[tdwg-tag] TDWG ontology revisited ... a newcomer'sperspective [SEC=UNCLASSIFIED]

Peter DeVries pete.devries at gmail.com
Fri May 15 22:08:09 CEST 2009 

In theory it should be possible for providers to use a simple excel-like
format which GBIF harvests, processes and exposes in one ormore of the more
complicated formats. The processed version could be made available in
different formats that correspond to different
ontologies. One could be an OWL DL based structure, another a simpler RDF
structure and the third as standard xml.

The downside is that this simpler format might need to have far fewer
fields.

Some of these could be repopulated by the harvester service.

For instance, if you know the state / province, the harvester should be able
to populate the continent.

- Pete


On Fri, May 15, 2009 at 2:51 PM, Chuck Miller <Chuck.Miller at mobot.org>wrote:

>  Bob,
>
> Well, Lynette is from Atlas of Living Australia and Rupert Wilson is from
> Royal Horticultural Society – neither natural history museum nor herbarium.
> But, even so, the “non-major” museums, zoos, aquaria, gardens, arboreta and
> herbaria (whoever they might be) are not a small bunch and I have to presume
> are not just limited to Excel spreadsheets, but there certainly are some no
> doubt.
>
>
>
> We simply have to recognize the existence of these thousands of nonacademic
> folks with biodiversity data systems out there.  And frankly, the high
> school Java programmer reference might not be that far off in some corners
> of the world’s data sources.  Excel, maybe too. It’s just a reality that
> TDWG needs to accept and support somehow.  And, again, I’m not saying we
> don’t need the semantic inferencing tools and standards, which we do. And I
> still think there should be a standard TDWG Ontology, hard as that may be to
> do.
>
>
>
> I just think we need to hedge the TDWG standards some for the sake of the
> Lynettes and Ruperts of the world.  If IPT were the universal integrator,
> adaptable to all sources and receivers, then I suppose that would make it
> like the “oil light” and end of discussion.
>
>
>
> Chuck
>  ------------------------------
>
> *From:* Bob Morris [mailto:morris.bob at gmail.com]
> *Sent:* Friday, May 15, 2009 1:27 PM
> *To:* Chuck Miller
> *Cc:* Lee Belbin; tdwg-tag at lists.tdwg.org
>
> *Subject:* Re: [tdwg-tag] TDWG ontology revisited ... a
> newcomer'sperspective [SEC=UNCLASSIFIED]
>
>
>
> OK. I'll put the elephant back in the room.  But first I'll go Chuck one
> further: once the major natural history museums and herbaria are taken out
> of the discussion, the biodiversity data holding community is made up of
> people who don't want to hear about anything except Excel(tm) spreadsheets,
> and well they shouldn't.
>
> Elephant wise, there is a case to be made that it is not standards bodies,
> but rather funded, mandated organizations like GBIF whose job is development
> of tools and training in their use,  even when assistance of the
> standards-making participants is needed in the technical implementation of
> the tools.  GBIF was pretty successful in that regard with their DiGIR
> provider, and is well on their way to another success with the Integrated
> Publishing Toolkit.
>
> Usually, standards bodies are made up of people who contribute because they
> \are/ tool builders and want to make sure their tools have the required
> level of interoperability with whatever other tools they perceive
> interoperability is in their users' interests.
>
> The global automotive industry is a good model (but so is the
> OpenGeospactial Consortium [note "Consortium" in their name].  ) .  With no
> real data, I'll wager that an insignificant fraction of private owners of
> automobiles have no clue what is the appropriate motor oil to use in their
> car, much less how to understand how to choose a motor oil, or understand
> such things as the relation between SAE10W30  designated motor oil and
> something corresponding to it in an EU standard. In fact, what most people
> want is simply a light to come on in their car when it is time to take the
> car to someone who knows what is the appropriate thing to do to make that
> light go out and keep the car safe and valuable.  Using a "change oil"
> indicator is an easy thing to learn.  Designing cars with useful indicator
> lights is not.  Even selling or servicing cars is not an easy thing to
> learn, and maybe those are  the analogy of the community in pain being put
> forth in these threads. If developing, deploying, and maintaining
> biodiversity information systems were not technically demanding enterprises,
> Mobot could fire its technical staff and hire a bunch of high school
> students who have had a course in Java and are masters of Twitter and
> Facebook. There are a lot of those for hire.
>
>
> Bob Morris
>
>
>
>  On Fri, May 15, 2009 at 12:47 PM, Chuck Miller <Chuck.Miller at mobot.org>
> wrote:
>
> Lee,
> As you know, I am a proponent of the simple and the understandable,
> particularly for the folks like Lynette.  I am glad to see a couple of
> appeals from the gallery to counterpoint the continuing pursuit of the
> complex issues. The biodiversity informatics/data community like it or not
> is primarily made up of those who do not spend their time expanding the
> limits of web-based semantic inference.  It may very well be that the only
> viable solutions for some of the use cases of biodiversity can only be
> reached by semantic inference.  But, the barrier to entry for folks like
> Lynnette (and there are many, many) is just too high and so solving those
> use cases by web-based semantics is simply out of reach for them.  We must
> accept that.
>
> We positively must enable the folks who do not understand triples, RDF,
> OWL, SPARQL and the rest to still be able to play in the global biodiversity
> data sandbox. We must continue to offer methods and techniques that do not
> require this level of knowledge. Call it a "light" version, or whatever you
> will, but I strongly believe the community at large needs it.
>  Unfortunately, that "community at large" doesn't speak up on Taxacom or
> TDWG much. I fear it's because they can't follow the technical threads and
> like Lynette are baffled and discouraged.
>
> TDWG has to continue to recognize the need to keep it simple, at least in
> part. It's always an 80-20 situation I think.  That does not preclude
> continuing work on the deeper, triples-based approaches for the 20%.  But,
> we must additionally and in parallel provide simpler, compatible approaches
> for the 80%.  We need to listen to that 80%.
>
> Chuck
>
>
> -----Original Message-----
> From: tdwg-tag-bounces at lists.tdwg.org [mailto:
> tdwg-tag-bounces at lists.tdwg.org] On Behalf Of Lee Belbin
> Sent: Thursday, May 14, 2009 7:38 PM
> To: tdwg-tag at lists.tdwg.org
> Subject: Re: [tdwg-tag] TDWG ontology revisited ... a newcomer'sperspective
> [SEC=UNCLASSIFIED]
>
> Hi Lynette, Greg, Gregor et al.,
>
> I've only just caught up with this thread, but feel obliged to post (I
> sound like Rich).
>
> A few months ago (and not for the first time), I came to exactly the same
> conclusion as you Lynette. There is I fear, a growing gap between the more
> technical members of TDWG and those who are joining TDWG from applications
> areas such as biology, taxonomy etc. As time goes on, this gap seems more
> evident, and nowhere is this more apparent than with the 'TDWG ontology'.
>
> The TDWG ontology is probably the most important priority we currently
> have. Your comments about the use of the ontology to help newcomers
> understand the domain is spot on. I'd also say that the newcomers are in
> many cases, domain experts who have a lot to contribute to the ontology, but
> really can't in its present form. The ontology is also mandatory if we want
> to efficiently cross link all the various TDWG activities/groups. Recent
> comments about Darwin Core and the TDWG ontology is a prime example!
>
> The ontology is priority-1 for TDWG, BUT (it is a big but), we need
> effective tools (preferably A web based tool) that would EASILY enable
> anyone (not just Protégé experts) to view (in various forms that were
> suitable for the purpose), manage, build, annotate, document, import and
> export bits or all of the ontology/vocabularies is helpful formats.
>
> If TDWG has these issues with developing and using an effective ontology,
> plenty of others must have also! Surely?
>
> I discussed this with Donald and he agreed and said that Greg and Garry
> were thinking about this as well (as Greg has suggested). I also discussed
> the ontology issue with Gail Kampmeier as she has a graduate student looking
> for a biodiversity informatics project - and this is a beauty. Markus Döring
> also said at the Fremantle meeting that he was keen to lead work on the
> ontology. I also discussed this same issue a month or so ago with Roger
> (post TONTO :), but I fear that Roger is in the 'techie' category and didn't
> fully grasp what I was trying to get across about SIMPLE etc. That's
> probably my fault. Your email Lynette seems to have got the point across
> better than I've done.
>
> There is a meeting about the ontology scheduled on the Tuesday evening at
> eBiosphere where Donald, Eamonn, Karen Stocks, hopefully Roger and a few
> others plan to discuss the issues. Please let me know the key issues that
> COULD be addressed at that meeting. Thankfully there seems to be some
> critical mass building about quickly moving forward on the ontology. I'd
> like to see what I can do to ensure that it happens.
>
> There is obviously nothing stopping work on aspects of the ontology such as
> Roger and Peter have suggested. If I can do anything about setting up a Wiki
> or similar easy tasks, please let me know.
>
> Lee
>
> Lee Belbin
> TDWG Secretariat
>
>
> -----Original Message-----
> From: tdwg-tag-bounces at lists.tdwg.org [mailto:
> tdwg-tag-bounces at lists.tdwg.org] On Behalf Of Greg Whitbread
> Sent: Thursday, 14 May 2009 7:09 PM
> To: Lynette.Woodburn at csiro.au
> Cc: tdwg-tag at lists.tdwg.org
> Subject: Re: [tdwg-tag] TDWG ontology revisited ... a newcomer's
> perspective [SEC=UNCLASSIFIED]
>
> Lynette,
>
> Yes. I agree.  To this end we (Garry is the one with the Twiki skills) are
> experimenting with ways of doing this using the TDWG wiki, one term per page
> described using dcmi /terms/ namepaces
> http://dublincore.org/documents/dcmi-terms/ , but alternatives do need to
> be considered before we make a start. I have just had another look at the
> MRTG Schema at http://www.keytonature.eu/wiki/MRTG_Schema_v0.7 for
> instance. A solution supporting export to a formal representation would be
> ideal though if it came to the choice, accessibility should take priority.
> Somewhere between Roger's lsid vocabularies and the MRTG schema page there
> must be a way to achieve this.
>
> Is Semantic-mediawiki an option?
>
> greg
>
> On Thu, 2009-05-14 at 13:30, Lynette.Woodburn at csiro.au wrote:
> > Back to basics ...
> >
> >
> >
> > Anyone new to biodiversity informatics (in general) and TDWG (in
> > particular) might be expected, as a first step, to seek a broad
> > understanding of the scope of the knowledge domain which is of
> > interest to the community they've just joined.  Next, they're likely
> > to want to gain an understanding of each of the main concepts and to
> > discover how those concepts relate to one other.  Delving yet deeper,
> > curiosity will lead them to seek details about features used by the
> > community to characterise each of those main concepts.  So, gradually,
> > it is anticipated that newcomers will gain an understanding of the
> > meaning associated by their fellow community members with elements
> > (concepts, features, relationships) within the knowledge domain.
> > (Those elements are, after all, the chief subjects of discourse
> > amongst community members.)
> >
> >
> >
> > This fantastic voyage of discovery, these first steps into Aladdin's
> > Cave, ought to be made easy for any newcomer.  Instead, TDWG presents
> > a dizzying array of perspectives on disparate subsets of elements
> > within the knowledge domain, often with only cryptic, tenuous links
> > binding them together.  'Horses-for-courses'-drivers clearly exist for
> > these subsets, but where is the common community understanding of
> > where each element fits into the broader, shared knowledge domain
> > which is TDWG's scope?
> >
> >
> >
> > I fully support any initiative which more effectively leads newcomers
> > (and not-so-newcomers) to that place: that place where I would hope to
> > find, in plain expressions devoid of techno-speak, a description of
> > each real world element (concept, feature, relationship), together
> > with a simple representation (a label?) by which the TDWG community
> > prefers each to be referred; that place which evolves, but endures,
> > independently of technological fashions and particular
> > implementations; that place I can visit to paint a picture in my
> > mind's eye of TDWG's own Aladdin's Cave.
> >
> >
> >
> > Lynette Woodburn
> >
> > Atlas of Living Australia
> >
> >
> >
> >
> >
> > ______________________________________________________________________
> > _______________________________________________
> > tdwg-tag mailing list
> > tdwg-tag at lists.tdwg.org
> > http://lists.tdwg.org/mailman/listinfo/tdwg-tag
> --
>
>
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> --
> Robert A. Morris
> Professor of Computer Science
> UMASS-Boston
> ram at cs.umb.edu
> http://bdei.cs.umb.edu/
> http://www.cs.umb.edu/~ram
> http://www.cs.umb.edu/~ram/calendar.html
> phone (+1)617 287 6466
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-- 
---------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
------------------------------------------------------------
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