December 2009 - tdwg-content

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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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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Re: [tdwg-content] [tdwg-tag] 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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DwC Basis of Record & dcterms:type
by Roger Hyam 09 Dec '09

09 Dec '09

I apologise if I come to this debate a little late but prompted by John and my renewed interest in the TDWG Ontology I feel I should. I have several short points. I hope I am not out of scope not being fully conversant with the debate so far. Generally we judge the class of an object by its properties. i.e. If it walks like a duck and quacks it is probably a duck (apologies to ornithologists) The sender and receiver often have a different classification systems for messages. e.g. Published specimen data is often(perhaps usually) received and treated as occurrence data. I assume DwC is an generic way for marking up messages rather than a full blown ontology. The basisOfRecord and dcterms:type should therefore be thought of as hints on how to interpret a record rather than declarations of class membership. Class membership is decided by the receiver. An "unmissable special offer" to the sender may be a "useful fire lighter" to the receiver. dcterms:type is used by the world and so should probably contain a generic term for systems/people who don't understand basisOfRecord. basisOfRecord should contain anything that is well defined in natural language. I suppose I am saying I don't understand the problem. Can some one summarise it? Thanks, Roger

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