March 2011 - tdwg-content - lists.tdwg.org

An individual identified to a higher group like Order, is still an instance of a species - just a species that is currently unspecified
by Peter DeVries 25 Sep '11

25 Sep '11

What I would recommend is that you treat a specimen that is identified to an order (Perciformes) with something like the following. Species => Order Perciformes species undetermined. The individual is still an instance of a species, however that species has yet to be determined. What would work best is to have some standard way of writing the green string above. This would allow the occurrences that are of individuals identified only to the Order Perciformes, to be interpreted as a species that falls somewhere within the Order Perciformes. - 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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A Little More on the TDWG BioBlitz Records
by Peter DeVries 29 Mar '11

29 Mar '11

Here is a little more on the latest version of the TDWG BioBlitz records. This bit.ly link will run a SPARQL query to give you what you need SPARQL Query for TableView of TDWG BioBlitz Records http://bit.ly/gcA3ox Here is the query used: Note it returns those records that have identifications and a lat/long but includes those without a photo. PREFIX foaf: <http://xmlns.com/foaf/0.1/> PREFIX txn: <http://lod.taxonconcept.org/ontology/txn.owl#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX dcterms: <http://purl.org/dc/terms/> PREFIX geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> PREFIX time: <http://www.w3.org/2006/time#> select distinct ?s, ?area, ?lat, ?long, ?kingdom, ?phylum, ?class, ?order, ?family, ?scientific_name, ?collector, ?recorder, ?individual, ?date, ?day_of_year, ?depiction where { ?s rdf:type txn:Occurrence. ?s dcterms:isPartOf txn:TDWG2010_BioBlitz. ?s geo:lat ?lat. ?s geo:long ?long. ?s txn:startDate ?date. ?s time:dayOfYear ?day_of_year. ?s txn:occurrenceHasArea ?area. ?s txn:kingdom ?kingdom. ?s txn:phylum ?phylum. ?s txn:class ?class. ?s txn:order ?order. ?s txn:family ?family. ?s txn:hasScientificName ?scientific_name. ?s txn:hasCollector ?collector. ?s txn:recordedBy ?recorder. ?s txn:occurrenceHasIndividual ?individual. OPTIONAL {?s foaf:depiction ?depiction }. } ORDER BY ASC(?area) limit 1000 =========== Here is a map base view of those records. http://bit.ly/ids5hX It uses the following query: PREFIX foaf: <http://xmlns.com/foaf/0.1/> PREFIX txn: <http://lod.taxonconcept.org/ontology/txn.owl#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX dcterms: <http://purl.org/dc/terms/> PREFIX geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> PREFIX time: <http://www.w3.org/2006/time#> describe ?s where { ?s rdf:type txn:Occurrence. ?s dcterms:isPartOf txn:TDWG2010_BioBlitz. ?s geo:lat ?lat. ?s geo:long ?long. ?s txn:startDate ?date. ?s time:dayOfYear ?day_of_year. ?s txn:occurrenceHasArea ?area. ?s txn:kingdom ?kingdom. ?s txn:phylum ?phylum. ?s txn:class ?class. ?s txn:order ?order. ?s txn:family ?family. ?s txn:hasScientificName ?scientific_name. ?s txn:hasCollector ?collector. ?s txn:recordedBy ?recorder. ?s txn:occurrenceHasIndividual ?individual. ?s foaf:depiction ?depiction . } limit 1000 This PivotView (requires Silverlight) is an interactive way to look at the data. It shows the TDWG Observations by Observer http://bit.ly/fzR3cv * It maybe a little slow to load (~1000 records) Here are two screenshots to give you an idea of what this looks like Small Version http://assets.taxonconcept.org/ss/PivotView_BioBlitz_by_Ob_800x457.png Large Version http://assets.taxonconcept.org/ss/PivotView_BioBlitz_by_Ob_1614x923.png Respectfully, - 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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Original TDWGBioblitz needs geo:lat geo:long fixed to match geo vocabulary
by Peter DeVries 29 Mar '11

29 Mar '11

I noticed this when someone wrote me about querying the original tdwgbioblitz RDF. In the file available here: http://www.cs.umbc.edu/~jsachs/occurrences/TechnoBioblitzOccurrences.rdf the geo:lat and geo:long are geo:latitude and geo:longitude. I separated the original version from my modified version. They are in two separate graphs on in my SPARQL endpoint. Original <urn:org:linkedopenspeciesdata:dataspace:tdwg2010bioblitz> The modified version is in the graph <urn:org:linkedopenspeciesdata:dataspace:taxonconcept> I can reload a fixed version of the original RDF when it is ready. The new version can be seen here: http://ocs.taxonconcept.org/ocs/index.html The highlighted species names takes you to the species concepts, while the "HTML" and "RDF" take you to the HTML and RDF for the occurrences themselves. For instance here is one observation http://ocs.taxonconcept.org/ocs/e08c6f06-ee59-4f2b-8f46-a3f66a65431e.html Here is the RDF for that observation http://ocs.taxonconcept.org/ocs/e08c6f06-ee59-4f2b-8f46-a3f66a65431e.rdf There are still some issues with the identifications, and I think that there are multiple rows "observations" for an individual observation. It seems as if one "observation" was made for the gps and another for the photograph but it is hard to tell. - 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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Stability of tdwg-content postings?
by Steve Baskauf 28 Mar '11

28 Mar '11

I have been reviewing some posts in the tdwg-content archives and got to this one: http://lists.tdwg.org/pipermail/tdwg-content/2010-August/000060.html It references a number of previous posts related to background on the DwC standard, such as http://lists.tdwg.org/pipermail/tdwg-content/2009-June/000019.html However, those links don't seem to do anything any more. There are other emails whose URLs begin with http://lists.tdwg.org/pipermail/tdwg-content/2009-June/ found in the June 2009 archives: http://lists.tdwg.org/pipermail/tdwg-content/2009-June/thread.html but not the ones referenced in the August 2010 message. I have been assuming that although it is a bit inconvenient to look things up in the list archives, the messages that have been sent would nevertheless be permanently archived. Is that not true? 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

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FW: Habitat classifications?
by Tony.Rees＠csiro.au 25 Mar '11

25 Mar '11

Apologies for cross-posting - below is a message I just sent to the TAXACOM list, but if there are TDWG persons not on TAXACOM who have not seen it and may have useful information, I'd be happy to receive it. Regards - Tony > -----Original Message----- > From: taxacom-bounces(a)mailman.nhm.ku.edu [mailto:taxacom- > bounces(a)mailman.nhm.ku.edu] On Behalf Of Tony.Rees(a)csiro.au > Sent: Thursday, 17 March 2011 2:22 PM > To: Taxacom(a)mailman.nhm.ku.edu > Subject: [ExternalEmail] [Taxacom] Habitat classifications? > > Dear all, > > I am interested in extending the habitat classification presently used in > my IRMNG genera and species database from the present "very basic" > (marine/nonmarine/both) to something a bit more detailed - maybe marine, > freshwater, terrestrial with up to perhaps a dozen or so subcategories of > each, as appropriate (e.g. end up with a little nested hierarchy of maybe > 30-50 terms total). > > So, I am looking for suggestions of such classifications as may already be > in use in order to either pick one up more or less unchanged, or develop > something with the best features of several. For example I am familiar > with the following off the top of my head: > > http://sn2000.taxonomy.nl/SyntaxHabitat.htm - 23 terms, coverage a bit > uneven > > http://mave.tweakdsl.nl/tn/syntax.html - scroll down to the section headed > "% HABITAT" -- 56 terms, looks quite useable. > > Something like the EUNIS classification e.g. as accessible via > > http://eunis.eea.europa.eu/habitats-code-browser.jsp possibly gets too > detailed too quickly at this time for my needs, but you never know what > may end up being of value. > > If list persons can point me at any other resources worth looking at, or > comment on details of the above, I would be very appreciative. It also > occurs to me that some people may have been through this exercise > previously, e.g. for "species / structured descriptive data" purposes, so > any pointers to the results of those deliberations would also be useful. > > Thanks in advance, > > Tony Rees > Manager, Divisional Data Centre, > CSIRO Marine and Atmospheric Research, > GPO Box 1538, > Hobart, Tasmania 7001, Australia > Ph: 0362 325318 (Int: +61 362 325318) > Fax: 0362 325000 (Int: +61 362 325000) > e-mail: Tony.Rees(a)csiro.au > Manager, OBIS Australia regional node, http://www.obis.org.au/ > Biodiversity informatics research activities: > http://www.cmar.csiro.au/datacentre/biodiversity.htm > Personal info: > http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566 > > > > _______________________________________________ > > Taxacom Mailing List > Taxacom(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom > > The Taxacom archive going back to 1992 may be searched with either of > these methods: > > (1) http://taxacom.markmail.org > > Or (2) a Google search specified as: > site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here

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Forgot to mention: MS Pivot Heuristics are putting non-gps occurrences in NC, sorry
by Peter DeVries 12 Mar '11

12 Mar '11

I forgot to mention in the earlier email that MS Pivot Heuristics are putting non-gps occurrences in NC, sorry. I hope to have this fixed in the future. - 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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Not condemning DarwinCore, but trying to support my argument for the development of an additional LOD RDF format
by Peter DeVries 11 Mar '11

11 Mar '11

I thought I should be clear that my point is not that there is something wrong with the DarwinCore for what it is good for, it is that I think we should develop some additional form that works well as LOD data. Perhaps expressed after processing by GBIF? Also the web applications just serve as a framework for exposing the data structure. I would *not* suggest that my occurrence example web app is ideal for showing / editing BioBlitz records. The idea I am trying to get across is meshups and possibilities of structured LOD data For example this view from Sig.ma http://sig.ma/search?pid=ba0db41b7772e1b06231a8975dcf903b <http://sig.ma/search?pid=ba0db41b7772e1b06231a8975dcf903b>I recently changed the occurrence RDF slightly and ID'd two previously unidentified wasps. http://ocs.taxonconcept.org/ocs/9f0fc9c7-a522-44d8-a0c3-327fea9351f0.html http://ocs.taxonconcept.org/ocs/e08c6f06-ee59-4f2b-8f46-a3f66a65431e.html In the listing of the occurrence records here http://ocs.taxonconcept.org/ocs/index.html The occurrence HTML and RDF are linked at the end of each row. The species names on the table link to the species concepts (the most interesting thing there is the RDF structure and LOD representations) A new Pivot View should be online shortly. The entire dataset is described with a void file and CKAN description http://ckan.net/package/taxonconcept I am sorry if some had problems with the earlier Pivot SPARQL query. The bit.ly link runs a SPARQL query which feeds into MS Pivot for viewing. For some people Pivot had problems parsing the results of the SPARQL query. In the future the current working Pivot example will be available here: http://www.delicious.com/taxonconcept.org <http://www.delicious.com/taxonconcept.org>This and other Pivot example can be found here: http://www.delicious.com/kidehen/pivot_collection_app * The MS Pivot example require Silverlight, which you might already have if you use netflix or similar apps, but they won't work on iPhone or iPad. :-( Respectfully, - 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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New views and RDF representations of the TDWG BioBlitz data
by Peter DeVries 09 Mar '11

09 Mar '11

Hi TDWG'ers, I decided that rather than tweak Joel's RDF by hand it might make more sense to just import the data and express in a different RDF representation. These examples are not about the web application or relatively small differences in how to name fields, they are more about how in general to format occurrence records in a way that maximizes their utility. I added the identified TDWG records to my small set of occurrence examples here: http://ocs.taxonconcept.org/ocs/index.html Here is one example http://ocs.taxonconcept.org/ocs/a5bd890c-c1db-4194-8347-796621105ae6.html On that page are highlighted links that take you into a view of the entity in my sparql endpoint knowledgebase. The data is also on the URIburner endpoint which allows a browsable Pivot interface. Here is the short link http://t.co/03WriMA The actual URI looks like this since it contains a SPARQL query: < http://uriburner.com/PivotViewer/?url=http%3A%2F%2Furiburner.com%2Fsparql%2… > There are still things that are not ideal in these examples, or instance I was not able to add the occurrenceRemarks simply but I hope to do so in the future. This also allows me to host the original DarwinCore RDF for comparison. Here is the url to the endpoint view of one of those records. Current DarwinCore < http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Fwww.cs.umbc.edu%2F~j…> Bit.ly < http://bit.ly/i1gfCK > Current TaxonConcept < http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/a…> Bit.ly < http://bit.ly/ezU2BA > Respectfully, - 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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data provenance; was Re: Updated TDWG BioBlitz RDF Example with Pivot View and Data Browsing
by Bob Morris 02 Mar '11

02 Mar '11

Your arguably reasonable recoding of the geo uri's of your example illustrates an issue on which so much metadata is silent: provenance. Once exposed, it is probably impossible for someone to know how the uncertainty (or any other data that might be the subject of opinion or estimate) was determined and whether the data is fit for some particular purpose, e.g. that the species were observed near each other. BTW, the IETF geo proposal was adopted in 2010, in the final form given at http://tools.ietf.org/html/rfc5870 . One interesting point is http://tools.ietf.org/html/rfc5870#section-3.4.3 which says "Note: The number of digits of the values in <coordinates> MUST NOT beinterpreted as an indication to the level of uncertainty." The section following is also interesting, albeit irrelevant for your procedure. It implies that when uncertainty is omitted (and therefore unknown), then "geo:41.53000000,-70.67000000" and "geo:41.53,-70.67" identify the same geo resource. Bob Morris On Wed, Feb 23, 2011 at 4:56 PM, Peter DeVries <pete.devries(a)gmail.com>wrote: > > [...] > > 5) I added in my proposed "area" so that it is easy to see what species > were observed near each other. Since there was no measure of radius in these > longitude and latitudes I made the radius 100 meters. > Normally I would estimate the radius for a GPS reading to be within 10 > meters but some of these observations were made where the GPS reading was > taken and the readings were given only to two decimals. > > Area = long, lat; radius in meters following the ietf proposal but with the > precision of the long and lat standardized > example "geo:41.53000000,-70.67000000;u=100" > > [...] > -- 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://efg.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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More Strange Monkey Business-like things in GBIF KOS Document
by Peter DeVries 02 Mar '11

02 Mar '11

More Strange Monkey Business-like things in GBIF KOS Document. Does this accurately characterize my project? "in the GeoSpecies project104 based on a small purpose-built ontology105 of mosquito-borne human pathogens." Did they bother to read any of the seven other examples on this page? Or here http://www.taxonconcept.org/ or here http://www.delicious.com/kidehen/pivot_collection_app+linked_geo_species or here http://www.slideshare.net/pjdwi/biodiversity-informatics-on-the-semantic-web Also note that this particular link they used in the document 104 does not work http://about.geospecies.org/index.htm While this http://about.geospecies.org/ or this does http://about.geospecies.org/index.html Also the "small" TaxonConcept SPARQL endpoint has ~27 million triples. It might also be useful to explain how reasoning can be used on the larger data sets. Do they have an example of reasoning that works on a data set over 100 million triples? Is there some reason why there is so much "push" towards specialized near proprietary solutions like LSID's and LOD unfriendly vocabularies? Respectfully, - 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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