- tdwg-content - lists.tdwg.org

Re: [tdwg-content] tdwg-content Digest, Vol 89, Issue 6
by Deborah Paul 14 Mar '17

14 Mar '17

Hi Steve, Matt, et al On 2017-03-14 7:00 AM, tdwg-content-request(a)lists.tdwg.org wrote: > We are now midway through the 30 day public comment period on the SDS and so > far, that issue has not come up. I was recently listening to the recording > of John Wieczorek's nice Darwin Core Hour presentation on controlled > vocabularies and it was apparent to me that the creation of controlled > vocabularies is an issue of interest to many in the community. So I've > written a blog post > (http://baskauf.blogspot.com/2017/03/controlled-values-again.html) that > attempts to explain in non-technical terms how the SDS specifies that > controlled vocabularies should be expressed in machine-readable form. For > those who are interested in the gory details, I've also included at the end > a more detailed explanation of the rationale for specifying that controlled > vocabularies should, in most cases, be described as SKOS concept schemes > rather than ontologies. For those of you interested in the on-going controlled vocabularies discussion, please do come to the next iDigBio Darwin Core Hour, brought to you by the iDigBio Data Mgmt Interest Group. You'll discover a bit more about what's found in some of these 23 fields where dwc suggests use of a cv. Paula Zermoglio presents: Darwin Core Hour: Thousands of shades for “Controlled” Vocabularies <https://www.idigbio.org/content/darwin-core-hour-thousands-shades-%E2%80%9C…>. Having TDWG members present at dwc hours is invaluable - as the broader community in the webinar strives to understand what the related data quality issues are, and what they can do about them at from their vantage point. > If you care about the creation of controlled vocabularies, you should take a > look at this post and create an official comment if there are things you > don't like about the approach taken in the proposed specification. Our > review manager, Dag Endresen, has requested that issues be raised on the > issue tracker athttps://github.com/tdwg/vocab/issues . However, > historically back-and-forth discussion about proposed standards has also > taken place on this list, so I think that responding here for clarification > and discussion would be appropriate prior to submitting an official comment. I'd also like to suggest if you think of a topic for another dwc hour / and you've someone in mind to present (yourself maybe?), please send us your ideas - using the Darwin Core Hour Input Form: https://tinyurl.com/zja2muz Best, Deb, et al in the iDigBio Data Mgmt Interest Group -- -- 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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Information about how controlled vocabularies would be handled under the draft Standards Documentation Specification
by Steve Baskauf 13 Mar '17

13 Mar '17

At the TDWG meeting in December, I led an informative session describing the main points of the draft Standards Documentation Specification (SDS) and its sister standard, the draft Vocabulary Management Specification. At that session, some participants seem to be taken aback at the prescription by the SDS that controlled vocabularies should be SKOS concept schemes rather than ontologies. There wasn't enough time at the meeting to fully explore that issue and I hoped that it would come up for further discussion during the public comment period. We are now midway through the 30 day public comment period on the SDS and so far, that issue has not come up. I was recently listening to the recording of John Wieczorek's nice Darwin Core Hour presentation on controlled vocabularies and it was apparent to me that the creation of controlled vocabularies is an issue of interest to many in the community. So I've written a blog post (http://baskauf.blogspot.com/2017/03/controlled-values-again.html) that attempts to explain in non-technical terms how the SDS specifies that controlled vocabularies should be expressed in machine-readable form. For those who are interested in the gory details, I've also included at the end a more detailed explanation of the rationale for specifying that controlled vocabularies should, in most cases, be described as SKOS concept schemes rather than ontologies. If you care about the creation of controlled vocabularies, you should take a look at this post and create an official comment if there are things you don't like about the approach taken in the proposed specification. Our review manager, Dag Endresen, has requested that issues be raised on the issue tracker at https://github.com/tdwg/vocab/issues . However, historically back-and-forth discussion about proposed standards has also taken place on this list, so I think that responding here for clarification and discussion would be appropriate prior to submitting an official comment. Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu http://vanderbilt.edu/trees

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2nd Darwin Core Hour Recording, Resources, and Upcoming Events of Interest
by Deborah Paul 08 Mar '17

08 Mar '17

Hi TDWG'ers, Thank you so much to all the TDWG community who added their voices to the Darwin Core Hour yesterday, very rich conversations and community / cross-discipline expertise and experience sharing :-) In case you weren't one of the 90-or-so folks who joined us and you want to hear Darwin Core Hour #2 presentation and discussion about controlled vocabularies, or if you want to share the conversation with your colleagues, here are places where you can go to do that. 1. iDigBio Calendar Announcement for DwC Hour #2 https://www.idigbio.org/content/darwin-core-hour-even-simple-hard has link to the recording. An mp4 version is in-the-works. 2. Explore the Darwin Core Questions & Answers wiki! https://github.com/tdwg/dwc-qa/wiki - where all Darwin Core Hour materials can be found. 3. See what questions have been asked and answered so far https://github.com/tdwg/dwc-qa/issues 4. Submit your question / volunteer (yourself or someone) to do a webinar on your darwin core topic: https://tinyurl.com/zja2muz 5. See what's inside some of the dwc fields that suggest using a controlled vocabulary (from GBIF, iDigBio, VertNet, and soon ALA too): https://github.com/tdwg/dwc-qa/tree/master/data Upcoming Events of Interest. A. The iDigBio Paleo Digitization Interest Group brings a talk by Erica Clites (University of California Museum of Paleontology, Berkeley, CA):**Serving your georeferencing data via data aggregators. Thursday, March 16, 2017 - 3:00pm to 4:00pm EDT. This webinar will define and discuss common Darwin Core terms related to georeferencing and discuss factors to consider when serving your georeferencing data online. If you are currently serving your georeferencing data, come prepared with the list of terms you serve or just bring your questions! https://www.idigbio.org/content/paleo-working-group-webinar-0 B. Our next formal Darwin Core Hour is Tuesday April 4th, 2017 by Paula Zermoglio: Thousands of shades for “Controlled” Vocabularies https://www.idigbio.org/content/darwin-core-hour-thousands-shades-%E2%80%9C… Happy Darwin Core and Data Quality, :-) Deb, et al from the iDigBio Data Mgmt Interest Group and the Darwin Core Hour Team (please excuse cross-postings) -- -- 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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Fwd: 'Data Quality' Task Group 2 - Tests and Assertions
by Lee Belbin 02 Mar '17

02 Mar '17

Dear TDWG-Content(ed) *Task Group 2 (Tests and Assertions) of the 'Data Quality' Interest Group seek your comments.* A select group of TDWGians (highlighted on the Members worksheet on the link below) have invested time to produce what I am calling a *core suite of standard tests and associated assertions that can be applied to occurrence records*. These tests are to help identify potential occurrence record issues. Why are we doing this? Largely to try to better align Data Publishers/Data Aggregators/Biodiversity Research Infrastructures/Data Custodians, and hopefully anyone who generates occurrence data. Users would appreciate consistency. A practical example: Merging records from say GBIF and the ALA etc would be greatly facilitated if they both applied the same set of tests. As a start and to keep it simple, these tests are based on one or more Darwin Core terms. We realize that tests could be applied to all Darwin Core terms, but we wanted a core set that would cover the significant terms that could be implemented relatively easily by all. The spreadsheet can be found at *https://tinyurl.com/h49zwof*. Note that this spreadsheet contains a series of worksheets. Please start by reviewing the Principles as they provide a context for what has been learnt during the process. The main worksheet is "Tests-current". We have to start somewhere, and this is the start. *PLEASE: Only add comments on the tests/principles to the Comments worksheet, but any additions to KEY references and tools worksheets would also be appreciated.* Comments would also be appreciated by 31/3/2017. Lee Lee Belbin The Atlas of Living Australia Tasmania http://spatial.ala.org.au

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

02 Mar '17

Hi everyone, A quick announcement, the GBIF Secretariat is currently seeking applications for a Web Developer, see complete details here: http://www.gbif.org/newsroom/news/web-developer-job-2017 Deadline for applications is Monday, 20 March 2017. Please be aware that the successful candidate will be locally recruited (no-relocation involved), according to the GBIF Staff Rules 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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1st Darwin Core Hour - 7 February 2017 @ 1 PM EST, 6 PM UTC
by Deborah Paul 28 Feb '17

28 Feb '17

Hello Everyone, You're invited! To: Darwin Core Hour 7 February 2017 @ 1 PM EST, 6 PM UTC Details: https://www.idigbio.org/content/darwin-core-hour-webinar-series Got questions? Get answers! Provide answers! For the best Darwin Core Hour experience, add your input here Darwin Core Hour Form https://goo.gl/forms/YCaJ8zjTaW3n6BKr1 Chapter Abstract In this first webinar in the Darwin Core Hour series, the basics of how Darwin Core functions in the biodiversity community as a dynamic standard will be covered. Topics will include what the standard consists of, how to use it, how it can be changed, sources of information, and where to go for help. Presenter: John Wieczorek Your input: 1) improves Darwin Core documentation (examples, definitions) 2) helps those in the Standards community address gaps and implementation of the standard terms 3) provides a forum for everyone to learn about each others data mapping, data sharing, software needs, standards issues and insights. 4) facilitates higher data quality! Go here for details: https://www.idigbio.org/content/darwin-core-hour-webinar-series In anticipation of our 1st Darwin Core (Happy) Hour, Debbie Paul, et al 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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Public review for TDWG Vocabulary documentation and maintenance standards
by Dag Endresen 27 Feb '17

27 Feb '17

Hi everyone, A brief reminder to participate in the public review <https://github.com/tdwg/vocab/blob/master/README.md> for the Vocabulary documentation and maintenance standards - as announced with the TDWG Announcements newsletter last week. The Documentation Specification will proscribe the format of human- and machine-readable documents that form TDWG (vocabulary) standards. The Vocabulary Maintenance Specification proscribes the process by which TDWG vocabularies will be modified and amended. https://github.com/tdwg/vocab/blob/master/README.md Please submit any comments, questions, or criticisms as "issues" in the issue tracker. If you would like to register an issue anonymously, please send it via email to the review manager, Dag Endresen <dag.endresen(a)gmail.com?subject=Issue%20with%20Vocabulary%20standards>. Public review will be open at least through March 27th, and may be extended if a valuable discussion is on-going. https://github.com/tdwg/vocab/issues (sorry for cross-posting)

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TDWG 2017 meeting announcement and call for symposia
by Stanley Blum 30 Jan '17

30 Jan '17

Dear TDWG list subscribers, (Please excuse our cross-posting.) We are excited to announce that Agriculture and Agri-Food Canada and the Canadian Museum of Nature will host the 2017 Biodiversity Information Standards (TDWG) conference in Ottawa, Canada, Oct. 1 - Oct. 6. Below, we describe the conference and solicit proposals for workshops and symposia. The deadline for submissions is March 1, 2017. A call for contributed papers and posters will be made in April 2017 after the symposia and workshops have been selected and announced. Standards for the description and exchange of biodiversity information help promote research, support decision-making for conservation and planning, and provide a means of communicating observations across taxa, sub-disciplines, and political boundaries. The annual TDWG conference serves two purposes: - it is a forum for developing, refining and extending standards in response to new challenges and opportunities; and - it is a showcase for biodiversity informatics - much of which relies on the specifications provided by TDWG and other standards organizations. Our theme this year is "Data Integration in a Big Data Universe: Associating Occurrences with Genes, Phenotypes, and Environments". For more information on the conference, including links to accommodations, please visit https://tdwg.github.io/conferences/2017. We invite you to submit proposals for workshops and symposia, which can be organized around already established themes, or which can be used to explore emerging topics of interest. At TDWG, 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 facilitating consensus around a key issue. Symposia and workshops addressing the conference theme are encouraged, but other topics relating to biodiversity information management, integration, analysis, and standards are also welcomed, such as: - knowledge graphs - metagenomics - citizen science - semantics and ontologies (e.g., sampling, traits) - biological field station data management - collections - data visualization - data quality assessment and improvement - agricultural biodiversity - conservation informatics - illuminating dark data - phyloinformatics - ePublications - standards for image processing (e.g. computer vision for organismal identification) - wikis for biodiversity knowledge. For full consideration, please submit your proposal via email to conf-submissions(a)tdwg.org by 1 March 2017. Proposals should be fewer than 400 words, and should include the following: 1. Names, email addresses, and affiliations of all organizers. 2. Whether the proposal is for a workshop or a symposium. 3. Whether the organizer(s) will accept unsolicited abstract submissions (vs. inviting all speakers themselves). 4. Number of 90 minute sessions requested. Please note: As mentioned above, this is a call for workshop and symposium proposals only. The general call for contributed papers and posters will be announced in April 2017, after the symposia and workshops have been selected and announced. Please address questions to conference(a)tdwg.org. Sincerely, The 2017 TDWG Program Committee

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Tags to describe descriptions, keywords and frequency?
by Antonio Rojas Castro 26 Jan '17

26 Jan '17

Dear list, I am new to the Darwin Core World, so I apologize in advance if I am missing any basics. I am working on a project that aims to describe plants according to Haller. We are using DwC to encode information with XML; however, I am missing the following elements: - an element to store small descriptions of plants; - an element to store the place where plants may be found — by that I am not meaning the actual location where the plant was identified but its habitat in general terms. - an element to store the frequency of the plant, in other words, if it is common or not. I am currently using my own terms to store this information: <hllr:addition> <hllr:description>foliis subhirsutis, ovato lanceolatis, acute serratis, peiolis florigeris ramosis, folia superantibus.</hllr:description> <hllr:keyword>Wegränder</hllr:keyword> <hllr:keyword>Gebüsch</hllr:keyword> <hllr:keyword>felsig</hllr:keyword> <hllr:frequency>verbreitet</hllr:frequency> </hllr:addition> I am wondering whether I could store that information in DwC tags instead — or should I be using Dublin Core tags to describe this kind of information? Many thanks. Best, -- Dr. Antonio Rojas Castro Research assistant, Cologne Center for eHumanities Communication coordinator, EADH <http://www.antoniorojascastro.com>

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minor issues with DWCA Validator
by Matt Yoder 11 Jan '17

11 Jan '17

Hi there, As we implement a DWCA generator I've stumbled on a number of minor bits in reference to http://tools.gbif.org/dwca-validator/. I understand how to get around these things, but resolving them might lower the barrier to entry for others. When I validate a DWCA 1) then I see a link 'Dublin Core' (http://code.google.com/p/darwincore/source/browse/trunk/dwca-reader/src/tes…) that link is broken 2) and I have no metadata file then the instructions under Metadata as to what to do to resolve the problem (i.e. do next) are essentially unusable for the non-technically oriented 3) and I read this: "All null values are empty strings." in green and I get this immediately after "Error scanning records: java.lang.NullPointerException" then I am confused I would be less confused with a literal example of the issue 4) and I have an id column in [0], and that id column is mapped to nothing then I see under Darwin Core Occurrence 'Core Record ID mapped to nothing' and I think 'OK' then at the bottom of that list I see 'Unknown term http://purl.org/dc/terms/identifier mapped to column 0' and I am confused as to this (auto-mapping?) that has a namespace (http://purl.org/dc/terms/) and a term (identifier), both of which I have not referenced and I don't know what todo Cheers, Matt

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