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Dear all:<br>
<br>
Our joint paper
(<a class="moz-txt-link-freetext" href="https://journals.ku.edu/index.php/jbi/article/view/3927/3790">https://journals.ku.edu/index.php/jbi/article/view/3927/3790</a>; you
may just look at "Summary and Outlook at the end)) and also Dave
Thau's other publications (<a class="moz-txt-link-freetext" href="http://wwwcsif.cs.ucdavis.edu/~thau/">http://wwwcsif.cs.ucdavis.edu/~thau/</a>;
perhaps start with the 2007 Ecol. Inform. publication) provide *a*
vision for usage. There are others since ontology development is
purpose dependent.<br>
<br>
1. Dahdul et al. 2010
(<a class="moz-txt-link-freetext" href="http://sysbio.oxfordjournals.org/content/59/4/369.full.pdf+html">http://sysbio.oxfordjournals.org/content/59/4/369.full.pdf+html</a>)
provide a rationale from the viewpoint of large-scale,
phylogeny-informed, ontology-driven analyses of evolutionary traits.
Quote:<br>
<br>
"A more complex investigation of morphology, such as a comparison of
structures across a monophyletic group of species, requires
processing such a large amount of data that it is rarely undertaken
except by the most determined domain experts. Yet larger-scale
analyses of the patterns of morphological evolution across multiple
clades are simply not tractable." [Inference: they would be if we
had suitable ontologies].<br>
<br>
2. Schulz et al. 2008
(<a class="moz-txt-link-freetext" href="http://bioinformatics.oxfordjournals.org/content/24/13/i313.full">http://bioinformatics.oxfordjournals.org/content/24/13/i313.full</a>)
address the potential benefits of organizing data from the model
organism and biomedical community (roughly) according to an
ontology-driven taxonomic übersystem (thanks for that one, Spanish
accents!):<br>
<br>
"To sum up, biological taxa constitute an overarching and systematic
ordering principle that is relevant in practically all biological
subject areas. In this article, we will show how the realm of
biological<br>
systematics can be embedded into an ontological framework. It is
structured as follows: We start with a summary introduction of
domain ontologies in general, as well as in the context of the
biology, addressing the OBO ontologies and the BioTop biomedical
topdomain ontology. Then we provide a formal account of different
aspects of the conceptualization of biological taxa and demonstrate
how this is implemented in BioTop. Finally, we briefly describe our
tentative implementation supporting our claim that an overarching
ontological framework for biology must have a conclusive and
practical account of biological taxa."<br>
<br>
3. Our own (Dave Thau's and mine) view of areas of usage is as
follows; this is all from the perspective of representing the
interests of taxonomy past, present and future, which - as some may
cheerfully argue - has roughly the same relationship to TDWG as
university administrations have to their faculty. <br>
<br>
A. An ontology of strictly nomenclatural relationships. Potentially
very useful for connecting literature, names, types, and ancillary
data in ways that name and synonymy relationships cannot. To my
knowledge this has neither been fleshed out nor implemented, but is
imo very worthwhile exploring.<br>
<br>
B. A full-blown ontology of (parts of) the tree of life (cf. Schulz
et al. 2010 => representing phylogeny, classification, names,
characters, specimens). Will probably only make sense for taxa whose
classification is largely stable. Not clear whether there is much
benefit for taxonomy proper.<br>
<br>
C. Ontology-based reasoning facilitates semantic integration of
multiple alternative taxonomies in taxonomic concept world. Once two
taxonomies are represented in an ontological framework and some
basic mappings of equivalence among their concepts are done
(typically by a specialist), then reasoning can infer millions of
additional relationships. This would presumably make the whole
taxonomic concept approach and mapping more palatable and scalable.
Dave Thau has shown how this can work.<br>
<br>
(D.) An emerging and growing set of anatomical ontologies (spiders,
wasps, plants, fishes, etc. => OBO Foundry) would benefit from
all or any of A-C, I suppose.<br>
<br>
I think it's also worth pondering whether, in addition trying to
represent today's data and practices in something like OWL-DL -
which will probably be both challenging and somewhat deflating -
TDWG can develop and formulate recommendations and examples of more
"ontology-compatible practices" in taxonomy and taxonomic
databasing/integretation. That is, practices that don't necessarily
use OWL just yet but adopt a semantic perspective that's more
aligned with logics than was/is often the case. A lot of that has to
do with unstated metadata-type information, I think. <br>
<br>
Bottom line of this view: reasoning in (and for!) taxonomy
can/should help with data integration, based on names (A) and
concepts (C).<br>
<br>
Regards,<br>
<br>
Nico<br>
<br>
<br>
On 11/15/2010 9:55 AM, Arlin Stoltzfus wrote:
<blockquote cite="mid:493D46F9-1ADD-4676-91A2-109EE6BD20DD@umd.edu"
type="cite">
<div>
<div>
<div>On Nov 13, 2010, at 5:17 AM, Roger Hyam wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
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<div bgcolor="#FFFFFF">
<div>I think we need a mother of all points at the
beginning</div>
<div><br>
</div>
<div>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.</div>
</div>
</span></blockquote>
<div><br>
</div>
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.
</div>
<div><br>
</div>
<div>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). </div>
<div><br>
</div>
<div>Are there any examples of this approach? </div>
<div><br>
</div>
<div>Arlin</div>
<div><br>
<blockquote type="cite"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
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<div bgcolor="#FFFFFF">
<div>Who is it for? What will it enable them to do? Do
they want/need to do it? <br>
<div><br>
</div>
</div>
<div><br>
On 13 Nov 2010, at 08:30, Kevin Richards <<a
moz-do-not-send="true"
href="mailto:RichardsK@landcareresearch.co.nz">RichardsK@landcareresearch.co.nz</a>>
wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>'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.<span
class="Apple-converted-space"> </span><br>
<br>
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.<br>
<br>
Kevin<br>
<br>
Sent from my HTC<br>
<br>
<div id="htc_header">----- Reply message -----<br>
From: "Lee Belbin" <<a moz-do-not-send="true"
href="mailto:leebelbin@gmail.com">leebelbin@gmail.com</a>><br>
Date: Sat, Nov 13, 2010 3:42 pm<br>
Subject: [tdwg-content] Relation of GNA to TDWG
vocabularies<br>
To: "<a moz-do-not-send="true"
href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>"
<<a moz-do-not-send="true"
href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>><br>
<br>
</div>
<font size="2">
<div class="PlainText">Well stated Stan, but I'd
add a third-<br>
<br>
3. Effective tool/s for viewing (graph,
sub-graph, tables, properties etc.),<br>
add/delete/modify with adaptable governance
control (e.g., assigned management<br>
to sub-graph domains), annotate (with full
logging of who did what, when and<br>
how...). This is in effect a collaboration tool.<br>
<br>
Until we have a tool (preferable to tools) that
can be intuitive and effective<br>
for building, managing and deploying /exporting
vocabs or ontologies, we will<br>
struggle with this socially and technically
tough, but very necessary task. The<br>
social issues are the hardest, but an effective
collaboration tool would be a<br>
big help.<br>
<br>
A tool that will be readily embraced by #2 (the
domain specialists) seems far<br>
more important than the tools I've seen so far
that are embraced by #1 (e.g.<br>
Protégé).<br>
<br>
That we don't have a TDWG ontology is an
increasing worry.<br>
<br>
Lee<br>
<br>
Lee Belbin<br>
Geospatial Team Leader<br>
Atlas of Living Australia<br>
<br>
<br>
-----Original Message-----<br>
From:<span class="Apple-converted-space"> </span><a
moz-do-not-send="true"
href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a><br>
[<a moz-do-not-send="true"
href="mailto:tdwg-content-bounces@lists.tdwg.org">mailto:tdwg-content-bounces@lists.tdwg.org</a>]
On Behalf Of Blum, Stan<br>
Sent: Saturday, 13 November 2010 9:43 AM<br>
To:<span class="Apple-converted-space"> </span><a
moz-do-not-send="true"
href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
Subject: Re: [tdwg-content] Relation of GNA to
TDWG vocabularies<br>
<br>
Progress on the TDWG ontology seems to require:<br>
<br>
1) one or more people with good sense of what
can be done with ontologies, both<br>
in the near-term and long-term; and<br>
2) one or more people who understand the way
information is partitioned in this<br>
domain and how it could fit together.<br>
<br>
I think we have a lot of #2, but not many of #1.<br>
<br>
FYI, we have seed money to bring these
categories together.<br>
<br>
-Stan<br>
<br>
<br>
On 11/12/10 2:25 PM, "Bob Morris" <<a
moz-do-not-send="true"
href="mailto:morris.bob@gmail.com">morris.bob@gmail.com</a>>
wrote:<br>
<br>
> On Fri, Nov 12, 2010 at 4:57 PM, Richard
Pyle<span class="Apple-converted-space"> </span><br>
> <<a moz-do-not-send="true"
href="mailto:deepreef@bishopmuseum.org">deepreef@bishopmuseum.org</a>><br>
> wrote:<br>
><span class="Apple-converted-space"> </span><br>
>> [...] the current status of the
TDWG-Ontology efforts. The Google<span
class="Apple-converted-space"> </span><br>
>> Code website seems a bit anemic,<br>
><span class="Apple-converted-space"> </span><br>
> Ooh, I love that line. I think I'll put it
in the script of my next<span
class="Apple-converted-space"> </span><br>
> animation, to be titled: "Alpha and Beta
discuss the current status of<span
class="Apple-converted-space"> </span><br>
> of the TDWG-Ontology efforts"<br>
><span class="Apple-converted-space"> </span><br>
> Thanks for correcting the URL.<br>
><span class="Apple-converted-space"> </span><br>
> Bob<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Robert A. Morris<br>
> Emeritus Professor of Computer Science
UMASS-Boston<br>
> 100 Morrissey Blvd<br>
> Boston, MA 02125-3390<br>
> Associate, Harvard University Herbaria<br>
> email:<span class="Apple-converted-space"> </span><a
moz-do-not-send="true"
href="mailto:morris.bob@gmail.com">morris.bob@gmail.com</a><br>
> web:<span class="Apple-converted-space"> </span><a
moz-do-not-send="true"
href="http://bdei.cs.umb.edu/">http://bdei.cs.umb.edu/</a><br>
> web:<span class="Apple-converted-space"> </span><a
moz-do-not-send="true"
href="http://etaxonomy.org/mw/FilteredPush">http://etaxonomy.org/mw/FilteredPush</a><br>
><span class="Apple-converted-space"> </span><a
moz-do-not-send="true"
href="http://www.cs.umb.edu/%7Eram">http://www.cs.umb.edu/~ram</a><br>
> phone (+1) 857 222 7992 (mobile)<br>
>
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<div style="font-size: 12px;">-------</div>
<div style="font-size: 12px;">Arlin Stoltzfus (<a
moz-do-not-send="true" href="mailto:arlin@umd.edu">arlin@umd.edu</a>)</div>
<div style="font-size: 12px;">Fellow, IBBR; Adj. Assoc.
Prof., UMCP; Research Biologist, NIST</div>
<div style="font-size: 12px;">IBBR, 9600 Gudelsky Drive,
Rockville, MD</div>
<div style="font-size: 12px;">tel: 240 314 6208; web: <a
moz-do-not-send="true" href="http://www.molevol.org">www.molevol.org</a></div>
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