- tdwg-content - lists.tdwg.org

Re: [tdwg-content] RFC 2119: Re: Public comment on the Darwin Core RDF Guide
by Paul J. Morris 29 Nov '14

29 Nov '14

On Sat, 29 Nov 2014 17:08:36 -0500 Jonathan A Rees <rees(a)mumble.net> wrote: > Do you know of any precedent for 2119 language to be used in a > vocabulary specification? I'd be very interested to see that... http://www.w3.org/Submission/sioc-related/ http://rdfs.org/resume-rdf/ http://www.openarchives.org/ore/1.0/vocabulary https://dvcs.w3.org/hg/gld/raw-file/default/people/index.html http://www.openannotation.org/spec/alpha2/ http://socsem.open.ac.uk/ontologies/curio/ http://www.w3.org/community/odrl/two/vocab/ http://www.w3.org/TR/HTTP-in-RDF10/ http://www.w3.org/TR/vocab-people/ http://www.w3.org/TR/vocab-data-cube/ http://www.w3.org/TR/EARL10-Guide/ -Paul -- Paul J. Morris Biodiversity Informatics Manager Harvard University Herbaria/Museum of Comparative Zoölogy mole(a)morris.net AA3SD PGP public key available

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Public comment on the Darwin Core RDF Guide
by Steve Baskauf 26 Nov '14

26 Nov '14

The Darwin Core standard contains several non-normative documents that describe how Darwin Core terms can be used in various contexts such as simple text [1] and XML [2]. Members of the RDF/OWL Task Group [3] have authored a guide describing how Darwin Core terms can be used in RDF. This guide has been subjected to extensive review by the Task Group and has been recommended by the Task Group as an addition to the Darwin Core standard under the Darwin Core Namespace Policy [4]. If ratified, the guide will be another non-normative document that is part of the standard, and a parallel guide to the existing text and RDF guides. The purpose of this email is to initiate the required 30 day public comment period before the proposed addition advances to the Executive Committee for ratification. Before commenting on the proposal, please begin by reading the cover page at https://code.google.com/p/tdwg-rdf/wiki/DwcRdf . The cover page includes the rationale for the guide, links to the proposed guide itself, supporting ancillary documents, and a history of the development of the guide. To comment, post to the tdwg-content email list (tdwg-content(a)lists.tdwg.org). Please use a descriptive subject line that differentiates your comment from other comments that deal with different aspects of the proposal. Comments will be tracked on the RDF/OWL Task Group's issue tracker [5]. The comment period will continue through at least 2014-12-26, but may be extended if discussion is ongoing. Steve Baskauf TDWG RDF/OWL Task Group co-convener [1] http://rs.tdwg.org/dwc/terms/guides/text/index.htm [2] http://rs.tdwg.org/dwc/terms/guides/xml/index.htm [3] https://code.google.com/p/tdwg-rdf/ [4] http://rs.tdwg.org/dwc/terms/namespace/index.htm [5] https://code.google.com/p/tdwg-rdf/issues/list -- 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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NIH Request for Information on Making Big Data Usable
by Ramona Walls 19 Nov '14

19 Nov '14

Hi everyone, The NIH currently has an RFI on making big data usable: http://grants.nih.gov/grants/guide/notice-files/NOT-ES-15-002.html. "The NIH is interested in exploring how the BD2K initiative can contribute to the improvement of policies, governance, administrative procedures, and funding to support community-based standards (CBS) efforts to develop and/or extend data and/or metadata standards, and how these activities relate to other ongoing or nascent biomedical research activities. Within this context, ‘community’ encompasses a broad range of stakeholders who may be engaged in the process of data standards development and use, including technical developers, librarians, science domain experts, researchers, information scientists, vendors, funders, publishers, and other end users. - See more at: http://grants.nih.gov/grants/guide/notice-files/NOT-ES-15-002.html#sthash.S… " I know most of us do NSF, not NIH funded research, but I think that the work we do on biodiversity informatics has a lot of relevance to NIH research (particularly documentation of microbial biodiversity), and the lessons learned about community by TDWG are worth sharing and promoting. I was planning to draft a response from the point of view of the biodiversity ontology development, but we could also make it a larger biodiversity informatics response, and include all of TDWG. Alternatively, there could be one response from TDWG and one from the BCO/PCO groups, if someone is interested in taking the lead on a TDWG response. 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

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New Darwin Core Release
by John Wieczorek 10 Nov '14

10 Nov '14

Dear all, Congratulations to our community for advancing the Darwin Core standard! The TDWG Executive Committee recently ratified various changes [1] to the Darwin Core, resulting in a new release that incorporates consensus in public commentary on proposed ideas, some of which have been under discussions for several years. The highlights of the changes are as follow: 1) A new class Organism [2] has been added, with associated terms and with a rearrangement of some terms from the Occurrence class. This change also resulted in the depracation of the individualID term in favor of the new organismID term. 2) The terms in the Darwin Core type vocabulary have been removed in favor of equivalent terms in the normal Darwin Core namespace. For those of you who care about namespaces, this is much cleaner than what we had before. For those of you who don't care about namespaces, you still benefit from cleaned up definitions of the Darwin Core classes, as well as not having to look on an obscure page to find out what a MachineObservation [3] is, for example. 3) Best practice recommendations have been added for how to populate the content of Darwin Core terms that support lists, such as higherClassification [4] and higherGeography [5]. The format of the content of the dynamicProperties [6] term is now recommended to be JSON on a single line. 4) The Dublin Core term "license" [7] is now recommended for use in Darwin Core in place of the "rights" term. In cases where a legal document proferring rights, such as the CC0 Public Domain Dedication [8], can be cited, license is the term in which that information should be captured, while the agent granting those rights would go in the rightsHolder term and any non-legally binding documentation about the expected behavior with respect to the information (community norms, for example - see those for Canadensys [9] and VertNet [10]) would go in the accessRights term. All of the documentation within the standard has been updated. Maintainers of tools and further documentation (including translations) should be aware of these changes and make updates accordingly. In an effort to facilitate more open maintenance of Darwin Core, the standard will be maintained on Github [11], while related documentation for the the terms and their translations will be maintained on the GBIF Semantic Media/Wiki [12], and further documentation will be moved from the Google Code development site [13] to a Darwin Core documentation repository in Github [14]. Issues related to the Darwin Core standard, including requests for clarification, changes, or additions, should be entered in the Github issue tracker for the Darwin Core Standard [15]. If you have any doubt about where to find Darwin Core documentation or tools, refer to the References section [16] of the Darwin Core Introduction. Now that the new release has been published, the Darwin Core Task Group, charged with the maintenance of the standard, will turn toward the following activities: 1) Complete the move to Github. 2) Generate more documentation with numerous examples of how to construct Simple Darwin Core for various types of data records. 3) Facilitate updates to profiles and software affected by these changes such as the Occurrence Core extension [17], the Darwin Core Archive Reader[18], and the Darwin Core API[19] ) 4) Facilitate the updates to the Darwin Core RDF Guide and integrate it into the body of the standard. 5) Facilitate the processing of new and outstanding proposals for changes to the Darwin Core. Broad topics currently include additions or changes for terms related to the classes Taxon (ranks and a ScientifName class), Event (sampling), MaterialSample (preparations and sequences), and Occurrence (environment). 6) Work with the Executive Committee to define the TDWG Standards maintenance process. 7) Update the archived release on the TDWG site as soon as the site reorganization is done. I hope this all comes as good news and that the efforts to accommodate the changes are painless, swift, and worthwhile. Cheers, John [1] http://rs.tdwg.org/dwc/terms/history/decisions/#Decision-2014-10-26_14 [2] http://rs.tdwg.org/dwc/terms/index.htm#organismindex [3] http://rs.tdwg.org/dwc/terms/index.htm#machineobservationindex [4] http://rs.tdwg.org/dwc/terms/index.htm#higherClassification [5] http://rs.tdwg.org/dwc/terms/index.htm#higherGeography [6] http://rs.tdwg.org/dwc/terms/index.htm#dynamicProperties [7] http://rs.tdwg.org/dwc/terms/index.htm#dcterms:license [8] http://creativecommons.org/publicdomain/zero/1.0/legalcode [9] http://www.canadensys.net/about/norms [10] http://www.vertnet.org/resources/norms.html [11] https://github.com/tdwg/dwc [12] http://kos.gbif.org/wiki/DarwinCore [13] https://code.google.com/p/darwincore/ [14] https://github.com/tdwg/dwc-documentation [15] https://github.com/tdwg/dwc/issues [16] http://rs.tdwg.org/dwc/index.htm#references [17] http://tools.gbif.org/dwca-validator/extension.do?id=http://rs.tdwg.org/dwc… [18] https://github.com/gbif/dwca-reader [19] https://github.com/gbif/dwc-api

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Floristic regions of the world
by Markus Döring 06 Nov '14

06 Nov '14

Hello, TDWG lists as one of its prior standard the "Floristic regions of the world”: http://www.tdwg.org/standards/104/ Unfortunately we do not give any information about it at all. It seems to me that the work of Takhtajan, A. 1986 is the actual endorsed standard. Can someone verfiy this? Takhtajan, A. 1986. Floristic regions of the world, pp. vii-xiii. University of California Press http://www.isbnsearch.org/isbn/0520040279 http://en.wikipedia.org/wiki/Phytochorion#Takhtajan.27s_floristic_regionali… Thanks, Markus

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Knowledge Representation in Systematic Biology - Edited book proposal
by Nico Franz 04 Nov '14

04 Nov '14

Looking for comments, ideas, potential contributors. Cheers, Nico http://taxonbytes.org/knowledge-representation-systematic-biology-edited-bo… *Nico M. Franz, Ph.D.* Associate Professor & Curator of Insects School of Life Sciences PO Box 874501 Arizona State University Tempe, AZ 85287-4501 Lab: (480) 965-2850 Collection:(480) 965-2036 Fax: (480) 965-6899 E-mail: nico.franz(a)asu.edu Website: http://taxonbytes.org Twitter: https://twitter.com/taxonbytes ASUHIC: http://symbiota4.acis.ufl.edu/scan/portal/collections/misc/collprofiles.php… WoNA: http://symbiota4.acis.ufl.edu/scan/portal/checklists/checklist.php?cl=1

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Wrapping up public comment on 204 - 226
by joel sachs 16 Oct '14

16 Oct '14

Hi Everyone, The following is a summary of the comments received since announcing the proposals encapsulated in Issues 204 - 226 [1]. Comment came in two forms - posts to tdwg-content, and comments in the Darwin Core Issue Tracker [2]. Only one issue attracted comment on tdwg-content, and five issues attracted (mostly clarifying) comments in the Tracker. (This is encouraging, since the proposals were the result of a years-long consensus building process.) The issue that was the subject of discussion on this list was Issue 205, the proposal to add a dwc:Organism class. The first comment came from Rob Guralnick, who did not see the need for this new class [3]. In reply, Steve Baskauf pointed out that we already have an Organism class, implied by the existing term dwc:individualID, and that the proposal simply describes what kinds of things could reasonably have their identifier be the value of dwc:individualID. There was concurrence with Steve from Rich Pyle and Bob Morris, with no further comment. The other comments on this issue were related to my suggestion [4] that the proposal be amended to i) remove the reference to OBI in our definition, and ii) to give the new class an opaque identifier. In regards (i), Rich, Bob, and Steve were in favour, and Hilmar opposed. In regards (ii), Bob was in favour, while Rich and Hilmar were initially opposed. After some conversation, however, it seemed acceptable to them that the term be given an opaque identifier, with organism as the label. Eamonn also seemed on board with an opaque identifier. Meanwhile, the Issue Tracker saw the following: Issue 204, the umbrella Issue for all the changes Bob wondered how we might notify those whose DwC Archives would be affected by the proposed changes. Steve and Markus argued that existing DwCAs would not be affected, for reasons they explain in their comments Issue 211, dwc:NomenclaturalChecklist JohnW pointed out that dwctype:NomenclaturalChecklist was to be replaced by dwctype:Nomen, which suggests that the correct label for the new term is dwc:Nomen. Issue 212, dwc:Occurrence I suggested expanding the definition of occurrence to include non-organismal things like genes, rocks, and metagenomic samples. For reasons I explain in my comment, I dont think we need to do this now. Issue 214, dwc:Event Some clarifying remarks from Bob and Steve. Issue 222, organismID Clarification from Steve (and an indication of support from Bob). Issue 226, AssociatedOrganisms Some questions from Bob, answered by Steve. --- If I have mischaracterized anything above, please let me know. Thanks! Joel.

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Audubon Core for STL media type?
by Stoner, Dan 08 Oct '14

08 Oct '14

The STL media type is used to store 3d geometry information (consumable by CAD software and 3D printing systems). iDigBio has one or more providers who are (or will be) generating STL files by scanning (stereolithography?) museum specimens to generate a 3D model. The 3D model is an example of digital media that is related to a physical specimen. I am attempting to determine the proper way to reference this "new" type of media in Audubon Core (dc:format). Wolfram Alpha suggests "application/sla": http://reference.wolfram.com/language/ref/format/STL.html However, other 3d model formats are listed in IANA as "model" types such as "model/x3d-vrml". The STL format is not listed as an IANA Media Type: http://www.iana.org/assignments/media-types/media-types.xhtml Is there a place to see pending types or those that are under future consideration? Any advice or pointers would be appreciated. Dan Stoner iDigBio / ACIS Laboratory University of Florida

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Re: [tdwg-content] [tdwg-tag] another poke about Audubon Core status
by Tim Robertson 29 Sep '14

29 Sep '14

Hi Dan, Thanks for your offer. As far as I recall, the TDWG executive decided at the last meeting to move onto a whole new platform and put contractor money aside to make it happen. I’m reluctant to point you at the tangled mess of the current system when I suspect it is to be replaced anyway. It really is a convoluted mess of Typo3 plugins, which try and keep a bunch of backend systems in sync and dues to bugs in there it does not work as expected. I really don’t think it is something you want to get into, but I sympathise that the TDWG site is broken and no-one is maintaining it… a simpler vanilla CMS solution that even requires more manual text editing etc. will be a far more manageable solution in my opinion. @TDWG Executive folks - is it still the intention to contract out and do a basic CMS site? If not, I’ll try and pull up the code but I’d need your approval to get him a DB dump as it holds user credentials / subscriptions etc. Please can you advise us? Anything we can do to help? Thanks, Tim On 19 Sep 2014, at 23:05, Stoner, Dan <dstoner(a)acis.ufl.edu> wrote: > I see in the tdwg-tag mailing list archives that the status of the Audubon Core Standard has been discussed recently: > > http://lists.tdwg.org/pipermail/tdwg-tag/2014-June/002558.html > > > So consider this another poke about getting the web site updated with the official status of the Standard. > > If there is anything I can do to facilitate the web site update, please let me know (as in, I am volunteering to hack code or whatever is needed). > > > Thanks, > > Dan Stoner > iDigBio / ACIS Laboratory > University of Florida > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag >

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Comments on Darwin Core Issue 205 (the proposed Organism term)
by joel sachs 18 Sep '14

18 Sep '14

Everyone, I'd like to comment on the proposed addition to Darwin Core of an "organism" class (https://code.google.com/p/darwincore/issues/detail?id=205). I am one of the submitters of this proposal, but I have some reservations/suggestions/questions about both the definition and the name. Taking them in turn: The Definition The proposed definition is: "A particular organism or defined group of organisms considered to be taxonomically homogeneous. An organism in the sense used here is defined as OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026). Instances of the Organism class are intended to facilitate linking of one or more Identification instances to one or more Occurrence instances. Therefore, things that are typically assigned scientific names (such as viruses, hybrids, and lichens) and aggregates whose occurrences are typically recorded (such as packs, clones, and colonies) are included in the scope of this class." There are a few things to note here: i. The definition of OBI:0100026 is "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." This definition is not internally consistent, since it delineates organisms as being either unicellular or multi-cellular, while at the same time explicitly including viruses, which are acellular. ii. The reference to OBI:0100026 does not add clarity to the DwC definition, since the DwC definition goes on to include the clarifying aspects of the OBI definition (viruses and lichens are organsims), while leaving out the muddying aspects of the OBI definition (organisms are unicellular or multicellular). The DwC definition also extends the the OBI defintion (to include wolf packs). iii. The rdf definition of OBI:organism inherits axioms from the Basic Formal Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to any particular upper ontology, as there is no consensus upper ontology. (Some scientific communities use Dolce, some use SUMO, and many have deliberately chosen to use none at all.) In general, I like the notion of Darwin Core as a glossary of terms, on top of which various data models can be built. When we import terms that carry with them an abundance of ontological commitment, it raises the stakes for those who choose to use TDWG vocabularies. (In contrast, when Darwin Core imported "Location" from Dublin Core, it did so at no cost, since Dublin Core is not tied to any particular upper world-view.) The Name There have been multiple debates about a good name for this class, and there was never consensus. (In addition to "Organism", candidates included "Individual", "OrganismalIndividual", "TaxonIndividualOrGroup", "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms", "OccurringThing".) I agree that we're unlikely to agree on a consensus name, but I question why we need a name at all. Although TDWG has traditionally used transparent identifiers for terms, this has been by convention, and is not a requirement. Is it time to test the "opaque identifier" waters? Are there potential problems with having a mix of transparent and opaque identifiers in our vocabularies? If not, could we call this class dwc:12345? Should we? Thoughts on any of the above? Many thanks, Joel.

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