Re: [tdwg-content] Relation of GNA to TDWG vocabularies
'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
_______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz
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.
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-
- 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:
- 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
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
I completely agree with Roger. - Pete
On Sat, Nov 13, 2010 at 4:17 AM, Roger Hyam rogerhyam@mac.com wrote:
I think we need a mother of all points at the beginning
- 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.
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-
- 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 tdwg-content-bounces@lists.tdwg.org [ tdwg-content-bounces@lists.tdwg.org mailto:tdwg-content-bounces@lists.tdwg.orgtdwg-content-bounces@lists.tdwg.org] On Behalf Of Blum, Stan Sent: Saturday, 13 November 2010 9:43 AM To: tdwg-content@lists.tdwg.orgtdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] Relation of GNA to TDWG vocabularies
Progress on the TDWG ontology seems to require:
- 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.commorris.bob@gmail.com web: http://bdei.cs.umb.edu/http://bdei.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush
http://etaxonomy.org/mw/FilteredPush
http://www.cs.umb.edu/~ramhttp://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile) _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.orgtdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
http://lists.tdwg.org/mailman/listinfo/tdwg-content
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Just FYI, there *are* mechanisms to obtain funding for exactly this. NSF funds workshops, though perhaps this would be too "applied" of a topic, but specifically BioSynC and NESCent fund working groups that want to meet and collaborate face-to-face on synthetic questions. The Comparative Data Analysis Ontology (CDAO). for example, was (one of) the result(s) of a NESCent working group called "Evolutionary Informatics".
-hilmar
On Nov 13, 2010, at 5:17 AM, Roger Hyam wrote:
I think we need a mother of all points at the beginning
- 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.
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-
- 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:
- 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
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
On Nov 13, 2010, at 5:17 AM, Roger Hyam wrote:
I think we need a mother of all points at the beginning
- 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-
- 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:
- 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
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz _______________________________________________ tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
<ATT00001.txt>
------- 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
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
- 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 mailto: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 mailto: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 mailto:tdwg-content@lists.tdwg.org" <tdwg-content@lists.tdwg.org mailto:tdwg-content@lists.tdwg.org>
Well stated Stan, but I'd add a third-
- 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 [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 mailto:tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] Relation of GNA to TDWG vocabularies
Progress on the TDWG ontology seems to require:
- 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 mailto:morris.bob@gmail.com> wrote:
On Fri, Nov 12, 2010 at 4:57 PM, Richard Pyle <deepreef@bishopmuseum.org mailto: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 mailto:morris.bob@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@lists.tdwg.org mailto:tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
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Arlin Stoltzfus (arlin@umd.edu mailto: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 http://www.molevol.org
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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-no... [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@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@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@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-
- 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:
- 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
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
<ATT00001.txt>
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
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
--
participants (7)
-
Arlin Stoltzfus -
Bob Morris -
Hilmar Lapp -
Kevin Richards -
Nico Franz -
Peter DeVries -
Roger Hyam