December 2011 - tdwg-content

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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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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