February 2011 - tdwg-content

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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data provenance; was Re: Updated TDWG BioBlitz RDF Example with Pivot View and Data Browsing
by Bob Morris 01 Mar '11

01 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 01 Mar '11

01 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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Updated TDWG BioBlitz RDF Example with Pivot View and Data Browsing
by Peter DeVries 23 Feb '11

23 Feb '11

I have updated my earlier revision of the TDWG BioBlitz RDF. I commend Joel for his RDF and think that any suboptimality was because of problems in trying to use the existing Darwin Core as Linked Data. Some earlier issues that have been fixed in the new examples are: 1) The names for people were not standardized. Even as a text string you could not find who collected what. To fix this I created URI's for all the individuals involved and linked the occurrences to the URI for the person that made the observation 2) The names for species were not standardized or spell checked. It took a while but I was able to figure out what I think people "meant" by the various name and linked them to species concepts. For those occurrences with multiple identifications, I linked the last identification to the occurrences species concept. *Future BioBlitz's might benefit from a pick list at least to genus. 3) Virtuoso out of the box does not recognize "associatedMedia" as an image that can be displayed. In order to get these to show up on the map view I had to add each image as a foaf:depiction. Also associatedMedia is a bit vague and this should probably be broken into different media types like images, sounds etc. 4) In my other RDF representations I make statement about the geonames locations in which the species concept was observed so the continent, state and county have "expectationsOf" the species and the species is "expectedIn" those areas. I have added these statements to the example RDF so that both the locations and the species concepts are linked to the occurrences. 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" The example data are available at the following URL's Occurrences: http://lod.taxonconcept.org/tdwg2010bioblitz/TechnoBioblitzOccurrences_date… People: http://lod.taxonconcept.org/people/tdwg2010bioblitz.rdf This bit.ly link will show clickable map with all the occurrences. (It is a little slow to load) The actual URL is < http://lsd.taxonconcept.org/isparql/view/?query=DESCRIBE%20%3Fx%20WHERE%20%… > But I don't expect that will go through everyone's emails correctly. This Pivot view shows occurrences by investigator http://bit.ly/eW3fgm Here is are view of two of the records, note how you can browse between people, species concepts, identifications, areas etc. http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/oc…<http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/oc…> http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/oc… Here is a browsable view of one of the areas bit.ly http://bit.ly/hBtVFL http://lsd.taxonconcept.org/describe/?url=geo:41.53000000,-70.67000000;u%3D… Here is the view of the species concept for the Honey Bee that is now linked to these occurrence records. http://bit.ly/g1zzJC In summary, I think it make sense to follow LOD best practices because this maximizes the utility of the data and allows you to take advantage of all the available tools. <http://bit.ly/eW3fgm>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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Example RDF for Occurrence Records following Linked Open Data practices
by Peter DeVries 21 Feb '11

21 Feb '11

I thought I would explain how I have been marking up occurrence records in RDF in this blog post. http://www.taxonconcept.org/taxonconcept-blog/2011/2/21/species-occurrence-… The quad store view of the different RDF entities mentioned in the blog can be seen here: Via this bit.ly bundle http://bit.ly/fnlTZd * Note that some of these links get change in email so you might want to use the bit.ly bundle above The RDF page: http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f… The Occurrence: http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f… The Area: http://lsd.taxonconcept.org/describe/?url=geo:44.86528100,-87.23147800;u=10 The Species Concept: http://lsd.taxonconcept.org/describe/?url=http://lod.taxonconcept.org/ses/I… The Individual: http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f… The Identification: http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f… The Continent: http://lsd.taxonconcept.org/describe/?url=http://sws.geonames.org/6255149/ The County: http://lsd.taxonconcept.org/describe/?url=http://sws.geonames.org/5250768/ Although the exact format of these could be changed there are several existing advantages and some possible future advantages. 1) Each data provider could expose their own data to the web without a central authority. This could be in the form of RDF, RDFa, or as gzipped RDF dump files. (records.rdf.gz) They would be automatically discoverable on the LOD cloud. A third party service could add value by pointing to the various repositories, perhaps with an annotation system like or as part of CKAN. ( http://ckan.net/) 2) Data validation in terms of being "well-formed" could be checked with the existing RDF and RDFa validators. http://www.w3.org/RDF/Validator/ http://validator.w3.org/ 3) The next level of validation e.g: Is this a valid geographic coordinate? Does the coordinate match the geographical names listed *(You could even have a service that takes the geo area and determines the correct geographic names etc.) Does the scientific name match a known species? Are the other required fields present and well formed. Is this a new record for that species in that specific geographic area Would have to be done by a validator created for the community, but it would benefit from the existing tools. 4) All the third party LOD tools and services would be able to use these records. 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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ShootOut at the Not OK Corral: namespaces in OWL (technical)
by Bob Morris 04 Feb '11

04 Feb '11

If you have ever been in pain over namespaces in OWL ontologies and RDF data, you may want to read this year-old day-time television soap opera script, errr...ummmm... I mean, highly technical discussion about namespaces. My guess is that this pain will be with us for a long time. http://comments.gmane.org/gmane.org.w3c.semantic-web/11878 FWIW, gmane seems to be a rather nice syndication mechanism for mailing lists, making it quite a bit easier than looking in gnu-mailman archives to follow old threads . My only complaint is that you have to poke a bit to find the originals (whereupon you are grateful to gmane) Bob -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob(a)gmail.com web: http://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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Audubon Core NameSpace
by Bob Morris 03 Feb '11

03 Feb '11

We dropped discussion of this, and I know Steve Baskauf and perhaps others want to start using it with minimal risk of having to redo data. I found little consensus in the discussion, and no compelling reason why the prefix had to end in "c". Therefore, I'd like to put back(?) on the table and resolve it quickly. Gail or others will guide us as to whether the Executive Committee cares about what we settle on: http://adbn.tdwg.org recommended prefix adbn --Bob -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob(a)gmail.com web: http://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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