December 2018 - 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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Call for Registration - U.S. Semantic Technologies Symposium Series (us2ts 2019)
by Hilmar Lapp 13 Dec '18

13 Dec '18

Apologies for cross-posting. ============================================================ U.S. Semantic Technologies Symposium Series US2TS Call for Registration <https://urldefense.proofpoint.com/v2/url?u=http-3A__us2ts.org_2019_&d=DwMFa…> http://us2ts.org/2019/posts/registration.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__us2ts.org_2019_posts_re…> ============================================================ Registration -------------------------------------- Early Registration deadline: Jan 22, 2019. Registration link: http://us2ts.org/2019/posts/registration.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__us2ts.org_2019_posts_re…> US2TS -------------------------------------- Semantic Web is an inherently multi-disciplinary field. With an ever-growing dependence on the Web and the continuously increasing importance of large-scale data sharing, integration, and reuse, natural science researchers, geoscience, biology, library science, health care, the humanities, just to name a few, have also taken an increasing interest in the Semantic Web. The U.S. Semantic Technologies Symposium (US2TS) series provide a forum to ease the division between computer science, natural science, and academia/government/industry. The list of program sessions is now available at http://us2ts.org/2019/posts/program.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__us2ts.org_2019_posts_pr…> Contact -------------------------------------- All questions about submissions should be emailed to contact-us2ts2019(a)googlegroups.com<mailto:contact-us2ts2019@googlegroups.com> Sponsors -------------------------------------- The following sponsors<http://us2ts.org/2019/posts/sponsor.html> have expressed their financial support for US2TS 2019: National Science Foundation<https://urldefense.proofpoint.com/v2/url?u=https-3A__nsf.gov_&d=DwMFaQ&c=im…>, Alfred P. Sloan Foundation<https://urldefense.proofpoint.com/v2/url?u=https-3A__sloan.org_&d=DwMFaQ&c=…> , Artificial Intelligence Journal<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.journals.elsevier.…> Platinum sponsors: Mobi<https://urldefense.proofpoint.com/v2/url?u=https-3A__mobi.inovexcorp.com_&d…>, Raytheon BBN<https://www.raytheon.com/ourcompany/bbn>, data.world<http://data.world/> Standard sponsors: IOS Press<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.iospress.nl_subjec…> [image.png] U.S. Semantic Technologies Symposium Series March 11-13, 2019 at Duke University in Durham, NC http://us2ts.org/2019/<https://urldefense.proofpoint.com/v2/url?u=http-3A__us2ts.org_2019_&d=DwMFa…>

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Re: [tdwg-content] Darwin Core and dcterms:location
by Tim Robertson 12 Dec '18

12 Dec '18

Hi Kim, (moving our private discussion onto this list) Thanks for the links. As far as I can see the “custom” dublin_core.xsd existed in all DwC releases from 2009 up until 2013-10-23 where it was removed. In that removal, the references to the location were also commented out (I presume meaning the modified XSD was no longer needed) though. For you to still find references to it suggests you might be using an older version of the Darwin Core XSD – is that possible? John / Peter: Do you recall why it was removed? To save searching, the modification to the DC xsd appeared to contain only the following:  <xs:element name="Location" substitutionGroup="dwc:anyClass"> <xs:complexType> <xs:choice maxOccurs="unbounded"> <xs:element ref="dwc:anyIdentifier"/> <xs:element ref="dwc:anyLocationTerm"/> <xs:element ref="dwc:anyRecordLevelTerm"/> </xs:choice> </xs:complexType> </xs:element> The commented out reference in the DwC xsd:  (see https://dwc.tdwg.org/xml/tdwg_dwc_class_terms.xsd) From: tdwg-content <tdwg-content-bounces(a)lists.tdwg.org> on behalf of Kim Mortimer <K.Mortimer(a)dal.ca> Date: Wednesday, 12 December 2018 at 20.34 To: "tdwg-content(a)lists.tdwg.org" <tdwg-content(a)lists.tdwg.org> Subject: Re: [tdwg-content] Darwin Core and dcterms:location To the TDWG mailing list and whomever it may concern, Darwin Core uses a Dublin Core element, dcterms:location, in its definition of classes and elements. However, no current XSD files for Dublin Core (that I can find) define location as an element. For reference, the current Dublin Core XSD files that I am familiar with are available at http://dublincore.org/schemas/xmls/qdc/ Given that dcterms:location is therefore an undefined element, the Darwin Core XML is invalid. This is important to me, and my employer MERIDIAN, because we are implementing Darwin Core in a GeoNetwork metadata schema plugin for our repository. To allow other documents to be validated against our schema within GeoNetwork, the entire plugin XML (which for us includes the Darwin Core XML) must be valid. I previously sent an email about this in September but did not receive any useful advice at the time. Development on our metadata repository has progressed without this element since then, as we have been tracking down other errors in GeoNetwork, but this is the current 'blocking' problem for us. The Darwin Core XSD files reference a dublin_core.xsd in their comments, which is said to contain dcterms:location. My best guess at what this refers to is https://github.com/tdwg/dwc/blob/2011-10-26/xsd/dublin_core.xsd - which is from a previous version of Darwin Core, and appears to be a custom version of http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd - so it unclear whether this is correct or not. Given that TDWG is responsible for Darwin Core, I am hopeful that someone will have a tip or solution. My alternative is to define dcterms:location myself as a custom insertion into Dublin Core, but based on the comments in Darwin Core files I believe some suitable XSD must exist. Thank you very much for your time, Kim Mortimer [mage removed by sender. MERIDIAN on blue circle containing many numbers,] Kim Mortimer Data Manager MERIDIAN - Marine Environmental Research Infrastructure for Data Integration and Application Network Institute for Big Data Analytics, Faculty of Computer Sciences, Dalhousie University p: + 1 902 494 1812 m: +1 902 880 1863 a: 6050 University Ave, Halifax, NS, B3H 4R2, Canada w: https://meridian.cs.dal.ca e: k.mortimer(a)dal.ca<mailto:k.mortimer@dal.ca>

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Re: [tdwg-content] Darwin Core and dcterms:location
by Kim Mortimer 12 Dec '18

12 Dec '18

To the TDWG mailing list and whomever it may concern, Darwin Core uses a Dublin Core element, dcterms:location, in its definition of classes and elements. However, no current XSD files for Dublin Core (that I can find) define location as an element. For reference, the current Dublin Core XSD files that I am familiar with are available at http://dublincore.org/schemas/xmls/qdc/ Given that dcterms:location is therefore an undefined element, the Darwin Core XML is invalid. This is important to me, and my employer MERIDIAN, because we are implementing Darwin Core in a GeoNetwork metadata schema plugin for our repository. To allow other documents to be validated against our schema within GeoNetwork, the entire plugin XML (which for us includes the Darwin Core XML) must be valid. I previously sent an email about this in September but did not receive any useful advice at the time. Development on our metadata repository has progressed without this element since then, as we have been tracking down other errors in GeoNetwork, but this is the current 'blocking' problem for us. The Darwin Core XSD files reference a dublin_core.xsd in their comments, which is said to contain dcterms:location. My best guess at what this refers to is https://github.com/tdwg/dwc/blob/2011-10-26/xsd/dublin_core.xsd - which is from a previous version of Darwin Core, and appears to be a custom version of http://dublincore.org/schemas/xmls/qdc/2008/02/11/dcterms.xsd - so it unclear whether this is correct or not. Given that TDWG is responsible for Darwin Core, I am hopeful that someone will have a tip or solution. My alternative is to define dcterms:location myself as a custom insertion into Dublin Core, but based on the comments in Darwin Core files I believe some suitable XSD must exist. Thank you very much for your time, Kim Mortimer [MERIDIAN on blue circle containing many numbers, with an orange wave pulse to the right.] Kim Mortimer Data Manager MERIDIAN - Marine Environmental Research Infrastructure for Data Integration and Application Network Institute for Big Data Analytics, Faculty of Computer Sciences, Dalhousie University p: + 1 902 494 1812 m: +1 902 880 1863 a: 6050 University Ave, Halifax, NS, B3H 4R2, Canada w: https://meridian.cs.dal.ca e: k.mortimer(a)dal.ca<mailto:k.mortimer@dal.ca>

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I am seeking speakers for a proposed Biodiversity Next symposium
by Simpson, Annie 06 Dec '18

06 Dec '18

Hello, TDWG list members, I've submitted the following abstract to Biodiversity Next and would like to know if any of you would like to give a talk? I've requested a 90-minute slot. If you are interested, please email me with your name, affiliation, title, and 300 word (or less) abstract, and we will see where this goes. How can specialized databases integrate information and work better together? Is following Darwin Core enough? Invasive species databases and other specialized biodiversity information systems are being called more and more to share their information with one another (Zeller et al. 2005; Holdren 2013). Because of differences in data content and database purpose, much information from smaller datasets can be lost during the integration process into larger databases such as BISON, iDigBio, GBIF, and others (Costello et al. 2013). The effort required for cross-walking data fields and for modifying database structure to accommodate new information is significant (Diepenbroek et al. 2014). Darwin Core extensions have been, and continue to be, created to facilitate the sharing of specialized datasets (Byrd 2018). However, following the guidelines set out in these extensions can be insufficient when their structure leans toward the flexible vs. requiring the use of controlled terms. Participants in this symposium will be encouraged to share examples -- both challenges and successes -- they have encountered during their efforts to combine specialized datasets. - Byrd C (2018) Adaptation of Darwin Core Standards and Development of New Standards for Geologic Specimens. Biodiversity Information Science and Standards 2: e25929. https://doi.org/10.3897/biss.2.25929 - Costello MJ, Michener MK, Gahegan M, Zhang ZQ, Bourne PE (2013) Biodiversity data should be published, cited, and peer reviewed. Trends in Ecology & Evolution. https://doi.org/10.1016/j.tree.2013.05.002 - Diepenbroek M, Glöckner FO, Grobe P, Güntsch A, Huber R, König-Ries B, Kostadinov I, Nieschulze J, Seeger B, Tolksdorf R, Triebel D, (2014) Towards an integrated biodiversity and ecological research data management and archiving platform: the German federation for the curation of biological data (GFBio). In: Plödereder E, Grunske L, Schneider E, Ull, D (Eds.), Informatik 2014. Bonn: Gesellschaft für Informatik e.V. p1711-1721. https://dl.gi.de/handle/20.500.12116/2782 - Holdren JP (2013) Increasing Access to the Results of Federally Funded Scientific Research. Office of Science and Technology Policy Memorandum, United States Government, Washington, DC. https://obamawhitehouse.archives.gov/sites/default/files/microsites/ostp/os… - Zeller D, Froese R, and Paulya D (2005) On losing and recovering fisheries and marine science data. Marine Policy 29(1):69-73. https://www.sciencedirect.com/science/article/pii/S0308597X04000193 *Annie Simpson, biologist & information scientist* asimpson(a)usgs.gov +1 703 648 4281 desk http://orcid.org/0000-0001-8338-5134 *BISON project (http://bison.usgs.gov <http://bison.usgs.gov>)* EcoScience Synthesis Branch *Science Analytics and Synthesis Program* *U.S. Geological Survey, MS 30212201 Sunrise Valley DriveReston, Virginia 20192*

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