January 2012 - 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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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 27 Jan '12

27 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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