October 2010 - tdwg-content

What I learned at the TechnoBioBlitz
by joel sachs 14 Oct '10

14 Oct '10

One of the goals of the recent bioblitz was to think about the suitability and appropriatness of TDWG standards for citizen science. Robert Stevenson has volunteered to take the lead on preparing a technobioblitz lessons learned document, and though the scope of this document is not yet determined, I think the audience will include bioblitz organizers, software developers, and TDWG as a whole. I hope no one is shy about sharing lessons they think they learned, or suggestions that they have. We can use the bioblitz google group for this discussion, and copy in tdwg-content when our discussion is standards-specific. Here are some of my immediate observations: 1. Darwin Core is almost exactly right for citizen science. However, there is a desperate need for examples and templates of its use. To illustrate this need: one of the developers spoke of the design choice between "a simple csv file and a Darwin Core record". But a simple csv file is a legitimate representation of Darwin Core! To be fair to the developer, such a sentence might not have struck me as absurd a year ago, before Remsen said "let's use DwC for the bioblitz". We provided a couple of example DwC records (text and rdf) in the bioblitz data profile [1]. I think the lessons learned document should include an on-line catalog of cut-and-pasteable examples covering a variety of use cases, together with a dead simple desciption of DwC, something like "Darwin Core is a collection of terms, together with definitions." Here are areas where we augemented or diverged from DwC in the bioblitz: i. We added obs:observedBy [2], since there is no equivalent property in DwC, and it's important in Citizen Science (though often not available). ii. We used geo:lat and geo:long [3] instead of DwC terms for latitude and longitude. The geo namespace is a well used and supported standard, and records with geo coordinates are automatically mapped by several applications. Since everyone was using GPS to retrieve their coordinates, we were able to assume WGS-84 as the datum. If someone had used another Datum, say XYZ, we would have added columns to the Fusion table so that they could have expressed their coordiantes in DwC, as, e.g.: DwC:decimalLatitude=41.5 DwC:decimalLongitude=-70.7 DwC:geodeticDatum=XYZ (I would argue that it should be kosher DwC to express the above as simply XYZ:lat and XYZ:long. DwC already incorporates terms from other namespaces, such as Dublin Core, so there is precedent for this. 2. DwC:scientificName might be more user friendly than taxonomy:binomial and the other taxonomy machine tags EOL uses for flickr images. If DwC:scientificName isn't self-explanatory enough, a user can look it up, and see that any scientific name is acceptable, at any taxonomic rank, or not having any rank. And once we have a scientific name, higher ranks can be inferred. 3. Catalogue of Life was an important part of the workflow, but we had some problems with it. Future bioblitzes might consider using something like a CoL fork, as recently described by Rod Page [4]. 4. We didn't include "basisOfRecord" in the original data profile, and so it wasn't a column in the Fusion Table [5]. But when a transcriber felt it was necessary to include in order to capture data in a particular field sheet, she just added the column to the table. This flexibility of schema is important, and is in harmony with the semantic web. 5. There seemed to be enthusiasm for another field event at next year's TDWG. This could be an opportunity to gather other types of data (eg. character data) and thereby i) expose meeting particpants to another set of everyday problems from the world of biodiversity workflows, and ii) try other TDWG technology on for size, e.g. the observation exchange format, annotation framework, etc. Happy Thanksgiving to all in Canada - Joel. ---- 1. http://groups.google.com/group/tdwg-bioblitz/web/tdwg-bioblitz-profile-v1-1 2. Slightly bastardizing our old observation ontology - http://spire.umbc.edu/ontologies/Observation.owl 3. http://www.w3.org/2003/01/geo/ 4. http://iphylo.blogspot.com/2010/10/replicating-and-forking-data-in-2010.html 5. http://tables.googlelabs.com/DataSource?dsrcid=248798

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Why we may need both a more XML-like DarwinCore and a to be developed truly semantic one later.
by Peter DeVries 14 Oct '10

14 Oct '10

I am starting to see some reasons why there might be a need for an more XML type version of the DarwinCore and a separate, still undefined buy truly "semantic", version that still need to be worked out. Part of this is that I think it that most people don't understand the semantic issues and will not for sometime. So for those who are submitting their data to GBIF, I don't know if they have to understand all the somewhat counterintuitive semantic issues. Here is an example from one of our earlier discussions - I realized only later that I should have brought this up at the time. For XML using "scientificName" makes a lot of sense. However: 1) The current semantic web cannot have literals as subjects. 2) Also if you represent knowledge as triples without ontology-based inferencing, you need to define predicates that for both "directions" in a particular relationship. (In general) So if we had a URI for each scientific name we would need to make both of the following kinds of statements. <concept> *hasScientificNameURI* <name_uri> <name_uri> *isScientificNameURI_Of* <concept> In the LOD cloud, you cannot assume that everyone will load and be able to infer against your specific vocabulary. This is, in part, the result of vocabularies not always playing well together. Also, it is not clear to what extent inferencing will work well on really large data sets or for particular projects. Eventually this will get figured out, but for now we need predicates that can be used to represent both directions. (most of the time) Without them you can only query in one direction. This was not completely obvious to me until I had a test set and realized why I was not able to query it in the ways I wanted. So for the more XML-centric DarwinCore there is no problem with using * scientificName.* For the fully semantic web version, the following pattern might be easiest to clearly interpret. hasScientificName "Puma concolor (Linnaeus 1771)" hasScientificNameURI < http://gni.globalnames.org/name_strings/6c3dc35f-d901-5cc5-b9c8-ad241069b9f8 > This makes it clear that the first form is to be used for a literal while the second form is to be used for a conventionally resolvable URI. Why do we need these name URI's at all? Because some groups will need to relate name strings to each other and name strings to concepts etc. Hard to do when you can't use a literal as a subject. :-) 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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Extending the geo vocabulary to include a "radius" in meters example, with example ontology and RDF file
by Peter DeVries 11 Oct '10

11 Oct '10

I thought that some of the semantic web community might be able to provide some insight as to how we might be able to extend the geo vocabulary without breaking compatibility with existing tools and services. I think it would be best to try the suggestion below with some additional sample data to see if it works as we expect before making any real decision. Also note that this is most relevant to the fully semantic RDF version of the DarwinCore, and less relevant in the XML/CSV implementations. Below is my original question, my test vocabulary and RDF as well as abbreviated versions of the suggestions from others: # Original Question There was some discussion about ways to record species observations using the geo vocabulary at a recent biodiversity informatics meeting. Some see the advantages of using the geo standard, but we really need to have a way to incorporate and error or extent in meters. What would be the best way to extend the current geo vocabulary so that it includes this radius measure but still works well with geo aware tools and services? The addition would be defined as the total extent including calculated error (PointRadiusSpatialFit). This would be used to record that a species or "thing" was observed or collected within this geographical defined area. Something like the example below, but I suspect that this might not make it a real geo:Point? <geo:Point> <geo:lat>55.701</geo:lat> <geo:long>12.552</geo:long> <dwc:radius>10</dwc:radius> </geo:Point> This should work so that if I have 10,000 records recorded from within this same area, I can define it once and then refer to that area description RDF in the 10,000 species occurrence records with one simple URI to that area definition. One solution would be for the geo authors to add the radius to the geo vocabulary. Also there may be unrelated groups that might like the radius attribute for some other use. Another alternative would be to somehow extend the geo vocabulary within a separate vocabulary. It is not clear to me what is the best way to do this and still retain geo compatibility. I look forward to ideas and suggestions, # End of Original Question ... After reviewing the feedback I created a test vocabulary and RDF file. The test vocabulary is in it's own namespace and called dwc_area. It is here: http://lod.taxonconcept.org/ontology/dwc_area.owl The HTML Document is here http://lod.taxonconcept.org/ontology/dwc_area_doc/index.html (For some reason it did not include the imported geo vocabulary) I also made up a small test file that uses both the new geo URI and an shows the suggested way to include a radius measure. It is here: http://lod.taxonconcept.org/rdf/area_example.rdf It should show up in URIburner and Sindice soon. I did submit an earlier incorrect version into Sindice so that might show up as well. Here is what the RDF looks like in URIBurner < http://linkeddata.uriburner.com/about/html/http/lod.taxonconcept.org/rdf/ar…> To get to each of the three "Areas" you need to click on the links in the * topics* list * Note that the final location of the vocabulary is unclear. It will probably end up in the DarwinCore vocabular or in my txn vocabulary. # Below is background info and the suggestions from the LOD community. 1) There is proposed standard that everyone should know about *A Uniform Resource Identifier for Geographic Locations ('geo' URI)* http://tools.ietf.org/html/rfc5870 (from Sean Gillies) * Not clear that all the systems understand this but URIburner and Virtuoso interprets these as a URN type thing so they work but are not understood in the way that the "geo" vocabulary is understood. Note that if and when this becomes a standard it will allow these "Areas" to be universally understood. What this means is that I can markup my 10,0000 mosquito records from one location with one URN type id. 2) I got the following back from Bernard Vatan. > What about something as the following, since the radius is not really a property of the point ... * Note this differs from my final examples <dwc:Area> <geo:center> <geo:Point> <geo:lat>55.701</geo:lat> <geo:long>12.552</geo:long> </geo:Point> </geo:center> <dwc:radius>10</dwc:radius> </dwc:Area> 3) I also got this back from Paul Houle, > For Ookaboo I've worked out an internal data model for points; Ookaboo also knows about real shapes, but the fact is that most people out there will throw points at you and only know how to consume points. > Here are a few bits of extra data that are useful to add to a point > (1) provenance > (2) datum (I try to stick to WGS84, but points from freebase occasionally have a Datum attached, so I store it) > (3) circular error (the accuracy of the determination of the point, for instance the technical limitation of a GPS receiver) > (4) scale length of feature (how accurate do we have to be? it's not worth getting into an edit war over the exact point that represents, say, Finland.) > (5) an overall quality rating (so if we've got ten points we can pick the best) # I am looking forward to comments and suggestions. If people want, this can be incorporated into the DarwinCore, but it would be best if it was done that did not entail some specific TDWG domain and ranges. This would allow it to be use by others, (perhaps for completely different kinds of things) without having to tie their work into some specific conceptualization. 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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What RDF is (Was Re: Idea for Discussion, Differentiating between "type's" of identifiers)
by Bob Morris 07 Oct '10

07 Oct '10

On Wed, Oct 6, 2010 at 8:53 AM, Peter DeVries <pete.devries(a)gmail.com> wrote: >[...] > I think part of the problem we are having is that people are not recognizing > how different RDF is from straight XML. > ... It's way worse than that. RDF is not XML at all. RDF/XML is merely a serialization of RDF It's not even the most human readable serialization. In fact it is one of the \worst/ for humans who need to figure out what triples are actually in play. It is so ubiquitous only because there are more tools that can process RDF/XML than any of the other RDF serialization syntaxes (syntices???). The persistent myth that human readability is an advantage of XML pretty much ignores all the use cases that humans have for reading something. It's about as readable as Lisp. Indeed, a Lisp loving colleague said of XML on the occasion of its first W3 recommendation : "I get it. It's Lisp with pointy brackets." 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://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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FYI: I am currently using the DBpedia URI's for TaxonAuthors where appropriate
by Peter DeVries 04 Oct '10

04 Oct '10

Steve and I have again run into similar issues when trying to create something that works well as LOD RDF. I have started to link to the DBpedia entries for those taxonomic authors that I recognize and exist in DBpedia. In one case, I created a page for an arachnologist so that he would have a resolvable URI. There is some lag between creating a Wikipedia page and it showing up in DBpedia but that is shortening. Also these Wikipedia pages are not as stable as I would like, but I think the DBpedia people probably can devise some solution. In this species concept I include both a link to the species description PDF and to the URI for the Author. HTML http://lod.taxonconcept.org/ses/2mqjL.html <http://lod.taxonconcept.org/ses/2mqjL.html>RDF http://lod.taxonconcept.org/ses/2mqjL.rdf <http://lod.taxonconcept.org/ses/2mqjL.rdf> Note that these species concepts have as a "Part" an original description, which has it's own section in the RDF. <txn:SpeciesOriginalDescription rdf:about=" http://lod.taxonconcept.org/ses/2mqjL#OriginalDescription">  <dcterms:title>Original Published Description relating to Species Concept Hentzia alamosa se:2mqjL</dcterms:title> <dcterms:identifier> http://lod.taxonconcept.org/ses/2mqjL#OriginalDescription </dcterms:identifier> <dcterms:description>LOD metadata about the original species description relating to Species Concept Hentzia alamosa se:2mqjL</dcterms:description> <dcterms:isPartOf rdf:resource=" http://lod.taxonconcept.org/ses/2mqjL#Species"/> <txn:hasAuthorURI rdf:resource=" http://dbpedia.org/resource/David_B._Richman"/> <txn:basionymName>Hentzia alamosa Richman, 2010</txn:basionymName> <txn:year>2010</txn:year> <txn:hasPDFVersion rdf:resource=" http://www.americanarachnology.org/JoA_free/JoA_v38_n1/arac-38-01-73.pdf"/> <txn:speciesOriginalDescriptionHasSpeciesConcept rdf:resource=" http://lod.taxonconcept.org/ses/2mqjL#Species"/> </txn:SpeciesOriginalDescription> Here is the view of this concept from within my triple store * Note that some email clients - notably AppleMail tries to change the encoded URI so the link below might not work for you. You can get to this same view by clicking on icon next to "Salticidae" on the html page < http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org… > - 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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Request to be added to the TDWG Google Project
by Peter DeVries 02 Oct '10

02 Oct '10

I did not see how to request to be added to the project on the google site. Could I be added to the list? Thanks :-) - 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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