August 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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iDigBio Train-the-Trainers Georeferencing Workshop Oct 8 - 12, 2012
by Deb Paul 09 Aug '13

09 Aug '13

** Hi Everyone, The Georeferencing Working Group at iDigBio is pleased to announce our first "Train-the-Trainers" Georeferencing Workshop for Thematic Collections Networks (TCNs) and others in engaged in the digitization of biological collections in the United States. See: https://www.idigbio.org/content/idigbios-first-train-trainers-georeferencin… for details. Three slots are still available in this workshop that is designed to focus on training participants to teach others to georeference. If you are interested, please send an application describing the reason(s) for your interest in the workshop, the current and future projects that will benefit from your attendance, and any previous experience you have with georeferencing to iDigBio's Program Assistant, Cathy Bester, cbester(a)flmnh.ufl.edu What: Train-the-Trainers -- Georeferencing Workshop Where: University of Florida, Gainesville, FL Who: Interested members of current TCNs and others in the biodiversity natural history collections community. When: October 8-12, 2012 Contact: Deborah Paul dpaul(a)fsu.edu for further information. Best, Deb and the iDigBio Georeferencing Working Group Deborah Paul User Services, iDigBio Institute for Digital Information, iDigInfo Florida State University Tallahassee, Florida 32308 850-644-6366

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Change of DwC terms stateProvince, county, and municipality?
by Markus Englund 06 Sep '12

06 Sep '12

Hi everyone, I have noticed that use of the Darwin Core terms stateProvince, county, and municipality sometimes can be quite confusing. This confusion may arise when a term name does not reflect the content, like when the term stateProvince does not refer to a state or province, or when the term county does not refer to a county. Take my own country Sweden for example, where the Darwin Core term stateProvince refers to the name of a county, the term county refers to the name of a municipality, and the term municipality refers to the name of a parish... As long as everyone stick to the definitions, literal meaning of term names doesn't really matters. Unfortunately, however, people sometimes tend to focus more on the literal meaning of term names than on the actual meaning of defined concepts. To make the Darwin Core terminology less confusing, I think words associated with geographic ranks should be removed from the term names. I suggest the following changes (you may come up with better ones yourself!): “stateProvince” --> “countryFirstOrderSubdivision” “county” --> “countrySecondOrderSubdivision” “municipality” --> “countryThirdOrderSubdivision” After having delved into the Darwin Core geography specifications, I also feel that these three terms would benefit from more consistent and clear-cut definitions. I have included proposed new definitions at the end of this mail. My intention is not to alter the meaning of any of the existing terms, just to make the definitions more precise. Each proposed new definition is also accompanied by a revised comment with examples. To conclude, here are some questions to think about: 1) Would it be desirable to have other names for the terms stateProvince, county, and municipality? If so, what names should be used instead? 2) Are the current definitions of the terms stateProvince, county, and municipality sufficiently good? If not, how should they be defined? Does the definitions proposed here make things clearer? 3) Would more elaborate examples in the comments like the ones presented here improve the Darwin Core standard? Looking forward to hear of any response! Markus Englund Department of Biodiversity Informatics Swedish Museum of Natural History P.O. Box 50007 SE-104 05 Stockholm, Sweden -------------------- SOME RELATED LINKS Wikipedia: Table of administrative divisions by country http://en.wikipedia.org/wiki/Table_of_administrative_country_subdivisions_b… UN Second Administrative Level Boundaries http://www.unsalb.org UN Gazetetteer - a global place name database and search engine http://dma.jrc.it/services/gazetteer GADM database of Global Administrative Areas http://www.gadm.org -------------------- PROPOSED NEW DEFINITIONS AND COMMENTS Term Name: countryFirstOrderSubdivision Definition: The full, unabbreviated name of the primary administrative division below country level in which the Location occurs. The named region should be a subdivision of the region referred to in the country term. Comment: Examples: "Montana" (a federal state in the USA), "Minas Gerais" (a federative unit in Brazil), "Neuquén" (a province in Argentina), "Hesse" (a federal state in Germany), "Stockholms län" (a county in Sweden). Term Name: countrySecondOrderSubdivision Definition: The full, unabbreviated name of the second-order administrative division below country level in which the Location occurs. The named region should be a subdivision of the region referred to in the countryFirstOrderSubdivision term. Comment: Examples: "Missoula" (a county located in the federal state Montana, USA), "Los Lagos" (a department located in the province Neuquén, Argentina), "Darmstadt" (a government district located in the federal state Hesse, Germany), "Sigtuna" (a municipality located in the county Stockholms län, Sweden). Term Name: countryThirdOrderSubdivision Definition: The name of the third-order administrative division below country level in which the Location occurs. The named region should be a subdivision of the region referred to in the countrySecondOrderSubdivision term. Comment: Examples: "Hainburg" (a municipality located in the government district Darmstadt in Hesse, Germany), "Norrsunda" (a parish located in the municipality Sigtuna in Stockholms län, Sweden)

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DwC - Java Reader failing to read archives
by Christopher Gwilliams 29 Aug '12

29 Aug '12

Hello All, I have recently created a small dwc archive that validates fine (with some minor column errors) on the validator online. However, the jar fails to read any values from each record, printing null, although the validator shows the values fine. I have attached the archive if it is of any use but I am assuming it is due to the lack of updates for the jar? Thanks, Chris Gwilliams

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iDigBio Augmenting OCR October Workshop, February Hackathon Invitation
by Deb Paul 22 Aug '12

22 Aug '12

Invitation to Augmented OCR Best Practices Workshop and Hack-a-thon Planning iDigBio (https://www.idigbio.org/) is running a workshop (October 1-2, 2012) and hack-a-thon (February 2013) to identify best practices and develop tools to get information from museum labels into computers. We are seeking individuals to participate in the "iDigBio Augmenting OCR" workshop on October 1-2. The objective of the workshop is to improve OCR output and subsequent manipulation by algorithms to extract the content of biological collection specimen labels and notes and have them efficiently and accurately inserted into a database for future use. Participants in the October workshop plan to narrow the hack-a-thon focus down to specific programmatic goals for software developers working at a hackathon to be held in February of 2013. Most broadly there can be four main steps to digitization: create an image, process the image to text using Optical Character Recognition (OCR) and/or human typists, break the content of the text into semantically useful fields such as family, scientific name, collector, date collected, location, habitat, growth habit and other fields and finally format this information for injection into a database. The participants will help to identify and collect images that are representative of those that will be needed by the biology community. This collection of images will serve as the working set for developers in the February Hack-a-thon. The October workshop participants plan to identify OCR output products that will be useful for the community as well as metrics that help evaluate how well different automation approaches produce these products. This may include measures of accuracy of the OCR but also accuracy of automated error correction, effectiveness of breaking text into meaningful semantic units such as precision, recall and F-Score. We seek biologists, programmers and others involved in the digitization process to participate in this October workshop to plan the February hack-a-thon and participate in the hackathon itself. Anyone can view our wish list at http://tinyurl.com/OCRHackathonWishList of some possible goals we have for optimizing machine and natural language processing algorithms used on OCR output from specimen labels. If interested in participating and you would like to know more please email asap to: Debbie Paul, dpaul(a)fsu.edu Deadline Thursday, August 30th to participate in the Oct 1 - 2 workshop. Looking forward to your participation, From all of us in the iDigBio Augmenting OCR Working Group Please forward to other interested listserves - thanks! -- Deborah Paul User Services, iDigBio Institute for Digital Information, iDigInfo Florida State University Tallahassee, Florida 32308 850-644-6366

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BCI et al. merger
by Bob Morris 10 Aug '12

10 Aug '12

Can anyone tell me authoritatively what is the status of the merger of BCI, Biorepositories.org and Index Herbariorum? In particular, what will the new portal be called and at what URL? I need to update some Audubon Core citations as we near the AC public comment effort. Thanks Bob -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Harvard University Herbaria Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram === The content of this communication is made entirely on my own behalf and in no way should be deemed to express official positions of The University of Massachusetts at Boston or Harvard University.

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