December 2009 - tdwg-tag - lists.tdwg.org

character encodings
by Bob Morris 10 Jan '10

10 Jan '10

Does SDD (resp. tdwg) have any best-practice about character encodings and character sets in XML. The sad fact of life is that many printed, and word processing, systematics and ecology documents have odd symbols even in characters and states, e.g. the degree sign, +- sign, the circled 'x', em-dashes, ..., which are not always rendered by browsers. -- Robert A. Morris Professor of Computer Science (nominally retired) UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: ram(a)cs.umb.edu web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/FilteredPush http://www.cs.umb.edu/~ram phone (+1)617 287 6466

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Re: [tdwg-tag] [tdwg-content] taxonomic rank terms
by Kevin Richards 21 Dec '09

21 Dec '09

Right. I might have a look at the occurrence stuff myself. Kevin Sent from my HTC ----- Reply message ----- From: "Roger Hyam" <rogerhyam(a)mac.com> Date: Mon, Dec 21, 2009 10:46 PM Subject: [tdwg-content] [tdwg-tag] taxonomic rank terms To: "Kevin Richards" <RichardsK(a)landcareresearch.co.nz> Cc: "tdwg-tag(a)lists.tdwg.org" <tdwg-tag(a)lists.tdwg.org>, "peter.midford(a)gmail.com" <peter.midford(a)gmail.com>, "tdwg-content(a)lists.tdwg.org" <tdwg-content(a)lists.tdwg.org> Yes we said we would move it into the google code repository and work on it there. I am working on the taxonomy side and will try and produce a mapping to the GBIF recommended way of using DwC for checklists. Not sure what is happening with Occurrence stuff. Would like to delete a lot of the existing LSID vocs in this area. Roger On 21 Dec 2009, at 09:43, Kevin Richards wrote: Was anything done at tdwg about aligning the various overlapping ontologies? Ie lsid vocabs and dwc. Sent from my HTC ----- Reply message ----- From: "Roger Hyam" <rogerhyam(a)mac.com<mailto:rogerhyam@mac.com>> Date: Mon, Dec 21, 2009 10:07 PM Subject: [tdwg-content] [tdwg-tag] taxonomic rank terms To: "Kevin Richards" <RichardsK(a)landcareresearch.co.nz<mailto:RichardsK@landcareresearch.co.nz>> Cc: "Peter Midford" <peter.midford(a)gmail.com<mailto:peter.midford@gmail.com>>, "tdwg-tag(a)lists.tdwg.org<mailto:tdwg-tag@lists.tdwg.org> mailing list" <tdwg-tag(a)lists.tdwg.org<mailto:tdwg-tag@lists.tdwg.org>>, "tdwg-content(a)lists.tdwg.org<mailto:tdwg-content@lists.tdwg.org>" <tdwg-content(a)lists.tdwg.org<mailto:tdwg-content@lists.tdwg.org>> Peter/Kevin, Sorry for delayed reply. The warning note on the top of the TDWG ontology really does mean what it says. I have just been working through TaxonConcept, TaxonName and TaxonRank. Although I hope to change the files are arranged this won't effect the URIs or their meaning - especially the ranks. The only area in the taxon name/concept vocabularies where I would like to use the hatchet is in the taxon Relationship. I believe this is superfluous and just plain confusing. Instead of being able to simply say SpeciesA includes SpeciesB we have to say SpeciesA has a Relationship and the relationship has a target taxon of SpeciesB and is of type includes! Here I'd like to cut things down to simple properties of TaxonConcept. I will write a fuller explanation of any proposed changes when I have finished so that we can fully discuss it. I'll do this on the tdwg-content list and we can spin it out into issues in a tracker of some kind. All the best, Roger N.B. I am only looking at the bit that concerns me at the moment i.e. Taxon stuff not all the occurrence stuff. On 20 Dec 2009, at 19:21, Kevin Richards wrote: > Yes, I am also curious what the state of the various schemas and vocabs is after the recent TDWG meeting. > I have previously expressed what I considered a priority, to review the various overlapping standards, and then re-model, refine, align/map equivalences, etc, to clarify the situation. > > This was something that was said may happen during/around the TDWG meeting. Has this been achieved/started? > > Kevin > > -----Original Message----- > From: tdwg-tag-bounces(a)lists.tdwg.org<mailto:tdwg-tag-bounces@lists.tdwg.org> [mailto:tdwg-tag-bounces@lists.tdwg.org] On Behalf Of Peter Midford > Sent: Friday, 18 December 2009 5:01 p.m. > To: tdwg-tag(a)lists.tdwg.org<mailto:tdwg-tag@lists.tdwg.org> > Cc: roger(a)hyam.net<mailto:roger@hyam.net> > Subject: [tdwg-tag] taxonomic rank terms > > Hi Roger and others, > I know that the tdwg ontology effort is currently in a state of flux, but I have a specific question that perhaps someone can answer here. What is or will be the fate of the vocabulary of rank terms at http://rs.tdwg.org/ontology/voc/TaxonRank? The disclaimer at the top of the page includes that the http URIs of 'key concepts' will be maintained, but are these rank terms going to be preserved? If so, will their URI's remain stable? Are there plans to prune any out? > > Thanks, > > Peter Midford > > > > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org<mailto:tdwg-tag@lists.tdwg.org> > http://lists.tdwg.org/mailman/listinfo/tdwg-tag > > Please consider the environment before printing this email > Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. > The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz<http://www.landcareresearch.co.nz/> > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org<mailto:tdwg-content@lists.tdwg.org> > http://lists.tdwg.org/mailman/listinfo/tdwg-content ________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz<http://www.landcareresearch.co.nz/> ________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

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Re: [tdwg-tag] [tdwg-content] taxonomic rank terms
by Kevin Richards 21 Dec '09

21 Dec '09

Was anything done at tdwg about aligning the various overlapping ontologies? Ie lsid vocabs and dwc. Sent from my HTC ----- Reply message ----- From: "Roger Hyam" <rogerhyam(a)mac.com> Date: Mon, Dec 21, 2009 10:07 PM Subject: [tdwg-content] [tdwg-tag] taxonomic rank terms To: "Kevin Richards" <RichardsK(a)landcareresearch.co.nz> Cc: "Peter Midford" <peter.midford(a)gmail.com>, "tdwg-tag(a)lists.tdwg.org mailing list" <tdwg-tag(a)lists.tdwg.org>, "tdwg-content(a)lists.tdwg.org" <tdwg-content(a)lists.tdwg.org> Peter/Kevin, Sorry for delayed reply. The warning note on the top of the TDWG ontology really does mean what it says. I have just been working through TaxonConcept, TaxonName and TaxonRank. Although I hope to change the files are arranged this won't effect the URIs or their meaning - especially the ranks. The only area in the taxon name/concept vocabularies where I would like to use the hatchet is in the taxon Relationship. I believe this is superfluous and just plain confusing. Instead of being able to simply say SpeciesA includes SpeciesB we have to say SpeciesA has a Relationship and the relationship has a target taxon of SpeciesB and is of type includes! Here I'd like to cut things down to simple properties of TaxonConcept. I will write a fuller explanation of any proposed changes when I have finished so that we can fully discuss it. I'll do this on the tdwg-content list and we can spin it out into issues in a tracker of some kind. All the best, Roger N.B. I am only looking at the bit that concerns me at the moment i.e. Taxon stuff not all the occurrence stuff. On 20 Dec 2009, at 19:21, Kevin Richards wrote: > Yes, I am also curious what the state of the various schemas and vocabs is after the recent TDWG meeting. > I have previously expressed what I considered a priority, to review the various overlapping standards, and then re-model, refine, align/map equivalences, etc, to clarify the situation. > > This was something that was said may happen during/around the TDWG meeting. Has this been achieved/started? > > Kevin > > -----Original Message----- > From: tdwg-tag-bounces(a)lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org] On Behalf Of Peter Midford > Sent: Friday, 18 December 2009 5:01 p.m. > To: tdwg-tag(a)lists.tdwg.org > Cc: roger(a)hyam.net > Subject: [tdwg-tag] taxonomic rank terms > > Hi Roger and others, > I know that the tdwg ontology effort is currently in a state of flux, but I have a specific question that perhaps someone can answer here. What is or will be the fate of the vocabulary of rank terms at http://rs.tdwg.org/ontology/voc/TaxonRank? The disclaimer at the top of the page includes that the http URIs of 'key concepts' will be maintained, but are these rank terms going to be preserved? If so, will their URI's remain stable? Are there plans to prune any out? > > Thanks, > > Peter Midford > > > > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag > > Please consider the environment before printing this email > Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. > The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content ________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

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taxonomic rank terms
by Peter Midford 21 Dec '09

21 Dec '09

Hi Roger and others, I know that the tdwg ontology effort is currently in a state of flux, but I have a specific question that perhaps someone can answer here. What is or will be the fate of the vocabulary of rank terms at http://rs.tdwg.org/ontology/voc/TaxonRank? The disclaimer at the top of the page includes that the http URIs of 'key concepts' will be maintained, but are these rank terms going to be preserved? If so, will their URI's remain stable? Are there plans to prune any out? Thanks, Peter Midford

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Typing in LSID RDF
by Steve Baskauf 02 Dec '09

02 Dec '09

In anticipation of actually being able to use LSIDs now that the TDWG GUID Applicability Statement is moving toward becoming a standard, I have been trying to figure out what exactly I would be putting in RDF for particular types of LSIDs that I would be likely to create. In particular, I have been thinking about the Recommendation "Objects in the biodiversity information domain that are identified by an LSID should be typed using the TDWG ontology or other accepted vocabularies in accordance with the TDWG common architecture." and how it would apply to the types of resources for which I want to create LSIDs. There are three types of things that I'm concerned about: herbarium specimens, digital still images (which could be either images of individual organisms in the wild or images of herbarium specimens), and individuals (in the sense of a URIref object of dwc:individualID). (The following examples assume the standard namespace declarations.) 1. For an herbarium specimen, it seems like I could use either: <rdfs:type rdf:resource="http://rs.tdwg.org/ontology/voc/TaxonOccurrence"/> or <rdfs:type rdf:resource="http://rs.tdwg.org/ontology/voc/Specimen"/> In the spirit of the new DwC standard, it seems like the first alternative would be better since specimen-related elements are now categorized by the more generic term Occurrence. I could then assert the physical nature of the specimen by <dcterms:type rdf:resource="http://purl.org/dc/dcmitype/PhysicalObject"/> 2. For a digital image of either a live plant in the wild or of an herbarium specimen, I could use: <rdfs:type rdf:resource="http://rs.tdwg.org/ontology/voc/TaxonOccurrence"/> or <rdfs:type rdf:resource="http://rs.tdwg.org/ontology/voc/DigitalImage"/> Again in the spirit of the new DwC standard, the first alternative would seem to be preferable, with <dcterms:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/> to establish that the resource was an image. However, if I do that there is nothing in the RDF to indicate that the LSID refers to a digital image rather than a 35mm slide gathering dust somewhere. Under that option, it seems like the only way that an application receiving a resolution of the LSID will know whether the still image is digital or film (physical) is to try a getData() call and succeed, or to possibly include information about file format. 3. For the individual organism (let's say a particular tree in my back yard), I am at a loss of what to use for rdfs:type. None of the types in the TDWG ontology seem right for this. There should be a type for it if I'm going to use dwc:individualID as a property of my live plant images (which I intend to do) given that dwc:individualID "may be a golbal unique identifier...". I can assert the physical nature of the tree by <dcterms:type rdf:resource="http://purl.org/dc/dcmitype/PhysicalObject"/> but that really only tells me that I can't retrieve the tree over the Web and does nothing to let me know that I'm talking about the tree and not a specimen from it or (film) picture of it. I could impart additional information by using basisOfRecord. That would clarify what kind of Occurrence the herbarium specimen was (PreservedSpecimen), but would not help with knowing that the images were digital [i.e. that they would return data for a getData() call], since the suggested value of basisOfRecord for a digital image would be "StillImage" - the same information that's in the dcterms:type statement. It seems to me that basisOfRecord might not even be appropriately applied to individual organisms, since the example values of basisOfRecord seem to provide information about the nature of the token that we use to know that an organism was present somewhere, rather than that the resource is the organism itself. But it seems from previous discussion that basisOfRecord can mean pretty much anything that the people using it decide it should mean, so maybe I could just start using "Individual" as a value for basisOfRecord. I hope that there is a relatively straightforward answer to this question. I'm talking about three very common and uncomplicated things that as a very practical matter need to be labeled with LSIDs. If the typing of LSIDs is really intended to achieve this goal: "Machine and human clients that retrieve the metadata associated with an LSID will use the associated typing information to decide how to process the metadata and any associated data.", then the object of a <rdfs:type rdf:resource="http://xxx"/> statement should allow the client to make this decision in a clear and uncomplicated way. A client resolving the LSID of a specimen should know to expect typical metadata about specimens but know that there is nothing deliverable via the web. A client resolving the LSID of an individual should know to expect metadata that might make it possible to put a dot on a map and to locate any specimens or images that exist for that individual. A client resolving the LSID of a digital image should expect that there will be a (data) representation for a human to look at on a computer monitor and be able to access metadata that would tell them how they would be allowed to use that image if they wanted. It is not clear to me how this goal (deciding how to process data/metadata) would be achieved using the current TDWG ontology. The creation of an "http://rs.tdwg.org/ontology/voc/Individual" class might help at least in the case of individuals in the environment. As a representative of many non-IT-trained potential users of LSIDs and as a TDWG "outsider", I urge the TAG to provide clear and simple answers to this and other questions related to how we can as soon as possible start using HTTP URIs and LSIDs. The TDWG GUID Applicability Statement goes a long way to achieving this, but the requirement that GUIDs be resolvable before they can be assigned creates a technical burden that could effectively "shut out" small players from using them. I know few herbarium curators and plant photographers who are willing to put in the kind of time that I have to try to understand how HTTP URIs/LSIDs work, and even I still have major questions. Thanks for all of the help and hard work that has been put into the development of these tools. Steve Baskauf -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 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) 343-6707 http://bioimages.vanderbilt.edu

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proxying rs.tdwg.org to google code
by "Markus Döring (GBIF)" 01 Dec '09

01 Dec '09

Hi TAG, we had talked about proxying some of the rs.tdwg.org subversion site to different google code projects. I have setup 2 test proxies for darwin core and the new ontology project using these URLs: http://rs.tdwg.org/dwc2/terms/index.htm http://rs.tdwg.org/ontology2/ I wasnt sure if this solution was fully agreed on at TDWG, so I am seeking for advice. I very much like this solution, which gives us the advantage of having google code exposed via the tdwg.org domain. And it frees us from having to sync different copies. If there are no objections I would love to replace the /dwc and potentially also the /ontology part of rs.tdwg.org. But before making this switch some files on google seem to need adjustments in regards of absolute/relative links and html redirects. Markus

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Darwin Core term management - dc:type, basisOfRecord, and recordClass
by John R. WIECZOREK 01 Dec '09

01 Dec '09

Dear TAG, On 23 October a solution to existing problems with the use of dwc:basisOfRecord and dcterms:type as published in the current Darwin Core standard was proposed. Discussions on tdwg-content leading up to and since that proposal support the addition of a term called recordClass as the pragmatic approach that requires less ongoing management than an alternative invoking a new type vocabulary. This message is to forge the way to the first Darwin Core term changes following the published Namespace Policy (http://rs.tdwg.org/dwc/terms/namespace/index.htm#classesofchanges). The proposed changes fall under two of the classes of changes, 3.3 (Semantic changes in Darwin Core terms) and 3.4 (Addition of Darwin Core terms declarations to existing Darwin Core namespaces). I propose to draft Decisions (see http://rs.tdwg.org/dwc/terms/history/decisions/index.htm) for review by the TAG following the 30-day prescribed review period (next week). I just wanted to send this introductory message in anticipation to open up the floor for any questions or commentary, as this is the first time this process has been invoked. John

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