April 2013 - tdwg-content - lists.tdwg.org

iDigBio Train-the-Trainers Georeferencing Workshop Oct 8 - 12, 2012
by Deb Paul 09 Aug '13

09 Aug '13

** Hi Everyone, The Georeferencing Working Group at iDigBio is pleased to announce our first "Train-the-Trainers" Georeferencing Workshop for Thematic Collections Networks (TCNs) and others in engaged in the digitization of biological collections in the United States. See: https://www.idigbio.org/content/idigbios-first-train-trainers-georeferencin… for details. Three slots are still available in this workshop that is designed to focus on training participants to teach others to georeference. If you are interested, please send an application describing the reason(s) for your interest in the workshop, the current and future projects that will benefit from your attendance, and any previous experience you have with georeferencing to iDigBio's Program Assistant, Cathy Bester, cbester(a)flmnh.ufl.edu What: Train-the-Trainers -- Georeferencing Workshop Where: University of Florida, Gainesville, FL Who: Interested members of current TCNs and others in the biodiversity natural history collections community. When: October 8-12, 2012 Contact: Deborah Paul dpaul(a)fsu.edu for further information. Best, Deb and the iDigBio Georeferencing Working Group Deborah Paul User Services, iDigBio Institute for Digital Information, iDigInfo Florida State University Tallahassee, Florida 32308 850-644-6366

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New Darwin Core terms proposed relating to material samples
by John Wieczorek 24 Jun '13

24 Jun '13

Dear all, TDWG could see a lot of activity in 2013 in anticipation of the meeting in Florence in October. Much of the activity is related to enabling integration across multiple parts of our domain. We have the Audubon Core under review for biodiversity-related media and an impending RDF Guide to supplement the already extant Text and XML Guides for Darwin Core. This message is to bring your attention to another integrative initiative, to introduce terms into Darwin Core that will form a nexus between Occurrences and the interesting things that happen with physical materials that result from them, such as, but not limited to, genetic sequencing. A series of meetings for a little over the past year have inspired our colleagues in the Genomics Standards Consortium (GSC) to propose to their constituency to align their terms with Darwin Core, including adopting some of the Darwin Core terms in place of their own that have the same meaning. Out of these discussions has come the realization that neither community has terms to accommodate the concept of an identifiable (objectively, not taxonomically), trackable material sample. This message constitutes such a proposal. This proposal would have no impact on those publishing purely taxonomic data. It would also have no impact on those publishing occurrence data unless they want to increase their capacity to distinguish material samples from organisms more rigorously than is now possible using only the dwc:preparations term. The initial request for new terms can be found in the Darwin Core Issue tracker as http://code.google.com/p/darwincore/issues/detail?id=167. Below I have elaborated nad formalized the request into the three distinct terms under consideration, initiating the 30 day minimum public review process to seek consensus on their inclusion in the Darwin Core standard. Your job, should you choose to accept it, is to discuss the merits or any perceived problems in the inclusion of these three terms in Darwin Core. Below I will give the proposed properties of three terms as they would appear in the Darwin Core Quick Reference Guide, though these properties would be included in the RDF of the normative form of the documentation. A new MaterialSample class: This is for the purpose of organizing properties, just as the existing classes (Occurrence, Event, Location, GeologicalContext, Identification, Taxon, etc.) do, without having any terms declare this class as their domain. Term Name: MaterialSample Identifier: http://rs.tdwg.org/dwc/terms/MaterialSample Namespace: http:/rs.tdwg.org/dwc/terms Label: Material Sample Definition: The category of information pertaining to the physical results of a sampling (or subsampling) event. In biological collections, the material sample is typically collected, and either preserved or destructively processed, with the intention of being representative of a greater whole. Comment: For discussion see http://code.google.com/p/darwincore/wiki/MaterialSample (this page will not exist until the term is ratified). Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: proposed Date Issued: 2013-03-28 Date Modified: 2013-04-08 Has Domain: Has Range: Version: MaterialSample-2013-03-28 Replaces: IsReplaceBy: Class: ABCD 2.0.6: not in ABCD (someone please confirm or deny this) A Darwin Core Type Vocabulary value for basisOfRecord is needed to represent this new class of information. Luckily, a term already exists in the Ontology for Biomedical Investigations ( http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org…) We and the GSC both propose to reuse this class within Darwin Core as below, making it the cross-ver point between the two domains. Term Name: MaterialSample Identifier: http://rs.tdwg.org/dwc/terms/MaterialSample Namespace: http://purl.obolibrary.org/obo/OBI_0000747 Label: material sample Definition: A material entity that has the material sample role Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines:http://purl.obolibrary.org/obo/OBI_0100051 Status: recommended Date Issued: 2013-03-28 Date Modified: 2013-03-28 Has Domain: Has Range: Version: MaterialSample-2013-03-28 Replaces: IsReplaceBy: Class: ABCD 2.0.6: not in ABCD In keeping with all other classes in Darwin Core, the Material Sample class would have a corresponding identifier property. The Genomics Standards Consortium (GSC) is in the process of proposing this term. If it is accepted, we propose to use it, and its properties would be as below, otherwise, the properties would be the same, but have the Darwin Core namespace and identifier URI. Term Name: materialSampleID Identifier: http://gensc.org/ns/mixs/materialSampleID Namespace: http://gensc.org/ns/mixs Label: Material Sample ID Definition: An identifier for the MaterialSample (as opposed to a particular digital record of the material sample). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the materialSampleID globally unique. Comment: For discussion see http://code.google.com/p/darwincore/wiki/MaterialSample (this page will not exist until the term is ratified). Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: http://purl.org/dc/terms/identifier Status: proposed Date Issued: 2013-03-28 Date Modified: 2013-04-08 Has Domain: Has Range: Version: materialSampleID-2013-03-28 Replaces: IsReplaceBy: Class: http://purl.obolibrary.org/obo/OBI_0000747 ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

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Completion of Audubon Core public review
by Steve Baskauf 25 Apr '13

25 Apr '13

More than the minimum 30 days required for the public review of Audubon Core have passed and I've received comments from everyone who told me that they planned to comment. I am therefore closing the public review period. The review guidelines at http://www.tdwg.org/fileadmin/documentation/guidance_docs/ReviewManagerGuid… require that Public Review comments be visible to all. Since many of the comments I received were emailed directly to me rather than to the tdwg-content list or posted on the Issues Tracker, I've posted a digest of the comments at http://code.google.com/p/auduboncore/wiki/RecordOfPublicReview for public inspection. As a result of these comments, a number of issues have been opened by commenters or by me based on the submitted comments. These issues can be viewed at the Audubon Core Issue Tracker http://code.google.com/p/auduboncore/issues/list I would like to thank everyone who took the time to read the specification and comment. I think that the standard will be strengthened based on your comments and look forward to working with the authors to implement many of your suggestions. Steve Baskauf Audubon Core Review Manager -- 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

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New listserv: Domain Modelling in Flower-Visiting
by Willem Coetzer 23 Apr '13

23 Apr '13

Please visit https://lists.ru.ac.za/mailman/listinfo/dmfv to subscribe. Looking forward to continuing the discussion about the semantics of flower-visiting and flower-visitors. [cid:image54ec2c.PNG@77a2217a.4d8c34f3] Somerset Street Willem Coetzer Grahamstown, 6139 Biodiversity Information Manager Private Bag 1015 Tel: +27 46 603 5841 Grahamstown, 6140 Fax: +27 46 622 2403 South Africa Email: W.Coetzer(a)saiab.ac.za<mailto:W.Coetzer@saiab.ac.za> http://www.saiab.ac.za/<http://http://www.saiab.ac.za/> Disclaimer:<http://www.nrf.ac.za/email-legal-notice.php> http://www.nrf.ac.za/email-legal-notice.php Please consider the environment before printing this message.

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What is the purpose of dcterms:accessRights in Darwin Core?
by Steve Baskauf 19 Apr '13

19 Apr '13

I have been struggling with some difficult terms while working on the draft Darwin Core RDF Guide. At the moment, the term that I've been struggling with is dcterms:accessRights, which is imported by Darwin Core from Dublin Core as a record-level term. In the case of dcterms:accessRights (defined as "Information about who can access the resource or an indication of its security status." with comment "Access Rights may include information regarding access or restrictions based on privacy, security, or other policies."), the range is given as dcterms:RightsStatement (i.e. a non-literal value is expected rather than a string literal). Thus a client interpreting a dcterms:accessRights property should expect a URI reference pointing to another resource that is a Rights Statement, defined as "A statement about the intellectual property rights (IPR) held in or over a Resource, a legal document giving official permission to do something with a resource, or a statement about access rights." So dcterms:accessRights seems to be a rather vague term that is intended to point to additional information about: 1. intellectual property rights (i.e. copyright) 2. permission to do something with a resource (i.e. licensing information) 3. access rights (i.e. to what extent access to the resource is controlled) These are actually three rather different types of information about a resource. It seems to me that the first two items are about created intellectual property - the territory of Audubon Core. Audubon Core has a pretty rich vocabulary for describing these kinds of properties that media are likely to have. But they don't seem to apply so much to Darwin Core, which is more about data and specimens, neither one of which can be copyrighted or licensed as far as I can know. So it seems to me that item 3 is the most relevant to Darwin Core, since data can be embargoed, access to specimens can be restricted, loans prohibited, etc. The ancient history on the accessRights term at http://dublincore.org/usage/meetings/2002/10/accessRights.shtml seems to indicate that the term was originally intended to serve to describe the limitations of access but that it got thrown together with intellectual property rights and licensing when the range was declared to be "RightsStatement" several years later. Anyway, I'm not how this term would get used in the context of specimens and observations. The DwC comment give the example "not-for-profit use only" which sounds more like a licensing statement such as Creative Commons-NC . When Audubon Core comes online, xmpRights:UsageTerms and xmpRights:WebStatement will be available to provide that kind of information for images and other media. We also have dwc:informationWithheld to tell people that some information is not available to the public. So under what circumstances would I actually use dcterms:accessRights? Is there anybody who uses it as a property in their metadata and can give me some real examples of its use? I'm sure there was a reason given when Darwin Core was undergoing ratification, but I don't remember the discussion, and it is too overwhelming to think of digging through the email archives to look for it. 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

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Re: [tdwg-content] tdwg-content Digest, Vol 48, Issue 4
by Éamonn Ó Tuama [GBIF] 16 Apr '13

16 Apr '13

The best practice that we should encourage is that terms should not be defined adhoc when creating Darwin Core extensions, but rather come from a published vocabulary (ideally expressed in RDF). The vocabulary work at GBIF supported by the EU ViBRANT project recognized this and it is something we are taking forward in the TDWG vocabulary management task group [1]. Éamonn [1] http://community.gbif.org/pg/groups/21382/vocabulary-management/ Message: 2 Date: Mon, 15 Apr 2013 15:58:32 +0000 From: Chuck Miller <Chuck.Miller(a)mobot.org> Subject: Re: [tdwg-content] Darwin Core To: "<tuco(a)berkeley.edu>" <tuco(a)berkeley.edu> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <A378AC48-A491-4D38-9CD5-04AD8C941792(a)mobot.org> Content-Type: text/plain; charset="us-ascii" On this same subject, what about the various Darwin Core term extensions at GBIF that are used by the GBIF Darwin Core Archive Validator? http://tools.gbif.org/dwca-validator/extensions.do There are a number of terms being created outside NCD and Darwin Core and TDWG. What does this mean to the TDWG Ontology and TDWG Vocabularies in general? Do we need formal multi-term synonymy or cross referencing to embrace the emerging real world of multiple overlapping terms standards? Chuck On Apr 15, 2013, at 10:45 AM, "John Wieczorek" <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu>> wrote: Dear all, I have been asked to cross-post here from a comment on the GBIF Community site discussion of "The Management of TDWG Ontologies and Darwin Core" (http://community.gbif.org/pg/forum/topic/29426/discussion-of-management-of- the-tdwg-ontologies-and-darwin-core/). Given the subject matter, I feel like the whole discussion should take place in the broader audience reached by this list. While managing the Darwin Core, I advocated not to re-use any term that had no status as a standard. It was partially for this reason that geo:lat and geo:long were rejected (see http://code.google.com/p/darwincore/issues/detail?id=82) It worries me a little to see a non-standard term (ncd:taxonCoverage, adopted in turn from the TDWG Ontology, also not a standard, see http://rs.tdwg.org/ontology/voc/Collection#taxonCoverage) being proposed for adoption into the Audubon Core (see http://terms.gbif.org/wiki/Audubon_Core_Term_List_%281.0_normative%29#ncd:ta xonCoverage). Does that bother anyone else? The alternative, sadly, is to make up a new term for ratification with the new standard. So, questions. If Audubon Core is ratified with the Natural Collections Descriptions (NCD) term in it, does that one term from NCD become a standard term? Under what governance? What about the rest of the NCD namespace? What about the TDWG Ontology. A lot of work went into both of those, but each lost its champions and they remain incompletely reviewed, especially in the context of all that has come to pass since they were active. I know that people refer to the TDWG Ontology fairly often in discussions, and that activity is still fomenting around that work with the imminent publication of the RDF Guide for Darwin Core. But what about NCD. What should we do with it? Does more than one person, group, or project still want to use it? If not, there isn't a lot of reason to go to the trouble of creating a data sharing standard if no one will use it to share. But if its need is still alive and active, who can take up the standard and promote its completion, review, and ratificatio n? Cheers, John _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org<mailto:tdwg-content@lists.tdwg.org> http://lists.tdwg.org/mailman/listinfo/tdwg-content

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(no subject)
by John Wieczorek 15 Apr '13

15 Apr '13

Dear all, I have been asked to cross-post here from a comment on the GBIF Community site discussion of "The Management of TDWG Ontologies and Darwin Core" ( http://community.gbif.org/pg/forum/topic/29426/discussion-of-management-of-…) Given the subject matter, I feel like the whole discussion should take place in the broader audience reached by this list. While managing the Darwin Core, I advocated not to re-use any term that had no status as a standard. It was partially for this reason that geo:lat and geo:long were rejected (see http://code.google.com/p/darwincore/issues/detail?id=82) It worries me a little to see a non-standard term (ncd:taxonCoverage, adopted in turn from the TDWG Ontology, also not a standard, see http://rs.tdwg.org/ontology/voc/Collection#taxonCoverage) being proposed for adoption into the Audubon Core (see http://terms.gbif.org/wiki/Audubon_Core_Term_List_%281.0_normative%29#ncd:t…) Does that bother anyone else? The alternative, sadly, is to make up a new term for ratification with the new standard. So, questions. If Audubon Core is ratified with the Natural Collections Descriptions (NCD) term in it, does that one term from NCD become a standard term? Under what governance? What about the rest of the NCD namespace? What about the TDWG Ontology. A lot of work went into both of those, but each lost its champions and they remain incompletely reviewed, especially in the context of all that has come to pass since they were active. I know that people refer to the TDWG Ontology fairly often in discussions, and that activity is still fomenting around that work with the imminent publication of the RDF Guide for Darwin Core. But what about NCD. What should we do with it? Does more than one person, group, or project still want to use it? If not, there isn't a lot of reason to go to the trouble of creating a data sharing standard if no one will use it to share. But if its need is still alive and active, who can take up the standard and promote its completion, review, and ratification? Cheers, John

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[Fwd: RE: [lpig] magnification/extent of objects present in images]
by Steve Baskauf 06 Apr '13

06 Apr '13

I don't think this actually went out on tdwg-content, so I'm forwarding it. Steve -------- Original Message -------- Subject: RE: [lpig] magnification/extent of objects present in images Date: Fri, 5 Apr 2013 20:27:54 +0000 From: Boyce Tankersley <btankers(a)chicagobotanic.org> To: steve.baskauf(a)vanderbilt.edu <steve.baskauf(a)vanderbilt.edu>, TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> References: <515C9790.3040507(a)vanderbilt.edu> For those living specimens where measurements are critical we include a scale next to the plant part in the image. We currently have 25 photographers using their own cameras and I am not sure how we would be able to determine and/or document magnification levels without the use of a scale. If we were working with a single make and model of a camera attached to a microscope I think the issue of magnification of the raw image would be easier to determine. Boyce Tankersley Director of Living Plant Documentation Chicago Botanic Garden -----Original Message----- From: live-plant-image-group(a)googlegroups.com [mailto:live-plant-image-group@googlegroups.com] On Behalf Of Steve Baskauf Sent: Wednesday, April 03, 2013 3:57 PM To: TDWG Content Mailing List Cc: live-plant-image-group(a)googlegroups.com Subject: [lpig] magnification/extent of objects present in images I am cross-posting this to the Live Plant Image email list in addition to tdwg-content because this is a subject that was previously discussed there. However, as this is part of the public review of the draft Audubon Core TDWG standard, I would request that you reply only to the tdwg-content list, so that any additional discussion will take place there for the record. If you aren't on that list and would like to reply, please send your responses to steve.baskauf(a)vanderbilt.edu and I will post it for you. This subject came up as part of a comment on Audubon Core from Andréa Matsunaga: "In iDigBio (http://tinyurl.com/MISC-Media) some people have expressed the desire to have information about the magnification being used (to have a rough idea of the size of the object, potentially from data that is automatically retrieved from the capturing device) as well as the real world size depicted by a pixel (for the purposes of allowing one to make measurements on the image; this would require one to have a scale on an image and perform some arithmetic). Would it be possible to add such terms?" There are terms in the SpatialMetrics terms (section 9.1) of the MIX vocabulary (http://www.loc.gov/standards/mix/ ) that can encode this kind of information. However, I would be interested in opinions about whether expressing this kind of information is a narrow need that is outside the scope of a fairly broad standard like Audubon Core or if the need for such terms is perceived as widespread. 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 -- -- You received this message because you are subscribed to the Google Groups "Live Plant Image Group" group (homepage: https://sites.google.com/site/liveplantimagegroup) To post to this group, send email to live-plant-image-group(a)googlegroups.com To unsubscribe from this group, send email to live-plant-image-group+unsubscribe(a)googlegroups.com --- You received this message because you are subscribed to the Google Groups "Live Plant Image Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to live-plant-image-group+unsubscribe(a)googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. . -- 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

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magnification/extent of objects present in images
by Steve Baskauf 03 Apr '13

03 Apr '13

I am cross-posting this to the Live Plant Image email list in addition to tdwg-content because this is a subject that was previously discussed there. However, as this is part of the public review of the draft Audubon Core TDWG standard, I would request that you reply only to the tdwg-content list, so that any additional discussion will take place there for the record. If you aren't on that list and would like to reply, please send your responses to steve.baskauf(a)vanderbilt.edu and I will post it for you. This subject came up as part of a comment on Audubon Core from Andréa Matsunaga: "In iDigBio (http://tinyurl.com/MISC-Media) some people have expressed the desire to have information about the magnification being used (to have a rough idea of the size of the object, potentially from data that is automatically retrieved from the capturing device) as well as the real world size depicted by a pixel (for the purposes of allowing one to make measurements on the image; this would require one to have a scale on an image and perform some arithmetic). Would it be possible to add such terms?" There are terms in the SpatialMetrics terms (section 9.1) of the MIX vocabulary (http://www.loc.gov/standards/mix/ ) that can encode this kind of information. However, I would be interested in opinions about whether expressing this kind of information is a narrow need that is outside the scope of a fairly broad standard like Audubon Core or if the need for such terms is perceived as widespread. 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

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