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Re: [tdwg-content] Treatise on Occurrence, tokens, and basisOfRecord [SEC=UNCLASSIFIED]
by Richard Pyle 29 Oct '10

29 Oct '10

Thanks, Julian -- I somehow missed Stan's post (among a flurry of other emails - both from this list, and from other sources). Sorry about that, Stan! So, after now having read Stan's post, I do agree that the "who and how" (I'm leaving out the "what they did", to avoid people mistaking it for the "what they saw") -- that is, the "action" (in my terms) of the Event -- should, indeed, be regarded as part of the Event, and not part of the Occurrence (although I still maintain it could legitimately be interpreted either way). I should also take this opportunity to mention MUSE and FishGopher as being among the very early efforts to organize this sort of information in a form that could be distributed over the proto-Net. Aloha, Rich > -----Original Message----- > From: Julian H [mailto:humphries@mail.utexas.edu] > Sent: Thursday, October 28, 2010 1:09 PM > To: Richard Pyle > Cc: tdwg-content(a)lists.tdwg.org > Subject: Re: [tdwg-content] Treatise on Occurrence, tokens, > and basisOfRecord [SEC=UNCLASSIFIED] > > > As Stan said in an earlier message today: > > "Back to the issue of event definition: If Event is defined > as just the conjunction (association, intersection, join) of > space and time, there is nothing to tell you why this > particular interval is of interest." > > In other words the who and how and what they did that made > the event of interest. > > julian > > > At 02:30 PM 10/28/2010, Richard Pyle wrote: > > > Yeah, some act took place at that place and time. In the > context of > > > Occurrence, probably an act of sampling or collecting, and so one > > > should expect metadata documenting that act (who, how, etc) > > > >As I alluded to in my previous post, it's not clear to me > whether the > >who, how, etc. are intrinsic properties of the Event, or if > the "Event" > >simply represents the single coordinate in 4-D space-time; and the > >other stuff is more a function of the Occurrence (i.e., more > metadata > >about documenting the tuple of Event+Individual). I can see > rational > >arguments either way. My inclination is that the word "Event" goes > >beyond merely the space-time coordinate, and implies some sort of > >"action". As such, my inclination is to define the "Event" as more > >than just the 4D space-time coordinate, and include who, > how, etc. as part of the "action" of the Event. > > > >As is probably obvious, I haven't throught this through extensively > >yet, so I reserve the right to change my mind. > > > >Rich > > > > > >_______________________________________________ > >tdwg-content mailing list > >tdwg-content(a)lists.tdwg.org > >http://lists.tdwg.org/mailman/listinfo/tdwg-content >

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Painted Lady Butterfly in from within the LOD Cloud via URIburner
by Peter DeVries 28 Oct '10

28 Oct '10

Painted Lady Butterfly in from within the LOD Cloud via URIburner http://bit.ly/aCLXmF The Occurrence RDF http://ocs.taxonconcept.org/ocs/a71fda68-024a-4020-a34c-64dce7935e5f.rdf <http://ocs.taxonconcept.org/ocs/a71fda68-024a-4020-a34c-64dce7935e5f.rdf>The Species Concept RDF http://lod.taxonconcept.org/ses/dwAmr.rdf <http://lod.taxonconcept.org/ses/dwAmr.rdf>I had added a urn for the individual so that individuals can be tracked between several occurrences. This SPARQL Query Which you can run on any endpoint that has the data set loaded will show the occurrences of this species. Here is the query embeded in a URL: (Toggle "Visualization" to get the map) < http://lsd.taxonconcept.org/isparql/view/?query=PREFIX%20txn%3A%20%3Chttp%3… > If that does not survive your email client, here is the bit.ly link http://bit.ly/crqr6G This will also run on the LOD cloud. http://bit.ly/aBBFCA (but you don't have to toggle the visualization) - Pete --------------------------------------------------------------- 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-content] practical details of recording a determination What is an Occurrence?
by Kevin Richards 28 Oct '10

28 Oct '10

I can't help but feel we are getting into a much more complicated area of biodiversity ( or any observation oriented field for that matter ) and that there must be other ontologies or models that we could follow or reuse. Our strength at TDWG is obviously the more biodiversity specific details such as taxonomy, invasiveness, etc. I might have an investigation of possible models to reuse - unless someone has already done this and has a suggestion. Kevin Sent from my HTC ----- Reply message ----- From: "Richard Pyle" <deepreef(a)bishopmuseum.org> Date: Thu, Oct 21, 2010 8:11 pm Subject: [tdwg-content] practical details of recording a determination What is an Occurrence? To: "'Steve Baskauf'" <steve.baskauf(a)vanderbilt.edu> Cc: "tdwg-content(a)lists.tdwg.org" <tdwg-content(a)lists.tdwg.org> I see dwc:establishmentMeans as being very clearly a property of "Individual At Place" (again, scoping "Individual" up to at least population). The closest thing we have to that in the diagram1 is Occurrence. The only hitch is that Occurrence isn't exactly "Individual At Place", so much as "Individual At Event[=Place+Time]" Some people have suggected that dwc:establishmentMeans is a function of Time as well as Place, in which case it is very clearly (to me) a property of Occurrence. Rich ________________________________ From: Steve Baskauf [mailto:steve.baskauf@vanderbilt.edu] Sent: Wednesday, October 20, 2010 3:25 PM To: Richard Pyle Cc: tdwg-content(a)lists.tdwg.org Subject: Re: [tdwg-content] practical details of recording a determination What is an Occurrence? Well, I also feel pretty good about most of that diagram, but I'm still struggling with the whole "token" thing. I feel the need to discuss basisOfRecord=LivingSpecimen which is the most complicated case and is also related to the previous discussion about dwc:establishmentMeans as well as my proposal to move it to the proposed Individual class. It is also related to another issue that I haven't broached here but which is discussed in my paper - "Occurrences" that aren't directly derived from an individual. I'm beginning to think that part of what I wrote there (in the paper) was wrong, but I'm not sure what the alternative is. That issue will probably come up if I comment about what Cam wrote in his email. So there may be more to hash out, but I can't handle it today because I've got too many other things to do. I've been mentally composing what I hope is a lucid presentation, but it hasn't hit the keyboard yet. Steve I have to say, this has been about the most productive (if volumunous) list-discussion I've had in...well...maybe ever. It seems we've both been equally persuasive, and equally willing to concede. How rare that happens in an internet forum! I'm not sure there's anything left that we disagee about. If the "diagram1" seems to resonate with everyone as the most "normalized" ER diagram we'll likely ever need, and if we can somehow accommodate flexibility in RDF for collapsing attributes to different classes (but only from the "one" side to the "many" side) -- then we might have achived the elusive Holy Grail of biodiversity informatics: true consensus. Thanks for your great feedback and for challenging my statements. I need that! Likewise! Aloha, Rich . -- 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-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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Increased List Traffic
by "Markus Döring (GBIF)" 28 Oct '10

28 Oct '10

Dear list subscribers, there has been a large increase in activity on this mailing list lately. I wanted to remind you that if you seek to reduce your incoming mails you can change your subscription to a digest mode that will bundle mails to a single one per day. Of course you can also leave this list if you want to. Both changes can be done after logging into your account here: http://lists.tdwg.org/mailman/listinfo/tdwg-content If you have lost your password you can request it to be resend to you on the very same page. Regards, Markus

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Example American Toad Occurrences SPARQL Query of the LOD Cloud
by Peter DeVries 27 Oct '10

27 Oct '10

American Toad Occurrences SPARQL Query are now working on the LOD Cloud http://bit.ly/9j7nlq -- --------------------------------------------------------------- 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-content] Data Licenses; Was: Re: Occurrence Records, with Individuals and Identifications
by Peter DeVries 24 Oct '10

24 Oct '10

Hi Bob, I need to think about this a little more, but these are records that I had previously exposed on GeoSpecies as cc with attribution., so they were a change. Also they include a photograph as supporting evidence, see foaf:depiction. These were mainly done to create examples that showed an Occurrence, Individual, Identification and used the ietf proposal for an "Area" geo e.g. "geo:44.86528100,-87.23147800;u=10". The example creates these in one RDF file, but assertions etc. can be made about these individual entities as if they were separate things. I think most data sets will probably need some sort of license that allows them to be used but with some sort of attribution. I would be interested in hearing people's opinion on what they would recommend. Also these records were created for purposes of the discussion, there are some other aspects that I will probably change in the future. Below is the actual RDF for the #Occurrence element. <txn:Occurrence rdf:about=" http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurr… "> <dcterms:title>Boloria selene Occurrence Shivering Sands Natural Area Woods 2005-07-24/2005-07-24</dcterms:title> <dcterms:isPartOf rdf:resource=" http://lod.taxonconcept.org/ontology/void#this"/> <dcterms:identifier> http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurr… </dcterms:identifier> <cc:license rdf:resource="http://creativecommons.org/publicdomain/"/> <cc:attributionURL rdf:resource="http://lod.taxonconcept.org"/> <cc:attributionName>Peter J. DeVries</cc:attributionName> <cc:morePermissions rdf:resource="http://about.geospecies.org/projects/"/> <dcterms:created>2010-10-21T00:00:00-0500</dcterms:created> <dcterms:modified>2010-10-22T00:10:51-0500</dcterms:modified> <txn:occurrenceHasSpeciesOccurrenceTag rdf:resource=" http://lod.taxonconcept.org/ses/ICmLC#Occurrence"/> <txn:occurrenceHasSpeciesConcept rdf:resource=" http://lod.taxonconcept.org/ses/ICmLC#Species"/> <txn:occurrenceHasIndividual rdf:resource=" http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Indivi… "/> <txn:hasScientificName>Boloria selene</txn:hasScientificName> <txn:continent>North America</txn:continent> <txn:countryCode>US</txn:countryCode> <txn:country>United States</txn:country> <txn:stateProvince>Wisconsin</txn:stateProvince> <txn:county>Door</txn:county> <txn:localityText>Town of Sevastopol</txn:localityText> <txn:locationName>Shivering Sands Natural Area Woods</txn:locationName> <txn:occurrenceHasArea rdf:resource="geo:44.86528100,-87.23147800;u=10"/> <geo:lat>44.86528100</geo:lat> <geo:long>-87.23147800</geo:long> <txn:georeferenceProtocol rdf:resource=" http://lod.taxonconcept.org/ontology/txn.owl#GeoProtocol_GPS"/> <txn:georeferenceVerificationStatus rdf:resource=" http://lod.taxonconcept.org/ontology/txn.owl#GeoVerifiedByCollector"/> <txn:occurrenceInContinent rdf:resource="http://sws.geonames.org/6255149/ "/> <txn:occurrenceInStateProvince rdf:resource=" http://sws.geonames.org/5279468/"/> <txn:occurrenceInCounty rdf:resource="http://sws.geonames.org/5250768/"/>  <txn:startDate>2005-07-24</txn:startDate> <txn:endDate>2005-07-24</txn:endDate> <txn:samplingProtocol rdf:resource=" http://lod.taxonconcept.org/ontology/txn.owl#SamplingProtocol_IndividualObs… "/>  <txn:collector rdf:resource=" http://lod.taxonconcept.org/ontology/people.owl#Peter_J_DeVries"/> <txn:identifiedBy rdf:resource=" http://lod.taxonconcept.org/ontology/people.owl#Kyle_E_Johnson"/>  <txn:identificationDate>2008</txn:identificationDate> <txn:identifiedAs rdf:resource=" http://lod.taxonconcept.org/ses/ICmLC#Species"/>  <txn:institutionCode>IRCW</txn:institutionCode> <txn:collectionCode>PJDPO</txn:collectionCode> <txn:catalogCode>PJDPO000179</txn:catalogCode> <txn:individualStatus rdf:resource=" http://lod.taxonconcept.org/ontology/txn.owl#IndividualStatus_Unknown"/> <txn:basisOfRecord rdf:resource=" http://lod.taxonconcept.org/ontology/txn.owl#BasisOfRecord_StillImage"/> <foaf:depiction rdf:resource=" http://assets.geospecies.org/spec_concept_uuid/e096643b-ff98-4f51-bd80-3ff0… "/> <foaf:page rdf:resource=" http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.rdf"/> </txn:Occurrence> Respectfully, - Pete On Sun, Oct 24, 2010 at 12:14 PM, Peter DeVries <pete.devries(a)gmail.com>wrote: > Hi Bob, > > Thanks for this. I will look into fixing this. > > - Pete > > > On Sun, Oct 24, 2010 at 11:35 AM, Bob Morris <morris.bob(a)gmail.com> wrote: > >> On Fri, Oct 22, 2010 at 12:47 AM, Peter DeVries <pete.devries(a)gmail.com> >> wrote: >> > I have redone my occurrence records to match the single example I had >> posted >> > before. (Go to the last example, if you just want something pretty) >> > Here is the >> > RDF: >> http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.rdf >> >[...] >> >> > - Pete >> >> Without regard to the structure of your RDF but rather to your license >> attribute on txn:Occurrence, you might care that >> (a) the CC Public Domain Mark license is intended to apply to work >> that was once copyrighted but now isn't. >> (b)For lots of reasons, CC now recommends against the use of CC >> licenses for data ( [1], [2] ). >> (c)Without regard to whether data is copyrightable, CC licenses >> only apply to copyrightable material; in all countries subscribing to >> the Copyright Convention, only creative works are copyrightable; I'm >> pretty sure you don't intend that an Occurrence is a creative work (or >> even that its expression is--at least an expression in a standard >> form). >> >> [1] >> http://sciencecommons.org/projects/publishing/open-access-data-protocol/ >> [2] http://sciencecommons.org/resources/faq/database-protocol/ >> >> 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) >> > _______________________________________________ >> > tdwg-content mailing list >> > tdwg-content(a)lists.tdwg.org >> > http://lists.tdwg.org/mailman/listinfo/tdwg-content >> > >> > >> > > > > -- > --------------------------------------------------------------- > 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/> > ------------------------------------------------------------ > -- --------------------------------------------------------------- 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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Data Licenses; Was: Re: Occurrence Records, with Individuals and Identifications
by Bob Morris 24 Oct '10

24 Oct '10

On Fri, Oct 22, 2010 at 12:47 AM, Peter DeVries <pete.devries(a)gmail.com> wrote: > I have redone my occurrence records to match the single example I had posted > before. (Go to the last example, if you just want something pretty) > Here is the > RDF: http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.rdf >[...] > - Pete Without regard to the structure of your RDF but rather to your license attribute on txn:Occurrence, you might care that (a) the CC Public Domain Mark license is intended to apply to work that was once copyrighted but now isn't. (b)For lots of reasons, CC now recommends against the use of CC licenses for data ( [1], [2] ). (c)Without regard to whether data is copyrightable, CC licenses only apply to copyrightable material; in all countries subscribing to the Copyright Convention, only creative works are copyrightable; I'm pretty sure you don't intend that an Occurrence is a creative work (or even that its expression is--at least an expression in a standard form). [1] http://sciencecommons.org/projects/publishing/open-access-data-protocol/ [2] http://sciencecommons.org/resources/faq/database-protocol/ 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) > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > >

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"resolution" of URIs usually used improperly
by Bob Morris 22 Oct '10

22 Oct '10

Is it too pedantic to wish that people would not use "resolve" when they mean "dereference"? The terms are distinguished in RFC 3986[1]: "URI "resolution" is the process of determining an access mechanism and the appropriate parameters necessary to dereference a URI; this resolution may require several iterations. To use that access mechanism to perform an action on the URI's resource is to "dereference" the URI." [1] I bet the concensus answer to my question is "Yes". Sigh. [1]http://www.rfc-editor.org/rfc/rfc3986.txt Bob (The Pedant) 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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Occurrence Records, with Individuals and Identifications
by Peter DeVries 22 Oct '10

22 Oct '10

I have redone my occurrence records to match the single example I had posted before. (Go to the last example, if you just want something pretty) Here is the RDF: http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.rdf In TXNburner you can step through the various elements starting with the RDF that describes the file itself, the other elements are "topics' of the page. http://lsd.taxonconcept.org/about/html/http/ocs.taxonconcept.org/ocs/f52244… There is some repetition between the "#" elements of this record, that I intend to cleanup. We don't really need to use geo in both the #Occurrence and #Area, but if for now if you want the #Occurrence records to show up as dots on a map then you do. Here is what it looks like on the LOD Cloud via Sindice. http://sig.ma/search?pid=5e39335bd5ff1a1e6f9a6ad0bfc91102 - Pete P.S. Sleep ... I remember what that was like :-) ---------------------------------------------------------------- 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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To the list administrators
by Amanda Neill 20 Oct '10

20 Oct '10

I am enjoying all the posts, but I'm getting them all twice, to the two different e-mail accounts I used to sign up for the listserves (three times if you count the g-mail that goes to my phone too)! Can I suggest these conversations have moved long beyond bioblitz issues and are now back to addressing the general things that have always found a forum in the tdwg-content list? Could we just ask the bioblitz subscribers to subscribe to tdwg-content if they are still interested? And quit cross posting more general discussions to both lists? That would be awesome. Thanks, Amanda K. Neill Director of the Herbarium (BRIT-SMU-VDB) Botanical Research Institute of Texas 500 E. 4th St. Fort Worth TX 76102 USA phone 817-332-4441 ext. 217 fax 817-332-4112 aneill(a)brit.org www.brit.org www.atrium-biodiversity.org atrium.brit.org www.andesamazon.org atrium.andesamazon.org ng.atrium-biodiversity.org

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