October 2009 - tdwg-content

Conflict between DarwinCore and DublinCore usage of dcterms:type / basisOfRecord
by Gregor Hagedorn 01 Nov '09

01 Nov '09

Dear John we (Gregor Hagedorn, Bob Morris, Steve Baskauf) realize that the public review period for DarwinCore (DwC) is over, but we believe we need to bring a potentially highly problematic issue to your attention. This issue has been found originally by Steve Baskauf. Essentially, it is an issue that is not very appearant when reading DarwinCore for review, but detected when trying to implement it in combination with other technologies. Steve describes the problem on: http://www.keytonature.eu/wiki/MRTGv08_Type_term_inconsistent_with_DwC DarwinCore seems to use dcterms:type in a way that is inconsistent with the DublinCore (DC) recommendations for publication artifacts, which is the way most users of DC are likely to use dcterms:type. Steve pointed out that MRTG's use, which does follow the DC recommendation, is inconsistent with DwC. We believe that this is not a problem of MRTG; the problem equally occurs, e. g., where natural history collections collaborate with the culture and library initative Europeana.eu, which equally uses DublinCore type in the original sense. DublinCore dcterms:type has an explicit type vocabulary: http://dublincore.org/documents/dcmi-terms/#terms-type whose annotations says: "Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMITYPE]." This vocabulary: http://dublincore.org/documents/dcmi-type-vocabulary/ defines values like StillImage, Sound, MovingImage, Text. In contrast, the DwC type vocabulary acts on an abstract level of recording occurrences that are independent of physical records. These occurrences can then be vouchered by physical resources like specimens, photos, movies, etc. The actual resources treated in DublinCore are therefore only potential vouchers for a DarwinCore resource. The terms recommended for DublinCore "type" are therefore expected in the DarwinCore "basisOfRecord" property. We do not mean to imply that there is anything wrong with the DarwinCore perspective. Unfortunately, we believe that DarwinCore cannot coexist with DublinCore data, as long as DarwinCode does not define its own dwc:type/dwc:abstractType property. ------------- Test case: An image showing a taxon observation shall be documented both in DarwinCore and DublinCore. DarwinCore prescribes or recommends dcterms:type=Occurrence, plus: basisOfRecord:StillImage. DublinCore recommends dcterms:type=StillImage. ------------- We have internally begun to discuss possible solutions. In DublinCore, dcterms:type does not express a particular type of metadata record, but is metadata about the underlying resource. We therefore consider replacing the DwC use of dcterms:type with something in the dwc namespace, and replacing dwc:basisOfRecord with dcterms:type as an option that minimizes the necessary design changes in DwC. We can see some other issues arise that depend on how one tries to bring DwC into closer coherence with the DublinCore recommendations, but perhaps these are best put forth on a wiki. Here we would like only to point out that we believe that the values for basisOfRecord fit into the dcterm:type vocabulary. Observations (dwc:HumanObservation and dwc:MachineObservation) may be placed as subtypes of http://purl.org/dc/dcmitype/Event. and specimens (dwc:PreservedSpecimen, dwc:FossilSpecimen, dwc:LivingSpecimen) as subtypes of http://purl.org/dc/dcmitype/PhysicalObject. For different communities, the dwc specimen types may have to be further subtyped as "Seed", "TissueSample", "DNA_Sample". However, we believe it is not possible to create a hierarchy like "StillImage - isSubtypeOf - Image - isSubtypeOf - Occurrence" because this is a use-case dependent view: A character image may be a subtype of a taxon representation, and it may or may not be a subtype of an occurrence representation. ------------- Best wishes Gregor, Bob, Steve -- --------------------------------- Dr. Gregor Hagedorn Heinrich-Seidel-Str. 2 12167 Berlin skype: g.hagedorn This message is sent on a personal basis and does not constitute an activity of the German Federal Government or its research institutions. Together with any attachments, this message is intended only for the person to whom it is addressed and may not be redistributed or published without permission.

9 35

[tdwg-spm] Subscribing to TDWG sessions
by Cynthia Parr 27 Oct '09

27 Oct '09

For those of you on this list attending TDWG 2009 in Montpellier, today is the deadline for submitting preferences for the sessions. I strongly encourage you to submit your preference to attend the SPM/Biological Description Interest group working sessions which are Sessions 6 and 7 on Tuesday. Gregor and I have planned back-to-back sessions as scope of standards like SPM and SDD range from general descriptive summaries to more atomized descriptions, and one of the things we need to do is discuss how best to ensure semantic connections across databases and schemas so that discovery and analysis can proceed intelligently, no matter what the scale of the original data. In Session 6 we will have only two or three introductory talks to set the stage for discussion on a mechanism for proposing and approving new terms and relationships that takes advantage of the fact that SPM is an RDF-oriented standard. What I have in mind is taking advantage of GBIF's vocabulary server to extend SPM; we'd also take maximum advantage of this as we aggregate information on Encyclopedia of Life. The general idea is to promote inclusiveness in vocabulary while ensuring that SPM can help tie species-level descriptions together in machine readable ways. We'll also talk about refining some of the definitions of existing terms that have proven difficult in practice. I will send out some background material this week in preparation for this discussion. Perhaps Gregor can comment on the goals for Session 7. Cyndy Cyndy -- Cynthia Sims Parr Director of the Species Pages Group Encyclopedia of Life http://www.eol.org Office: 202.633.8730 Fax: 202.633.8742 parrc(a)si.edu Mailing address: National Museum of Natural History P.O. Box 37012 MRC 106 Washington, DC 20013-7012

2 1

Public Review of GUID and LSID Applicability Statement
by Richardson, Ben 26 Oct '09

26 Oct '09

TDWG is pleased to announce the commencement of the Public Review of the Globally Unique Identifier (GUID) and Life Sciences Identifier (LSID) Applicability Statements. Applicability Statements provide guidance for use of external standards within the TDWG domain. The GUID statement provides general recommendations and the LSID one covers the specific GUID currently recommended by TDWG. Since being officially submitted, the Applicability Statements have 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 applicability statement during the Public Review period from 23rd October till at least 23rd November 2009. How to Participate: You can participate in the review of the GUID-LSID AS 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 GUID-LSID AS Wiki space. You can post comments to the Open Journal System (which may be anonymous) at http://www.tdwg.org/stdtrack/article/view/150. The abstract is displayed and on the right hand side of the page is a link to add a comment. Please note: you must be registered and logged in to the TDWG web site to post a comment, however registration is free. Down the bottom of the page, there is a link to download the complete applicability statement. You can also comment direct in a copy of the document as follows: · At the previous URL, download a copy of the Microsoft Word format document. · Once you have downloaded it, turn on track changes and make your notes and comments. · Submit that file at http://wiki.tdwg.org/twiki/bin/view/GUID/GUIDAndLSIDASReview. Please DO NOT add any comments to the Wiki page, comment only through the two methods outlined above. Questions about the process should be directed to me at ben(dot)richardson(at)dec.wa.gov.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 for their contribution to the document. In addition, the guidance of Lee Belbin through the review process has been invaluable and greatly appreciated. Links: · GUID and LSID AS comment area in OJS http://www.tdwg.org/stdtrack/article/view/150. · LSID Wiki space: http://wiki.tdwg.org/twiki/bin/view/GUID/GUIDAndLSIDASReview · LSID Resolution Project home page: http://lsids.sourceforge.net/ · LSID Specification: http://lsids.sourceforge.net/quick-links/lsid-spec/ Please accept my apology if you’ve received this multiple times from various mailing lists. Regards, Ben Richardson This email, together with any attachments, is intended for the addressee only. It may contain confidential or privileged information. If you are not the intended recipient of this email, please notify the sender, delete the email and attachments from your system and destroy any copies you may have taken of the email and its attachments. Duplication or further distribution by hardcopy, by electronic means or verbally is not permitted without permission.

1 0

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

1 0

Question about Simple Darwin Core
by Jaime Bosque 20 Oct '09

20 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

3 5

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 -------------------------------------------------------

1 1

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

3 5