- tdwg-content - lists.tdwg.org

Re: [tdwg-content] Conflict between DarwinCore and DublinCore usage of dcterms:type / basisOfRecord
by Steve Baskauf 24 Oct '09

24 Oct '09

In a similar vein as Bob mentioned (below), I would like to see how this proposal would be applied to the specific case where images taken directly of living organisms are used to document occurrences (my original issue posted on the MRTG wiki, http://www.keytonature.eu/wiki/MRTGv08_Type_term_inconsistent_with_DwC) I routinely collect this kind of image and have made the case that live organism images can and should be used in the same way as physical specimens to document occurrences (http://www.cals.ncsu.edu/plantbiology/ncsc/vulpia/pdf/Baskauf_&_Kirchoff_Di…) Thus as occurrence records, the metadata for such images should be in conformity with DwC as well as the media-specific MRTG schema. In the example of a live plant image from http://www.cas.vanderbilt.edu/bioimages/species/frame/oslo.htm I would assign image record /DwC:recordClass/ = Occurrence /DwC:basisOfRecord/ = StillImage /dcterms:type/ = StillImage /mrtg:subtype/ = Photograph [Note that DwC:basisOfRecord is not synonymous with mrtg:subtype as it currently stands. Would it have to be under John's proposal?] In the example of an image of an herbarium sheet shown at http://www.morphbank.net/Show/?pop=Yes&id=142009 I would assign the record for the herbarium sheet itself: /DwC:recordClass/ = Occurrence /DwC:basisOfRecord/ = PreservedSpecimen /dcterms:type/ = PhysicalObject and for the record of the specimen image: /DwC:recordClass/ = Occurrence /DwC:basisOfRecord/ = StillImage /dcterms:type/ = StillImage /mrtg:subtype/ = Photograph Is this the idea? Again, I note that it is not particularly useful in this situation to consider /basisOfRecord/ a subtype of /dcterms:type/ as they have the same value for the images. Steve Baskauf Bob Morris wrote: > For any proposed solutions, I'd like to see a few use cases, e.g., > examples of biodiversity multimedia resources, and how the proposals > play out for them. For MRTG's concerns, my favorites are: > > * http://bit.ly/AudubonOspreyDescription an original Audubon > manuscript describing the Osprey in the Audubon Osprey drawing > * http://bit.ly/AudubonOspreyPrint an original of the Audubon Osprey > print, for sale at a gallery, or as in a stable Collection > * http://bit.ly/AudubonOspreyDigitalImage N.Y. Public Library Digital > Image of Audubon Osprey print. > * http://www.flickr.com/photos/mikebaird/324182767/ a cc licensed > picture on Flickr of an Osprey, georeferenced to named location. > > > --Bob > > > > On Fri, Oct 23, 2009 at 4:20 PM, John R. WIECZOREK <tuco(a)berkeley.edu> wrote: > >> Gregor, >> >> That sounds like a good solution to all of the problems. I would >> propose that the basisOfRecord IS the the same thing as your proposed >> dwc:subtype, so we should keep basisOfRecord. >> >> Net solution: >> >> 1) keep dcterms:type >> 2) use DCType vocabulary to control dcterms:type (so, StillImage, >> PhysicalObject, Event, etc.) >> 3) keep basisOfRecord >> 4) use our DwC-specific subtypes (PreservedSpecimen, FossilSpecimen, >> HumanObservation, etc.) as the controlled vocabulary for basisOfRecord >> without a formal type vocabulary (very close to how it is now, just >> some of the terms would go to dcterms:type). >> 5) add a recordClass term >> 6) use the DwCType vocabulary to control the recordClass term instead >> of the dcterms:type term. >> >> This solutions fixes the Dublin Core - Darwin Core controlled >> vocabulary problem, retains all existing terms, isolates the >> controlled vocabulary that is specific to our domain, making it very >> easy to expand without changes to the standard. >> >> Any objections? >> >> John >> >> On Fri, Oct 23, 2009 at 12:33 PM, Gregor Hagedorn >> <g.m.hagedorn(a)gmail.com> wrote: >> >>>> How about we retain basisOfRecord, but have it refine dcterms:type, >>>> drop dcterms:type and add a "recordClass" term in its place that is >>>> governed exactly as dcterms:type is currently being used in the >>>> recently ratified version of the Core? >>>> >>> recordClass for Taxon/Occurrence/Event sounds good. >>> >>> I am less sure about keeping the "perspective-dependent" >>> basisOfRecord-term in a place where dcterms:type. The dcterms:type >>> vocabulary is, in principle, extensible, and meant to be extended. >>> Except, of course, some specific xml-implementation of dublin core >>> prevent this... To avoid problems with this one might desire to have >>> only the strict resource type vocabulary in dcterms:type. Then this >>> could by PhysicalObject/Event and a dwc:subtype added to express >>> PreservedSpecimen/MachineObservation etc. Essentially, MRTG intends to >>> use such a mrtg:subtype as well to differentiate different StillImage >>> or Text subtypes: >>> http://www.keytonature.eu/wiki/MRTG_Schema_v0.8#Subtype >>> >>> This would then mean, DarwinCore might support: >>> dwc:recordClass >>> dcterms:type >>> dwc:subtype >>> >>> Gregor >>> >>> > > > > -- 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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Question about Simple Darwin Core
by Jaime Bosque 19 Oct '09

19 Oct '09

Hi list, this is my first e-mail in a list like this so hope I'm doing it right at the right place :) I'm developing a web application about orchids observations from users and would like to allow them to download the observation (or a group of them) in Simple Darwin Core formatted as XML. I've been reading a useful guide in http://rs.tdwg.org/dwc/terms/simple/index.htm and have written my PHP generator but I'm still having some questions regarding to the use of it. 1.- I guess I should use Occurrence in dc:type 2.- Can I add any taxonomical information even if its an Occurrence? I think I can and in fact I should, as in the guide says: "Support (provide data in) as many fields as you can.". So, with this facts, is this a correct Simple Darwin Core xml file? <?xml version="1.0" encoding="UTF-8"?> <SimpleDarwinRecordSet xmlns="http://rs.tdwg.org/dwc/dwcrecord/" xmlns:dc="http://purl.org/dc/terms/" xmlns:dwc="http://rs.tdwg.org/dwc/terms/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://rs.tdwg.org/dwc/dwcrecord/ http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd"> <SimpleDarwinRecord> <dctype:type>Ocurrence</dc:type> <dcterms:modified>2009-08-03</dcterms:modified> <dcterms:language>es</dcterms:language> <dcterms:rights>Contenido bajo licencia Creative Commons 3.0</dcterms:rights> <dcterms:rightsHolder>Asociación Ibérica de Orquideología</dcterms:rightsHolder> <dcterms:accessRights>Para uso no comercial únicamente</dcterms:accessRights> <dwc:institutionID>NIF AIO: XXXXXXX</dwc:institutionID> <dwc:institutionCode>AIO</dwc:institutionCode> <dwc:basisOfRecord>HumanObservation</dwc:basisOfRecord> <dwc:informationWithheld>Consultar a la Asociación Ibérica de Orquideología para más detalles acerca de la observación</dwc:informationWithheld> <dwc:dataGeneralizations>La información mostrada se muestra con una imprecisión variable de 11 metros a 11 kilómetros. Para una información más precisa consultar a la Asociación Ibérica de Orquideología</dwc:dataGeneralizations> <dwc:catalogNumber>160</dwc:catalogNumber> <dwc:occurrenceDetails>http://localhost/pfc/app/base.php?contet=view_observation&id=160</dwc:occurrenceDetails> <dwc:occurrenceRemarks>una apífera en jaca</dwc:occurrenceRemarks> <dwc:recordedBy>510183 </dwc:recordedBy> <dwc:individualCount> </dwc:individualCount> <dwc:disposition>photograph</dwc:disposition> <dwc:associatedMedia>http://localhost/pfc/app/uploads/da77dc5ea69b06b66ce6cbb9f069ea2b.jpeg</dwc:associatedMedia> <dwc:country>Spain</dwc:country> <dwc:stateProvince>Huesca</dwc:stateProvince> <dwc:county>Aragón</dwc:county> <dwc:municipality>Borau</dwc:municipality> <dwc:verbatimElevation>935 m</dwc:verbatimElevation> <dwc:verbatimCoordinateSystem>decimal degrees</dwc:verbatimCoordinateSystem> <dwc:verbatimSRS>WGS84</dwc:verbatimSRS> <dwc:decimalLatitude>42.63500</dwc:decimalLatitude> <dwc:decimalLongitude>-0.58500</dwc:decimalLongitude> <dwc:geodeticDatum>WGS84</dwc:geodeticDatum> <dwc:coordinateUncertaintyInMeters>1111</dwc:coordinateUncertaintyInMeters> <dwc:scientificName>Ophrys apifera</dwc:scientificName> <dwc:kingdom>Plantae</dwc:kingdom> <dwc:phylum>Magnoliophyta</dwc:phylum> <dwc:class>Liliopsida</dwc:class> <dwc:order>Orchidales</dwc:order> <dwc:family>Orchidaceae</dwc:family> <dwc:genus>Ophrys</dwc:genus> <dwc:specificEpithet>apifera</dwc:specificEpithet> <dwc:taxonRank>species</dwc:taxonRank> </SimpleDarwinRecord> </SimpleDarwinRecordSet> Thanks in advance, Jaime

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Public Review of TAPIR
by Piers Higgs 15 Oct '09

15 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 14 Oct '09

14 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 22 Sep '09

22 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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