[tdwg-content] Relation of GNA to TDWG vocabularies

Nico Franz nico.franz at upr.edu
Mon Nov 15 15:45:10 CET 2010


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 at landcareresearch.co.nz 
>> <mailto: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 <mailto: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 
>>> <mailto:tdwg-content at lists.tdwg.org>" <tdwg-content at lists.tdwg.org 
>>> <mailto: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>
>>> [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 <mailto: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 
>>> <mailto:morris.bob at gmail.com>> wrote:
>>>
>>> > On Fri, Nov 12, 2010 at 4:57 PM, Richard Pyle
>>> > <deepreef at bishopmuseum.org <mailto: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 <mailto:morris.bob at gmail.com>
>>> > web:http://bdei.cs.umb.edu/
>>> > web:http://etaxonomy.org/mw/FilteredPush
>>> >http://www.cs.umb.edu/~ram <http://www.cs.umb.edu/%7Eram>
>>> > phone (+1) 857 222 7992 (mobile)
>>> > _______________________________________________
>>> > tdwg-content mailing list
>>> >tdwg-content at lists.tdwg.org <mailto: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 <mailto: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 <http://www.molevol.org>
>
>
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