August 2017 - 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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Darwin Core Hour 8: A bite from the core - testing for data quality
by Deborah Paul 04 Sep '17

04 Sep '17

Hi Everyone, RE: Darwin Core Hour 8: A bite from the core - testing for data quality In this upcoming episode of Darwin Core Hour (DCH), we head down under to join Arthur D. Chapman and Lee Belbin for a conversation about Darwin Core and Data Quality. We'll hear about collaborative efforts across the aggregator community (specifically GBIF, VertNet, ALA, and iDigBio) to harmonize data quality algorithms for the downstream data use by researchers, developers, etc. These efforts are the result of the Biodiversity Information Standards (TDWG) Data Quality Interest Group (DQIG) work to develop a suite of common, shared tests and data format expectations for use by aggregators. TIME: (please check carefully, the international dateline is involved in this DCH) 7 AM Wednesday Sept 6th (Tasmania) 5 PM Tuesday Sept 5th (USA EDT) 6 PM Tuesday Sept 5th (Buenos Aires) 21:00 UTC Tuesday Sept 5th DETAILED Abstract: https://www.idigbio.org/content/darwin-core-hour-bite-core-testing-data-qua… WHERE: http://idigbio.adobeconnect.com/room Read more about these Test and Assertions on the DQIG Wiki https://github.com/tdwg/bdq/wiki/Task-Group-2-(Tests-and-Assertions)-of-the-'Data-Quality'-Interest-Group-seek-your-comments Related Links Your questions here: https://tinyurl.com/zja2muz BDIQ GitHub: https://github.com/tdwg/bdq Data Quality Tests: http://bit.ly/2uY3FoA Principles: http://bit.ly/2vqoGsK Brought to you by the Darwin Core Hour Team - Connecting Biodiversity Data Communities Deb Paul, et al PS Check out past and future DCH Webinars https://github.com/tdwg/dwc-qa/wiki/Webinars Hints for best Adobe Connect experience: https://www.idigbio.org/wiki/index.php/Web_Conferencing Let us know if you'd like to moderate / present / plan future Darwin Core Hours https://tinyurl.com/zja2muz -- -- Upcoming iDigBio Eventshttps://www.idigbio.org/calendar -- Deborah Paul, iDigBio Digitization and Workforce Training Specialist iDigBio -- Steering Committee Member, SPNHC Liaison and Member-At-Large, SYNTHESYS3 Representative Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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Darwin Core Hour 7 (Part Three): The Aggregator's Viewpoint - (More Than Vert)Net
by Deborah Paul 28 Aug '17

28 Aug '17

Hi Everyone! At this Darwin Core Hour (DCH): it is VertNet's turn to share what happens to museum specimen data when it is shared with them as data aggregator. Please join us for: DCH 7 (Part Three!): The Aggregator's Viewpoint - (More Than Vert)Net When: *Tu**esday, August 29th, 2PM EDT, 3PM (Buenos Aires), 7 PM (London), 6 PM UTC (18:00)* Where: https://idigbio.adobeconnect.com/room DETAILS: https://www.idigbio.org/content/darwin-core-hour-aggregators-viewpoint-more… *Presenters (VertNet)**:* John Wieczorek - Information Architect, Museum of Vertebrate Zoology, University of California, Berkeley *Moderators:* Paula Zermoglio, Deborah Paul Abstract. In this Darwin Core Hour we will follow up in the series on aggregator perspectives with a view from VertNet. Though the taxonomic scope of VertNet as a biodiversity data aggregator is focused on Chordates, VertNet serves a broader biodiversity data mobilization role that has no taxonomic or geographic boundaries. As an Associate Participant in GBIF, VertNet is also involved in a wide variety of other community services, including the development of, promotion of, and training on biodiversity data standards and data quality. In this webinar we will explore the series of services that VertNet provides, such as migration and data quality processes, as well as its unique extracting and searching capabilities, which allow content such as trait data (e.g., body mass and length) to be sought and retrieved. We will discuss VertNet's role in the broader data mobilization framework and how that relates to other biodiversity data sharing initiatives. As always, we encourage people to bring or submit questions and to have open discussions in each webinar. Brought to you by the Darwin Core Hour Team - Connecting Biodiversity Data Communities Deb Paul, et al PS Check out DCH 7 Parts One and Two (GBIF and iDigBio) https://www.idigbio.org/content/darwin-core-hour-aggregators-viewpoint-gbif… Hints for best Adobe Connect experience: https://www.idigbio.org/wiki/index.php/Web_Conferencing Let us know if you'd like to moderate / present / plan future Darwin Core Hours https://tinyurl.com/zja2muz -- -- Upcoming iDigBio Events https://www.idigbio.org/calendar -- Deborah Paul, iDigBio Digitization and Workforce Training Specialist iDigBio -- Steering Committee Member, SPNHC Liaison and Member-At-Large, SYNTHESYS3 Representative Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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TDWG 2017: deadlines for registration and hotel
by joel sachs 16 Aug '17

16 Aug '17

Dear Colleagues, The TDWG 2017 conference is fast approaching and the organising committee would like to urge you to both register and book your accommodation as soon as possible. We have a great line up of key note speakers and symposia, workshops, posters and software demos based on this year's theme - Data Integration in a Big Data Universe: Associating Occurrences with Genes, Phenotypes, and Environments. We also have an exciting line up of social/networking opportunities including a welcoming reception, "A night at the Museum", hike in the Gatineau mountains to see the Fall colours, collection tours, and a banquet open to all participants and guests. Please come and help make this conference a great success, as well as joining Canada in celebrating its 150th anniversary! At this stage, we are suggesting that you immediately book a hotel room at the conference venue (Delta Hotel) as the hold on the rooms will expire on August 29. There are still some rooms available. Also, standard registration will expire on Aug. 31, after which the registration fee will increase. All the information you need to register, learn about the conference and venue, and book accommodation is on the conference website: https://tdwg.github.io/conferences/2017/ We look forward to seeing everyone in October! On behalf of the 2017 organizers, James and Joel

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Darwin Core Hour 7: GBIF and iDigBio present the Aggregator's Viewpoint
by Deborah Paul 14 Aug '17

14 Aug '17

Hi Everyone! Please join us tomorrow to learn about what happens to museum specimen data when it is shared with a data aggregator. Title: Darwin Core Hour: GBIF and iDigBio present the Aggregator's Viewpoint Part ONE: GBIF: free and open access to global biodiversity data Part TWO: iDigBio - aggregating and enhancing vouchered global biocollections data When: Tuesday, August 15th, 10 AM EDT, 9AM CDT, 4 PM CEST Where: https://idigbio.adobeconnect.com/room DETAILS: https://www.idigbio.org/content/darwin-core-hour-aggregators-viewpoint-gbif… **NOTE: this DwC Hour could potentially go slightly over its scheduled hour.** Abstract. In this next Darwin Core Hour Series, we shift to the viewpoint of large biodiversity data aggregators. In this session, we welcome GBIF and iDigBio. GBIF aggregates the world's biodiversity data from observations to checklists to biological specimen data. iDigBio aggregates vouchered specimen data with related media, genetic information and trait data. The Darwin Core Standard plays a key role in the standardization of biodiversity data and in the design and implementation of strategies to improve data quality. Many people wonder what happens to their data after they provide it to an aggregator. Find out the answers to such questions as: what does the aggregator do to assess fitness of the data?, what are the most common data issues seen?, what does the aggregator do to data to make it easier to find when searching an aggregator database?, and how does sharing data with an aggregator benefit me as a collection manager/curator/researcher/data scientist? As always, we encourage people to bring or submit <https://tinyurl.com/zja2muz> questions and to have open discussions in each webinar. Brought to you by the Darwin Core Hour Team - Connecting Biodiversity Data Communities Deb Paul, et al Hints for best Adobe Connect experience: https://www.idigbio.org/wiki/index.php/Web_Conferencing Let us know if you'd like to moderate / present / plan future Darwin Core Hours https://tinyurl.com/zja2muz Sincere apologies for cross-posting! -- -- Upcoming iDigBio Events https://www.idigbio.org/calendar -- Deborah Paul, iDigBio Digitization and Workforce Training Specialist iDigBio -- Steering Committee Member, SPNHC Liaison and Member-At-Large, SYNTHESYS3 Representative Institute for Digital Information, 234 LSB Florida State University Tallahassee, Florida 32306 850-644-6366

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