- tdwg-content - lists.tdwg.org

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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Fwd: ANN: LOD Cloud - Statistics and compliance with best practices
by Peter DeVries 19 Oct '10

19 Oct '10

I thought that people might find this useful and informative. - Pete ---------- Forwarded message ---------- From: Anja Jentzsch <anja(a)anjeve.de> Date: Tue, Oct 19, 2010 at 10:33 AM Subject: ANN: LOD Cloud - Statistics and compliance with best practices To: "public-lod(a)w3.org" <public-lod(a)w3.org> Hi all, in the last weeks, we have analyzed which data sources in the new version of the LOD cloud comply to various best practices that are recommended by W3C or have emerged within the LOD community. We have checked the implementation of the following nine best practices: 1. Provide dereferencable URIs 2. Set RDF links pointing at other data sources 3. Use terms from widely deployed vocabularies 4. Make proprietary vocabulary terms dereferencable 5. Map proprietary vocabulary terms to other vocabularies 6. Provide provenance metadata 7. Provide licensing metadata 8. Provide data-set-level metadata 9. Refer to additional access methods The compliance with the best practices was either checked manually or by using scripts that downloaded and analyzed some data from the data sources. We have added the results of the evaluation in the form of tags to the LOD data set catalog on CKAN [1]. We are now happy to release the first statistics about the structure of the LOD could as well as the compliance of the datasets with the best practices. The statistics can be found here: http://www4.wiwiss.fu-berlin.de/lodcloud/state/ The document contains an initial, preliminary release of the statistics. If you spot any errors in the data describing the LOD data sets on CKAN, it would be great if you would correct them directly on CKAN. For information on how to describe datasets on CKAN please refer to the Guidelines for Collecting Metadata on Linked Datasets in CKAN [2]. After your feedback and corrections, we will then move the corrected version of the statistics to http://www.lod-cloud.net/ (around October 24th). Have fun with the statistics and the encouraging as well as disappointing insights that they provide. Cheers, Chris Bizer, Anja Jentzsch and Richard Cyganiak [1] http://www.ckan.net/group/lodcloud [2] http://esw.w3.org/TaskForces/CommunityProjects/LinkingOpenData/DataSets/CKA… -- ---------------------------------------------------------------- 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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Idea for Discussion, Differentiating between "type's" of identifiers
by Peter DeVries 19 Oct '10

19 Oct '10

I have been thinking about the following pattern. In part after looking at the GBIF vocabulary. I am not sure if it is even a good idea but might be worth some discussion. For those fields that have both a string and "ID" form maybe the following pattern might be useful hasScientificName = string form hasScientificNameURI = Resolvable LOD compliant identifier hasScientificNameLSID = LSID identifier which could be resolvable once you add the "http:proxy" etc. This allows all three forms to be included if desired, it also provides a hint as to how the field should be interpreted or resolved. One group could also provide a mapping service so that each record does not need to include all three forms, but would allow systems to find the matching LSID for a given URI or vs. versa. My concern was that it would be difficult to infer how a scientificNameID should be interpreted by other systems. Is this an LSD, is it a URI, is it a UUID etc. ? This impacts the structure of the RDF. * Note that the actual identifiers might not be correct, the example below is more about the form of the RDF * For instance, I don't think it is probably correct to see the COL LSID as just a namestring * Also in this example the GNI name does not exactly match the string name <dwc:hasScientificName>Puma concolor (Linnaeus 1771)</dwc:hasScientificName> <dwc:hasScientificNameURI rdf:resource=" http://gni.globalnames.org/name_strings/6c3dc35f-d901-5cc5-b9c8-ad241069b9f8 "/> <dwc:hasScientificNameLSID rdf:resource="urn:lsid:catalogueoflife.org: taxon:24e7d624-60a7-102d-be47-00304854f810:ac2010"/> Some system may choke on the LSID form assuming that it uses a standard resolution mechanism So it might be best to use this form <dwc:hasScientificNameLSID>urn:lsid:catalogueoflife.org: taxon:24e7d624-60a7-102d-be47-00304854f810:ac2010</dwc:hasScientificNameLSID> - 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/> ------------------------------------------------------------ _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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Example of Cloud Compatible, Semantic RDF for Occurrences and Individual Specimens
by Peter DeVries 17 Oct '10

17 Oct '10

I thought that it might be useful and illustrative to create some examples of an Occurrence record using the new extension of the geo vocabulary and a record for an individual with two identification annotations. These are designed mainly to work well on the Linked Open Data Cloud and allow me to do the kinds of queries that I need to. There are points where if I assumed inferencing I could have slimmed down the RDF, but you cannot always assume that there will be inferencing so I choose to be explicit. Also these two examples are linked together and browsable in the way one would expect. The have not been completely assimilated in to the cloud, and there may be some errors in them but the serve as pretty good demonstrations. They also serve to illustrate how different the conceptualizations may need to be between a DarwinCore for submitting records and one that will work well on the cloud. (See my earlier proposal) *Linking Species Concepts to Occurrences and Individual Specimens* I have created an example RDF below that demonstrates markup for an individual specimen (the American Toad http://lod.taxonconcept.org/ses/kQmp4.html) http://lod.taxonconcept.org/inds/abdd0381-7f82-42ff-bb88-a30237fa8684.rdf - Note that includes two separate identifications in the RDF and another example RDF for an occurrence record that uses the new extended geo vocabulary. http://lod.taxonconcept.org/ocs/a3c39dad-6756-4129-9a61-fbd32883d369.rdf Occurrence: *RDF Document for Bufo americanus Occurrence Shivering Sands Natural Area Beach 2008-07-04/2008-07-04* RDF: http://lod.taxonconcept.org/ocs/a3c39dad-6756-4129-9a61-fbd32883d369.rdf TXNburner: http://lsd.taxonconcept.org/about/html/http/lod.taxonconcept.org/ocs/a3c39d… Sig.ma: http://sig.ma/search?pid=dd44aabc1a68b8c75898d9c743f95f00 Individual: *RDF Document for Individual Bufo americanus specimen Shivering Sands Natural Area Beach 2008-07-04/2008-07-04* RDF: http://lod.taxonconcept.org/inds/abdd0381-7f82-42ff-bb88-a30237fa8684.rdf TXNburner: http://lsd.taxonconcept.org/about/html/http/lod.taxonconcept.org/inds/abdd0… Sig.ma: http://sig.ma/search?pid=88b8af943c0734ae3c2322e0d6787417 This SPARQL Query works on my Virtuoso Endpoint, this query will also start working on the Cloud once the RDF has been assimilated PREFIX txn: <http://lod.taxonconcept.org/ontology/txn.owl#> PREFIX american_toad: <http://lod.taxonconcept.org/ses/kQmp4#Species> DESCRIBE ?x WHERE { ?x txn:areaHasObservedSpecies american_toad:. } ---------------------------------------------------------------- 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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