[tdwg-content] Relation of GNA to TDWG vocabularies

Bob Morris morris.bob at gmail.com
Mon Nov 15 22:11:35 CET 2010


One example is the methodology of "competency questions", whether in
natural language or something formal, or both.  These are explicit
questions that the target information systems should be able to
address, and if inclusive enough will help reveal the terms and
relationships needed. [1] touches on them. [2] is a specific
biodiversity set of competency questions by Dave Thau, (the only
biodiversity competency questions  I know about, but there may be
others now lurking in ALA, or elsewhere.)  [3] Is a nice paper with
rather explicit detail about how they designed and exploited their
competency questions.

[1]  http://protege.stanford.edu/publications/ontology_development/ontology101-noy-mcguinness.html
[2]  http://code.google.com/p/ala-bie/wiki/OntologyCompetency
[3]  A Semantic Web Ontology for Small Molecules and Their Biological Targets
JooYoung Choi, Melissa J. Davis, Andrew F. Newman, Mark A. Ragan
Journal of Chemical Information and Modeling 2010 50 (5), 732-741


Bob Morris

Robert A. Morris
Emeritus Professor  of Computer Science
UMASS-Boston
100 Morrissey Blvd
Boston, MA 02125-3390
Associate, Harvard University Herbaria
email: morris.bob at gmail.com
web: http://bdei.cs.umb.edu/
web: http://etaxonomy.org/mw/FilteredPush
http://www.cs.umb.edu/~ram
phone (+1) 857 222 7992 (mobile)


On Mon, Nov 15, 2010 at 8:55 AM, Arlin Stoltzfus <arlin at umd.edu> wrote:
> On Nov 13, 2010, at 5:17 AM, Roger Hyam wrote:
>
> I think we need a mother of all points at the beginning
> 0) Clearly defined use-cases/scenarios/competency questions that have enough
> detail to act as tests of any proposed solutions. Without these we will
> continue to bob around in the sea of good ideas and never arrive at any
> destination.
>
> I often have thought the same thing.  Folks working on ontologies tend to
> focus on philosophical issues of conceptualization, i.e., painting a
> detailed picture of the "things" involved.  This quickly leads to problems
> because, to the extent that the world actually can be understood via
> "classes" and "properties", domain experts simply do not agree on what these
> classes and properties are.  Yet one of the (frequently implicit)
> assumptions of ontology-building is that the domain experts have an
> agreed-upon description of the world, or they can talk themselves to the
> point of having one.
> The alternative is to focus on the process of reasoning from inputs to
> correct outputs, i.e., test-driven ontology development.  Perhaps domain
> experts would agree much more thoroughly on what inferences are valid, and
> what ones are invalid, from a given set of inputs.  In an ideal world, the
> domain experts would provide a rich set of hypothetical information inputs,
> and then they would provide a rich set of inferences from them, and perhaps
> an equally rich set of invalid inferences, and then the knowledge
> engineering folks would build the ontology to avoid all the invalid
> inferences and support as many of the valid inferences as they can (until
> the money runs out).
> Are there any examples of this approach?
> Arlin
>
> Who is it for? What will it enable them to do? Do they want/need to do it?
>
>
> On 13 Nov 2010, at 08:30, Kevin Richards <RichardsK at landcareresearch.co.nz>
> wrote:
>
> 'Effective tools' to do X, Y & Z always seem to be on the agenda, but I'm
> not sure it is the tools that are the hold up.  Unfortunately I think it
> boils down to funding... I'm sure if we had adequate funding to get people
> together for the required length of time, working on the right stuff etc,
> etc, then we would make fantastic progress.
>
> I'm thinking a really good session with a basic UML tool would be a big step
> forward.  I have got hold of a UML tool and intend to have a go at a core
> tdwg model.  I think it would be great then if we could organise a session
> on working on this model.
>
> Kevin
>
> Sent from my HTC
>
> ----- Reply message -----
> From: "Lee Belbin" <leebelbin at gmail.com>
> Date: Sat, Nov 13, 2010 3:42 pm
> Subject: [tdwg-content] Relation of GNA to TDWG vocabularies
> To: "tdwg-content at lists.tdwg.org" <tdwg-content at lists.tdwg.org>
>
> Well stated Stan, but I'd add a third-
>
> 3. Effective tool/s for viewing (graph, sub-graph, tables, properties etc.),
> add/delete/modify with adaptable governance control (e.g., assigned
> management
> to sub-graph domains), annotate (with full logging of who did what, when and
> how...). This is in effect a collaboration tool.
>
> Until we have a tool (preferable to tools) that can be intuitive and
> effective
> for building, managing and deploying /exporting vocabs or ontologies, we
> will
> struggle with this socially and technically tough, but very necessary task.
> The
> social issues are the hardest, but an effective collaboration tool would be
> a
> big help.
>
> A tool that will be readily embraced  by #2 (the domain specialists) seems
> far
> more important than the tools I've seen so far that are embraced by #1 (e.g.
> Protégé).
>
> That we don't have a TDWG ontology is an increasing worry.
>
> Lee
>
> Lee Belbin
> Geospatial Team Leader
> Atlas of Living Australia
>
>
> -----Original Message-----
> From: tdwg-content-bounces at lists.tdwg.org
> [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Blum, Stan
> Sent: Saturday, 13 November 2010 9:43 AM
> To: tdwg-content at lists.tdwg.org
> Subject: Re: [tdwg-content] Relation of GNA to TDWG vocabularies
>
> Progress on the TDWG ontology seems to require:
>
> 1) one or more people with good sense of what can be done with ontologies,
> both
> in the near-term and long-term; and
> 2) one or more people who understand the way information is partitioned in
> this
> domain and how it could fit together.
>
> I think we have a lot of #2, but not many of #1.
>
> FYI, we have seed money to bring these categories together.
>
> -Stan
>
>
> On 11/12/10 2:25 PM, "Bob Morris" <morris.bob at gmail.com> wrote:
>
>> On Fri, Nov 12, 2010 at 4:57 PM, Richard Pyle
>> <deepreef at bishopmuseum.org>
>> wrote:
>>
>>> [...] the current status of the TDWG-Ontology efforts.  The Google
>>> Code website seems a bit anemic,
>>
>> Ooh, I love that line.  I think I'll put it in the script of my next
>> animation, to be titled: "Alpha and Beta discuss the current status of
>> of the TDWG-Ontology efforts"
>>
>> Thanks for correcting the URL.
>>
>> Bob
>>
>>
>> Robert A. Morris
>> Emeritus Professor  of Computer Science UMASS-Boston
>> 100 Morrissey Blvd
>> Boston, MA 02125-3390
>> Associate, Harvard University Herbaria
>> email: morris.bob at gmail.com
>> web: http://bdei.cs.umb.edu/
>> web: http://etaxonomy.org/mw/FilteredPush
>> http://www.cs.umb.edu/~ram
>> phone (+1) 857 222 7992 (mobile)
>> _______________________________________________
>> tdwg-content mailing list
>> tdwg-content at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>
>
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> <ATT00001.txt>
>
> -------
> Arlin Stoltzfus (arlin at umd.edu)
> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
> IBBR, 9600 Gudelsky Drive, Rockville, MD
> tel: 240 314 6208; web: www.molevol.org
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