June 2012 - tdwg-content - lists.tdwg.org

Re: [tdwg-content] If you need something for referring to a population, then it is probably best to do it as a related class
by Nico Franz 05 Jun '25

05 Jun '25

Hello all: I have a few inserted comments, hopefully with some clarifying effect: On 5/4/2011 10:54 AM, Peter DeVries wrote: > Hi Steve, > > I may have overloaded the term specimen to make the explanation easier > to follow. > > A specimen could be an individual or it could be part of an individual. > > To some extent you need to think about how these models will be used. > > If you subscribe to the model that a species is whatever a taxonomists > says it is then it is difficult to make statements like. > > X% of the world's species will be extinct by 2050. > > If you mean a species as defined by the concept documented at this URI > which is supported by these specimens, images, and DNA then you are on > firmer ground. > > Species in the natural world do a pretty good job recognizing those > individuals that are appropriate mates. In other words members of > their own species. > > Are we modeling species or variations in human conceptualizations of > species? > >> Assuming that there was only one individual organism identified >> there is really one one species (or hybrid). > Aaaaaaaaaaaaaah! Please Nico C., don't take this one up! > > > I stick with this. Assuming you don't have a hybrid individual. That > individual is one species. The fact that human may disagree on what > species it is a human issue. > > Again, Are we modeling species or variations in human > conceptualizations of species? NMF: I believe there is a history of biodiversity database engineering that actually led some people, initially in Australia (Greg Whitbread?) and Europe (Berendsohn's group) to place more emphasis on modeling human conceptualizations of taxa. I understand this happened in the late 80s / early 90s. The motivation was, apparently, that no long-term consensus seemed available to model a single and sufficiently widely accepted taxonomy of, say, Central European vascular plant species or mosses. I believe that projects such as the Euro + Med PlantBase (http://www.emplantbase.org/home.html) are examples of the persistence (success?) of this 20+ year old practice. I think this is the kind of background that Steve is referring to. > > Which of these is of primary importance to decision makers and > non-taxonomist biologists? > Part of the problem with various publications relating to ontologies > and taxonomy is that their species models entail a specific > phylogenetic hypothesis. > > In the real world taxa are not as clean as some would like to make > them out to be. > > Each individual is a unique combination of thousands of separate gene > lineages which often do not follow clean monophyletic paths. > > I would argue that most of those who work with species related data > see them as useful typological constructs which in general follow the > biological species model. NMF: The solution of how to properly model things such as species in RDF, OWL (etc.) should ideally accommodate all "species concepts" (BCS, ESC, PSC, GSC, there's dozens), i.e. it should be neutral towards this issue. The examples below are too simple, ignoring for example cases such as pro parte synonymy, or a concept ("species") that appears unique and monophyletic to one author but (vastly) polyphyletic to another. To do an accurate mapping in that latter case (which is not super-common but it's real), I think one would have to come down on saying we're modeling human conceptualizations. They are not just that, so really it's not a strict dichotomy, meaning that by modeling conceptualizations we do not have to say "the species only exist on our heads", or "well, then anything goes". I agree (sheepishly) that it does come down to what the input data look like, and what the expectations are towards just accommodating the user community versus pushing them in a particular direction. Some of this also on p. 47 of this PDF: https://journals.ku.edu/index.php/jbi/article/view/3927/3852 > > /Aedes triseriatus/ owl:sameAs /Ochlerotatus triseriatus/ > > Others seem to see them as phylogenetic end nodes which entail a > specific phylogenetic history. > > /Aedes triseriatus/ distinctFrom /Ochlerotatus triseriatus/ > / > / > If you are primarily interested in understanding issues of ecology, > disease, diversity and conservation the former model is more > appropriate than the later. > > Respectfully, > > - Pete Regards, Nico Nico M. Franz, Ph.D. Assistant Professor Director, UPRM Invertebrate Collection Department of Biology University of Puerto Rico Call Box 9000 Mayagüez, PR 00681-9000 Phone: (787) 832-4040, ext. 3005 Fax: (787) 834-3673 E-mail: nico.franz(a)upr.edu Laboratory website: http://academic.uprm.edu/~franz/ UPRM-INVCOL: http://uprm-invcol-project.tumblr.com/

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use of the terms dcterms:rightsHolder and dcterms:accessRights in existing databases
by Steve Baskauf 03 Jul '12

03 Jul '12

The terms dcterms:rightsHolder and dcterms:accessRights are "imported" from Dublin Core into the Darwin Core record-level vocabulary. I am interested in them for two reasons: there are several issues with the use of those terms as RDF predicates, and they differ from the terms suggested for use in rights management in the draft Audubon Core vocabulary. What I am wondering is how widely are they actually used in databases by our community? If you maintain a database, do you use them? 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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Job announcement: Biodiversity Informatics Manager for Canadensys
by Peter Desmet 28 Jun '12

28 Jun '12

Dear colleagues, The Université de Montréal Biodiversity Centre is seeking to hire a Biodiversity Informatics Manager for the Canadensys network (http://www.canadensys.net) An excerpt from the position description: The Biodiversity Informatics Manager will maintain, improve and expand the Canadensys biodiversity network, to ensure its relevance, usefulness and visibility. He/she will design and implement innovative tools to publish, synthesise and display biodiversity data, building upon the current infrastructure, which includes a community portal (http://www.canadensys.net) blog (http://www.canadensys.net/blog) explorer (http://data.canadensys.net/explorer) repository (http://data.canadensys.net/ipt) and checklist database (http://data.canadensys.net/vascan) ... The full description - including how to apply - can be found attached or at http://www.canadensys.net/job-announcement.pdf. Evaluation of applications will begin July 15, 2012. Best regards, Peter Desmet p.p. Anne Bruneau PS: Apologies for cross-posting.

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Re: [tdwg-content] LSID Resolution Service using DDDS/DNS
by Julien Cigar 20 Jun '12

20 Jun '12

Thank you all for those clarifications, I'll not go further with LSID and rather use the usual URLs. On 06/19/2012 23:41, Jonathan A Rees wrote: > Sadly nobody ever registered urn:lsid: with IETF, or even specified it > well enough that it would be able to pass IETF NID review if > submitted. LSIDs aren't URNs or URIs in any standards sense. Jonathan > > On Mon, Jun 18, 2012 at 10:51 AM, Julien Cigar<jcigar(a)ulb.ac.be> wrote: >> Hi Roderic, >> >> Thanks for your reply. >> >> But I've almost the same feeling. The more I read about LSIDs, the more I >> feel that there are no real huge benefits over URLs, .. although it looks >> like different concept to me: I see more an URL as the location of the >> resource, and the LSID the identifier of that resource. >> >> It's frustrating because at first glances all the models and the "to be >> compliant you must ..." rules that come with the spec seemed pretty >> >> Some advantages I see compared to URLs: >> - the separation of data and metadata (through the .getData / .getMetadata >> methods and the WSDL files), .. although you could achieve more or less the >> same by playing on the Accept header of the HTTP request >> - the versioning >> - the resolution services/discovery services.. although there are a lot of >> "assuming that..." in the spec >> - protocol independent >> - other things ... ? >> >> Best regards, >> Julien >> >> >> On 06/18/2012 15:15, Roderic Page wrote: >>> Hi Julien, >>> >>> Firstly, let me say "run, run away now". Unless you need to support >>> resolving existing LSIDs (e.g., Index Fungorum, IPNI) then I can see no >>> reason to use LSIDs. The future landscape of identifiers is essentially URLs >>> and DOIs. The difference between the two boils down to whether you want your >>> identifiers to have a degree of management or not (you can add management to >>> URLs but the DOI infrastructure for this seems more established). >>> >>> My understanding has been that querying the DNS for the SRV record is >>> enough. This is what my LSID tester >>> http://darwin.zoology.gla.ac.uk/~rpage/lsid/tester/ >>> <http://darwin.zoology.gla.ac.uk/%7Erpage/lsid/tester/> does. Reading the >>> LSID spec I get the sense that, had it been more widely adopted, there was a >>> mechanism to resolve LSID authorities centrally at a server >>> "lsidauthority.org<http://lsidauthority.org>" (option [a]). If this >>> mechanism didn't exist, we would do a regular DNS lookup of the domain in >>> the LSID we were trying to resolve (option [b]). Option (a) was never >>> implemented, so it's option (b). >>> >>> >>> That said, >>> >>> Regards >>> >>> Rod >>> >>> On 18 Jun 2012, at 13:04, Julien Cigar wrote: >>> >>>> Hello, >>>> >>>> I'm reading the LSID spec and there are some things that are some things >>>> that are a little cloudy to me. >>>> >>>> The spec says that the client should query the DNS for NAPTR records for >>>> the domain name "lsid.urn.arpa", but it seems that the URN NID part "lsid" >>>> has not been established at IANA (lsid.urn.arpa is unresolvable) ? Why ? >>>> I wondered if it's enough to query the DNS of the "authority >>>> identification" part of the LSID (domain name) for a _lsid._tcp SRV record >>>> and assume that this entry is a valid resolution service for the given LSID >>>> ? If not, what's the proper way to find a resolution service for, let's say, >>>> "urn:lsid:blah.my.domain:foo:12345" ? >>>> >>>> Thank you >>>> >>>> Best regards, >>>> Julien >>>> >>>> -- >>>> No trees were killed in the creation of this message. >>>> However, many electrons were terribly inconvenienced. >>>> >>>> <jcigar.vcf>_______________________________________________ >>>> tdwg-content mailing list >>>> tdwg-content(a)lists.tdwg.org<mailto:tdwg-content@lists.tdwg.org> >>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content >>> >>> --------------------------------------------------------- >>> 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<mailto:r.page@bio.gla.ac.uk> >>> >>> Tel: +44 141 330 4778 >>> Fax: +44 141 330 2792 >>> Skype: rdmpage >>> AIM: rodpage1962(a)aim.com<mailto:rodpage1962@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 >>> >> >> -- >> No trees were killed in the creation of this message. >> However, many electrons were terribly inconvenienced. >> >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> -- No trees were killed in the creation of this message. However, many electrons were terribly inconvenienced.

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LSID Resolution Service using DDDS/DNS
by Julien Cigar 20 Jun '12

20 Jun '12

Hello, I'm reading the LSID spec and there are some things that are some things that are a little cloudy to me. The spec says that the client should query the DNS for NAPTR records for the domain name "lsid.urn.arpa", but it seems that the URN NID part "lsid" has not been established at IANA (lsid.urn.arpa is unresolvable) ? Why ? I wondered if it's enough to query the DNS of the "authority identification" part of the LSID (domain name) for a _lsid._tcp SRV record and assume that this entry is a valid resolution service for the given LSID ? If not, what's the proper way to find a resolution service for, let's say, "urn:lsid:blah.my.domain:foo:12345" ? Thank you Best regards, Julien -- No trees were killed in the creation of this message. However, many electrons were terribly inconvenienced.

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