Dear all:

   Our joint paper (https://journals.ku.edu/index.php/jbi/article/view/3927/3790; you may just look at "Summary and Outlook at the end)) and also Dave Thau's other publications (http://wwwcsif.cs.ucdavis.edu/~thau/; perhaps start with the 2007 Ecol. Inform. publication) provide *a* vision for usage. There are others since ontology development is purpose dependent.

1. Dahdul et al. 2010 (http://sysbio.oxfordjournals.org/content/59/4/369.full.pdf+html) provide a rationale from the viewpoint of large-scale, phylogeny-informed, ontology-driven analyses of evolutionary traits. Quote:

"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].

2. Schulz et al. 2008 (http://bioinformatics.oxfordjournals.org/content/24/13/i313.full) 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!):

"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
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."

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.

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.

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.

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.

(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.

   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.

   Bottom line of this view: reasoning in (and for!) taxonomy can/should help with data integration, based on names (A) and concepts (C).

Regards,

Nico


On 11/15/2010 9:55 AM, Arlin Stoltzfus 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@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@gmail.com>
Date: Sat, Nov 13, 2010 3:42 pm
Subject: [tdwg-content] Relation of GNA to TDWG vocabularies
To: "tdwg-content@lists.tdwg.org" <tdwg-content@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@lists.tdwg.org
[mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Blum, Stan
Sent: Saturday, 13 November 2010 9:43 AM
To: tdwg-content@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@gmail.com> wrote:

> On Fri, Nov 12, 2010 at 4:57 PM, Richard Pyle 
> <deepreef@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@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@lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> 

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Arlin Stoltzfus (arlin@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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