- tdwg-content - lists.tdwg.org

[tdwg-geospatial] TDWG mailing list consolidation
by "Markus Döring (GBIF)" 08 Sep '10

08 Sep '10

Dear members of the TDWG mailing list tdwg-geospatial, TDWG has seen a proliferation of mailing lists over the years, most of which are inactive today. Traffic on most lists is rather little and usually limited to only a short period of time. As most lists also have very much the same subscribers, we are seeking to merge lists into just a few ones. The main 3 mailing lists we want to maintain in the future being: tdwg(a)lists.tdwg.org A list with very low traffic for official TDWG announcements from the executive committee http://lists.tdwg.org/mailman/listinfo/tdwg tdwg-content(a)lists.tdwg.org A list for all non technical discussions covering all TDWG working groups / standards http://lists.tdwg.org/mailman/listinfo/tdwg-content tdwg-tag(a)lists.tdwg.org The technical architecture group list that will host discussions about the technical details of standards http://lists.tdwg.org/mailman/listinfo/tdwg-tag Within the next days we will automatically add all subscribers of this list to tdwg and tdwg-content and will merge all existing archives of the mailing list tdwg-geospatial into tdwg-content. The list tdwg-geospatial will be closed and removed once the archives have been merged. Best wishes, Markus Döring

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[Biogeosdi] TDWG mailing list consolidation
by "Markus Döring (GBIF)" 08 Sep '10

08 Sep '10

Dear members of the TDWG mailing list biogeosdi, TDWG has seen a proliferation of mailing lists over the years, most of which are inactive today. Traffic on most lists is rather little and usually limited to only a short period of time. As most lists also have very much the same subscribers, we are seeking to merge lists into just a few ones. The main 3 mailing lists we want to maintain in the future being: tdwg(a)lists.tdwg.org A list with very low traffic for official TDWG announcements from the executive committee http://lists.tdwg.org/mailman/listinfo/tdwg tdwg-content(a)lists.tdwg.org A list for all non technical discussions covering all TDWG working groups / standards http://lists.tdwg.org/mailman/listinfo/tdwg-content tdwg-tag(a)lists.tdwg.org The technical architecture group list that will host discussions about the technical details of standards http://lists.tdwg.org/mailman/listinfo/tdwg-tag Within the next days we will automatically add all subscribers of this list to tdwg and tdwg-content and will merge all existing archives of the mailing list biogeosdi into tdwg-content. The list biogeosdi will be closed and removed once the archives have been merged. Best wishes, Markus Döring

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evil twin of "dcterms:replaces" in DwC rdf representation
by Bob Morris 08 Sep '10

08 Sep '10

dwcterms.rdf uses "rdfs:replaces" to implement the "Replaces" attribute of DwC term definitions. There is no rdfs:replaces in the RDFS recommendation. Probably what is desired is dcterms:replaces or, even better owl:PriorVersion, which will play nicely with reasoning on Annotation Properties. This matters if one is trying to make an OWL2 representation of DwC, which is very finicky about what Annotation Properties may be in the rdfs namespace (none, except as those listed in http://www.w3.org/TR/owl2-syntax/#Annotation_Properties). Bob Morris -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob(a)gmail.com web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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dwc:associatedOccurrences
by Mark Wilden 07 Sep '10

07 Sep '10

On Tue, Aug 24, 2010 at 6:24 AM, John Wieczorek <tuco(a)berkeley.edu> wrote: > Note that associatedOccurrences is one of the several terms that are meant > to allow lists of relationships between resources to be captured in a single > field. Others include associatedMedia, associatedReferences, > associatedSequnces, and associatedTaxa. The main purposes of these fields is > to provide a mechanism to share relationship information in a flat > application profile such as the Simple Darwin Core > (http://rs.tdwg.org/dwc/terms/simple/index.htm). If an application profile > isn't constrained by being flat, then there is a much more robust way to > capture relationships, using the ResourceRelationship class and it's > constituent terms (http://rs.tdwg.org/dwc/terms/index.htm#relindex). However, the values of the description of the relationship (http://rs.tdwg.org/dwc/terms/index.htm#relationshipOfResource) are not controlled, so this still doesn't provide a "community-defined" vocabulary that Bob was asking about. ///ark Web Applications Developer Center for Applied Biodiversity Informatics California Academy of Sciences

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Upcoming TDWG meeting
by Nico Cellinese 02 Sep '10

02 Sep '10

Hi all, we have reserved one full day for a Phylogenetics Standards hands-on activity at the upcoming TDWG conference. We asked for power strips and wireless network and tables that we can sit around and work together. The only thing that's missing right now is what exactly we should target. The options are wide open right now, with the two only major constraints being that (a) we have no funding this year to bring people in who wouldn't otherwise be there, and (b) abstract submission deadline is next Wednesday. Any feedback or ideas, wild or not, that you have would be welcome - send those our way. And BTW currently this workshops seems to be placed on the Wednesday of the conference week, so those of you blitzing the local biosphere will unfortunately have a conflict. Cheers, Nico & Hilmar <><><><><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Assistant Curator, Herbarium & Informatics Adjunct Assistant Professor, Department of Biology Florida Museum of Natural History University of Florida 354 Dickinson Hall, PO Box 117800 Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://www.flmnh.ufl.edu

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Re: [tdwg-content] [tdwg-tag] Do terms in the http://rs.tdwg.org/dwc/terms/ namespace actually resolve?
by Peter DeVries 01 Sep '10

01 Sep '10

Hi Steve, I originally replied to this in the tdwg-tag list, rather than the tdwg-content list. The resolvability of ontological terms is needed by services like Sindice to figure out how to interpret the RDF. As in this example: http://sig.ma/search?pid=02c02e379a5b11a344ed7519ff198222 Like Bob, I have also had problems incorporating the TDWG vocabulary into Protege, which is one reason that I had trouble getting it to work. My current thinking is that it might be best to keep the TDWG vocabulary as it is for submitting data to GBIF etc, while designing a more efficient vocabulary that works well on the LOD. By "efficient", I mean a vocabulary that uses standard resolvable URI's instead of literals for standard terms etc. This solution would also avoid the problem that Markus just mentioned. I am also wondering if the "individual" definition should be changed to mean one individual organism rather than a potential collection of individuals. Individuals from the same colony could be represented using a separate related vocabulary. Allowing multiple individuals will cause problems for consuming applications. For instance, is the queen a separate individual or not? How do you differentiate between a photo of the queen vs. a photo of one of the workers. There are also potential problems even if the individuals are all workers. I have been thinking that for some attributes like character states, it might be best to have a family level ontology. In this example, you might have a "formicidae_ontology", that could be used to deal with individuals from the same colony as well as ant specific character states. xmlns:ant="http://rs.gbif.org/family_ontology/ant.owl#" <rdf:Description rdf:about="http://example.org/individual/123412"> <ant:colonyMateOf rdf:resource="http://example.org/individual/123414"/> </rdf:Description> This could be defined as a subproperty of dc:relation or something similar in the gbif/tdwg vocabulary. <http://sig.ma/search?pid=02c02e379a5b11a344ed7519ff198222>- Pete On Tue, Aug 24, 2010 at 6:43 PM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu > wrote: > I was doing some GUID testing using a Linked Data client and I noticed > that some Darwin Core terms did not seem to resolve to anything. I ran > a test using > http://demo.openlinksw.com/rdfbrowser2/ > http://api.talis.com/stores/iand-dev1/items/dipper.html > http://www5.wiwiss.fu-berlin.de/marbles/ > and > http://dataviewer.zitgist.com/ > I first I looked up > http://purl.org/dc/terms/creator > and all four clients reported the properties of the term. Then I tried > http://rs.tdwg.org/dwc/terms/basisOfRecord > and nothing happened with any of them. I ran a Vapour > http://validator.linkeddata.org/vapour > validation on the basisOfRecord URI and got the following message: > > Vapour was unable to complete the request due to the following exception: > > ForbiddenAddress: forbidden request from 98.87.45.8 to > http://rs.tdwg.org/dwc/terms/basisOfRecord (resolves to IP 192.38.28.106), > internal IP addresses are forbidden > > I have no idea what that means, but all of this seems to mean that > Darwin Core is currently "broken" from a Linked Data point of view. > > Steve > > -- > 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 > > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag > -- ---------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

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Re: [tdwg-phylo] Upcoming TDWG meeting
by Arlin Stoltzfus 27 Aug '10

27 Aug '10

Is anyone else interested? If there is interest, I'll start a planning document (TDWG phylo twiki?). Arlin On Aug 27, 2010, at 2:45 PM, Dan Rosauer wrote: > Hi Arlin and others > > I think that idea 1 below is a really valuable topic to address. > The ability to link tree tips to other sources of data by taxon name > or identifier is a threshold step for automating a whole range of > analyses and displays. For example, the software I work on, > Biodiverse, links phylogenies to species location data for > visualisation and analysis. It would be great to have it running > automatically online, linking (for example) trees from treebase to > distributions from GBIF. To do this (and many other things) however > we need a better solution to the taxon matching problem you describe. > > cheers > Dan > > From: tdwg-phylo-bounces(a)lists.tdwg.org [mailto:tdwg-phylo-bounces@lists.tdwg.org > ] On Behalf Of Arlin Stoltzfus > Sent: Friday, August 27, 2010 11:27 AM > To: tdwg-phylo(a)lists.tdwg.org > Subject: Re: [tdwg-phylo] Upcoming TDWG meeting > > I'm sending this reply to only the tdwg-phylo list (sending to > everyone seems like overkill). > > Here are two ideas based on the use of phylogenies: > > 1. For various reasons, its important to be able to associate > valid species sources or other universal identifiers (e.g., NCBI > gis) with the human-readable OTU identifiers used in tree files, but > this typically isn't done and it's not always easy. The goal of > this project is to enable ordinary phylogenetics & systematics users > to use current standards (Newick, NHX, phyloxml, ...) to associate > species names (possibly other tax ids) with phylogenies in their > usual workflows. The focus is on developing short-term tools and > strategies that might lead to better long-term solutions. In some > cases, its just a matter of knowing how to use the file format > properly, possibly aided by better tools for data input. For users > whose workflows rely on Newick, we would need a way to keep a > separate mapping of OTU ids and tax ids, along with tools to > interconvert or translate to one of the other formats (this could be > as simple as an Excel spreadsheet or as complex as a web service > that maintains your mapping and does the translation for you). > > 2. There is a huge variety of tree viewers. To some extent, users > need this variety due to their having different feature sets. But > users shouldn't have to choose the viewer based on data format > restrictions. The goal of this project is to improve the usability > of tree viewers. Assess the interoperability (standards > compatibility) of tree viewing software, develop strategies to > improve it, and get started on any strategies that can be > implemented. Its not possible to modify viewers whose source code > is unavailable, but there may be ways to work around this with > scripts and translation tools. > > Arlin > > On Aug 26, 2010, at 9:40 PM, Nico Cellinese wrote: > > > Hi all, > > we have reserved one full day for a Phylogenetics Standards hands-on > activity at the upcoming TDWG conference. We asked for power strips > and wireless network and tables that we can sit around and work > together. The only thing that's missing right now is what exactly we > should target. The options are wide open right now, with the two > only major constraints being that (a) we have no funding this year > to bring people in who wouldn't otherwise be there, and (b) abstract > submission deadline is next Wednesday. > > Any feedback or ideas, wild or not, that you have would be welcome - > send those our way. > > And BTW currently this workshops seems to be placed on the Wednesday > of the conference week, so those of you blitzing the local biosphere > will unfortunately have a conflict. > > Cheers, > Nico & Hilmar > > > <><><><><><><><><><><><><><><><><><><><> > Nico Cellinese, Ph.D. > Assistant Curator, Herbarium & Informatics > Adjunct Assistant Professor, Department of Biology > > Florida Museum of Natural History > University of Florida > 354 Dickinson Hall, PO Box 117800 > Gainesville, FL 32611-7800, U.S.A. > Tel. 352-273-1979 > Fax 352-846-1861 > http://www.flmnh.ufl.edu > > > > <ATT00001.txt> > > ------- > Arlin Stoltzfus (arlin(a)umd.edu) > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > IBBR, 9600 Gudelsky Drive, Rockville, MD > tel: 240 314 6208; web: www.molevol.org > > <ATT00001.txt> ------- Arlin Stoltzfus (arlin(a)umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org

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DwC formal semantics, was Re: dwc:associatedOccurrences
by Bob Morris 25 Aug '10

25 Aug '10

On Tue, Aug 24, 2010 at 9:14 PM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> wrote: > As I was stuck in traffic this morning I was thinking about my response to > Bob's comments. In retrospect, I should have simply said that indicating > that specimens are duplicates by assigning their dwc:individualID property > to the same URI is really not just one option, but rather that it is the > semantically correct thing to do. If "semantically correct" is meant to be something about formal semantics, I am not yet prepared to believe that the DwC rdf profile is amenable to useful OWL formal semantics as it stands. (It also makes no claims to do so, and for reasons I'm sympathetic to, probably shouldn't). A little about this later. > [... stuff about owl:sameAs and whale sharks] The paper by Halpin and Hays [1] shows that even for Linked Data, owl:sameAs is more complicated than may seem. (The paper also asserts that not much reasoning is presently done on Linked Data, so I suppose any particular use of owl:sameAs for anything but machine reasoning may in practice be harmless for present Linked Data tools.) My understanding from studying it is that dwcterms.rdf makes no pretense to be an OWL ontology, nor do its authors claim that. It uses rdf and rdfs with close to no formal semantics restrictions. Put another way, it is about as open world as it could get and still be valid rdf. Although I at first was annoyed by this(*), I have come to believe that it is probably a boon, because it allows multiple profiles to be built on dwcterms.rdf, using it as controlled vocabulary but allowing formal semantics to be determined by the axioms of the profile. I agree with your opinion "it is wrong to invent some other term to represent a relationship that can be clearly and unambiguously expressed using existing terms", but formal semantics imposes a definition of "unambiguously expressed" and practitioners of one domain may accept a particular unambiguous expression, while those in another don't. Information systems have to be accepted, not merely unambiguous. After I've tried to build a few DwC OWL profiles for distinguishable communities of collections practice, I'll look again at your arguments to see how much commonality I (and more importantly, my informants) think there is lurking in the profiles. I expect that some of these kinds of issues will be on the table at several of the proposed Wednesday/Thursday sessions at TDWG. Hope you're there. (*)A good example is this: wrestle dwcterms.rdf into Protege 4 and then go looking for dwc:basisOfRecord. You won't find it listed as a Property, and unless you understand the whole rdf stack, you'll be mystified why Protege is merely unhelpful, not broken, in this case. Bob [1] "When owl:sameAs isn’t the Same: An Analysis of Identity Links on the Semantic Web", Harry Halpin and Patrick J. Hayes http://events.linkeddata.org/ldow2010/papers/ldow2010_paper09.pdf -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob(a)gmail.com web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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dwc:associatedOccurrences
by Bob Morris 25 Aug '10

25 Aug '10

http://rs.tdwg.org/dwc/terms/index.htm#associatedOccurrences carries this description: associatedOccurrences Identifier: http://rs.tdwg.org/dwc/terms/associatedOccurrences Class: http://rs.tdwg.org/dwc/terms/Occurrence Definition: A list (concatenated and separated) of identifiers of other Occurrence records and their associations to this Occurrence. Comment: Example: "sibling of FMNH:Mammal:1234; sibling of FMNH:Mammal:1235". For discussion see http://code.google.com/p/darwincore/wiki/Occurrence Details: associatedOccurrences My questions: a. Are the names of the associations, and/or the syntax of the value meant to be community defined? b. If no to a. , where are those definitions? If yes, Have any communities defined any names and syntax? I am especially interested in "duplicate of" in the case of herbarium sheets." c. (May share an answer with b.) Is there any use being made by anyone in which associatedOccurrences is designed to have machine-readable values. If yes, where? Thanks Bob -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob(a)gmail.com web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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Replying to all doesn't
by Mark Wilden 24 Aug '10

24 Aug '10

It seems incorrect to me that doing "Reply to all" on this list doesn't actually reply to all (i.e., the list). The only way I see to actually "reply to all" is to remember to manually edit the To: line to put in tdwg-content. Granted, inadvertent "replies to all" when just "reply" was intended can be annoying and even embarrassing. However, it does seem that if you explicitly "reply to all," you should do just that. ///ark Web Applications Developer Center for Applied Biodiversity Informatics California Academy of Sciences

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