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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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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 22 Feb '11

22 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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Bioblitz as rdf: does this make sense?
by joel sachs 19 Jan '11

19 Jan '11

Hi Everyone, I've posted rdf of the bioblitz data. It's at http://www.cs.umbc.edu/~jsachs/occurrences/TechnoBioblitzOccurrences.rdf . Individual occurrences can be retrieved via http://www.cs.umbc.edu/~jsachs/occurrences/[occurrence_id] e.g. http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1835 Individual identifications can be retrieved via http://www.cs.umbc.edu/~jsachs/identifications/[identification_id] e.g. http://www.cs.umbc.edu/~jsachs/identifications/tdwg2010bioblitz_1835_id_1 The scripts behind this are on the kludgy side, so reports of errors and abnormalities will be warmly welcomed. Implicit in each of the following notes is the question "Is this a good way to do it?": 1. The data is "normalized" w.r.t. identification. "Normalized" is in quotes because I mean it in the sense that Steve Baskauf was using in his Fall 2010 series of posts. His meaning of the term makes sense to me, but many people (e.g. the OBO folks), take "normalized ontology" to mean "disentangled" (i.e. no multiple inheritance.) As an example, here's an occurrence with two crowdsourced determinations: http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644 2. I used sequential integers for observation and identification IDs; in practice, a mechanism needs to be in place to prevent two people from assigning the same id to their respective identifications. 3. My answer to Cam Webb's Question #1 from http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001720.html is "both". In other words, just as "Joel Sachs" is both me and also my name, so http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1668 is both an occurrence and an occurrence_id, expressed as: --- <dwc:Occurrence rdf:about="http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644"> <dwc:occurrenceID> http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644 </dwc:occurrenceID> <blah blah blah/> </dwc:Occurrence> --- 4. I was surprised to see that the Darwin Core Identification class has no "occurrenceID" or "specimenID" term. How is one supposed to tie an identification to an observation (assuming the identification is not in-lined, of course)? DeVries and Baskauf each mint their own terms for doing this (txn:identificationHasOccurrence, and sernec:basedOnOccurrence, respectively); I used dwc:occurrenceID as if it were a record level term. 5. We had scope for multiple taxonConceptID columns in the Fusion table, and assigned lsids where possible. I also mean to work with Pete to assign GUIDs from taxoncocept.org. In addition, I assigned ethan taxon concept ids, which look like this: http:.//spire.umbc.edu/ethan/Coffea_arabica In their argument over opaque vs. transparent taxonCoceptIDs, I was sympathetic to both Pete's and Gregor's arguments. Ultimately, if the tooling exists to always display the rdfs:labels every time I'm loooking at a list of opaqueIDs, then transparent IDs are unnecessary. But, for now, it's really helpful to look at an ID and know what it's referring to. (For species names not in the spire database, the rdf returned by http:.//spire.umbc.edu/ethan/$name is simply an rdfs:seeAlso to http://http://gni.globalnames.org/name_strings?search_term=$name) 6. It was easy to assert membership in RDF classes corresponding to various Cape Cod categories of concern - invasive species, threatenened species, indicators, etc. You can see these classes at http://spire.umbc.edu/ontologies/lists (Information of where these lists come from is included as rdfs:comments. I'll add further documentation, e.g. links to eml files.) Note that "ThingOfConcern" is defined as the superclass of all the other classes in the collection. The idea here is that people can create their own "ThingOfConcern" class, and then query for observations that are of concern to them. You can see sample sparql queries at http://www.csee.umbc.edu/~jsachs/occurrences/queries/sample.txt As an aside, I think we, as a community, should come up with a biodiversity benchmark suite of rdf data and corresponding sparql queries, that can be used to test the suitability and scalability of semantic web knowledge bases. I'll take this up in a future post (unless someone beats me to it). Comments, questions, and better ideas are welcome. Thanks - Joel.

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