, who has several years of
> > experience with
> > semantic processing and independent experience with taxonomic
> > data, was that
> > this would be an exploration in that direction. Dave would
> > formalize some
> > development objectives and scope during a 30 day contract
> > period and that we
> > would as a project (Taxon, SMS, Matt) then decide whether to
> > fund his work
> > plan for some additional months. Dave would be obligated by
> > the nature of
> > his role, to make sure what he proposes would have relevance
> > and eventually
> > intersect the work of the two groups. He would, as you point
> > out, not be
> > working within the current scope and activities of the Taxon
> > working group,
> > except to take our work as a departure and reference point
> > for some semantic
> > explorations. We discussed Thau's potential role in this
> > context during one
> > of our recent Taxon teleconference calls.
> >
> >
> >
> >
> >
> > -----Original Message-----
> > From: Robert K. Peet [mailto:peet at unc.edu]
> > Sent: Sun 9/14/2003 6:04 PM
> > To: Beach, James H
> > Cc: thau at learningsite.com; Kennedy, Jessie; Bertram
> > Ludaescher; Gauch, Susan
> > Evalyn; seek-taxon at ecoinformatics.org
> > Subject: Re: [seek-taxon] RE: some ideas
> >
> >
> >
> >
> >
> > Howdy,
> >
> > Dave Thau seems like a bright guy that we might benefit from.
> > However, it
> > seems like he would be working in isolation from our previous
> > work. We
> > are already working a bit too much as fragmented groups
> > rather than as a
> > coherent team. To add another fragment would likely not be
> > productive,
> > but rather just distract us. Is there a convenient way to
> > bring him up to
> > speed on the various things members of our group have done and then
> > interact with him regularly during the contract period so
> that he can
> > build on our our past work and help us to converge on a
> > common vision?
> >
> > Bob
> >
> >
> >
> >
> > On Sat, 13 Sep 2003, Beach, James H wrote:
> >
> > >
> > > Dave --
> > >
> > > Thanks for this interesting set of ideas. Let me forward
> > them to Matt
> > > Jones, Jessie Kennedy, Susan Gauch, and Bertram Ludaescher
> > to see what
> > they
> > > think. I will (and maybe they will hopefully also) get
> > back to you early
> > > next week and we'll make some decisions.
> > >
> > >
> > > Jessie, Bertram, Susan and Matt -- Would you have any
> > thoughts on these
> > > suggestions from Dave Thau on possible work areas for
> > semantic processing
> > of
> > > classifications. These are just early thoughts from Dave,
> > he has not
> > talked
> > > in depth with anyone of us yet.
> > >
> > > We have proposed to Dave that we would hire him as a
> > consultant on the
> > SEEK
> > > Taxon group for an initial 30 day period to research the scope of
> > challenges
> > > with the semantic processing of multiple classifications.
> > So this is just
> >
> > > very preliminary and it would be very useful for SEEK if
> > you had any
> > > thoughts for Dave on the challenges he describes.
> > >
> > > -- 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: thau at learningsite.com [mailto:thau at learningsite.com
> > <mailto:thau at learningsite.com> ]
> > > > Sent: 11 September, 2003 6:46 PM
> > > > To: Vieglais, David A; Beach, James H
> > > > Subject: some ideas
> > > >
> > > >
> > > > Howdy!
> > > >
> > > > I'd like to try out some SEEK ideas just to make sure I'm
> > > > thinking correctly. Let me know if any of these sound
> > > > particularly interesting or particularly irrelevant. Let me
> > > > know if I'm totally off base here too.
> > > > I haven't yet scheduled any meetings or phone calls with
> > > > anyone, so this
> > > > comes out of a bit of a vacuum.
> > > >
> > > > I've come up with four basic topics lurking around the TG/SMS
> > > > border so
> > > > far:
> > > >
> > > > 1. Using SMS representations and languages to reason over
> > > > multiple taxonomic hierarchies.
> > > >
> > > > 2. Using SMS to aid in building an index, registry,
> > > > collection of assertions, whatever it is that the TG will
> > be serving.
> > > >
> > > > 3. Figuring out what to do with data sets describing taxa at
> > > > different levels (e.g. genus level data vs. species
> level data).
> > > >
> > > > 4. Figuring out what to do with data sets containing
> > > > uncertain taxonomic information.
> > > >
> > > > Here are some more details about each of these. Read on, or
> > > > if it's too much for an email, let me know if a phone call
> > > > would be more appropriate.
> > > >
> > > >
> > > > 1. The SMS folks have various ontology representations and
> > > > inference engines. It may be a good idea for the taxon group
> > > > to use these representations and engines when doing things
> > > > like reasoning over multiple conflicting hierarcies, or
> > > > simply responding to SMS queries. There are a number of
> > > > things I could look into regarding that. Some quick ideas:
> > > > a. working on a way for new taxonomic concept providers to
> > > > share data
> > > > with SEEK
> > > > b. helping translate the rules developed by the TG into
> > > > more SMS-like representations (like F-Logic and OWL)
> > > > c. using the SMS stuff to navigate conflicting hierarchies
> > > > - one thing to point out is that I already have a database of
> > > > conflicting taxonomic hierarchies buried in the
> > > > www.speciestoolkit.org. Hidden in there are full > taxonomies
> > > > from species 2000, ITIS, Genbank, and a couple others.
> > > >
> > > > 2. Using SMS to support feature extraction techniques that
> > > > may be useful in determining taxonomic concepts in EML data
> > > > sets and other types of documents. I'm a bit unclear about
> > > > what data are going to reside in a "taxanomic name server"
> > > > and what data are going to be calculated over a distributed
> > > > fashion, but assuming there's going to be some sort of index
> > > > of names or collection of assertions, or registry, SMS could
> > > > be a help in growing that index, collection or registry.
> > > >
> > > > 3. The simple cases of SMS and TG working together are
> > > > a. SMS asks TG which of a set of names represent the
> > same critters
> > > > b. SMS gives TG as set of names and wants the accepted
> > names back
> > > > c. SMS wants a list of possible synonyms for some name
> > > >
> > > > However, these largely act within one level of a hierarchy.
> > > > I have some species names, I want the 'official' species
> > > > names. What happens when SMS wants to reason over data sets
> > > > which act at different levels? One data set may cover a
> > > > subset of a genus (e.g. Arizona desert Pheidoles) while
> > > > another might discuss a specific species (Pheidole titanus).
> > > > What role can the TG play in helping the SMS reason
> > > > accurately in cases like this?
> > > >
> > > > 4. There seems to be a bit of confusion about what to do
> > > > with data sets which are unclear about the species they're
> > > > representing. Those data sets may be rejected from analysis,
> > > > or perhaps the taxon group can help add a little certainty.
> > > > If a set of observations uses a common name, it may be
> > > > possible to narrow down which species they might mean using a
> > > > combination of information from that data set and some input
> > > > from the person contributing the set. This would definitely
> > > > help the SMS in its quest to find data to contribute to an
> > > > analysis, but information generated like this should be
> > > > tagged with a certainty value of some sort. This whole area
> > > > is pretty rich for investigation.
> > > >
> > > > Ok... that's it for now. Looking forward to your reactions.
> > > >
> > > > thau!
> > > >
> > > >
> > > >
> > > _______________________________________________
> > > seek-taxon mailing list
> > > seek-taxon at ecoinformatics.org
> > > http://www.ecoinformatics.org/mailman/listinfo/seek-taxon
> > <http://www.ecoinformatics.org/mailman/listinfo/seek-taxon>
> > >
> >
> >
> ====================================================================
> >
> > Robert K. Peet, Professor Phone: 919-962-6942
> > Department of Biology, CB#3280 Fax: 919-962-6930
> > University of North Carolina Cell: 919-368-4971
> > Chapel Hill, NC 27599-3280 USA Email: peet at unc.edu
> >
> > http://www.bio.unc.edu/faculty/peet/
> > <http://www.bio.unc.edu/faculty/peet/>
> >
> >
> ====================================================================
> >
>
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