October 2010 - tdwg-content

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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Re: [tdwg-content] "Wrong" RDF, was Re: What I learned at the TechnoBioBlitz
by Richard Pyle 17 Oct '10

17 Oct '10

Hi Steve, First of all, thank you for taking the time to carefully articulate your perspective on this. As someone who has written more than a few "epic" posts to these lists, I am personally grateful for the careful explanation. I know many people don't have time to read long messages, but I think that the lack of explicit descriptions of things has led to confusion, which, in the long run, has cost us all even more time. For much of your emails, I found myself nodding in agreement. I'm only commenting below on a few passages that caught my attention. I don't know how much your later posts supercede this one, but here are my comments to your first. >From your first post of Oct 15: > In the case of putting "dots on a map" to show the distribution of a > species, the case is simple if the occurrences are specimens where the > whole dead organism is collected. It is not so simple with other > types of occurrences. Let me illustrate with an example. There is > currently precisely one known individual of Crataegus harbisonii in > nature. I have given this individual the URI > http://bioimages.vanderbilt.edu/ind-baskauf/70905 . I have > approximately 62 images of that individual at > http://bioimages.vanderbilt.edu/ind-baskauf/70905.htm and > http://www.cas.vanderbilt.edu/bioimages/species/crha2.htm . > Each one of these images represents an occurrence in that I pressed > the shutter on my camera at different times for each one. Yes, technically, you could represent these 62 images as 62 separate Occurrence records (rather, as 62 separate events). But assuming the 62 shutter releases were all within a reasonable period of time (e.g., the same day), it would be perfectly appropriate to collapse these 62 events into a single event, which spanned in time from the first shutter-release to the last. The reason you would do that is that very, very few end-users would gain much wisdom about nature knowing the precise points in time that the organism occurred at that place. Most would be quite happy to infer that it also existed at the same place in-between the individual shutter-releases. Thus, representing a single event (anchored to the Occurrence) as a range of time from first shutter-release to last, would be adequate for essentially all use-cases. I relaize that each image contains with it the metadata for its moment of capture, but of course that is metadata that applies to the image (evidence of the occurrence); not the occurrence itself (which can be safely flattened to a single occurrence). For analagous reasons, many natural history collections aggregate multiple specimens of the same taxon collected at the same event into a single "lot", which gets a single catalog number, and is represented as a single occurrence. If I collect 100 individuals of [what I identify as] the same fish species at the same poison station, I will establish one specimen record, with individualCount set to 100, and represent it as a single Occurrence (even though technically, the 100 fish were captured at slightly different different times, and thus I could technically generate a different Event instance for each, and thus have 100 different occurrence records). > Ron Lance has collected tissue from this tree for grafting purposes > and now has an occurrence with basisOfRecord="LivingSpecimen" in his > arboretum in North Carolina. Andrea Bishop of the Tennessee Dept of > Environment and Conservation has seeds collected from the tree - I'd > call the collection of those seeds an occurrence record. I would probably do the same, assuming they weren't collected at the same time (plus or minus a few hours to a few days) as the tissue sample. But in either case, the tree at the place and time is the occurrence; the tissue sample and the seeds are just evidence of the occurrence. If either the time is substantially different (certainly possible!), or the location is different (not likely, it being a tree), then I would see justification for treating it as two separate occurrence records, so we know that the tree was at that place at those two (reasonably separate) times. And, of course, we'd want to join the two Occurrences via individualID. > So my > question to Marcus and others at GBIF is: how many dots will you put > on your map for this tree? My answer: one for each distinctly different moment in time that the tree was confirmed to be in that place (by whatever evidence). How does one define "distinctly different"? Well, I suspect that would be best judged by a biologist who could determine whether there is meaningful knowledge to be gained by knowning this tree was at this place at multiple points in time within the span of an hour, vs. multiple points in time within the spann of a day, or a month, or a year. Is diel variation important to document? Is lunar-cycle variation important to document? Is seasonal variation important to document? The answers to these questions would inform the decision of how many of these "potentially unique Occurrences" should be aggregated into a single occurrence, which would be represented by less-precision of time and/or place. > I anticipate that one response > to this question will be to call each imaging bout one "observation" > having a number of dwc:associatedMedia > references. That > collapses the number of occurrence records considerably, but not down > to one. It could be one. What is the time span of a "bout", compared to the time-span of the collection of all bouts combined? How important is it to resolve the time component of each bout individually, vs. aggregate them into a single bout, represented by a broader (less precise) window of time? > I took images of that tree on at least three separate instances over > the course of a year and Ron collected his graft tissue years before > that. Sounds to me like four occurrence records; presuming there is value in distingushing the occurrence of the tree at the place at different times of the year. > There is simply no way to reduce the number of occurrences for this > tree to one, nor should we want to. There is a way -- if you don't care about seasonal variation, you simply define the Event as a span of time covering all four visits to the tree. You probably wouldn't want to do that; but you certainly could. > A possible use > of multiple occurrence records (i.e. my first point above) of this > sort might be to establish how long individuals of Crataegus > harbisonii live and each occurrence record (whether separated by years > or by the seconds between shutter clicks) is a part of the record that > we should be able to (and want > to) preserve. Another use would be to track a non-sessile organism > (e.g. a whale) in both time and space. In that case, the record on a > map for an individual would be some kind of curve rather than a dot. > But in any case, recognizing the existence of an entity that I'm > calling an Individual facilitates these broader uses of occurrence > data and it's really hard for me to see how that is going to happen if > we ONLY have occurrences as separate entities. > Response Markus? > How does GBIF deal with whale tracks or multiple banded bird > observations for a single bird? If I understand your overall point correctly, it is something like this: Individuals potentially span multiple Occurrences. DwC uses individualID to link these multiple Occurrences together. However, there is no class for individualID, and hence no way to apply additional dwc metadata to the object represented by the individualID, other than through one or more occurrence records. Is that about right? I mean, we certainly can provide an individualID as a component of dwc:occurrence; but we have no way with dwc of assigning metadata specific to that individual, except through a series of occrence instances. > (In the oversimplified > examples I gave earlier, I applied a scientific name directly to an > individual. In actual practice, I relate individuals to > identifications and then relate the identifications to > taxa.) Good to know! This is, in my opinion, the right way to do it. > Again, to illustrate with a real-life example, when Bruce Kirchoff was > developing his Woody Plants of the Southeastern US learning software, > he asked a taxonomist to go through the images of mine that he was > using for the project to verify that they were identified correctly. > My old website just threw together all images of a particular species > onto one page without regard to the individuals from which they > originated (e.g. > http://www.cas.vanderbilt.edu/bioimages/species/sarar3.htm > and > http://www.cas.vanderbilt.edu/bioimages/species/soam3.htm). > It turns out that I had carelessly misidentified a vegetative Sambucus > racemosa ssp. > racemosa individual as Sorbus americana. The taxonomist asked me > which of the various bark, twig, leaf, etc. images were from the same > plant and the only way I could find out was through the laborious > process of looking for images with similar time/date values and my > hand written field notes. It was a nightmare finding all of the > particular image records that needed to have their identifications > fixed and then correcting them. On my new website (e.g. > http://bioimages.vanderbilt.edu/metadata.htm, then click on Quercus > chrysolepis), the images are connected to the individual from which > they originated. If I discover by looking at a particularly > informative image that I have misidentified the individual, I only > need to add an updated determination (i.e. identification) to that > individual's record and automatically all images from that individual > are displayed with the correct name and are placed on the correct > species page. Well...I would counter that you could achieve the same thing by representing things via Occurrence, and then cross-linking those Occurences that represent the same individual by using the shared individualID. The only thing you don't have is metdata specific to the individual anchored directly to the individualID. Instead, dwc denormalizes this a bit and aggregates those individual-specific metadata to other classes (Occurrence, Idnetification, etc.) It's not that I disagree that an "individual" is a useful class in the realm of biodiversity informatics. I also think there are a couple of important entities in taxon name/concept space that warrant their own classes. However, as John W. and Markus have both emphasized, DwC (necessarily) represents a compromise between a proper ontological mapping of the information classes, and a practical vehicle for information exchange amongst holders of biodiversity datasets. I find this constraining sometimes, but it helps when I remind myself of the following: DwC is a mechanism for exchanging data & metadata, not a database model or schema. As such, I think it covers most (but not all) of the need, with a reasonable (as opposed to normalized) set of classes and terms. If you have metadata for an individual, you can resolve (err...deference) that metdata by providing an appropriate individualID via dwc occurrence records. So, to re-state -- I don't disagree with your premise that there logically ought to be a class for individual; I'm just not sure it is necessary for DwC at this time. Having said that, and being a database-nerd with a tendency to hyper-normalize data models, I am mostly playing devil's advocate in my message here. In truth, I share your view that there should be (should have been) a class for Individual, and Occurrence should have simply been the union of an Individual and an Event. So....I reserve the right to stop playing Devil's Advocate, and join you in your efforts to make the case for an "individual" class. My only concern is that we may have different perspecives on how to scope "individual". In my mind, a better term would be "organism", rather than "individual"; because in my mind, once you allow a single coral head (as oppose to the individual polyps) to be represented as an "individual", you've just allowed for multiple "individuals" -- which opens the door to ever broader circumscriptions of multiple individuals (colony-->small group-->herd/school/flock-->population-->taxon concept). > I recognize that many "specimen-based" organizations aren't really > going to care one whit about this. That's fine. In their databases > and personal XML schemas they can ignore Individuals as it is their > prerogative. Actually, no we can't. Often is the case that a "lot" of 10 specimens is later determined to contain more than one taxon. In such cases, we *do* need to identify individuals, so we can separate the lot accordingly. I know it's not exactly the same as the examples you give, but fundamentally it's the same basic information flow: aggregated/abstract occurrence needs more precise recognition of individual organism. > But when we build > RDF templates, I believe strongly that for the benefit of those of us > who care about the broader applications of occurrences those templates > should use individuals to connect (one or more) occurrences and (one > or > more) identifications. For those with a technical bent, you can see > how I have done this for an herbarium specimen by looking at the page > source RDF of the example > http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0429.rdf > . For those of a non-technical bent, just look at the webpage that > shows up when you click on the link. It looks just like any other web > page for a specimen and you don't even have to know that the > underlying RDF supports using Individuals as a grouping mechanism. I guess my real question is: is the case for individual as a class because you cannot represent certain information within DwC (via individualID) at all? Or that you could do so more elegantly if individual was broken out as a class? I certainly agree that it would be more elegant to treat individual as a class; I'm just not convinced that the increase in elegance justifies the increase in complexity/normalization of DwC. > In summary, I think we need Individual as a DwC class to enable > understandable rdfs:typing of records of individuals and to create a > context in which instances of individuals can be placed (i.e. people > would assign and use identifiers for individuals when they document > occurrences). These instances (and their assigned URI GUIDSs) would > allow for "connecting" > identifications and occurrences in a more meaningful way. I am not > suggesting that the occurrence be dethroned as the center of > biodiversity records. Assuming that the xxxxID terms end up being > moved out of the various classes and into the record-level terms area > as was suggested recently, I think that there are really only about > two terms that should be put into a new Individual class: the other > new term I have proposed > (individualRemarks) and establishmentMeans (but that is the topic of > another email). It may seem odd to suggest a adding a class that has > very few terms in it, but if you follow my reasoning above you will > hopefully understand why I have done so. OK, I guess I should have read this paragraph first -- it would have saved me a lot of typing above. But the words are already typed above, and I don't have time to go figure out which ones are no longer necessary, so I'm leaving it as written (Sorry!). Anyway, the way you frame it here certainly clarifies things in my mind, and nudges me closer to joining your crusade for establishment of an individual class. But I'm not yet sure we fully agree on the scope of what an "individual" is. The most intruiging passage in your entire email (for me) is this one: > I think that there are really only about two terms that should be put > into a new Individual class: the other new term I have proposed > (individualRemarks) and establishmentMeans (but that is the topic of > another email) By including establishmentMeans in your attributes of individual, you've piqued my interest in reading your "another email".... :-) > I hope that the discussion (and criticism!) will continue. > Again, I'm interested in hearing alternatives. I'll find time later to read and contemplate your other emails. For now, Id be interested in whether my comments in this email are useful, or am I just misunderstanding your basic point. Aloha, Rich

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