June 2016 - 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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A proposal to improve Darwin Core for invasive species data
by Quentin Groom 25 Jun '16

25 Jun '16

I've been working on a proposal to improve Darwin Core for use with invasive species data. The proposal is detailed on GitHub at https://github.com/qgroom/ias-dwc-proposal/blob/master/proposal.md. The proposal is for a new term "origin" and suggested vocabularies for establishmentMeans and occurrenceStatus. I'd welcome your feedback on the proposal. >From my perspective it provides some needed clarity on the establishmentMeans and occurrenceStatus fields, but also adds the origin that is needed for invasive species research and for conservation assessments. I'm not sure of the best way to discuss this, but if you have concrete proposals for changes you might raise them as issues on GitHub, as well as mentioning them here. Regards Quentin Dr. Quentin Groom (Botany and Information Technology) Botanic Garden Meise Domein van Bouchout B-1860 Meise Belgium ORCID: 0000-0002-0596-5376 <http://orcid.org/0000-0002-0596-5376> Landline; +32 (0) 226 009 20 ext. 364 FAX: +32 (0) 226 009 45 E-mail: quentin.groom(a)plantentuinmeise.be Skype name: qgroom Website: www.botanicgarden.be

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Additional terms for sample event data in DwC
by Kyle Braak 17 Jun '16

17 Jun '16

Hi all, In compliance with the directions for requesting changes to the Darwin Core (DwC) vocabulary, I hereby submit to the TDWG Content list a proposal for four new terms to more faithfully express sample event data. The need for these four new terms is based on several inputs: EU Nodes workshop on sample event data<http://www.gbif.pt/EuropeanNodesMeeting/workshop>, April 2016<http://www.gbif.pt/EuropeanNodesMeeting/workshop>[1]; discussions on the Sample event data publishing interest group<http://community.gbif.org/pg/groups/47949/sample-event-data-publishing-inte…>[2]; experiences publishing the first round of sample event datasets<http://www.gbif.org/dataset/search?q=&type=SAMPLING_EVENT>[3]. While DwC already provides many terms that enable describing sample event data, these four new terms will allow a larger number of underlying protocols to be encoded in a standardised way. Notably the term samplingTaxaRange will also allow for accurate presence/absence data to be recorded. These four terms are: layer https://github.com/tdwg/dwc/issues/125 #Justification Required for describing the different layers within a location. Especially useful for describing the location of sampling when the sampling protocol uses stratification. For example, vegetation surveys (relevés) commonly stratify a plot into vegetation layers and describe each plant species' abundance within each layer. #Definition The layer within a Location. Recommended best practice is to use a controlled vocabulary such as the GBIF vegetation layer vocabulary<http://rs.gbif.org/vocabulary/gbif/vegetation_layer.xml>[4]. The elevation or depth of the layer should be well defined in the vocabulary. Otherwise describe the range of elevation using minimumElevationInMeters and maximumElevationInMeters or the range of depth using minimumDepthInMeters and maximumDepthInMeters. #Comment Examples: "tree", "shrub". #Term group Location siteID https://github.com/tdwg/dwc/issues/126 #Justification Required for identifying a specific sampling site at or within a location. This allows distinction from dwc:locationID, which is an identifier for the sampling location itself. Especially useful for describing permanent sampling sites that haven't been georeferenced. This also enables sampling sites to be referenced across datasets. #Definition An identifier for the sampling site at or within the Location. #Comment May be a global unique identifier or an identifier specific to the dataset. Example: "tr011-s1" identifies a sampling site within a location (locationID= "tr011"). #Term group Location samplingTaxaRange https://github.com/tdwg/dwc/issues/127 #Justification Required for describing the range of taxa that could be observed at the time and place of sampling given a) the sampling protocol or b) the taxonomic coverage of the study and the expertise of the personnel carrying out the identification. This would allow for accurate presence/absence data to be recorded. #Definition A short list (concatenated and separated) of taxa names or the URI of a timestamped checklist describing the range of taxa being sampled during a sampling event. For taxonomic and biogeographical/ecological reasons, however, this checklist should exist solely within the context of the sample event dataset. #Comment The recommended best practice varies depending on whether the list of taxa is short or long. For a short list, the recommended best practice is to separate the values with a vertical bar (' | '). Examples: "Lepidoptera | Coleoptera", "Lepidurus arcticus (Pallas, 1793)". For a long list, the recommended best practice is to use the URI of a timestamped checklist. Example: "http://danbif.au.dk/ipt/resource?r=checklist-bees-denmark" - checklist for the taxa of bees occurring in Denmark. #Term group Event siteTreatment https://github.com/tdwg/dwc/issues/128 #Justification Required for describing the treatments that were intentionally applied to a sampling site before sampling occurred. Especially useful for describing sample events where the underlying protocol tests a control-group versus a treatment-group. For example, an investigation looking at the effects of grazing on vegetation will have a control plot and a plot that has been permanently grazed. Note this is different from dwc:preparations, which only applies to a specimen. #Definition A list (concatenated and separated) of treatments for a sampling site. #Comment The recommended best practice is to separate the values with a vertical bar (' | '). Examples: "permanently grazed", "Imazapyr | Triclopyr" - two herbicides that have been applied. #Term group Event None of the existing DwC terms is sufficient for any of the proposed terms although two are somewhat related: locationID ("An identifier for the set of location information") and preparations ("A list of preparations and preservation methods for a specimen."). Neither are adequate - locationID is an identifier for the sampling location itself but not specific sampling sites within the location and preparations refers exclusively to specimens but not a sampling site. Thank you for your consideration of my proposal, Kyle Braak GBIF Secretariat [1] http://www.gbif.pt/EuropeanNodesMeeting/workshop [2] http://community.gbif.org/pg/groups/47949/sample-event-data-publishing-inte… [3] http://www.gbif.org/dataset/search?q=&type=SAMPLING_EVENT [4] http://rs.gbif.org/vocabulary/gbif/vegetation_layer.xml

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TDWG DwC Text schema references git head
by godfoder 15 Jun '16

15 Jun '16

Recently, iDigBio has seen some errors popping up in our logs related to fetching XML definitions from https. In tracing this problem we found that the current published text XSD: http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd References the darwin core terms with the URL: https://raw.githubusercontent.com/tdwg/dwc/master/xsd/tdwg_dwcterms.xsd For those of you not familiar with how git and github work, the URL being used is an unversioned URL pulling right from HEAD off of github (rather than a version tag or branch). This means that any committed change to the file on github will immediately change the behavior of schema validation in client programs, potentially invalidating a previously valid XML file (or simply breaking things if the commit contains errors). This seems to be related to a (potential) issue with the new DwC release process. I get that we're now moving towards more of a "living standard" model with small incremental update. I think we still need some form of release process. Rather than having defintions pulled right from github master, we could create a "latest" tag in github that everything references (in addition to tags for individual releases probably): https://raw.githubusercontent.com/tdwg/dwc/latest/xsd/tdwg_dwcterms.xsd Then, commits could be made to the DwC repo representing the ongoing work of improving the standard, and then when everyone is happy with the changes, the tag could be moved to indicate that the changes are now "published". If we want to leave the URL as is, we should document the commit procees in the contributor documentation. There is a well known pattern that exclusively uses branches that is often called git flow: http://nvie.com/posts/a-successful-git-branching-model/ We could also move to a "no commits to this repo" model, where all changes must come in as pull requests from forks of the main repo. - Alex

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Re: [tdwg-content] A proposal to improve Darwin Core for invasive species data (Quentin Groom)
by Ramona Walls 11 Jun '16

11 Jun '16

Quentin and all: I finally had a chance to read through this long list of emails. It's great to see the discussions inspired by Quentin's proposal. To bring this particular thread back into focus, Quentin, I think it would be helpful if you could summarize the comments and suggestions that pertain specifically to the proposed term changes, perhaps in the github doc if you think that is appropriate. I would like to see some concrete next steps for moving forward. I too am encouraged by Donald's remarks, as they capture much of what inspired work on the BCO and are consistent with the directions that I think TDWG needs to move to keep pace with biodiversity and data science. As important as those high level changes are, I want to make sure we we don't loose track of the much needed work on origin, occurrenceStatus and establishmentMeans. Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Senior Scientific Analyst, CyVerse, University of Arizona Research Associate, Bio5 Institute, University of Arizona On Sun, May 29, 2016 at 3:00 AM, <tdwg-content-request(a)lists.tdwg.org> wrote: > Send tdwg-content mailing list submissions to > tdwg-content(a)lists.tdwg.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/tdwg-content > or, via email, send a message with subject or body 'help' to > tdwg-content-request(a)lists.tdwg.org > > You can reach the person managing the list at > tdwg-content-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg-content digest..." > > >

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Term change: footprintSRS
by Kyle Braak 02 Jun '16

02 Jun '16

Hi all, I'd like to propose a change to the term footprintSRS<http://rs.tdwg.org/dwc/terms/#footprintSRS>[1] that would allow it to also be provided using the EPSG code as a controlled vocabulary (e.g. "EPSG:4326"). I welcome your feedback in the following GitHub issue<https://github.com/tdwg/dwc/issues/122>[2] where you can find more information about my proposed change. Thanks, Kyle GBIF Secretariat [1] http://rs.tdwg.org/dwc/terms/#footprintSRS [2] https://github.com/tdwg/dwc/issues/122

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