November 2015 - 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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Application deadline extended for Practical Hacking On Identifiers at BiOSphere 2 (PHOIBOS2), Feb. 17-19, 2015, Oracle, Arizona, USA
by Ramona Walls 24 Nov '15

24 Nov '15

The deadline for applications has been extended to Dec. 6th. Please apply online at http://bit.ly/1knvYoR Also, a reminder that there is funding available to support several participants from developing countries! Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Research Associate, Bio5 Institute, University of Arizona Laboratory Research Associate, New York Botanical Garden On Tue, Nov 10, 2015 at 1:24 PM, Ramona Walls <rlwalls2008(a)gmail.com> wrote: > In the era of big data and informatics, there is growing awareness among > scientists and scientific data managers of the need for permanent, globally > unique identifiers for both physical specimens and digital data, leading to > the development of new systems for minting, tracking, resolving, and > querying identifiers. However, existing identifier systems have not yet > been put to the test with the types of very large, multidisciplinary > datasets that loom on the horizon, and developing an identifier > infrastructure for really big data (pre- and post-publication) is crucial > next step. > > During the three day PHOIBOS2 > <https://github.com/identifier-services/phoibos2/wiki> workshop at the > world-renowned Biosphere 2 <http://b2science.org/> in Oracle, Arizona, > identifier practitioners and data generators will come together to > summarize the current state of the field, identify and elucidate the > technical issues, and develop solutions. PHOIBOS2 will incorporate elements > of a hackathon, but outputs may also include non-technical products like a > draft proposal, a survey, or educational materials. The agenda for the > meeting is modeled after the successful MIT Hacking Medicine > <http://hackingmedicine.mit.edu/>, in which groups of participants are > asked to identify a problem and articulate what a system that solved the > problem would look like, including technologies, support material, and a > business model. We aim to develop a vision of an identifier infrastructure > that spans the entire data lifecycle in the context of very large, complex, > multi-disciplinary, research-oriented datasets. > > If you are a scientist, or user or developer of identifier systems, and > would like to take part in this innovative experience, please complete the > online application available here > <https://docs.google.com/forms/d/1m1paDJjRigPLw0PaLFlS5D2bfvJ2iGwP6W_bsvcMEY…> > by November 30, 2015. The meeting is open to all, with room and board > covered for up to 30 participants, and limited funding available to support > travel costs, particularly for early career or under-represented > participants. Funding requests will be considered in early December, after > all applications are received. > > This workshop is funded by the U.S. National Science Foundation, with > logistical support provided by the iPlant Collaborative. > ------------------------------------------------------ > Ramona L. Walls, Ph.D. > Scientific Analyst, The iPlant Collaborative, University of Arizona > Research Associate, Bio5 Institute, University of Arizona > Laboratory Research Associate, New York Botanical Garden >

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Practical Hacking On Identifiers at BiOSphere 2 (PHOIBOS2), Feb. 17-19, 2015, Oracle, Arizona, USA
by Ramona Walls 10 Nov '15

10 Nov '15

In the era of big data and informatics, there is growing awareness among scientists and scientific data managers of the need for permanent, globally unique identifiers for both physical specimens and digital data, leading to the development of new systems for minting, tracking, resolving, and querying identifiers. However, existing identifier systems have not yet been put to the test with the types of very large, multidisciplinary datasets that loom on the horizon, and developing an identifier infrastructure for really big data (pre- and post-publication) is crucial next step. During the three day PHOIBOS2 <https://github.com/identifier-services/phoibos2/wiki> workshop at the world-renowned Biosphere 2 <http://b2science.org/> in Oracle, Arizona, identifier practitioners and data generators will come together to summarize the current state of the field, identify and elucidate the technical issues, and develop solutions. PHOIBOS2 will incorporate elements of a hackathon, but outputs may also include non-technical products like a draft proposal, a survey, or educational materials. The agenda for the meeting is modeled after the successful MIT Hacking Medicine <http://hackingmedicine.mit.edu/>, in which groups of participants are asked to identify a problem and articulate what a system that solved the problem would look like, including technologies, support material, and a business model. We aim to develop a vision of an identifier infrastructure that spans the entire data lifecycle in the context of very large, complex, multi-disciplinary, research-oriented datasets. If you are a scientist, or user or developer of identifier systems, and would like to take part in this innovative experience, please complete the online application available here <https://docs.google.com/forms/d/1m1paDJjRigPLw0PaLFlS5D2bfvJ2iGwP6W_bsvcMEY…> by November 30, 2015. The meeting is open to all, with room and board covered for up to 30 participants, and limited funding available to support travel costs, particularly for early career or under-represented participants. Funding requests will be considered in early December, after all applications are received. This workshop is funded by the U.S. National Science Foundation, with logistical support provided by the iPlant Collaborative. ------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Research Associate, Bio5 Institute, University of Arizona Laboratory Research Associate, New York Botanical Garden

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