- tdwg-content - lists.tdwg.org

Public Review of TAPIR
by Piers Higgs 16 Oct '09

16 Oct '09

Public Review of TAPIR TDWG is pleased to announce the commencement of the Public Review of the TDWG Access Protocol for Information Retrieval TAPIR - a method for sharing biodiversity information. Since being officially put forward as a draft, TAPIR has undergone a peer review, a review by the TDWG Executive and multiple revisions. Open Invitation: We invite all who may contribute and/or consume biodiversity information to examine this proposed standard during the Public Review period from 10th September through at least until the 10th November 2009. How to Participate: You can participate in the review of TAPIR in two ways; either through lodging a comment through TDWG's Open Journal System, or you can take the Microsoft Word document and edit it with track changes and resubmit it to the TAPIR Wiki space. To post comments to the Open Journal System (that can be anonymous), go to http://www.tdwg.org/stdtrack/article/view/449/39 <http://www.tdwg.org/stdtrack/article/view/449/39> . On the right hand side of the page is a link to add a comment. At the previous URL, you can also download a copy of the Microsoft Word format specification. Once you have downloaded it, turn on track changes and make your notes and comments. You can then submit that file at http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirReview <http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirReview> . Please DO NOT add any comments to the Wiki page, only via the OJS page. Questions about the process should be directed to me at piers(at)gaiaresources.com.au. Please share this opportunity for public comment and review with others you think may be interested. Acknowledgements: I'd like to thank the authors, the anonymous reviewers and the members of the Executive Committee who reviewed the standard. In addition, the guidance of Lee Belbin through the review process has been invaluable and greatly appreciated. Links expanded: TAPIR Specification in HTML - http://www.tdwg.org/dav/subgroups/tapir/1.0/docs/tdwg_tapir_specificatio n_2009-09-08.htm <http://www.tdwg.org/dav/subgroups/tapir/1.0/docs/tdwg_tapir_specificati on_2009-09-08.htm> Official TAPIR Website - http://www.tdwg.org/subgroups/tapir/ <http://www.tdwg.org/subgroups/tapir/> Various TAPIR software packages - http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirSoftware <http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirSoftware> Subscribe to tdwg-tag - http://lists.tdwg.org/mailman/listinfo/tdwg-tag Related Links: TDWG: http://www.tdwg.org/ <http://www.tdwg.org/> Other TDWG Standards: http://www.tdwg.org/standards/ <http://www.tdwg.org/standards/> TDWG Standards Track (in OJS): http://www.tdwg.org/stdtrack/index <http://www.tdwg.org/stdtrack/index> Apologies if you receive this multiple times from various mailing lists. Sincerely, Piers Higgs, Review Manager ------------------------------------------------------- Piers Higgs Gaia Resources p +61 8 92277309 m +61 411 754 006 w www.gaiaresources.com.au e piers(a)gaiaresources.com.au -------------------------------------------------------

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year of publication
by Kevin Richards 15 Oct '09

15 Oct '09

I have just been attempting to create some example DwC data and cannot find terms for "year of publication" and "year on publication". Do they exist? ta Kevin ________________________________ 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

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Darwin Core Public Review Officially Ended
by Gail Kampmeier 23 Sep '09

23 Sep '09

The Public Review of the proposed Darwin Core Standard, which began 11 July 2009 has ended today (23 September) with the posting of the response to the Public Review http://rs.tdwg.org/dwc/index.htm. The Terms may be found at http://rs.tdwg.org/dwc/terms and the code site http://code.google.com/p/darwincore/, which worked well in combination with this list, tdwg-content, made tracking and fixing of problems very easy. The next step in this process will be to seek ratification of the Darwin Core as an official TDWG Standard from the TDWG Exec Committee. John Wieczorek (MVZ) and his co-authors Markus Döring (GBIF), Renato De Giovanni (CRIA), Tim Robertson (GBIF), Dave Vieglais (KUNHM) have done an outstanding job in pulling together everything and surviving the process of bringing this pivotal standard to fruition. It has been my great privilege to help shepherd this process as Review Manager. I would also like to thank those who jumped into the fray (or started the fray) during the Public Review, offering their opinions, expertise, experiences as tests to the system. Attached (if it makes it through) is a summary of the changes and issues left to address in the future and why. Again, many thanks to all, particularly John Wieczorek --be sure to stand him the beverage of his choice when you see him! Gail Review Manager, Darwin Core +++++++ If you build castles in the air, your work need not be lost; that is where they should be. Now put the foundations under them. Henry David Thoreau Gail E. Kampmeier Sr. Research Entomologist Illinois Natural History Survey Institute of Natural Resource Sustainability University of Illinois at Urbana-Champaign +++++++

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Re: [tdwg-content] DwC taxonomic terms
by John R. WIECZOREK 23 Sep '09

23 Sep '09

Switching to tdwg-content for this thread as it will be of general interest. 1) The whole reason behind keeping the supplementary documentation separate is so that it can grow, adapt, and explain in perpetuity without affecting the standard and without causing any "standards process" to be activated. Changes are welcome and can be done at any time. Since the wiki system is backed by SVN version control and people can subscribe to see changes committed (I see everything that happens on the site), it will be easy enough roll back anything that is out of line, or to amend it if it is only slightly misaligned. 2) Yes, please. If you have a gmail account I can add you to the list of project committers. 2009/9/22 Richard Pyle <deepreef(a)bishopmuseum.org>: > > By the way: > >> Supplementary page for Taxon at >> http://code.google.com/p/darwincore/wiki/Taxon?ts=1253663045&u > pdated=Taxon >> has also been updated, though there is a lot more in the way >> of helpful information and examples that can be added here. > > Two questions: > > 1) Can this other helpful information and examples be added after you submit > the final DwC standard? Or must it all be intact before you "push the > button"? > > 2) Would you like me to add such information & examples to the Google Code > darwincore wiki page? If so, I'd be happy to help in that capacity. > > Aloha, > Rich > > >

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NESCent Phyloinformatics VoCamp - LAST CALL FOR PARTICIPATION
by Nico Cellinese 17 Sep '09

17 Sep '09

NESCent Phyloinformatics VoCamp LAST CALL FOR PARTICIPATION This is the second and last circular for the Phyloinformatics VoCamp event that will be co-located with the 2009 TDWG Conference. Please note that there is only 1 day left until the deadline for application, which is Friday September 18. The full Call for Participation is at http://docs.google.com/View?id=dhdjhbvd_66gr5cdqfq . The application consists of your cv and your responses to 6 questions about your experience, skills, objectives, support, and commitment to open software development through an online form at http://bit.ly/VoCamp_Form . The form is easy to fill out, so please do not let the approaching deadline deter you from applying if you are interested. We specifically encourage applications from members of under- represented groups. If you have questions, contact an organizer or write to vocamp1(a)nescent.org. Yours, The Organizing Committee Arlin Stoltzfus, Chair (University of Maryland Biotechnology Institute) Nico Cellinese (University of Florida) Karen Cranston (Field Museum of Natural History) Hilmar Lapp (NESCent) Sheldon McKay (Cold Spring Harbor Laboratory, iPlant Collaborative) Enrico Pontelli (New Mexico State University)

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Re: [tdwg-content] [Fwd: Re: NCD and DwC]
by John R. WIECZOREK 16 Sep '09

16 Sep '09

I'm moving this conversation into tdwg-content to weave together the conversation for all. Sorry about the confusion. The conversation has progressed in this side thread beyond my proposal in the tdwg-content list. I'm not sure what you mean by shield, but yes, the idea is to make sure they are minimally affected by whatever may happen to NCD. To me that means using a refinement, technically. Yes, at least from the process perspective there is still an opportunity to rework NCD, as it hasn't fully progressed through the standards process. It is now at essentially the same stage as Darwin Core, though I expect Darwin Core to be ready for Executive Review this week, while NCD may take longer. I agree that consistent conventions would be nice across standards. Ultimately it will help all of our stakeholders. But DwC is the first to follow the vocabulary-first paradigm in the footsteps of Dublin Core. I can imagine inertia or resistance for other standards in the TDWG family. On Tue, Sep 15, 2009 at 10:41 AM, <renato(a)cria.org.br> wrote: > Hi John, > > Initially I had the impression that you repeated the same proposal that > you sent to the mailing list, but now I see what you mean. Sorry. > > So the idea is to actually shield DwC terms, not exactly refine the NCD > ones. I would prefer to see NCD terms being directly used, but I > understand your position. Although we have the chance to change NCD, I > would feel better knowing Roger's opinion about this. It's a strange > situation because in theory we shouldn't be changing NCD. It is already > fully ratified (or am I wrong, Wouter?). So we shouldn't expect changes, > unless NCD decides to release a new version and go through the TDWG > process all over again. > > I definitely agree that we should try to define and use the same namespace > and naming conventions across our standards. > -- > Renato > >> I think my solution is already congruent with what you are saying, >> Renato. My proposed solution is to declare these DwC terms as formal >> refinements of the NCD terms. If the NCD terms change between now and >> when that standard gets ratified, all DwC will have to do is change >> the refines attributes - no one in implementation will be affected. >> That aside, I think it would be best if NCD followed the established >> DC pattern of term identification, not just for consistency, but also >> for usability. I can definitely foresee people wanting to use the >> fielded text solution for sharing NCD records, and the way the terms >> are identified now that will be a mess. >> >> Here are the terms I have proposed and their formal refinements. >> >> dwc:institutionCode refines http://rs.tdwg.org/ncd/terms/Institution#Code >> dwc:institutionID refines http://rs.tdwg.org/ncd/terms/Institution#Id >> dwc:collectionCode refines http://rs.tdwg.org/ncd/terms/Collection#Code >> dwc:collectionID refines http://rs.tdwg.org/ncd/terms/Collection#Id >> dwc:ownerInstitutionCode refines >> http://rs.tdwg.org/ncd/terms/Institution#Code > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > >

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Re: [tdwg-content] city to county
by Steve Baskauf 14 Sep '09

14 Sep '09

1. I support Gregor's call to internationalize the name of the "county" DwC element, although I do not have a strong opinion on the name or definition. 2. One reason why I don't have strong opinions about the location terms at various levels is that I think in the future they will become increasingly irrelevant. A GPS-derived decimal latitude and decimal longitude effectively serves as a GUID for locality. If a record has a decimal latitude and longitude it should be possible (and in many cases already IS possible) to determine all of the other geographic elements (continent, country, stateProvince, etc.) from the decimal latitude and longitude using software, and with a suitably accurate digital elevation model to determine the elevation for surface records as well. The only other element that is really important is the "terminal (most specific) named area" which is not likely to be something like a political subdivision that can be computer-derivable. It is more likely to be something like "west side of Smith's quarry" or "Jonesville Community Park" - something that would be useful to place the GPS coordinates in a local context. Until I read this thread it was never clear to me that this is what dwcterms:locality meant and I think that people have been using it in a variety of ways. Perhaps the name should be changed to make it more clear that locality means the lowest level rather than something more generic. Steve Baskauf -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

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Re: [tdwg-content] NCD and DwC
by John R. WIECZOREK 12 Sep '09

12 Sep '09

OK, if we're agreed in principle to share these terms in common and upgrade them to meet the more general uses, I propose to have the following terms in the Darwin Core namespace, then NCD can reuse them. The big reason is that we (DwC) would otherwise have to wait for NCD to be finalized, lest we be given a moving target. In Darwin Core we would leave these all as record-level terms, without assigning them to a "Collection" or "Dataset" class. institutionCode Definition: The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record. Comment: Examples: "MVZ", "FMNH", "AKN-CLO" institutionID Definition: An identifier for the institution having custody of the object(s) or information referred to in the record. Refines: http://purl.org/dc/terms/identifier collectionCode Definition: The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived. Comment: Examples: "Mammals", "Hildebrandt", "eBird" collectionID Definition: An identifier for the collection or dataset from which the record was derived. For physical specimens, the recommended best practice is to use the identifier in a collections registry such as the Biodiversity Collections Index (http://www.biodiversitycollectionsindex.org/). Comment: Example: "urn:lsid:biocol.org:col:34818" Refines: http://purl.org/dc/terms/identifier On Fri, Sep 11, 2009 at 4:21 AM, Wouter Addink <wouter(a)eti.uva.nl> wrote: > Dear Gail, > > > > I’ve good news. It looks like the people in the NCD group agree with all > suggested changes: > > > > 1) Dublin Core recommends the use of the dcterms rather than their > antiquated dc counterparts. Shouldn't NCD follow suit? Specific > example: instead of http://purl.org/dc/elements/1.1/source, use > http://purl.org/dc/terms/source. > > 2) NCD is using terms from the TDWG ontology, which is to date an > unfinished academic exercise without any review. This dependency > seems to me to guarantee that NCD will require revision when the > ontology is revised. This wouldn't necessarily be required if NCD took the > reigns and defined terms that aren't already in another standard (the > Ontology does not fit into this category) within its own domain. > > Specifically, abandon http://rs.tdwg.org/ontology/voc/ in favor of > http://rs.tdwg.org/ncd/terms/. > > 3) Reword some of the NCD term definitions so that NCD can be used > more generally for data sets (data collections), and not just for > object collections. > > I’ve not yet received feedback on this from Roger Hyam however. But, unless > he disagrees and comes with a better solution, I think we can conclude that > the changes are agreed and that NCD will be adapted for these changes. I am > not sure yet when exactly, but I want to have NCD finalized soon (aim is > this month). > > Wouter

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biostatus
by Kevin Richards 11 Sep '09

11 Sep '09

This is a bit out of the blue, and I haven't had the chance to look into it fully, but... is there allowance for Biostatus in the new Dariwn Core format? An imprtant, and common field - ie Biostatus occurrence, locality, and status, eg "Present Indigenous" Kevin ________________________________ From: tdwg-content-bounces(a)lists.tdwg.org [tdwg-content-bounces(a)lists.tdwg.org] On Behalf Of Nico Cellinese [ncellinese(a)flmnh.ufl.edu] Sent: Thursday, 10 September 2009 4:04 a.m. To: tdwg-content(a)lists.tdwg.org Subject: [tdwg-content] NESCent Phyloinformatics VoCamp NESCent Phyloinformatics VoCamp OPEN CALL FOR PARTICIPATION Integrating diverse biological data with the historical process of evolution is a grand challenge for 21st century biology. The interoperability of data from diverse fields (e.g., genetics, ecology, biodiversity, biomedicine) requires a technology infrastructure based on formalized, shared vocabularies. Developing such vocabularies is a community project. In order to build controlled vocabularies and ontologies, the National Evolutionary Synthesis Center (NESCent: http://nescent.org<http://nescent.org/>) is sponsoring a "Phyloinformatics VoCamp". We invite scientists from diverse sub-disciplines to apply for this event, as explained below. The application deadline is September 18, 2009. More information about motivation, plans, and preliminary ideas is available online at http://bit.ly/VoCamp_Proposal. Feel free to disseminate this notice to colleagues who may be interested.* A VoCamp (http://vocamp.org<http://vocamp.org/>) is an intense, hands-on, working meeting with face-to-face interactions between a diverse group of people focused on vocabulary and ontology design, development and application. The Phyloinformatics VoCamp will include ontology and vocabulary developers from relevant efforts, experts on knowledge representation and reasoning, and users and developers of integrative applications that use these ontologies. This event will partially overlap with the Biodiversity Information Standards (TDWG: http://tdwg.org<http://tdwg.org/>) Annual Conference in Montpellier, France, November 9-13, 2009. The VoCamp is an activity of the TDWG Interest Group on Phylogenetics Standards (http://wiki.tdwg.org/Phylogenetics) and is partly supported by TDWG and the Université Montpellier. GOALS AND ACTIVITIES -------------------- The objective of the event is to connect previously disparate ontology development efforts, stakeholder communities, and interoperability initiatives with shared objectives. Aside from sharing knowledge, expertise, and best practices, our goal is to build-out existing ontology resources in a hands-on manner in terms of ontological rigor, semantic richness, and modularity that supports effective reuse. We also plan to have programming expertise and activities present at the event, such as for necessary large-scale transformations, and especially for proof-of-concept applications that directly apply the ontologies being developed. On a long-term basis, we anticipate that the event, if successful, will give rise to similarly structured follow-up events organized by the participating stakeholder communities, such as TDWG, SONet (http://sonet.ecoinformatics.org<http://sonet.ecoinformatics.org/>), and OBO (http://www.obofoundry.org<http://www.obofoundry.org/>). ORGANIZATION ------------ The VoCamp will be 4 days in duration during November 7-11, 2009 and is co-located with the TDWG annual conference (http://www.tdwg.org/conference2009) in Montpellier, France. The first two days (Nov 7-8) will be dedicated entirely to VoCamp and the remainder of the event (Nov 10-11) will overlap with TDWG 'workshops days'. Participants will have the opportunity, and are encouraged, to interact with TDWG participants and attend conference sessions outside of the VoCamp. The specific vocabulary development targets will be selected by the participants partly in advance through a dedicated area on a wiki, a mailing list, and one or more conference calls, and partly on-site through an Open Space activity. The exact agenda for the event will be developed similarly, but will be largely devoted to ontology and vocabulary development time. At the event itself, participants will self-organize into small subgroups focused on particular targets. The VoCamp will conclude with a wrap-up session, and a report presented to the TDWG conference audience. We also anticipate that several "boot camps" will be needed to ensure a productive event for all participants, for example on ontology design and engineering, reasoning, and infrastructure for collaborative development of ontologies. We welcome comments and suggestions for issues in ontology development that are not explicitly addressed here or in our proposal but that could be addressed at the event. Please email the organizers at vocamp1(a)nescent.org<mailto:vocamp1@nescent.org> with any suggestions. HOW TO APPLY ------------ The application consists of your cv and your responses to 6 questions about your experience, skills, objectives, support, and commitment to open software development. To apply, please fill out the online form at http://bit.ly/VoCamp_Form by September 18, and submit your CV to the organizers at vocamp1(a)nescent.org<mailto:vocamp1@nescent.org>. NESCent will provide funds in support of expenses, including travel, accommodation, registration, and meals. Pending the final amount of funds available and the support requested by the participants, sponsorship may need to be capped. Logistical and travel details will be communicated to accepted and confirmed participants. We specifically encourage applications from members of under- represented groups, specifically women and minorities, and from graduate students and post-docs. If you have questions or are unsure whether to apply, please contact an organizer or write to vocamp1(a)nescent.org<mailto:vocamp1@nescent.org> . Please understand that funding and space for this event are limited. We also need to balance a critical mass of expertise in specific areas with broad participation. Therefore, not all qualified applicants can be guaranteed acceptance. Yours, The Organizing Committee Arlin Stoltzfus, Chair (University of Maryland Biotechnology Institute) Nico Cellinese (University of Florida) Karen Cranston (Field Museum of Natural History) Hilmar Lapp (NESCent) Sheldon McKay (Cold Spring Harbor Laboratory, iPlant Collaborative) Enrico Pontelli (New Mexico State University) * This announcement is being sent to the following lists: evoldir, TDWG, SSB, nexml, phylows, CDAO, SONet, GBIF, Ecolog, TAXACOM. ________________________________ 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

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DwC taxonomic terms
by Richard Pyle 10 Sep '09

10 Sep '09

Greetings, I only just now subscribed to this list, and I apologize for not coming into the discussion earlier. I've just finished reading this complete thread in the archives, and I want to make a few comments while it's frseh in mind (as fresh as one's mind can be at 3:30am). I will expand (expound?) some more tomorrow. I understand the desire to stick with familiar terms; but in the case of taxonomy, "familiar" can be a bad thing. Several critical words (e.g., "name", "concept", "taxon", etc.) mean slightly (sometimes not so slightly) different things to different people. As such, relying on the term itself to inform users of what the term represents (without referring them to the definition) can lead to disparate applications of the term in provided datasets. In my mind, it's better to use a less-familiar term that requires users to consult the definitoion, to reduce the chance of misapplication; rather than save the end user the trouble of consulting the definition by trying to use a familiar term that is definied differently by different people. Too much opportunity for a person to jump to the wrong conclusion about what content is expected in association with a particular term. One of the biggest complaints I had about TCS 1.0 was the distinction between "name" and "concept". It was always my intent to try to suppress or eliminate this distinction in TCS 2.0; so I'm less eager than Stan is to cling to the terms as they exist in TCS 1.0. Don't get me wrong -- I have been wrestling with data modelling of taxon names and taxon concepts since about 1990, so I am *VERY* familiar with what people mean when they distinguish names from concepts. But at an informatics level, I think Markus was absolutely right when he defined the "usage" as the most granular (and convenient) data object you can use to refer to either taxon concepts or taxon names. Our community has struggled with what to call this "thing" for a long time. Walter called it "Potential Taxon". I first started calling it "TaxonRef" (short for "Taxon Reference", based on pretty-much the same logic Dave Remsen alluded to). Then I started calling it "Assertion" (sensu: http://systbio.org/files/phyloinformatics/1.pdf). James Ytow had something similar called "Appearance"; but after years of conversations with him, we finally established that his "Appearance" was something slightly different (actually more granular). Others have called it a "Treatment" or "Taxon Treatment". In developing GNUB, we finally settled on "TaxonNameUsage", because that was both explicit, and generic (and also wouldn't likely be confused with anything else in our field). Yes, it's cumbersome, but I think it represents the right balance of self-describing but without potentially disparate preconceived notions. The definition is the usage or application of a taxon name within a particular documented context. "Documented context" is mostly published literature, but can also include any other forms of documentation, such as correspondence, unpublished manuscripts, single-copy documents such as field notes, specimen identification tags, etc. This is the core unit of information that GNUB will index and assign shared GUIDs to. I am absolutely convinced that it will become the standard currency for referencing taxon names and concepts. The point that Markus was trying to make is that a TaxonNameUsage instance carries both an implied (or explicit) taxon concept circumscription, and also the nomenclatural metadata associated with how that circumcription was labelled (i.e., the "name"). This doesn't mean it's ambiguous, because it is what it is: a discrete Usage Instance. The difference is in what set of metadata is harvested from the identified Usage Instance. For example, consider: 1. Aus bus Smith 1950 sec Smith 1950 2. Aus bus Smith 1950 sec Jones 1960 3. Xus bus (Smith 1950) sec Brown 1970 We have one species epithet, and three TaxonNameUsage instances (TNUs). #1 is the original taxonomic description of the species "bus", which was originally combined with the genus "Aus". This has both a name part (Aus bus Smith 1950), and an implied taxon concept (sec Smith 1950). If I resolve any of these TNUs for nomenclatural information, I get a genus name, species epithet, an author, and a year. If I resolve them for taxon concept information, I get all the name bits plus the according to stuff ("sec" stuff); plus any other taxon concept information that is resolvable through that particular usage instance. Thus, whether you're interested in the nomenclature or the concept circumscription, you get both (explicitly) from referencing a TNU instance. I'm too tired to write any more now, but I plan to expand on this tomorrow, with specific reference to the DwC terms and in the context of GNUB. Aloha, Rich Richard L. Pyle, PhD Database Coordinator for Natural Sciences and Associate Zoologist in Ichthyology Department of Natural Sciences, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef(a)bishopmuseum.org http://hbs.bishopmuseum.org/staff/pylerichard.html

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