- tdwg-content - lists.tdwg.org

Proposal to create a new DwC term for the class Individual
by Steve Baskauf 23 Jan '10

23 Jan '10

This issue is with reference to http://code.google.com/p/darwincore/issues/detail?id=69 I have proposed the creation of a new Darwin Core term, Individual, that is a class representing individual organisms in their environment (as opposed to live organisms in collections which would be Occurrences of type LivingSpecimen). The justification for this new term is given at the link above, but to summarize, this class is needed: 1. to establish the concept of an individual (in the sense of the object of dwc:individualID) and its relationship to other classes in the TDWG ontology. 2. to provide a way for users who assign a GUID as a value for the dwc term individualID to meet Recommendation 11 (regarding GUID typing) of the draft TDWG GUID Applicability Statement. I should also note that the problem that my proposal is intended to resolve may exist for other terms in the new Darwin Core standard that can refer to resources that can be identified with GUIDs. In particular, there may be no existing classes in the TDWG ontology http://tdwg-ontology.googlecode.com/svn/trunk/ontology/voc/ for GUID-labeled resources that are referenced by identificationID datasetID, eventID, and locationID . The lack of an appropriate means to type objects identified by GUIDs is only one of the impediments to the implementation of GUIDs in the biodiversity community, but it is one that can be solved relatively quickly by appropriate action on the part of the TDWG technical architecture group. 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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Has Domain and Has Range for DwC Terms
by Moen, William 18 Jan '10

18 Jan '10

As part of our work on the Apiary Project, http://www.apiaryproject.org/content/apiary-home, we are using DwC as the foundational vocabulary for our metadata requirements. The question we currently have relates to the Has Domain and Has Range parameters for the DwC terms as listed in the Complete Historical Record: http://rs.tdwg.org/dwc/terms/history/index.htm We have been reading a number of Dublin Core as well as DwC docs to get an understanding, but it would be very helpful to hear from those of you who have worked with these parameters in DwC. Thanks. Bill ---------------------------------------------------------------------------------------------- William Moen, Ph.D. Director of Research Director, Texas Center for Digital Knowledge (TxCDK) Associate Professor, Department of Library and Information Sciences College of Information, University of North Texas 1155 Union Circle 311068, Denton, Texas 76203-5017 Email: William.Moen(a)unt.edu Website: http://www.unt.edu/wmoen Voice: 940-565-2473 (TxCDK) or 565-3563 (LIS) Fax: 940-369-7872

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Re: [tdwg-content] Any RDF example? Is this what the standard authors intended?
by Paul.Alexander＠csiro.au 14 Jan '10

14 Jan '10

Hi Pete, Thank you for your example. I'm confused by the example's use of dcterms:identifier mainly because I understand that Identifier should point to the resource being described (resource from Dublin Core point of view). My interpretation of DublinCore is that title and publisher describe the resource if it is specifically referenced, i.e. the resource is pointed to by dcterms:identifier (An unambiguous reference to the resource within a given context.) On the other hand if the rdf:Description is pointing to the resource being described, then some alternatives to dcterms:identifier would be dcterms:References, dcterms:Abstract or dcterms:Source. Each indicate we are pointing to a resource that is associated in some way with the rdf:Description resource. One possibility is to discard dcterms:Identifier, so dcterms:title will not be specifically tied to a resource outside its own namespace and will therefore be associated with its containing element i.e. rdf:Description. I clicked through the various parts via uriburner, viewed the source code, looked at the dcterms:Title of each of the RDF files in the example, and re-read the posts on 23 and 24 December but I don't get it. I will have a more thorough look at Darwin Core. Perhaps it would help my understanding if you could put the files dcterms:titled: Pedilus serratus, Bufo americanus and Shivering Sands Natural Area Beach into context. Thank you in advance. Paul ----------------------------------------------------------- On Tue, 12 Jan 2010 02:33:08, Peter DeVries <pete.devries(a)gmail.com> wrote: Hi Jamie, I have mocked up this example, but I am not sure it is what the standard authors were intending. See my post on December 23rd. Here is my example http://rdf.geospecies.org/datasets/Bcb50c3c-13f5-4c0c-A6de-5f422e2b88c7.rdf <http://rdf.geospecies.org/datasets/Bcb50c3c-13f5-4c0c-A6de-5f422e2b88c7.rdf>You can click through the various parts via uriburner http://linkeddata.uriburner.com/about/html/http://rdf.geospecies.org/datase… I also have a lot of species information in RDF, (about 2 million triples) but it is not in DarwinCore at: http://lod.geospecies.org/ The about page is here: http://about.geospecies.org/ This data set is part of the Linked Open Web or LOD, which is explained here: http://linkeddata.org/ Here is the diagram of the Linked Open Data Cloud: http://www4.wiwiss.fu-berlin.de/bizer/pub/lod-datasets_2009-03-05.html I have some examples of SPARQL queries here: http://about.geospecies.org/sparql.xhtml Here the page for one of my species http://lod.geospecies.org/ses/iuCXz.html Here is the RDF for that species http://lod.geospecies.org/ses/iuCXz.rdf I have tried to follow the DarwinCore as close as I can without breaking what I have working. In the future, I plan to rework my occurrence RDF into something like my example above, but with some additional fields. I think I can come up with a version of RDF for occurrences in DarwinCore that also follows Linked Data best practices. Hope this helps. :-) - Pete

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Any RDF example?
by Jaime Bosque 13 Jan '10

13 Jan '10

Dear list, As far as I've been working with DWC I've been just using Simple Darwin Core in XML files but now I'd like to add semantic information and therefore I've planned to use RDF. I've been looking around but couldn't find any good example of a DWC RDF, could you please provide me with one? Even better if it contains the FOAF info of the author... :) Thanks in advance, Jaime

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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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Cross referencing of TDWG's rank terms in an OBO rank vocabulary
by Peter Midford 04 Jan '10

04 Jan '10

Hello, A few weeks ago I inquired about the stability of URI's for the rank terms that appear in the TDWG ontology. Here's why - I am preparing to submit a rank vocabulary to the OBO foundry that includes rank terms from both NCBI and terms from TDWG. In the case of terms that came from TDWG, I have included the TDWG URIs as OBO cross references for the terms. This message is to let the TDWG community know that, barring any objection from the TDWG maintainers, I will be submitting vocabulary, including terms I picked up from TDWG, to the OBO foundry for review. If you are someone involved in both TDWG and OBO foundry, the OBO request will follow soon. Let's please keep discussion of OBO-specific issues on obo-discuss. Thanks, Peter Peter E. Midford Phenoscape Ontology Curator Peter.Midford(a)gmail.com

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clarification of the use of dwc:recordedBy
by Steve Baskauf 04 Jan '10

04 Jan '10

John et al., I have been pondering the difference of the use of the terms dwc:recordedBy and dcterms:creator (http://purl.org/dc/terms/creator). dcterms:creator is defined as: "An entity primarily responsible for making the resource." dwc:recordedBy is defined as: A list (concatenated and separated) of names of people, groups, or organizations responsible for recording the original Occurrence. The primary collector or observer, especially one who applies a personal identifier (recordNumber), should be listed first. Except for the one word "original" in dwc:recordedBy, I would believe that these two terms would mean the same thing in the case of Occurrence resources. In some cases, such as the collection of a physical specimen or photographing a live organism, I think that they are the same thing. The entity that creates the resource (specimen or image) is the same entity that has recorded the Occurrence. However, in the situation where a specimen is imaged, the resulting image resource would have a dcterms:creator that was the person or institution that did the specimen imaging, while according to the way that I read the definition, dwc:recordedBy for the specimen image would have a value that specified the collector of the specimen (not the photographer). If I am correct in this interpretation, this distinction would be useful in the case of images because it would allow for a simple mechanism to distinguish between images that directly record the appearance of individual organisms and images that are simply digital representations of some other thing that records the appearance of an individual organism, i.e. if dcterms:creator= =dwc:recordedBy then the resource was collected directly from an organsim and if dcterms:creator !=dwc:recordedBy then the resource might represent some other resource that was collected directly from an organism. I am not sure how this would apply in situations other than images. For example, if a spider were collected and assigned a persistent identifier, then later for a character documentation project the body parts were separated and considered separate specimens with their own identifiers, would the metadata for a leg specimen resource have dcterms:creator as the person who made the leg prep and dwc:recordedBy be the person who collected the spider? Basically, I would like to know the intention of the use of the word "original" in the definition of dwc:recordedBy. 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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Test Example of Beetle Occurrence in DarwinCore
by Peter DeVries 23 Dec '09

23 Dec '09

Hi TDWG'ers, After Gail's ECN email I made up a demo/trial DarwinCore Occurrence Record of one of Dan's beetle records. Here is my example http://rdf.geospecies.org/datasets/Bcb50c3c-13f5-4c0c-A6de-5f422e2b88c7.rdf <http://rdf.geospecies.org/datasets/Bcb50c3c-13f5-4c0c-A6de-5f422e2b88c7.rdf>You can click through the various parts via uriburner http://linkeddata.uriburner.com/about/html/http://rdf.geospecies.org/datase… Happy Holidays! - Pete ---------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 GeoSpecies Knowledge Base About the GeoSpecies Knowledge Base ------------------------------------------------------------

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

21 Dec '09

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

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Re: [tdwg-content] [tdwg-tag] 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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