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July 2018

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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 19 Nov '25

19 Nov '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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Questionnaires: Integrating Changes into Collections Databases: Challenges and Opportunities
by Deborah Paul 17 Jul '18

17 Jul '18

*Surveys: Integrating Changes into Collections Databases: Challenges and Opportunities* The purpose of these surveys are to gather information from the collections community regarding your experience incorporating changes into your local collections databases. Our goals are to compile and sharefindings at /SPNHC-TDWG 2018/ <https://doi.org/10.3897/biss.2.26003>//as part of the SPNHC symposium <https://doi.org/10.3897/biss.2.26003>: Challenges for Implementing Collections Data Quality Feedback: synthesizing the community experience. Our interests are in the skills, processes, and resources needed (or missing) when collections staff work to integrate data from aggregators and/or crowd-sourced transcriptions back into their local databases. We plan to share the critical information collected in these surveys to help current and future programs design and implement improved data integration and data quality efforts.Many changes might need to be integrated into collection databases. These two surveys focus on : * data quality feedback suggestions from aggregators, and * information provided by crowdsourcing efforts (e.g., online transcription platforms), Please take either questionnaire, or both, as is appropriate. Each survey is estimated to take a maximum of 5 to 10 minutes. /Results will be shared at //SPNHC-TDWG 2018/ <https://doi.org/10.3897/biss.2.26003>/and with you as well if you provide contact information. / Survey 1: Integrating Data Quality Feedback from Aggregators into Collection Databases http://bit.ly/integrateDQ Survey 2: Integrating Crowdsourced Data into Collection Databases http://bit.ly/integrateCrowdData Thanks very much.In anticipation, Deb Paul (iDigBio) & Nicole Fisher (CSIRO) /please excuse cross-postings - aiming for worldwide reach - please share!/ *Nicole Fisher* Digital Collections and Informatics National Research Collections Australia (NRCA) CSIRO *E*nicole.fisher(a)csiro.au <mailto:nicole.fisher@csiro.au> *T*+61 2 6246 4261 *M*+61 (0) 475 972 827 Address : GPO Box 1700, Canberra ACT 2601, Australia www.csiro.au/en/Research/Collections <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.csiro.au_en_Researc…> -- -- Upcoming iDigBio Events https://www.idigbio.org/calendar -- Deborah Paul, iDigBio Digitization and Workforce Training Specialist iDigBio -- Steering Committee Member SPNHC Liaison, Member-At-Large and Member International Relations Committee SYNTHESYS3 Representative Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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