Hi Steve,
I try to take some time to think about your notes, sorry for the delay.
There are many different contexts that can be used when thinking about species and related data.
It is often useful to separate these contexts into different kinds of related entities.
Here are some contexts that I think are useful to separate
http://lod.taxonconcept.org/ses/mCcSp#Image - An image of a Cougar http://lod.taxonconcept.org/ses/mCcSp#Occurrence - An occurrence of a Cougar http://lod.taxonconcept.org/ses/mCcSp#Individual - An individual Cougar http://lod.taxonconcept.org/ses/mCcSp#Taxonomy - A Basic Taxonomy for the Cougar, one alternative among many potential classifications http://lod.taxonconcept.org/ses/mCcSp#NCBI_Taxonomy - The NCBI Taxonomy for Cougar, or starting at the lowest available clade http://lod.taxonconcept.org/ses/mCcSp#OriginalDescription - The Original Description of the Cougar, ideally with links to the PDF or BHL URI.
* Note that in this model a species can have several Taxonomies or classifications. This reflects the reality that the same species has one hierarchy in NCBI and a different one in CoL.
You can find all the tagged images of the Cougar by finding all those that are of the type http://lod.taxonconcept.org/ses/mCcSp#Image
Here is one example of an image that is tagged in this way. (From http://lod.taxonconcept.org/ses/v6n7p.html )
<foaf:Image rdf:about=" http://assets.taxonconcept.org/seuuids/603bebac-cc44-4168-bbf7-b11b976f9d79/... "> <rdf:type rdf:resource="http://lod.taxonconcept.org/ses/v6n7p#Image%22/%3E <dcterms:isPartOf rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p#Species%22/%3E <dcterms:source rdf:resource=" http://commons.wikimedia.org/wiki/File:Mountain_lion.jpg%22/%3E dcterms:contributorUnited States Department of Agriculture</dcterms:contributor> <cc:license rdf:resource="http://creativecommons.org/publicdomain/%22/%3E <wdrs:describedby rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p.rdf%22/%3E </foaf:Image>
You are correct in noting that an occurrence of a species could simply be typed in a similar way, and maybe that would be better than the somewhat awkward.
txn:occurrenceHasSpeciesOccurrenceTag
I originally went with this name because I wanted it to be clear that the subject and objects should be.
If we use this data set as and example http://ocs.taxonconcept.org/ocs/index.html (Mainly TDWG BioBlitz 2010)
We can demonstrate how this is useful for SPARQL Queries.
We can run a SPARQL describe query for all the observations of the Honey Bee with this query.
PREFIX txn: http://lod.taxonconcept.org/ontology/txn.owl#
describe ?s where { ?s txn:occurrenceHasSpeciesOccurrenceTag < http://lod.taxonconcept.org/ses/z9oqP#Occurrence%3E }
* It might be simpler to mark these observations up as having a type of http://lod.taxonconcept.org/ses/z9oqP#Occurrence.
In this case the query would look like this. (You can use "a" as a short cut meaning (http://www.w3.org/1999/02/22-rdf-syntax-ns#type)
PREFIX txn: http://lod.taxonconcept.org/ontology/txn.owl#
describe ?s where { ?s a http://lod.taxonconcept.org/ses/z9oqP#Occurrence }
* I would need to redo the occurrence record RDF for this new query to work
We can take that original query above and paste into the LOD SPARQL Endpoint http://uriburner.com/isparql/ (Advanced Tab)
Run the query
This link will run the query - will probably not go through all email system intact. See bit.ly link below. < http://uriburner.com/isparql/view/?query=PREFIX%20txn%3A%20%20%20%20%20%3Cht...
Bit.ly version http://bit.ly/lM6vWB
and get a esult (Not very pretty, or interpretable by humans)
We can select make "Make Pivot" from the top left corner of the Window.
This will run the query and feed the data to MS Pivot which parses and displays the result.
In theory, and I hope in the future, there will be an open source solution that does this as easily and does not require MS Silverlight.
The result is a Browsable Pivot View which you can select to view the result by Observer, Location etc.
This bit.ly will take you to a view by observer (the person who made the observation) http://bit.ly/lacRb1 This biit.ly will take you to a view by dwcArea http://t.co/eu55BaG
I have bundled all these examples including screenshots into one bit.lybundle so you won't need Sliverlight to get an idea on how this works.
http://bit.ly/iXg2y8 <- Link to Bit.ly bundle with screen shots etc.
I have included closeups of the Pivot settings in the top right corner so you can see how to change the attribute that Pivot uses to create the view.
Note also that if you go to the Knowledge Base View of the Honey Bee you can browse to the observations of that species.
http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%... Bit.ly Link http://bit.ly/g1zzJC
Since I have updated to the latest version of Virtuoso the strange URI links have been replaced with Human readable text from the label view for that entity.
This includes the links to occurrences, gni names strings, and links to GeoNames.
Part of the reasoning behind this structure is to make explicit to computers what context we are talking about.
The human brain makes these context switches automatically but computers do not.
That said there are areas where they could be improved or simplified.
Also I think that you will need a class for each species concept, but they are all instances of txn:SpeciesConcept - something allowed in OWL2.
My ontology has probably changed slightly since you last saw it.
OWL http://lod.taxonconcept.org/ontology/txn.owl
OWL Doc http://lod.taxonconcept.org/ontology/doc/index.html
Respectfully,
- Pete
On Mon, May 2, 2011 at 8:16 AM, Steve Baskauf steve.baskauf@vanderbilt.eduwrote:
OK, Pete, I'm going to try to write the other email that I mentioned in the previous one. This email relates to the actual suggestion that you made in the email, that is to use the URIs of the form like: "http://lod.taxonconcept.org/ses/mCcSp#Occurrence"http://lod.taxonconcept.org/ses/mCcSp#Occurrence. In the RDF that defines what this URI means, the URI is described as "A lightweight tag that can be used to label occurrences of this species". What I'm not sure about is what exactly one is supposed to do with it. From the example that I was talking about in the previous email ( http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.rdf), this "tag" is the object of the predicate txn:occurrenceHasSpeciesOccurrenceTag . So I guess that it is another way that one could query Occurrence records to find out which ones are Occurrences of the species having the identifier "ICmLC" (*Boloria selene*). But I'm not sure what the advantage of that is. The RDF for the Occurrence already tells me that the Occurrence has the txn:occurrenceHasSpeciesConcept property with object URI http://lod.taxonconcept.org/ses/ICmLC#Species . I can resolve that URI and "find out" that the "species concept" (sensu DeVries) is *Boloria selene* . But if I used the "lightweight tag" I'd also have to resolve its URI to find out about it and the RDF for the tag directs me to the http://lod.taxonconcept.org/ses/ICmLC#Species URI anyway via the dcterms:isPartOf property of the tag. I guess the point is that if one wants to "find out" about the Occurrence, it takes two steps to get to the species concept description if I use the tag (first through txn:occurrenceHasSpeciesOccurrenceTag, then through dcterms:isPartOf) which is no advantage over just getting there in one step (via txn:occurrenceHasSpeciesConcept). If the only point is to have something to put in as a search term, then why not just make the txn:occurrenceHasSpeciesOccurrenceTag a data property with the literal object the string "ICmLC"?
I suppose that one could say that an advantage of the "lightweight tag" approach would be that one is indicating that the particular Occurrence is an instance of a class that consists of all Occurrences of the species *Bororia selene*. That seems to be what the intention is. But this seems to be a case of creating many subclasses rather than having a general class and assigning it properties that help one to understand the nature of the instance of that class. It requires the creation of a class for every species on the planet. Instead of there being a relatively small number of classes that includes the basic kinds of resources (Occurrence, individual, Identification, taxon concept) there is a class for occurrences of every kind of taxon concept. Actually, there are several classes for every instance of taxon concept, because you are recommending that the "lightweight tag" approach be used for other types of things as well, such as individuals and (in your suggestion below, populations). There isn't anything intrinsically "wrong" with this approach, but with my bias toward preferring "well known" types/classes it just seems like a lot to expect consuming applications to "understand" what amounts to potentially millions of classes that this method would introduce.
I also don't quite understand what a txn:SpeciesOccurrenceTag is exactly. In the RDF that defines the txn:SpeciesOccurrenceTag instance for *Bororia selene* (http://lod.taxonconcept.org/ses/ICmLC#Occurrence) the dcterms:description says that it "allow species occurrences to be modeled as instances of SpeciesOccurrenceTag". But that doesn't seem to be what is actually occurring. When the Occurrence instance http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurre... described, it is not typed as the lightweight tag (which IS a txn:SpeciesOccurrenceTag because of the implicit typing caused by the XML container element name). The lightweight tag URI is the object of the txn:occurrenceHasSpeciesOccurrenceTag property, but that doesn't make the Occurrence an instance of SpeciesOcurrenceTag as would be the case (I think) if the lightweight tag URI were the object of a rdf:type property. Anyway, I'm confused about this.
The other issue that I would raise with this approach is that it brings up the same issue that I raised in the other email that I wrote. It essentially puts a burden of anticipating the results of a query onto the metadata provider. If one follows the model of allowing multiple Identifications for an organism, then it is possible that someone somewhere else might apply their own Identification instance to the individual represented in the Occurrence. As was the case in my earlier example, for txn:occurrenceHasSpeciesOccurrenceTag to be useful as a thing to be queried, the metadata provider would need to somehow know that this additional Identification had been made, and then create another txn:occurrenceHasSpeciesOccurrenceTag property for the Occurrence instance. This seems to somewhat at odds with the benefit that the Linked Data world has in allowing resources to be created by people all over the cloud and then linked rather than expecting a centralized authority to do everything.
Anyway, maybe you can explain what is going on so that I can understand it better and maybe explain why this approach is better than just creating a few classes and describing their instances by descriptive properties.
Steve
Peter DeVries wrote:
I am still somewhat puzzled why TDWG seems so opposed to adopting anything that comes from outside a small click?
I was thinking that it would be best to create a separate class that can be used for populations of a species.
This would require adding an additional tag to the TaxonConcept Species Concept Model, which currently includes several tags like entities
http://lod.taxonconcept.org/ses/mCcSp#Species <- The Species Concept for the Cougar
See http://lod.taxonconcept.org/ses/v6n7p.html HTML http://lod.taxonconcept.org/ses/v6n7p.rdf RDF
http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%... Base View (http://bit.ly bit.ly/gMFqR1
The model mints URI's for the following related entities. See RDF. or KB View
http://lod.taxonconcept.org/ses/mCcSp#Image - An image of a Cougar http://lod.taxonconcept.org/ses/mCcSp#Occurrence - An occurrence of a Cougar http://lod.taxonconcept.org/ses/mCcSp#Individual - An individual Cougar http://lod.taxonconcept.org/ses/mCcSp#Taxonomy - A Basic Taxonomy for the Cougar, one alternative among many potential classifications http://lod.taxonconcept.org/ses/mCcSp#NCBI_Taxonomy - The NCBI Taxonomy for Cougar, or starting at the lowest available clade http://lod.taxonconcept.org/ses/mCcSp#OriginalDescription - The Original Description of the Cougar, ideally with links to the PDF or BHL URI.
Here is how a subset of these would relate to the new #Population Tag and related semantic entities.
This tag is used an individual organism that that is an instance of the species concept pecies concept RDF. This allows you to refer to a individual cougar in a way that is separate from the concept of cougar and retains links to other data relating to that species concept.
<txn:SpeciesIndividualTag rdf:about=" http://lod.taxonconcept.org/ses/v6n7p#Individual%22%3E dcterms:titleA Tag for individuals of the species concept Puma concolor se:v6n7p</dcterms:title> skos:prefLabelA Tag-like resource that is used to label individuals of the species concept Puma concolor se:v6n7p</skos:prefLabel> dcterms:identifierhttp://lod.taxonconcept.org/ses/v6n7p#Individual </dcterms:identifier> dcterms:descriptionA lightweight tag that can be used to label individuals of this species. These allow individual organisms to be modeled as instances of SpeciesIndividualTag</dcterms:description> <dcterms:isPartOf rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p#Species%22/%3E <wdrs:describedby rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p.rdf%22/%3E </txn:SpeciesIndividualTag>
Add a tag for a species population to the species concept RDF. This allows you to refer to a population of cougars in a way that is separate for an individual cougar and retains links to other data relating to that species concept.
<txn:SpeciesPopulationTag rdf:about=" http://lod.taxonconcept.org/ses/v6n7p#Population%22%3E dcterms:titleA Tag for populations of the species concept Puma concolor se:v6n7p</dcterms:title> skos:prefLabelA Tag-like resource that is used to label populations of the species concept Puma concolor se:v6n7p</skos:prefLabel> dcterms:identifierhttp://lod.taxonconcept.org/ses/v6n7p#Population </dcterms:identifier> dcterms:descriptionA lightweight tag that can be used to label populations of this species. These allow populations of a species to be modeled as instances of SpeciesIndividualTag</dcterms:description> <dcterms:isPartOf rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p#Species%22/%3E <wdrs:describedby rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p.rdf%22/%3E </txn:SpeciesPopulationTag>
This is the RDF for a population, it has as one of it's parts an individual organism. It is typed to indicate that it refers to a population of Cougars.
<owl:Class rdf:about=" http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation%22%3E <rdf:type rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p#Population%22/%3E skos:prefLabelThe population of North American Cougars Puma concolor se:v6n7 </skos:prefLabel> <dcterms:hasPart rdf:resource=" http://ocs.taxonconcept.org/ocs/51cd124d-78c5-40aa-a7ff-2e3f58ca6ade#Individ... "/> <wdrs:describedby rdf:resource=" http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation.rdf%22/%3E </owl:Class>
Respectfully,
- Pete
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
Email: pdevries@wisc.edu
TaxonConcept http://www.taxonconcept.org/ & GeoSpecieshttp://lod.geospecies.org/ Knowledge Bases
A Semantic Web, Linked Open Data http://linkeddata.org/ Project
-- 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) 343-6707http://bioimages.vanderbilt.edu