June 2017 - 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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bioRxiv preprint: To increase trust, change the social design behind aggregated biodiversity data
by Nico Franz 30 Jun '17

30 Jun '17

Dear TDWG: Bit of a different, social angle here on the biodiversity aggregation/trust issue. Hopefully of interest to some. (and apologies for cross posting) Cheers, Nico http://www.biorxiv.org/content/early/2017/06/28/157214 Abstract Growing concerns about the quality of aggregated biodiversity data are lowering trust in large-scale data networks. Aggregators frequently respond to quality concerns by recommending that biologists work with original data providers to correct errors "at the source". We show that this strategy falls systematically short of a full diagnosis of the underlying causes of distrust. In particular, trust in an aggregator is not just a feature of the data signal quality provided by the aggregator, but also a consequence of the social design of the aggregation process and the resulting power balance between data contributors and aggregators. The latter have created an accountability gap by downplaying the authorship and significance of the taxonomic hierarchies - frequently called "backbones" - they generate, and which are in effect novel classification theories that operate at the core of data-structuring process. The Darwin Core standard for sharing occurrence records plays an under-appreciated role in maintaining the accountability gap, because this standard lacks the syntactic structure needed to preserve the taxonomic coherence of data packages submitted for aggregation, leading to inferences that no individual source would support. Since high-quality data packages can mirror competing and conflicting classifications, i.e., unsettled systematic research, this plurality must be accommodated in the design of biodiversity data integration. Looking forward, a key directive is to develop new technical pathways and social incentives for experts to contribute directly to the validation of taxonomically coherent data packages as part of a greater, trustworthy aggregation process.

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Registration and abstract submission now open for TDWG 2017
by James Macklin 15 Jun '17

15 Jun '17

Dear Colleagues, We are happy to announce that Registration and Abstract Submission for the TDWG 2017 meeting are now open. Registration is available at the conference website <https://tdwg.github.io/conferences/2017/>, and instructions for abstract submission can be found here <https://tdwg.github.io/conferences/2017/call-for-abstracts/instructions/>. The deadline for submission is July 14. Camera-ready copy will be due Sept. 5. In a change for TDWG, abstract submission this year will be done through the Pensoft ARPHA platform. Many of you are already familiar with ARPHA, which supports and facilitates collaborative authoring, manuscript review, feedback to authors, publication, and post-publication review and discussion. One of the benefits that will come from this is that abstracts will be published in Proceedings of TDWG, hosted by Pensoft. Published abstracts will be assigned DOIs, and will be available for post-publication review. The TDWG 2017 organizing committee has worked with Pensoft to customize the ARPHA workflow in a way that makes sense for TDWG. Please note that you can add references, a figure, a table, and supplementary materials without these being counted towards your total word limit. It is likely that there will be some hiccups, and we ask for your patience throughout the process. Help is available via the ARPHA tool's "Helpdesk" icon, or via email to tdwgproceedings(a)pensoft.net. As previously announced, TDWG 2017 has a rich collection of workshops and symposia <https://tdwg.github.io/conferences/2017/program/> to which you can contribute. Abstracts are required for oral presentations, computer demonstrations, and posters. The only exception is “wild ideas” (see below), which do not require abstracts. These categories are described below. Types of ContributionsSymposia or Workshop Presentations The backbone of a TDWG meeting are its symposia and workshops. A symposium is typically a collection of talks, sometimes with a panel or open discussion. A workshop may have talks, but typically encourages more active engagement through training activities or through facilitated discussion around a key issue. Accepted symposia and workshops are listed here <https://tdwg.github.io/conferences/2017/program/> <https://tdwg.github.io/conferences/2017/program/>along with an indication of whether or not the symposium/workshop organizers are accepting unsolicited submissions. If you would like to give a talk, you should first see if any open workshops/symposia match your topic. Other Oral Presentations If no workshop or symposium is suitable, you can submit your abstract to the "Other Oral Presentation" category. The organizing committee will attempt to schedule similar talks in the same session. Computer demonstrations We will provide an opportunity for live computer demonstrations. Note that rooms for these presentations may have WiFi connections only (not wired), and you are advised to have a backup plan should the internet connection not work to your satisfaction. Posters We will provide dedicated space for posters and at least one dedicated poster session on the agenda. Instructions on poster size will be announced closed to the conference, and posted on the FAQ <http://tdwg.us9.list-manage1.com/track/click?u=50f3cc44307841383062ca0d6&id…> . 5-Minute Wild Ideas/Unconference Towards the end of the conference, we will have a “Wild Ideas” session, with talks selected via an unconference <https://en.wikipedia.org/wiki/Unconference>-style procedure. Abstracts are not be required for this category of submission. We look forward to your contributions and to seeing you in Ottawa in October. Sincerely, The 2017 Program Committee

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DwC Hour 5: DwC Standards in Practice: Introduction to Sharing Data Using the GBIF IPT
by Deborah Paul 08 Jun '17

08 Jun '17

Hello TDWG!, Darwin Core (DwC) Hour #5 is almost here: DwC Standards in Practice: Introduction to Sharing Data Using the GBIF IPT. Go Here for Webinar Details and Meeting Link: https://www.idigbio.org/content/darwin-core-hour-dwc-standards-practice-int… ABSTRACT. This webinar introduces the GBIF IPT, the most widely used tool to publish and share biodiversity data through the GBIF network. Demonstrating how to publish a species occurrence dataset, special emphasis will be given to how to properly map fields to /DwC terms/ while complying with vocabularies and making sure to satisfy GBIF’s required and recommended terms. It will end with a brief look at the tool’s roadmap, with some essential information all IPT administrators need to be made aware of. Please bring or submit questions for open discussions in each webinar: https://tinyurl.com/zja2muz When: Tuesday, June 13th, 10 AM EDT, 9AM CDT, 4 PM CEST Where: https://idigbio.adobeconnect.com/room Presenters: Kyle Braak - IPT Product Manager for GBIF, Laura Russell - Program Officer for Participation and Engagement at GBIF, Carole Sinou - Research Officer in Biodiversity for Canadensys. Moderators: Gary Motz, Erica Krimmel EXTRAs. 1. Explore the Darwin Core Questions & Answers wiki! https://github.com/tdwg/dwc-qa/wiki - where all Darwin Core Hour (DwC) materials can be found. 2. See which of your questions have been asked and answered so far https://github.com/tdwg/dwc-qa/issues 3. Submit your question / volunteer (yourself or someone) to do a webinar on your darwin core topic: https://tinyurl.com/zja2muz 4. Here's a list of terms for which DwC recommends use of a controlled vocabulary - note many are in the Location class. https://github.com/tdwg/dwc-qa/wiki/Controlled-Vocabularies 5. See what's inside some of the DwC fields that suggest using a controlled vocabulary (data from GBIF, iDigBio, VertNet, and soon ALA): https://github.com/tdwg/dwc-qa/tree/master/data 6. Future DwC Hour webinars coming up feature discussions about Darwin Core locality terms and sharing georeferenced locality data, and Aggregators sharing how they process data provided by the community. See you soon! Happy Darwin Core and Data Quality, :-) Deb, et al from the iDigBio Data Mgmt Interest Group and the Darwin Core Hour Team (please kindly excuse cross-postings!) Webinar series brought to you by the iDigBio Data Management Interest Group (DMI). We welcome input for this series from everyone worldwide. We plan to make this happen 1x month. We use Adobe Connect for our webinars. See https://www.idigbio.org/wiki/index.php/Web_Conferencing for hints on best experience (hint: use headsets!) -- -- Upcoming iDigBio Events https://www.idigbio.org/calendar -- Deborah Paul, iDigBio Digitization and Workforce Training Specialist iDigBio -- Steering Committee Member, SPNHC Liaison, SYNTHESYS3 Representative Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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Job opening at the GBIF Secretariat
by Federico Mendez 02 Jun '17

02 Jun '17

Hi everyone, the GBIF Secretariat is currently seeking applications for a Software Developer, see complete details here: http://www.gbif.org/newsroom/news/gbif-seeks-software-developer<http://www.gbif.org/newsroom/news/web-developer-job-2017> Deadline for applications is Monday, 17 July 2017. The selected candidate is expected to live in Denmark, and a relocation package is available for internationally recruited staff. Please feel free to share this position with your own networks and contacts. Thanks, Federico Mendez fmendez(a)gbif.org<mailto:fmendez@gbif.org> skype: fede.mendez Lead Software Developer

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