- tdwg-content - lists.tdwg.org

Evidence/Token Class [was: New Darwin Core terms proposed relating to material samples]
by Richard Pyle 26 May '13

26 May '13

Thanks, Dan. I changed the subject line because I think your comment: > tissue converted to DNA extract is still tissue (the tissue is still > "material sample" after "destructive sampling", and still part of > the event, just as is a photograph of the beast in the museum. Relates to part of what Steve wrote: > We defined a class for evidence, but we also considered not having evidence > being an explicit class. Not defining an explicit Token class would have simplified > the diagram at the bottom of the page - one could just say that there should be > evidence and it should be linked to the resource it documents. > Token and THeE/IndividualOrganism are not disjoint classes - the physical entity > can be the evidence if somebody "owns" it and makes it available for people to examine. > However, in DSW, Token and THeE are not synonymous because we allow evidence > to include things that are not physically derived from the entity (e.g. images, sounds, > string data records) in addition to physical specimens. This is an area that at first seems subtle, but once we actually started working with data, starts to became more and more intuitive (at least to me, anyway). I first started thinking about this seriously during a 2007 meeting of ICZN Commissioners, when we were contemplating the question of what could/should, and what could/should not, fulfill the role of a type specimen under the ICZN Code. Needless to say, we did not come up with a complete answer to the question, but the discussion did help frame in my mind the question in much better detail. Under the ICZN Code (which differs in a few respects from the ICNafp Code in this area), the definition of a type specimen s fairly straight-forward: 1) It must be biological material. An image (e.g., illustration or photograph) cannot be a type specimen (I believe the ICNafp accommodates "iconotypes"). Rather, the organism depicted in an image is regarded as being the type specimen. 2) A type specimen consists of the entire organism. For example, in the case of a mammal that is captured and separated into its fur, skeleton, alcoholic-preserved tissues, and tissue samples for DNA analysis, all of these things together constitute the type specimen. In other words, the whole specimen is the type. This is in contrast to ICNafp, where a single specimen from a tree (for example) is the type, whereas other specimens taken from the same tree are isotypes, and the remainder of the tree is not a type at all. 3) It is understood that the community of organisms inhabiting a type specimen (e.g., parasites and commensals) do not form part of the type specimen. There are other issues as well (especially for ichnotaxa, colonies, and other specific cases), but the general point is that under the ICZN Code, a type specimen consists of the sum of all cells that contain the same DNA material that were part of the same biological individual (i.e., identical twins, clones, and parthenogenic and other asexually reproducing organisms potentially contain the same DNA material, but are different "individuals"). Most of the above is pretty straight-forward. Where it gets a bit squishy is when you go down below the "tissue sample" level into smaller and smaller subunits. Can a single cell containing intact DNA be a type specimen for a multicellular organism? Can a single DNA molecule be a type specimen? Can a single chromosome be a type specimen? Can a PCR product be a type specimen? ...you can add as many hair-splitting examples as you wish. Conversations like this let me to draw a distinction between matter that is actually from an organism, vs. stuff that is representative of the organism but lacks any material connection to the organism. Coming back to Dan Janzen's comment; I would conclude that most things that would full under the term "materialSample" include actually matter from a biological organism. A PCR product is borderline, because it presumably does contain actual matter from the organism, but the vast majority of matter in the PCR product was not from the organism. Once you lose all the matter from the organism, you are no longer talking about the "individual", but instead are now talking about "Evidence of the Individual". This applies to images of the individual (whether taken in-situ, or in a lab), DNA "sequences" (rendered as text), images of the results of DNA sequencing analysis (in various forms), and various other non-biological derivatives. So, this leads me to the comment from Steve about "Evidence" (which, if I understand correctly, is conceptually the same as the DSW "Token": https://code.google.com/p/darwin-sw/wiki/ClassToken). In our model, a specimen is *not* a Token or Evidence -- it is an individual. This has proven (in my mind at least -- Rob W. still has reservations) to be a MUCH more practical way to think of, and manage data for, specimens. This email will be WAY too long if I try to explain all the subtleties of this, so I'll just leave it at that. But clearly there are some differences between our notion of "Evidence", and the DSW concept of "Token" -- although both seem to be intended to solve the same problem. Enough for now.... Aloha, Rich

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Fwd: SANBI Post Doctoral Fellowships
by John Wieczorek 08 May '13

08 May '13

Forwarding relevant opportunity announcement from South Africa. ---------- Forwarded message ---------- From: Gloria Cupido <G.Cupido(a)sanbi.org.za> Date: Wed, May 8, 2013 at 5:17 AM Subject: SANBI Post Doctoral Fellowships To: Paula Hathorn <P.Hathorn(a)sanbi.org.za> Dear all **** ** ** Please see on the SANBI website adverts for the two biodiversity informatics post doctoral fellowships based at the University of the Western Cape http://www.sanbi.org/jobs/post-doctoral-fellowship-interrogation-biodiversi… http://www.sanbi.org/jobs/post-doctoral-fellowship**** ** ** Please circulate these adverts to potential candidates who will add value to the programme we are establishing.**** ** ** Kind regards**** ** ** Paula**** ** ** ** ** Paula Hathorn**** Learning Network Manager**** Biodiversity Information Management **** South African National Biodiversity Institute **** Tel: +27 21 799 8885**** Cell: +27 82 2608584**** Fax2email: 0865208130**** ** ** ------------------------------ Please visit our website www.sanbi.org for more information about the South African National Biodiversity Institute . Think before you print. Please consider the environment before printing this email. NOTE: This email and any attachments are intended for the addressee only, and contain information that may be legally privileged and / or confidential and / or the subject of copyright that is protected by law. Any unauthorised usage, disclosure, alteration or dissemination is prohibited. The SANBI accepts no responsibly for any loss whether it be direct, indirect or consequential, arising from information made available and actions resulting there from. No liability is accepted by the SANBI or the sender. The views or opinion expressed in this email message may not necessarily be that of the SANBI or the SANBI Management. The SANBI reserves the right to monitor all email communication. Please consider the environment before printing this email. The disclaimer is located at http://www.sanbi.org/node/5672

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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 18 Apr '13

18 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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AC Comment: terms for phylocode and DNA barcode
by Steve Baskauf 25 Mar '13

25 Mar '13

Rob Stevenson made another helpful comment with regards to the proposed Audubon Core standard: "Rather than have Term Name: associatedSpecimenReference as a place for phylocode and a DNA barcode, should the standard support specific fields for a phylocode and a DNA barcode? These seem to be independent approaches that might help anchor or tie together multimedia observations. I can image people taking a picture of an insect and getting a DNA barcode but not having a Taxon Name or a set of characters completed. It seems that molecular data are becoming more and more important and their collection is becoming more and more automated. For microbes, molecular characterization seems to be the main approach uses". I have not opened an issue for this item because although it is an important issue, I'm not sure it is in scope for Audubon Core. AC imports terms from other vocabularies when possible (notably Darwin Core), but generally only mints terms when they deal specifically with multimedia and when existing vocabularies don't already provide such a term. The issue that Rob raises is a general one that needs to be discussed in the context of how vocabularies such as Darwin Core (which are currently designed primarily to facilitate "flat", specimen-oriented databases) can be adapted for use in more normalized databases which integrate information about many kinds of resources (e.g. specimens, DNA sequences, images, etc. ). This is a topic that is the subject of ongoing discussions with groups such as BiSciCol, RCN4GSC, and the TDWG RDF task group. But it may be too much for Audubon Core to take on at this point in time. Opinions? 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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