March 2014 - 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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synonyms in DwC Archives
by Hilmar Lapp 19 Mar '14

19 Mar '14

I'm looking for recommendations on how best to put synonyms for taxon records into DwC Archive format. I'm assuming that these would go into an extension file. Do I have this right? What I'm having more trouble with is determining the right column term. there's dwc:vernacularName, which is also in the examples, but what about synonyms of different types that come with taxonomies (such as NCBI's) or that result from merging taxonomies. There isn't an obvious candidate in DwC, and the list at http://rs.gbif.org/core/dwc_taxon.xmldoesn't have a suggestion either that would seem pertinent. Any suggestions, pointers to documentation or examples? -hilmar -- Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io

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why is relationshipOfResource defined as the inverse of what one would expect?
by Hilmar Lapp 19 Mar '14

19 Mar '14

Among the ResourceRelationship terms in DwC, we have the following key properties denoting subject and object of the asserted relationship: resourceID - "An identifier for the resource that is the subject of the relationship." relatedResourceID - "An identifier for a related resource (the object, rather than the subject of the relationship)." Then there is relationshipOfResource, which oddly and confusingly is defined as the inverse of a property relating subject to object: "The relationship of the resource identified by relatedResourceID to the subject (optionally identified by the resourceID)." The comment gives examples that do nothing to suggest that the definition has this backwards, or to disambiguate: "Examples: "duplicate of", "mother of", "endoparasite of", "host to", "sibling of", "valid synonym of", "located within"." The corresponding wiki page does not offer further clarification: https://code.google.com/p/darwincore/wiki/ResourceRelationship There is also a page on the TDWG-RDF wiki (which declares itself as obsolete, yet links to itself for further information): https://code.google.com/p/tdwg-rdf/wiki/ResourceRelationship The example on this page (Table 1) seems to assume (or is fooled or confused into thinking) that relationshipOfResource is not relating object to subject, but as one would expect subject to object. So is the definition wrong? And if it's not, why was the relationship chosen to point in the inverse direction of what one would expect? -hilmar -- Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io

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