- tdwg-content - lists.tdwg.org

Suggested changes to DwC documentation
by Steve Baskauf 03 Feb '12

03 Feb '12

I have submitted two issues related to documentation of Darwin Core: http://code.google.com/p/darwincore/issues/detail?id=133 regarding XSLT transformation of the normative document http://code.google.com/p/darwincore/issues/detail?id=134 regarding clearly identifying which documents are the normative documents I think they could be handled administratively without invoking the full process described in the namespace policy if the DwC task group (i.e. John Wieczorek) thinks they are advisable. Steve -- 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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Darwin Core extension on Freshwater Biodiversity Resources
by Dag Endresen (GBIF) 27 Jan '12

27 Jan '12

Dear Dr Michael Haft, I noticed your Tweet yesterday [1] and the reply from Laura regarding developing a Darwin Core extension [2]. Assuming that you might be interested to develop an extension for publishing data using the Darwin Core Archive format [3][4] I see this as a two step process. First you will need to identify the individual terms (data properties). The Darwin Core standard provides a vocabulary including the most important terms for describing primary biodiversity data records. You are strongly encouraged to reuse terms from the Darwin Core standard (and other standards) as far as is possible. New terms for the Darwin Core standard can be proposed using the link as provided by Laura [2]. Only terms of general utility for a broad range of biodiversity datasets are intended to be included in the Darwin Core standard. Terms with a more limited interest for a thematic community can be defined in a separate vocabulary to extend the list of Darwin Core terms. As an example, in the community for plant genetic resources (germplasm) we have developed such an "extension" [5] following the Darwin Core format and based on previously already established terms used in the plant genetic resources community [6][7]. If your community is already publishing a vocabulary of terms following a similar format as the Darwin Core and with individual term definitions accessible using a URI or another persistent identifier, then you may of course use your own community vocabulary of terms in the next step - without creating a new "extension" to the Darwin Core terms. The next step in the process for sharing your data using the Darwin Core Archive format is to develop an extension to the Darwin Core Archive schema. (Notice that there is a difference between the "extension" to the Darwin Core terms, and an "extension" to the Darwin Core Archive schema). The Darwin Core Archive is based on two core entities namely the Darwin Core Occurrence [8][9] or the Darwin Core Taxon [10][11]. The Darwin Core Archive format is only intended for sharing datasets with these unit types (rowType). Further work is required if you wish to share other data types using the Darwin Core Archive format. Would your data type perhaps be on the "Occurrence" [8][9] of organisms in Fresh Water Systems? The Global Biodiversity Information Facility (GBIF) provides a Sandbox [12] for testing new schema-extensions for the Darwin Core Archive format. Schema-extensions included here can be tested using the GBIF Integrated Data Publishing Toolkit (IPT) [13]. Notice that you need to select the "Sandbox mode" when installing the IPT and that you will need to reinstall the IPT if you later wish to use it in production mode. Remember also that you can use the Darwin Core Archive format without using the GBIF IPT. GBIF provides a Vocabulary Server [14] that may assist you with the development of your schema-extension (for the Darwin Core Archive). The GBIF Vocabulary Server can assist you in building the list of terms and providing the XML format for your extension that can be included to the Sandbox registry [12]. Notice that the Vocabulary Server is not automatically updating the GBIF Resources Registry [12] and that you will need to make contact with the GBIF secretariat (for example with me) to add your new extension to the Sandbox. I hope this is of help, and please don't hesitate to make further contact if you have questions or comments. I have copied this message to the TDWG mailing list to invite further comments on the development of Darwin Core extensions. Best regards Dag Endresen [1] https://twitter.com/#!/mikehaft/status/162552503228055553 [2] http://code.google.com/p/darwincore/wiki/SubmittingIssues [3] http://rs.tdwg.org/dwc/terms/guides/text/index.htm [4] http://tools.gbif.org/dwca-assistant/ [5] http://code.google.com/p/darwincore-germplasm/ [6] http://www.bioversityinternational.org/index.php?id=19&user_bioversitypubli… [7] http://apps3.fao.org/wiews/mcpd/MCPD_Dec2001_EN.pdf [8] http://rs.tdwg.org/dwc/terms/Occurrence [9] http://rs.gbif.org/core/dwc_occurrence.xml [10] http://rs.tdwg.org/dwc/terms/Taxon [11] http://rs.gbif.org/core/dwc_taxon.xml [12] http://rs.gbif.org/sandbox/extension/ [13] http://code.google.com/p/gbif-providertoolkit/ [14] http://vocabularies.gbif.org/extensions -- Dag Endresen, PhD Knowledge Systems Engineer Global Biodiversity Information Facility (GBIF) Universitetsparken 15, DK-2100 Copenhagen, Denmark http://community.gbif.org/pg/profile/dag.endresen

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DSW questions
by Hilmar Lapp 26 Jan '12

26 Jan '12

Hi Steve and Cam, I have a question re: your design of the current Semantic Darwin Core ontology. (And this is assuming that with the published 0.2 version I have the latest one in hand.) My understanding is that all classes in DSW are imported from either DwC or DC (or FOAF), in order to reuse those terms. While that's a good idea in principle, it seems that DSW is actually not saying much new (in a semantic sense) about them, except to declare them to be OWL classes, and to assert them as disjoint from each other (or equivalent in one case). DSW then adds a variety of object (and some data) properties, which distinguish themselves from those in DwC by declaring domain and range axioms for them. But that doesn't say anything about the classes either, nor does it, I would argue, about the properties - domain and range constraint really only say something about the instances for which one asserts those properties. So by itself the DSW won't allow me to infer anything about the classes and properties in the ontology (aside from disjointness), though it will allow me to make more inferences about instance data to which it is applied than DwC would. And those additional inferences would consist only of the instances' class memberships (and their non-memberships). I'm wondering a) whether I'm missing something here and am in error, and if not, b) whether the above was indeed the extent of what you wanted to achieve with DSW. Either way, what are your current plans with the ontology? It doesn't seem to have changed for a while. (And please forgive me if this isn't the right list to post to - I couldn't find a DSW-specific one on the Google code homepage.) Cheers, -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : ===========================================================

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New Paper at PLoS ONE; Darwin Core: An Evolving Community-Developed Biodiversity Data Standard
by David Bloom 25 Jan '12

25 Jan '12

A new paper about the Darwin Core Standard has been published at PLoS ONE; Darwin Core: An Evolving Community-Developed Biodiversity Data Standard. The paper at PLoS ONE: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0029715 Abstract: Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations. David Bloom VertNet Coordinator Museum of Vertebrate Zoology University of California, Berkeley 3101 Valley Life Sciences Building Berkeley, CA 94720-3160 Phone: 510.643.1620 Fax: 510.643.8238 Email: dbloom(a)vertnet.org Email: dbloom(a)berkeley.edu URL: http://www.vertnet.org VertNet Portals: MaNIS: http://www.manisnet.org HerpNET: http://www.herpnet.org ORNIS: http://www.ornisnet.org FishNet2: http://www.fishnet2.net

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Re: [tdwg-content] [Taxacom] Finding your species in Mendeley
by Roderic Page 08 Dec '11

08 Dec '11

Dear Ward, That's great! One quibble, I would expect the value for http://rs.tdwg.org/dwc/terms/#namePublishedInID to be a URI, not a string literal. In other words, instead of: <dwc:namePublishedInID> <![CDATA[ http://dx.doi.org/10.1371/journal.pone.0026243 ]]> </dwc:namePublishedInID> I would have: <dwc:namePublishedInID rdf:resource="http://dx.doi.org/10.1371/journal.pone.0026243" /> This means a client will interpret this as a resource and could decide to go and fetch it. If you store the DOI as a string clients won't know to "follow their nose" and retrieve details about the publication with that DOI. This isn't made clear in the Darwin Core spec, so I've cc'd this to the TDWG-Content mailing list in case anyone there has any comments. Regards Rod On 8 Dec 2011, at 12:20, Ward Appeltans wrote: > Dear Rod > > The original description references and DOIs are now also part of the WoRMS RDF output. > E.g. http://lsid.tdwg.org/summary/urn:lsid:marinespecies.org:taxname:590007 > > Note, the RDF seems to be cached at the TDWG site, because the new terms do not yet show up in older records. > > Thanks! > Best regards > Ward > > > From: Roderic Page [mailto:r.page@bio.gla.ac.uk] > Sent: woensdag 7 december 2011 16:40 > To: taxacom > Cc: gread(a)actrix.gen.nz; Ward Appeltans > Subject: Re: [Taxacom] Finding your species in Mendeley > > Dear Ward, > > On 7 Dec 2011, at 11:38, Ward Appeltans wrote: > > > Dear Rod, > > Good points, we have extended the WoRMS webservice, and added the elements 'link' and 'fulltext' to the Source output object. > > That's great. Will these appear in the LSID metadata as well, because that's what I use to harvest WoRMS records (and is arguably what anyone wanting to do Semantic Web-style integration will use. > > > > With regards to the mapping interface and colour blindness, there is a option to switch the base layers (to countries for example). Is this OK for you? > http://www.marinespecies.org/polychaeta/aphia.php?p=taxdetails&id=590097 > > I guess my point is that the default map should not be uninterpretable to people like me who have trouble distinguishing red and green when used together (the EOL maps are equally bad, where as GBIF is much better. > > > > Linking taxa to the original source reference (incl DOI/handle links and/or full texts if possible) is a priority in WoRMS, so I'm eager to look at more automated ways (if quality and citation completeness is acceptable). > > Automation we can do, quality depends heavily on the original citation, which for older literature can be pretty messy. If by completeness you mean completeness of the citation record you'd want to add to WoRMS, I'd argue this matters less than identifiers, because if you have a DOI you can retrieve the citation at any time (albeit with a few caveats). Obsessing with citations is what got us in this mess in the first place ;) > > Regards > > Rod > > > > > > Thanks. > Best regards > Ward > WoRMS/VLIZ > > -----Original Message----- > From: Geoffrey Read [mailto:gread@actrix.gen.nz] > Sent: woensdag 7 december 2011 9:22 > To: Roderic Page > Cc: taxacom; Ward Appeltans > Subject: Re: [Taxacom] Finding your species in Mendeley > > Hi Rod, > > Fine. Tech points Ward's business. I only want to point out that you have > only the bare minimum ION shows you, which is very far from "this record > complete". You don't seem to have the hierarchy even, just the names, and > no authors. If Thompson Reuters was in the business of creating WoRMS-like > records like that one (not difficult just takes someone a bit of time), we > volunteer database workers could all fold our tents and get back to the > taxonomic coalface (sorry, mixed metaphors there). Although they wouldn't > be allowing free access, now would they? Perhaps it's good they don't then > (see below). Plus you've matched the doi perfectly to ION's record. Which > is indeed clever. Of course Thompson Reuters could provide that initially > if they wanted to - but I imagine doing that would adversely affect some > of their middle man services. > > I like that ZooKeys is auto loading its new papers into the Species-Id > website. Ideally all taxonomy will be available structured like that, and > auto loadable into WoRMS and there would be little manual work for WoRMS > editors from the new pubs anymore. > > Geoff > > On Wed, December 7, 2011 7:43 pm, Roderic Page wrote: > > On 7 Dec 2011, at 01:15, Geoffrey Read wrote: > > > http://www.marinespecies.org/polychaeta/aphia.php?p=taxdetails&id=590097 > > Nice, but can't resist three comments: > > 1. It's great that this record has a DOI, but the same information doesn't > appear in the metadata for the LSID, which means the only way I could > extract this information from WoRMS is by screen scraping (yuck) > > 2. iTaxon already has this record complete with DOI > http://iphylo.org/~rpage/itaxon/?search=Notodasus+harrisae > > 3. When will map makers learn about red-green colour blindness! I can't > see the red dot indicating the type locality unless I zoom in and the > green background momentarily disappears. > > > > > > --------------------------------------------------------- > Roderic Page > Professor of Taxonomy > Institute of Biodiversity, Animal Health and Comparative Medicine > College of Medical, Veterinary and Life Sciences > Graham Kerr Building > University of Glasgow > Glasgow G12 8QQ, UK > > Email: r.page(a)bio.gla.ac.uk > Tel: +44 141 330 4778 > Fax: +44 141 330 2792 > AIM: rodpage1962(a)aim.com > Facebook: http://www.facebook.com/profile.php?id=1112517192 > Twitter: http://twitter.com/rdmpage > Blog: http://iphylo.blogspot.com > Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > > --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r.page(a)bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962(a)aim.com Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html

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RDF sandboxes
by joel sachs 07 Dec '11

07 Dec '11

I'd like to bring to everyone's attention the RDF sandboxes that have been set up and made available for our use - see http://code.google.com/p/tdwg-rdf/ These are a great resource - they allow projects to start exploring RDF without the hassle of setting up infrastructure (triplestores, sparql endpoints, etc.), and they allow all of us to load data into a common space for querying (as Cam did with Rod's frog data [1]). (I've found the 4store instance to be particularly satisfying - for example, the bioblitz invasives testcases [2] load and execute painlessly.) (And if anyone has the time and inclination ... it would be great to have a sandbox with rule processing capabilities.) Cheers, Joel. 1. http://code.google.com/p/tdwg-rdf/wiki/RodPageChallenge 2. http://bit.ly/vN3DvX

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Commercial usage of shape files
by Ronny Scholz 01 Dec '11

01 Dec '11

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Darwin Core changes published
by John Wieczorek 18 Nov '11

18 Nov '11

Dear all, I have finally been able to implement all of the Darwin Core proposed changes that were approved by the TDWG Executive Committee on 16 Oct 2011. Changes include corrections to minor errors that have been brought to my attention since the previous release as well as changes resulting from issues submitted to the Darwin Core Issue Tracker and resolved through open commentary and review. This revision of the Darwin Core Standard is the first one to have added terms (namePublishedInYear, dcterms:references, georeferencedDate, and identificationVerificationStatus). It is also the first revision in which a term has been deprecated (occurrenceDetails), albeit in favor of a broader existing term from the Dublin Core (dcterms:references). Not all proposed changes were accepted. Specifically, issues 115-117 calling for the inclusion of the Dublin Core terms StillImage, MovingImage, and Sound in the Darwin Core Type vocabulary have been deferred for further research. Also, issue 122 calling for an alias attribute for Darwin Core terms was rejected. The reasoning behind the decisions is included in the comments for each issue in the Issue Tracker (http://code.google.com/p/darwincore/issues/list). You can search for a specific issue by entering its number in the text box next to the "Search" button, then click on the button. The brief summary of each of the decisions is recorded on the Darwin Core Decision History page at http://rs.tdwg.org/dwc/terms/history/decisions/index.htm Anyone interested in the specific changes to the actual documents of the standard may browse the list of committed changes on the Darwin Core Google Code site at http://code.google.com/p/darwincore/source/list Specifically, revisions numbered 1469-1472, 1477, 1481, and 1484 show the recent changes related to the standard. Other revisions on the list are related to the Darwin Core Reader software, not to the standard. Files associated with the standard have all been updated. These include the archive file (darwincore_2011-10-16.zip), which contains the full standard and web page documentation. Utility files for this revision have also been created and added as featured downloads visible on the Darwin Core Project home page at http://code.google.com/p/darwincore/ Files that are no longer up to date with the standard have been deprecated, but may still be found on the downloads tab if you search for deprecated downloads. Please let me know if you have any comments or questions, Cheers, John On Mon, Oct 3, 2011 at 3:57 PM, John Wieczorek <tuco(a)berkeley.edu> wrote: > Dear all, > > This is an update to let you know that I have just submitted a summary > with a request to the TDWG Executive Committee for authorization to > make changes to the Darwin Core terms. The specific changes requested > are those that have achieved an unopposed consensus on this list > during the public review period that began 4 July 2011 (and ended when > I sent the message to the Executive today). For reference, the > specific changes for which authorization was sought are those having > the status "Vote" on the Darwin Core Issue Tracker and listed below: > > Issue 84: new term namePublishedInYear > Issue 96: new term dcterms:references, deprecate dwc:occurrenceDetails > Issue 104: new term georeferencedDate > Issue 105: new term identificationVerificationStatus > Issue 109: remove subclassing from dwctype:Occurrence > Issue 110: remove subclassing from dwctype:PreservedSpecimen > Issue 111: remove subclassing from dwctype:FossilSpecimen > Issue 112: remove subclassing from dwctype:LivingSpecimen > Issue 113: remove subclassing from dwctype:HumanObservation > Issue 114: remove subclassing from dwctype:MachineObservation > Issue 115: new term dcmitype:StillImage to Darwin Core Type Vocabulary > (value for basisOfRecord) > Issue 116: new term dcmitype:MovingImage to Darwin Core Type > Vocabulary (value for basisOfRecord) > Issue 117: new term dcmitype:Sound to Darwin Core Type Vocabulary > (value for basisOfRecord) > > In addition, there have been requests to add two attributes to all > Darwin Core terms to facilitate applications: > > Issue 121: add English term label attribute > Issue 122: add term alias attribute > > For details on these and all other open issues for the Darwin Core, > see http://code.google.com/p/darwincore/issues/list. > > Cheers, > > John >

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RDF/OWL - Please answer these questions.
by joel sachs 16 Nov '11

16 Nov '11

Hi Everyone, One of the action items out of the kick-off meeting of the new RDF/OWL best practices group was a questionnaire with two purposes: i) to assess people's expectations and wishes for the group; and ii) to serve as an RDF audit, a partial "state of the semantic web in TDWG". The questionnaire is at http://code.google.com/p/tdwg-rdf/wiki/Survey All are encouraged to participate (especially the 20 or so people who volunteered to do so at the kick-off). Filling out the survey myself, I realized that it can actually take a lot of time to present and explain an organization's rdf . So please, don't be shy about answering in parts. Take ten minutes to provide some pointers now, and then return later to provide more detailed explanations. For the first ten people to complete the survey, I will buy beer at iEvoBio 2012 (or whenever I next see you). Thanks! Joel.

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Please don't answer these questions.
by joel sachs 02 Nov '11

02 Nov '11

Hi Everyone, One of the action items out of the kick-off meeting of the new RDF/OWL best practices group was a questionnaire with two purposes: i) to assess people's expectations and wishes for the group; and ii) to serve as an RDF audit, a kind "state of the semantic web in TDWG". We agreed that we'd iterate once over the questionnaire, so here is draft 1 (pasted below). Suggestion are welcome - please make them off-list. In a couple of days, we'll circulate the real questionnaire, and ask for answers. Thanks! Joel. ------ 1. What are your expectations for the RDF/OWL Task Group? 2. Is there anything specific you'd like other members of the group to share? 3. Are you currently using, or do you have immediate plans to use RDF? If yes, can you give a brief description of the data being served, and/or provide links (if possible) to some subset of: data dumps, SPARQL endpoints, design documents or project proposals, a bubble diagram (or even just a list) of the classes and properties you are using (with namespaces, of course), a list of classes and properties that you need but that are *not* readily available, anything elses that would shed light on what you're up to?

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