April 2011 - tdwg-content - lists.tdwg.org

An individual identified to a higher group like Order, is still an instance of a species - just a species that is currently unspecified
by Peter DeVries 25 Sep '11

25 Sep '11

What I would recommend is that you treat a specimen that is identified to an order (Perciformes) with something like the following. Species => Order Perciformes species undetermined. The individual is still an instance of a species, however that species has yet to be determined. What would work best is to have some standard way of writing the green string above. This would allow the occurrences that are of individuals identified only to the Order Perciformes, to be interpreted as a species that falls somewhere within the Order Perciformes. - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

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Question about "vocabulary" in Darwin Core Archives assistant
by Steve Baskauf 23 May '11

23 May '11

I am playing around with Darwin Core Arcives, in particular the DwC-A Assistant (http://tools.gbif.org/dwca-assistant/) One thing that I am not exactly clear about is how to use the "Vocabulary" column in the assistant. The description that comes up when you mouse over the column heading says that it should ideally be a URI that identifies the vocabulary and resolves to some machine readable form like RDF. So what I'm wondering is whether I can put what effectively amounts to as a namespace in that spot. For example, a URI for the name "Acer rubrum L." that actually resolves to RDF is: http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:… I think that would qualify as a valid HTTP URI guid because it's the proxied form of an LSID. So I would like to use it as a value for the dwc:scientificNameID column in a DwC-A taxon record. However, the only part of the identifier that makes the string unique within uBio's domain is the last number - if I'm always using a uBio guid, the first approximately 75 characters will be the same for all of the guids. So can I just put "http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:" in the Vocabulary column and then just put the locally unique numbers (e.g. "456216") in the column for dwc:scientificNameID? Should an application using a DwC-A file be smart enough to append the "vocabulary" string on the front of the actual value in the text file? Or is that not how the "Vocabulary" column is intended to be used? 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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If you need something for referring to a population, then it is probably best to do it as a related class
by Peter DeVries 10 May '11

10 May '11

I am still somewhat puzzled why TDWG seems so opposed to adopting anything that comes from outside a small click? I was thinking that it would be best to create a separate class that can be used for populations of a species. This would require adding an additional tag to the TaxonConcept Species Concept Model, which currently includes several tags like entities http://lod.taxonconcept.org/ses/mCcSp#Species <- The Species Concept for the Cougar See http://lod.taxonconcept.org/ses/v6n7p.html HTML http://lod.taxonconcept.org/ses/v6n7p.rdf RDF http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org… Base View (http://bit.ly bit.ly/gMFqR1 The model mints URI's for the following related entities. See RDF. or KB View http://lod.taxonconcept.org/ses/mCcSp#Image - An image of a Cougar http://lod.taxonconcept.org/ses/mCcSp#Occurrence - An occurrence of a Cougar http://lod.taxonconcept.org/ses/mCcSp#Individual - An individual Cougar http://lod.taxonconcept.org/ses/mCcSp#Taxonomy - A Basic Taxonomy for the Cougar, one alternative among many potential classifications http://lod.taxonconcept.org/ses/mCcSp#NCBI_Taxonomy - The NCBI Taxonomy for Cougar, or starting at the lowest available clade http://lod.taxonconcept.org/ses/mCcSp#OriginalDescription - The Original Description of the Cougar, ideally with links to the PDF or BHL URI. Here is how a subset of these would relate to the new #Population Tag and related semantic entities. This tag is used an individual organism that that is an instance of the species concept pecies concept RDF. This allows you to refer to a individual cougar in a way that is separate from the concept of cougar and retains links to other data relating to that species concept. <txn:SpeciesIndividualTag rdf:about=" http://lod.taxonconcept.org/ses/v6n7p#Individual"> <dcterms:title>A Tag for individuals of the species concept Puma concolor se:v6n7p</dcterms:title> <skos:prefLabel>A Tag-like resource that is used to label individuals of the species concept Puma concolor se:v6n7p</skos:prefLabel> <dcterms:identifier>http://lod.taxonconcept.org/ses/v6n7p#Individual </dcterms:identifier> <dcterms:description>A lightweight tag that can be used to label individuals of this species. These allow individual organisms to be modeled as instances of SpeciesIndividualTag</dcterms:description> <dcterms:isPartOf rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p#Species"/> <wdrs:describedby rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p.rdf"/> </txn:SpeciesIndividualTag> Add a tag for a species population to the species concept RDF. This allows you to refer to a population of cougars in a way that is separate for an individual cougar and retains links to other data relating to that species concept. <txn:SpeciesPopulationTag rdf:about=" http://lod.taxonconcept.org/ses/v6n7p#Population"> <dcterms:title>A Tag for populations of the species concept Puma concolor se:v6n7p</dcterms:title> <skos:prefLabel>A Tag-like resource that is used to label populations of the species concept Puma concolor se:v6n7p</skos:prefLabel> <dcterms:identifier>http://lod.taxonconcept.org/ses/v6n7p#Population </dcterms:identifier> <dcterms:description>A lightweight tag that can be used to label populations of this species. These allow populations of a species to be modeled as instances of SpeciesIndividualTag</dcterms:description> <dcterms:isPartOf rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p#Species"/> <wdrs:describedby rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p.rdf"/> </txn:SpeciesPopulationTag> This is the RDF for a population, it has as one of it's parts an individual organism. It is typed to indicate that it refers to a population of Cougars. <owl:Class rdf:about=" http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation"> <rdf:type rdf:resource="http://lod.taxonconcept.org/ses/v6n7p#Population "/> <skos:prefLabel>The population of North American Cougars Puma concolor se:v6n7 </skos:prefLabel> <dcterms:hasPart rdf:resource=" http://ocs.taxonconcept.org/ocs/51cd124d-78c5-40aa-a7ff-2e3f58ca6ade#Indivi… "/> <wdrs:describedby rdf:resource=" http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation.rdf"/> </owl:Class> Respectfully, - Pete ------------------------------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries(a)wisc.edu TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://lod.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project ---------------------------------------------------------------------------------------

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DwC for the semantic web
by Steve Baskauf 04 May '11

04 May '11

Dear colleagues, With the exciting development of Semantic Web technologies, many of us already need a way to consistently express DwC in RDF. In particular, we need it to meet the requirements for GUID resolution (as expressed in the TDWG applicability guide) and to be able to share and aggregate diverse kinds of biodiversity metadata in the Linked Open Data world. After several months of development, stimulated by the tdwg-content discussions of last Fall, we would like to offer an ontology for consideration, based on Darwin Core terms: Darwin-SW: General site: http://code.google.com/p/darwin-sw/ Using namespace dsw = "http://purl.org/dsw/" It is a candidate for general usage, but we do not claim it is _the_ solution, and greatly respect the efforts by others to develop similar ontologies, from which we have learned much. However, for DSW, we wanted to use existing DwC terms for classes and data properties whenever possible and only create new terms when there were no existing terms that would do the job. We did feel that there was a need for clarity in how resources should be typed (i.e. rdf:type property) and for object properties that expressed the relationships among classes unambiguously. Please see the Rationale, DesignPrinciples and ClassesAndTypes wiki pages at the above address. In the ontology, we sought to embody relationships among classes based on our perception of the community consensus of what the classes represent and how they are related to each other, as expressed in posts to the tdwg-content list. Thus each class is documented carefully on the wiki with hyperlinked references to specific tdwg-content posts. We also sought to clarify or resolve issues that were raised in the list discussion, most notably the relationship among Occurrences and the evidence that documents them (i.e. tokens), and the role of "individuals". See wiki pages for the Token, Occurrence, and IndividualOrganism classes. The ontology is now in use at http://bioimages.vanderbilt.edu/, and we intend to use it more widely. We would value your opinions on the fitness of this ontology as a general solution for consistently expressing DwC concepts in RDF. Sincerely, Steve Baskauf and Cam Webb steve.baskauf(a)Vanderbilt.Edu cwebb(a)oeb.harvard.edu

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domains of object properties. was Re: DwC for the semantic web
by Bob Morris 29 Apr '11

29 Apr '11

I´ve been in Ecuador for two weeks with only a few hours of internet contact. Flying from Quite tonight. So I´ve only scanned the Design Document and may have done so too hastily. I´ll have more time next week to look at it and the ontology. However, meanwhile, I´ve posted the following unsurprizing comment there, and hope that anyone who responds here will also respond there. ----- It´s a little hard to understand why DSW object properteries should have domains but data properties should not. Keep in mind that the formal semantics of rdfs:domain is that if rdfs:domain P C then any use a P x forces a to have rdfs:type C. This constrains the extensibility of P and probably of the use of other ontologies where P might be useful. Specifying domains tends to close the world somewhat, and I see no advantage to that....Indeed, this is more naughty than anti'naughty sensu Bob Morris. ----- --Bob Morris On Wed, Apr 27, 2011 at 9:01 PM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> wrote: > Dear colleagues, > > With the exciting development of Semantic Web technologies, many of us already need a way to consistently express DwC in RDF. In particular, we need it to meet the requirements for GUID resolution (as expressed in the TDWG applicability guide) and to be able to share and aggregate diverse kinds of biodiversity metadata in the Linked Open Data world. > > After several months of development, stimulated by the tdwg-content discussions of last Fall, we would like to offer an > ontology for consideration, based on Darwin Core terms: > > Darwin-SW: > General site: http://code.google.com/p/darwin-sw/ > Using namespace dsw = "http://purl.org/dsw/" > > It is a candidate for general usage, but we do not claim it is _the_ solution, and greatly respect the efforts by others to develop similar ontologies, from which we have learned much. However, for DSW, we wanted to use existing DwC terms for classes and data properties whenever possible and only create new terms when there were no existing terms that would do the job. We did feel that there was a need for clarity in how resources should be typed (i.e. rdf:type property) and for object properties that expressed the relationships among classes unambiguously. Please see the Rationale, DesignPrinciples and ClassesAndTypes wiki pages at the above address. > > In the ontology, we sought to embody relationships among classes based on our perception of the community consensus of what the classes represent and how they are related to each other, as expressed in posts to the tdwg-content list. Thus each class is documented carefully on the wiki with hyperlinked references to specific tdwg-content posts. We also sought > to clarify or resolve issues that were raised in the list discussion, most notably the relationship among Occurrences and the evidence that documents them (i.e. tokens), and the role of "individuals". See wiki pages for the Token, Occurrence, and IndividualOrganism classes. > > The ontology is now in use at http://bioimages.vanderbilt.edu/, and we intend to use it more widely. We would value your opinions on the fitness of this ontology as a general solution for consistently expressing DwC concepts in RDF. > > Sincerely, > > Steve Baskauf and Cam Webb > steve.baskauf(a)Vanderbilt.Edu > cwebb(a)oeb.harvard.edu > > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Department of Organismal and Evolutionary Biology Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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Re: [tdwg-content] DwC for the semantic web
by Ke Chung Kim 28 Apr '11

28 Apr '11

Dear Steve: Thanks for getting us information on the tdwg-content via email discussion. I am a taxonomist/systematist working with diverse insects and for the last two decades have been actively involved in biodiversity issues, specifically insect biodiversity. Although I have not followed your continued discussion on the issue last fall, I thought I should raise several points on individual, population and species in the context of the tdwg-contents: DwC for the semantic web. I am impressed with enthusiasm and dedication of the tdwg for biodiversity informatics. Assuming your focus is primarily in the taxonomic context, your effort related to bio-informatics has a considerable impact on the issues related to biodiversity homogenization and biodiversity assessment. This involves the first detection and establishment of invasive species that is expressed in terms of individual (specimen), population, or species related to location of discovery/detection and establishment of population in specific habitat unit. Similarly, biodiversity assessment involves the defined spatial unit and community structure and assemblage that consists of individuals and population of resident species that could be small numbers to several hundreds of species. I have not seen any discussion on the application of your effort under tdwg, although you may have already dealt with these issues of application for your work through your discussion. I would like to know the position of your group on these application for your current discussion on hand. Thanks for your response. K. C. Kim Ke Chung Kim, Ph. D., Dipl.-ABFE Professor Emeritus and Curator Department of Entomology, Frost Entomological Museum, 127 Headhouse #3; Tel: 814-863-2863; Fax: 814-865-3048 (ENT); Director Emeritus, Center for BioDiversity Research PSIEE, Land and Water Research Bldg., Pennsylvania State University, University Park, PA 16802, U.S.A.; Tel: 814-863-0159; Fax: 814-865-3378 (PSIEE) Home: 213 Morningside Circle, State college, PA 16803-1347 Tel: 814-234-1718; Fax: 814-234-8327 Founding Chair, Board of the DMZ Forum, Inc., NY http://www.ento.psu.edu/Personnel/Faculty/kim.htm

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Official World Tapir Day Website
by Jim Croft 27 Apr '11

27 Apr '11

http://www.tapirday.org/ hope you guys are celebrating... Jim

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poking from TDWG wiki's
by Bob Morris 15 Apr '11

15 Apr '11

What if the list tdwg-content received a notification from each TDWG wiki when a page changed? These are fairly unobtrusive and presently infrequent (because most TDWG wiki's are inactive). They summarize the change and give links to the new content. I believe that they are set to notify only once a day. I \think/ this can be accomplished without more than edit privilege on the wikis, and if nobody raises major objection, I'll try to implement it for SDD, MRTG, and AnnotationsIG and we can see if it is a help or an annoyance. Pros: No need to make announcements or comments in two places. WikiLuddites can still respond in the mailing list. No need to opt-in for Wiki change notices. One click to relevant information. Cons: Default is to summarize changes, so people who want to respond in the mailing list have to proactively visit the relevant Wiki and perhaps cut/paste into their reply. Spammy feeling if a wiki suddenly become very active. Wiki users who do not subscribe to tdwg-content won't see email discussion of wiki pages. Another possibility is to do this in some other mailing list, perhaps even one devoted to entirely to the notifications. But to me, an active mailing list seems more productive. After all, wiki content is nothing if not TDWG content.... Bob Morris -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Department of Organismal and Evolutionary Biology Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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GBIF Darwin Core data publishing documents and tools
by David Remsen (GBIF) 11 Apr '11

11 Apr '11

Dear TDWG Content GBIF has produced a series of documents and supporting tools that focus primarily on Darwin Core publishing. They are divided into three profiles each of which presents a series of documents based on the different content types in which GBIF focuses: 1. primary biodiversity data, http://www.gbif.org/informatics/primary-data/publishing/ 2. checklists, http://www.gbif.org/informatics/name-services/publishing/ 3. resource metadata http://www.gbif.org/informatics/discoverymetadata/publishing/ While you may have seen the announcement of the GBIF Integrated Publishing Toolkit earlier in the year, we also have developed two additional tools for producing Darwin Core Archives, which are featured on these sites. First, we have produced a suite of MS Excel templates, currently under evaluation, which are coupled with a web service that processes completed files and returns a validated Darwin Core Archive. Templates exist for primary biodiversity data, simple checklists, and EML metadata. See http://tools.gbif.org/spreadsheet-processor/ Second, the Darwin Core Archive Assistant is a tool that composes a XML metafile, the only XML component of a Darwin Core Archive, for you. It presents a pick list of Darwin Core and extension terms, accessed dynamically from the GBIF registry, and presents these to the user who describe their data files. This allows Darwin Core Archives to be created for sharing with no installed software at all. See http://tools.gbif.org/dwca-assistant/ We would appreciate any feedback on any or all of this as we roll these tools and documents out to the GBIF community. Best, David Remsen ---------------------------------------------------------------------------- David Remsen, Senior Programme Officer Electronic Catalog of Names of Known Organisms Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321472 Fax: +45-35321480 Mobile +45 28751472 Skype: dremsen ----------------------------------------------------------------------------

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TDWG 2011 - New Orleans - October 16-21, 2011
by Chuck Miller 08 Apr '11

08 Apr '11

The TDWG Executive Committee is pleased to announce that the 2011 TDWG annual conference will be held on October 16-21, 2011 at the Astor Crowne Plaza Hotel in New Orleans, Louisiana located at the entrance to the famous Bourbon Street district. Hank Bart, Director of Tulane Museum of Natural History, will be the local sponsor. Information on accommodations, registration, program, abstract submission and other meeting details will soon be made available at www.tdwg.org. We hope to have an informative and productive meeting and a lot of fun in The Big Easy. Chuck Miller TDWG Chair

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