[tdwg-content] Idea for Discussion, Differentiating between "type's" of identifiers

Thu Oct 7 19:30:20 CEST 2010

I like Steve's idea of setting up some test data. I have found that this is
really helpful in figuring out how to represent entities in a way that
allows useful queries.

I also like Rogers idea of exploring of the taxonomic hierarchies using
SKOS.

I have something like this for the Catalog of Life classifications. It only
goes down to Class.

* I am not suggesting that this is the best way or the only way, and it may
not be the most appropriate way to
  model these in SKOS depending on your particular use case.

One thing thing that might be really interesting is following Roger's
suggestion and try this and see if we can create some hierarchy ontologies
which then can be run against each other to determine where they are the
same an where they are different.

There are two more issues that are worth mentioning. In some hierarchies
there are "unassigned" clades which have other clades nested inside of them.
You can see this in the Catalog of Life Fungi. To deal with this you need to
create some sort of "Fungi_Class_Unassigned" clade in which to place the
subordinate classes.

This seems and looks somewhat awkward at first, but it will make sense when
you start making you own.

The other issue is that you  to figure out a way to have the URI for each
clade be unique and since some clades have
the same name you might have to do something like plantGenus_Acer, to make
sure each is unique.

It might be useful to develop some common pattern for this and I would be
interested what Roger suggests.

Also in the case of the Catalog of Life the clades change each year so you
will have to plan for that.

Here is the http://lod.taxonconcept.org/ontology/phylo/CoL/CoL_2010_base.owl

Another pattern for this would be *
http://lod.taxonconcept.org/ontology/phylo/CoL/2010/base.owl*

* I use "base" because I anticipate that once you get below something like
order or family you might need to split
  the lower clades into separate files.

Here is the ontology documentation
  http://lod.taxonconcept.org/ontology/phylo/CoL/doc/index.html

This was made using Protege - which you can get here from Standford.edu
  http://protege.stanford.edu/

The particular reason I made this is described here:

http://www.taxonconcept.org/taxonconcept-blog/2010/6/10/a-species-has_many-classifications.html

Again this might not be structured in the best way for all people but some
might find the example useful
and we might be able to come up with a common solutions to dealing with
genera or other clades that
have identical names. The URI's for these clades needs to be different but
the rdfs:Label could be the same.

There are a lot of features of SKOS, for one thing it can easily handle
labels for the different clades in
many different languages. This is especially good for vernacular or common
names.

The only side effect of using SKOS is that it entails the classes as
skos:Concepts. Some in the LOD community think this might be a problem
others do not. In using SKOS to document a clade you are making it
skos:Concept, but classes can have many types, so something can be both a
skos:Concept and a dwc:Rank etc.

Here is a good resource on SKOS: http://www.w3.org/TR/skos-primer/

- Pete

On Thu, Oct 7, 2010 at 10:38 AM, Roger Hyam <rogerhyam at mac.com> wrote:

>
> I am only just keeping up with this thread so excuse me if I speak out of
> turn.
>
> I wonder if we should have a normative rendering of DwC in RDF at all.
>
> There will probably be many many decisions to take in developing such a
> model. The correct answer to each one of these decisions will depend on the
> use-case for the model. If we don't have at least one clear use-case for
> *consuming* the data then our decisions will be either arbitrary or we will
> argue around and around in circles unable to decide on the perfect answer. A
> use-case should involve answering a real world question not a hypothetical
> one and it should be testable.
>
> As an example I am of the growing opinion that taxonomic classifications
> would be rendered perfectly adequately in SKOS - each classification being a
> free standing thesaurus linked to other thesauri/classifications using the
> standard SKOS terms. Any tool that understood SKOS would then "understand"
> taxonomy. One could produce a mapping from DwC checklists to SKOS to do
> this. It would be totally inappropriate to convert DwC dataset of specimens
> into a SKOS thesaurus as specimens could never be considered concepts.
>
> I hesitate to formally propose the SKOS model (I thought about presenting
> it at TDWG) because I haven't found a decent SKOS browser even or an
> application that would demonstrate the utility of this approach - though I
> have ideas...
>
> Anyhow just my tuppence worth - before departing for a long weekend :)
>
> All the best,
>
> Roger
>
>
> On 7 Oct 2010, at 15:41, Steve Baskauf wrote:
>
>  I agree that it is best to avoid a proliferation of terms and I agree that
> it is best to keep Darwin Core technology independent to the maximum extent
> possible.  However, I think that the case of facilitating HTTP URIs is a
> special one because of the requirements of GUIDs/Persistent Identifiers.
> Both the TDWG and GBIF guidelines such as they currently stand say that
> GUIDs must be resolvable, that in their resolution they must return RDF, and
> that the RDF has to be in an XML format.  Like it or not, that is what we
> have.  Given the amount of time that it seems to have taken to settle on
> that much, I think it is best for us to decide to live with it, warts and
> all, rather than re-opening the discussion and delaying the implementation
> of GUIDs for another five years.
>
> Given that assumption, there needs to be within Darwin Core some way to
> support this particular "technology" (Linked Data, RDF/XML) even if we don't
> do "special" things to support other technologies such as LSID, DOI, etc.
> The point is well taken that most of those other technologies have
> mechanisms for turning their identifiers into URIs and the aforementioned
> guidelines lay out how owl:sameAs can be used within the RDF to associate
> the non-HTTP-resolvable forms with the URIs.  Based on my admittedly limited
> experience with trying to write RDF using Darwin Core terms, I think that in
> most cases there already exists appropriate terms for getting the job done.
> What may be lacking is concrete examples and community consensus on what
> terms to use for what.  I also think that there are probably some "ID" terms
> where it isn't really very important (from an RDF point of view) that there
> exist both a URI form and a text string form.  I'm thinking of something
> like dwc:identificationID, which is mostly likely to be needed to allow a
> machine to make a connection between some resource and its identification.
> The machine isn't going to care if there is a human-readable version.  In
> contrast, something like dwc:collectionID is likely to need both a URI
> version (e.g. proxied version of the BCI LSID) for the machines and a string
> version (the name of the collection as it would be displayed) for humans.  I
> think that trying to make example/template RDF for various types of
> resources will help make it clear in which cases one version (URI), the
> other (string), or both are actually necessary.
>
> I "volunteered" a couple weeks ago to have a go at writing an RDF guide for
> Darwin Core.  I am still willing to do this, although I'm still getting
> caught up at work from being at the TDWG meeting.  However, next week we
> have fall break and I will make it a priority to come up with a draft which
> can be the subject of discussion.  As a part of this process, I think it
> would be good to create one or more "boilerplate" RDF files for the various
> kinds of resources that are likely to be identified with GUIDs (e.g.
> Occurrences, Taxa, etc.).  This can also be a subject of discussion and I
> think it will help to clarify what will meet the actual needs that we have
> discussed in this thread.  I have a pretty clear picture of what I think
> Occurrence RDF should look like.  I'm going to have to depend on Pete and
> others to deal with the taxonomy part.
>
> Steve
>
> Markus Döring wrote:
>
> Steve, Pete,
>
> Id like to draw your attention on a basic DarwinCore design pattern. Dwc has the goal of being technology independent by simply providing a list of abstract terms one can use in various arenas such as xml, rdf, xhtml, csv etc. And even within those there might be various ways of using them (e.g. we have a normalised and a simple flat xml schema), thats why we should have a guideline for each of them on how to use them. We are missing such a guideline for rdf currently, hence this debate.
>
> Whether scientificName is a literal string or some complex object shouldnt matter - its defined to be a scientific name. Such a dwc rdf property could either hold a literal string or a url to some name rdf:resource (potentially with a rdfs:label).
>
> With the introduction if many ID terms we have diluted that idea a little already in my mind. We could have as well used scientificName in xml to hold some identifier for that name. All URNs tell you what they are by their urn prefix (not necessarily how to resolve them), so you can easily detect a UUID, LSID, http(s) url, ftp, doi and apply the conventional resolution mechanism. The hardest problem are the local ids and other plain identifers. For those mainly we created the ID terms (at least in my mind). I am feeling rather uncomfortable discussing the introduction of specific dwc terms for each type of id. Maybe we should remove all id terms in dwc and use the specific guidelines to specify these? At least if you really think having all those id terms for rdf is a good thing I would feel much more comfortable going down this route instead of diluting dwc by adding more and more rather redundant terms. The abstract concept is key to a dwc term, not the actual data type fo
>
> rced by the technology you are using it with. Would you want several date terms for various date formats? In fact we do that already to some degree (eventDate, eventTime, year, month, day, verbatimEventDate) and I always felt this is not a good idea. There are also a number of verbatimXXX terms in dwc which also contradict this pattern.
>
> Talking about new dwc terms - in the examples given properties like "hasScientificName" is not strictly the correct dwc term, which is simply scientificName. I think it would be fine to have the convention in the rdf guidlines to use hasDwcTerm instead of dwcTerm, this is exactly what an rdf guideline is for. On the flip side I am sure this only applies to some terms, recordBy for example is likely to remain as it is. Its unclear to me what is best to do really. Always stick to the original dwc terms? Refine them through some rdfs or owl schema and define the relation to the original term? Should we still use the same namespace in this case?
>
> As an rdf beginner even after a few years exposed I wonder if we cant simply stick to the non ID terms and use them either as literals or with a uri pointer. As in the rdf world a resolvable http is really required for resource relations to work, why not simply mandate this in the guidelines? If you only happen to have non resolvable uris like lsid or dois the guidelines should be asking you to use proxied versions, knowing it will break rdf frameworks and lod conventions otherwise. On the resolving side one could always include such urns with owl:sameAs (or sth alike) I believe. But how many non resolvable ids with no matching http counterpart are really out there yet?
>
> - Markus
>
>
> On Oct 6, 2010, at 9:02, Peter DeVries wrote:
>
>
>
>  Hi Steve,
>
> You are probably right that it might be best to use rdfs:Label, but I am thinking we might be able to get the same
> result my defining the string variants as subproperties of rdfs:Label.
>
> This would make them an rdfs:Label but a special kind of rdfs:Label.
>
> This is one of those things that I would test with Sindice and URIburner to see if they interpret these correctly.
>
> This would require a live vocabulary that Sindice could look at to determine that hasScientificName is to be
> treated as a  rdfs:Label.
>
> - Pete
>
> On Mon, Oct 4, 2010 at 10:41 AM, Steve Baskauf <steve.baskauf at vanderbilt.edu> <steve.baskauf at vanderbilt.edu> wrote:
> Although this specific example deals with taxonomic name identifiers, it is related to a previous discussion on this list about how we should use the dwc:xxxxxID terms and other terms (such as recordedBy and identifiedBy) that could have either a string (literal) or URI form.  Although I don't really want to see an unnecessary proliferation of Darwin Core terms, I think that in the interest of clarity (particularly where RDF is involved) there either should be multiple terms that make it clear what form of identifier is expected, or else there should be an understanding that in RDF the default for such a term is a URI which would then have an rdfs:Label property which was the string form.  I think the former would be preferable to the latter.
>
> I came to this opinion when trying to write RDF describing an herbarium specimen.  The collector should be the dwc:recordedBy property of the specimen.  Optimally, there would be a database in which known collectors were assigned URIs so that "Glen N. Montz", "Glen Montz", "G. N. Montz", etc. would all be different labels for the same resource.  However, realistically, I'm not going to drop what I'm doing to set up such a database (even if I were capable of doing it, which I'm not).  So I ended up just writing it as <dwc:recordedBy>Glen N. Montz</dwc:recordedBy> even though I knew it wasn't probably the best thing.  In a large Occurrence database that was compiled from the RDF created by a lot of people, there might end up being a mixture of strings and URIs for dwc:recordedBy properties of the specimens.  It seems to me like it would be better to have properties like dwc:recordedBy for strings and dwc:recordedByURI for a corresponding URI (and I suppose dwc:reco
>
> rdedByLSID if anyone wants to use it).  Of course, this would require a number of term additions to DwC and clarification in the DwC documentation that the generic version was intended for strings.
>
> With respect to the example
>
> <dwc:hasScientificNameLSID rdf:resource="urn:lsid:catalogueoflife.org:taxon:24e7d624-60a7-102d-be47-00304854f810:ac2010"/>
> I think you are right that (with the possible exception of rdfs:seeAlso) there is an expectation that an rdf:resource attribute will be a resolvable URI that produces RDF.  So
> <dwc:hasScientificNameLSID>urn:lsid:catalogueoflife.org:taxon:24e7d624-60a7-102d-be47-00304854f810:ac2010</dwc:hasScientificNameLSID>
> is probably better.
>
> Steve
>
>
> Peter DeVries wrote:
>
>
>  I have been thinking about the following pattern. In part after looking at the GBIF vocabulary.
>
> I am not sure if it is even a good idea but might be worth some discussion.
>
> For those fields that have both a string and "ID" form maybe the following pattern might be useful
>
> hasScientificName = string form
> hasScientificNameURI = Resolvable LOD compliant identifier
> hasScientificNameLSID = LSID identifier which could be resolvable once you add the "http:proxy" <http:proxy> etc.
>
> This allows all three forms to be included if desired, it also provides a hint as to how the field should be interpreted or resolved.
>
> One group could also provide a mapping service so that each record does not need to include all three forms, but would allow systems
> to find the matching LSID for a given URI or vs. versa.
>
> My concern was that it would be difficult to infer how a scientificNameID should be interpreted by other systems.
>
> Is this an LSD, is it a URI, is it a UUID etc. ?
>
> This impacts the structure of the RDF.
>
> * Note that the actual identifiers might not be correct, the example below is more about the form of the RDF
> * For instance, I don't think it is probably correct to see the COL LSID as just a namestring
> * Also in this example the GNI name does not exactly match the string name
>
> <dwc:hasScientificName>Puma concolor (Linnaeus 1771)</dwc:hasScientificName>
> <dwc:hasScientificNameURI rdf:resource="http://gni.globalnames.org/name_strings/6c3dc35f-d901-5cc5-b9c8-ad241069b9f8" <http://gni.globalnames.org/name_strings/6c3dc35f-d901-5cc5-b9c8-ad241069b9f8>/>
> <dwc:hasScientificNameLSID rdf:resource="urn:lsid:catalogueoflife.org:taxon:24e7d624-60a7-102d-be47-00304854f810:ac2010"/>
>
> Some system may choke on the LSID form assuming that it uses a standard resolution mechanism
>
> So it might be best to use this form
>
> <dwc:hasScientificNameLSID>urn:lsid:catalogueoflife.org:taxon:24e7d624-60a7-102d-be47-00304854f810:ac2010</dwc:hasScientificNameLSID>
>
> - Pete
>
> ----------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> TaxonConcept Knowledge Base / GeoSpecies Knowledge Base
> About the GeoSpecies Knowledge Base
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>
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> Steven J. Baskauf, Ph.D., Senior Lecturer
> Vanderbilt University Dept. of Biological Sciences
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> --
> ----------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> TaxonConcept Knowledge Base / GeoSpecies Knowledge Base
> About the GeoSpecies Knowledge Base
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> --
> 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
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