[tdwg-content] ITIS TSNID to uBio NamebankIDs mapping
Steve Baskauf
steve.baskauf at vanderbilt.edu
Sun Jun 5 14:17:56 CEST 2011
Thanks to all of you for taking the time to explain your perspective on
the issues relating to taxon names and their identifiers. I suspect
that some of this was probably explained last year in earlier threads
that I zoned out on, so thanks for your patience in "re-explaining" -
I'm understanding this better now. For example, I think I "get" the
reason for the use of UUIDs that Pete and Dima explained - thanks for
explaining that again. I see the problem with character encodings in
URIs, etc.
I think that part of the difficulty that we are having in nailing down
this issue is that different people have different things that they want
their identifiers to "do". In a sense this is a good thing because
"clever" GUIDs actually CAN do multiple things at once. Some of these
things are:
1. uniquely identifying a resource globally
2. use http as a resolution mechanism
3. providing a means for tracking provenance
4. providing a single, stable point of reference to which multiple
people/institutions can anchor the properties of their own resources
5. providing a way to unambiguously refer to the resource in a
publication (i.e. type-able)
6. providing a means for a human to find information about the thing via
a webpage
7. providing a means for a computer to find information about the thing
via RDF/XML
8. not change
Some people are primarily interested in a few of these things. Some
people are interested in others. If the identifier is for internal or
temporary use, then it doesn't really matter what the form of the
identifier is, or whether it only meets a few of these functions. For
example a URI that is used to identify your shopping cart when you make
a purchase on amazon.com is going to be globally unique, but not stable
or type-able. A private URI that you are using to call up information
within your organization (maybe with a query string on the end) may meet
some of these functions and might actually be globally unique. However,
I would not count either of these things as a "GUID" in the sense of an
identifier for permanent, public exposure and consumption, and intended
as an object for a property in somebody else's RDF. I would assert that
a "good" GUID in that sense ought to meet all of the 8 criteria that I
listed above. We know how to do those things. There are plenty of
resources online about how to achieve content negotiation, "cool" URIs
(http://www.w3.org/TR/cooluris/), GUID standards
(http://www.tdwg.org/standards/150/) and best practices
(http://www2.gbif.org/Persistent-Identifiers.pdf
http://links.gbif.org/persistent_identifiers_guide_en_v1.pdf), etc. that
tell us how to do this. We have examples in our community that show us
how to do these things and people who know how to do them. There is,
therefore, no excuse for us to be creating public GUIDs that only do
part of these things.
Rich provides these examples of identifiers:
A. A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523
B. urn:lsid:zoobank.org:act:A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523
C.
http://zoobank.org/urn:lsid:zoobank.org:act:A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523
D. http://zoobank.org/A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523
E.
http://lsid.tdwg.org/urn:lsid:zoobank.org:act:A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523
F. http://www.google.com/search?q=Danaus+plexippus+(Linnaeus+1758)
G.
http://lsid.tdwg.org/summary/urn:lsid:zoobank.org:act:A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523
H.
http://darwin.zoology.gla.ac.uk/~rpage/lsid/tester/?q=urn:lsid:zoobank.org:act:A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523&submit=Go
and then says:
"But really, from the perspective of the end-user, does it matter if
it's an identifier or a service? Ultimately, they ask the questions,
and the answers appear on their computer screens."
I would answer this question by saying "yes, it does matter!" - it is
important that a well-designed GUID do more than just throw something up
onto a human user's web browser. All of 8 these examples are globally
unique (test 1). However, many of them flunk one or more of the seven
other "tests" that I've laid out above. A and B flunk test 2. I
applied test 6 all 8 of them by pasting them into Firefox to see if they
would produce a human-friendly webpage and this test was flunked by A,
B, and E. I applied test 7 to all of them by checking them with the
OpenLink RDF browser (http://demo.openlinksw.com/rdfbrowser2/). Only E
passed that test. All of them are pretty rotten on test 5, although D
isn't too bad. The fact that there are at least five identifiers
suggested which might be appropriate for use in metadata (A through E)
makes the set as a whole flunk test 4. The bottom line is that not one
of the 8 suggested identifiers pass all 8 of the tests. To me that is
unacceptable. We simply should not be satisfied with that when it is
clear that we can create identifiers that will meet all 8 tests. Lest
anyone doubt me, here are three examples of "good" GUIDs created by
members of our community which pass all 8 tests; there are undoubtedly more.
http://biodiversity.org.au/apni.taxon/118883
http://lod.taxonconcept.org/ses/v6n7p
http://biocol.org/urn:lsid:biocol.org:col:35259
All three pass the "cool URI" test and clearly resolve to metadata for
both humans and computers. What I am wanting for taxon names is
identifiers that pass the 8 tests I listed.
An important question that I think has been underlying much of this
discussion is whether GUIDs are actually needed for names. If one takes
the position that a "name" can never be more than a string without
crossing the line into being something more complicated like a TNU or
TaxonConcept, then I think one could make the case that the answer to
this is "no". There isn't a whole lot that one would want to know about
the string that couldn't just be imparted by letting it be a string
literal. If one takes this position, then "Quercus alba L." is a
different "thing" (i.e. resource) from "Quercus alba" or "Quercus alba
Linnaeus". It seems that something like this is the position that Rich
and the GNI are taking. Under this scenario, there is little point in
creating URI GUIDs for the name strings.
On the other hand, if one takes the position that a name can be a
conceptual entity that has properties which include its name string(s)
and parts thereof, then it does make sense to apply GUIDs to that kind
of entity. I am thinking about a tn:TaxonName as defined in the TDWG
ontology (see
http://code.google.com/p/tdwg-ontology/source/browse/trunk/ontology/voc/TaxonName.rdf),
which comes out of the TCS schema (see
http://code.google.com/p/darwin-sw/wiki/ClassTaxon for info and links
regarding TCS). A tn:TaxonName is "An object that represents a single
scientific biological name..." i.e. an "object" NOT defined as a
string. Under the TCS, it is not kosher for a tn:TaxonName to have
properties that tell how it is related to higher taxa - this is reserved
for TaxonConcept instances. However, it is perfectly fine for an
instance of tn:TaxonName to have properties that define the parts of its
name (genus, species, and infraspecificEpithet if any) and other
metadata directly associated with the name. Assigning a "good" GUID to
a tn:TaxonName would be a desirable thing from the standpoint of test #4
because it would allow multiple people to assert that they were talking
about the same name without having to worry about whether they did or
did not include the author in the string and whether "Quercus lobata
Née" is the same thing as "Quercus lobata Nee". The "atomized" parts of
the name could be provided in a single unit of metadata rather than
having to repeat them for every concept like "Quercus alba L. sensu
Weakley 2010", "Quercus alba L. sensu Gleason and Cronquist 1991",
"Quercus alba L. sensu Radford et al. 1968", "Quercus alba L. sensu
Wofford and Chester 2002", etc.
Currently I'm following the approach for marking up Taxon metadata that
was outlined by Cam and me at
http://code.google.com/p/darwin-sw/wiki/ClassTaxon - it's based
primarily on ideas from TCS and influenced by RDF examples posted by
several people on this list (specifically it uses the Taxon Concept
parts of the unfinished TDWG ontology with is NOT a standard, but is
based on the TCS standard). We considered it to be relatively "safe"
because it was based primarily on TCS which is a ratified TDWG standard
and seems to mesh well with what most people seem to intend when they
are talking about Taxon/TaxonConcept instances. We hope that this would
avoid descending into "taxon concept hell" as would happen if we defined
our own personal idea of what we think a taxon concept is. (In the
interest of moving forward constructively in a relatively short period
of time we hope that others will follow the same practice.) What I'm
doing is creating temporary tc:TaxonConcept (a.k.a. tc:Taxon) resources
to which I'm linking the dwc:Identification instances. I call them
temporary because I don't really intend for others to use them and I'm
hoping eventually to replace them with links to GNUB URIs when such
things exist. In a nutshell, the RDF looks like this:
<tc:TaxonConcept
rdf:about="http://bioimages.vanderbilt.edu/taxon/19290-weakley2010">
<tc:nameString>Quercus alba L.</tc:nameString>
<tc:hasName rdf:resource
="http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:448328"/>
<tc:accordingToString>Weakley, A.S., 2010. Flora of the southern and
mid-Atlantic states, working draft of 8 March 2010. University of North
Carolina Herbarium, North Carolina Botanical Garden, Chapel Hill, NC,
US. http://www.herbarium.unc.edu/flora.htm</tc:accordingToString>
<tc:accordingTo rdf:resource="http://www.herbarium.unc.edu/flora.htm"/>
</tc:TaxonConcept>
In reality the RDF is more complicated than that but for the purposes of
discussion, these are the important features. [For now you can ignore
the "accordingTo parts because it's not really right according to TCS
and the URI is for a web page, not the actual reference.] For the
purposes of "stupid" clients (e.g. a Linked Data browser), the
tc:nameString and tc:accordingToString literals would give them
something to throw on a screen for humans to look at. A smarter client
might be able to parse out the name string and do something clever with
it. However, as someone who has listened to Pete's preaching and is
trying hard to be a Linked Data/Semantic Web Believer, I want to put a
functioning URI as the object of the tc:hasName property so that a real
smarty-pants client could do exceptionally clever things like decide
that maybe my /"Quercus alba/ L." pictures should go be put on the same
webpage as somebody else's /"Quercus alba"/ pictures and with a third
person's /"Quercus alba/ Linnaeus" pictures. I don't know how to do
that, but I have faith that there are people on the list who know how,
and so I want to give them the Linked Data resources to make that
possible. This is similar to the rationale for using the URI
http://bioimages.vanderbilt.edu/contact/baskauf to refer to me rather
than the strings "Steve Baskauf", "Steven J. Baskauf", "S. Baskauf",
etc. etc.
As I think about it, a primary purpose of providing a URI for a taxon
name is to allow a machine to know that names which are referred to in
two different taxon concepts are the same. This can be accomplished in
one of two ways. One is simply make sure that users who are trying to
look up two variant name strings for the same taxon name are directed to
the same identifier. This is essentially what happens when one looks up
a TSN on the ITIS website. If I search the ITIS website for either
"Quercus alba L." or "Quercus alba", I'm sent to the record for TSN
19290. In this scenario, there is a single identifier for all of the
lexical variants of Quercus alba L. When comparing two taxon instances
to see if they have the same taxon name part, a machine has virtually no
work to do in order to know that two name strings represent the same
tn:TaxonName because even if the tc:nameString literal for the taxon has
a different string literal value, as long as the URI object of
tc:hasName is the same, then the names are the same.
The situation at uBio is different. uBio assigns a different identifier
for each string and if one searches for different lexical variants, one
gets different identifiers (although as one types a name on their
website, the name version with the preferred author abbreviation shows
up at the top of the "suggestions" list). However, although uBio
provides separate identifiers for separate name strings, the RDF
metadata that is returned when the "urn:lsid:ubio.org:namebank:448328"
URI for "Quercus alba L." is resolved includes statements like
<ubio:lexicalVariant rdf:resource="urn:lsid:ubio.org:namebank:2645936"/>
whose object is the URI for "Quercus alba". So although two users who
are creating tc:Taxon records for taxa with the same tn:TaxonName may
get two different uBio ID numbers for two lexical variants, the
properties of a uBio name string includes metadata property connections
which could allow a client to figure out whether two name strings are
really the same tn:TaxonName.
Now what about the GNI? At the moment, if I search for either "Quercus
alba L." or "Quercus alba", I get a web page showing "Lexical Groups"
which I guess may or may not actually be the same conceptual name. I'm
not directed to any preferred version nor am I told which ones are
considered variants of others. I don't know the algorithm for
generating the UUIDs for these strings so I can't actually look up what
RDF is returned for those Quercus alba strings, but based on the
examples of other names that Pete gave, the RDF just seems to say "this
string is the scientific name Quercus alba" and has no information
telling me what other strings are variants. So what I'm struggling to
figure out is what purpose there actually would be for me to use any
kind of GNI URI as the object of my tc:hasName property. A URI based
either on the name string or a URI containing a UUID generated from the
name string would simply tell me that the thing that I'm talking about
is that name string. That is exactly the same information that I
already provide in the literal value of the tc:nameString property.
Maybe there is a plan at some time in the future to add RDF metadata of
the kind that uBio provides about variants and then I guess there would
be a point in using a URI with tc:hasName that resolves to that RDF.
But if the GNI is only a "dirty bucket" that accumulates every name
string that anybody has ever used in history but with little or no
metadata, then I can't see that I have any use for a URI point to it, at
least as something to which I would refer in RDF. I'm not saying that
there isn't a use for the GNI. I think what I'm saying is that there
doesn't seem to be any point in worrying about how to create URIs for
the GNI when those URIs don't "do" anything different from what a string
literal does. I think this is essentially what Rich was saying: "that
text string represents a perfectly suitable unique identifier. There is
no need to generate a surrogate identifier like an integer number or
UUID or LSID or whatever".
From the standpoint of what I think of as the "general Bob Morris
naughty test" (am I being naughty to assert that some resource has an
rdf:type that doesn't make sense?), I believe that one could technically
use either a uBio http proxied LSID or a resolvable identifier created
from an ITIS TSN (which unfortunately does not exist to my knowledge) to
represent a tn:TaxonName. Although Rich has been very cautionary about
maintaining the distinction between ITIS TSNs, which he believes to
represent some kind of minimal TNU and uBio IDs which he believes to
represent a name string, I haven't been able to find any evidence that
it would be "naughty" to assert that either one is a tn:TaxonName. The
RDF returned when a uBio LSID is resolved does not give any rdf:type.
It simply says that the resource has a dc:type of "scientific name".
This could really mean anything we want since scientific name is not a
part of the DC type vocabulary. There is also nothing in the RDF that
defines the resource as being of the string data type (although one of
its properties, ubio:canonicalName, does). So I can't see that I would
be creating any "collision" of rdf:types by asserting the resource to be
of type tn:TaxonName. The ITIS website does return tc:Taxon (a.k.a.
tc:TaxonConcept) type information when one looks up a TSN, but since as
far as I know ITIS doesn't provide any RDF describing the resources
identified by their TSNs, there isn't any collision if I assert that
such a resource is a tn:TaxonName. Also, if one reads the information
that was referenced earlier in the thread at
http://www.itis.gov/pdf/faq_itis_tsn.pdf , it seems pretty clear that
ITIS intends for the subject of their TSNs to be names, not taxon
concepts even if the metadata they send to humans on their website seems
to say otherwise.
As far as what URI I stick in my RDF as the object of the tc:hasName
property (which incidentally does not HAVE to be a tn:TaxonName, since
tc:hasName does not have a defined range), at this point I guess the
uBio URI is the only choice since there aren't ITIS http URIs (as far as
I know).
Steve
Nicolson, David wrote:
> Rich (et al.)... Just a quick comment re ITIS TSNs, since Rich posited:
> =======================
> My understanding (David N.: correct me if I'm wrong), is that all TSNs that correspond to "valid/accepted" names (where [taxonomic_units].[usage]='valid'|'accepted') essentially represent a taxon concept. The rest of the TSNs (where [taxonomic_units].[usage]='invalid'|'not accepted') represent a variety of things, ranging from different combinations to alternate spellings to subjective synonyms, each of which is referable to one of the "valid/accepted" names.
> =======================
>
> I would say "sort of".... The TSNs do not themselves correspond with much of anything other than a unique, persistent, non-intelligent identifier for a "scientific name" (I realize that begs your next question/point of what that term "means") record in the context of the ITIS data system. See this linked from the "About ITIS" page:
> http://www.itis.gov/pdf/faq_itis_tsn.pdf
>
> Re "Scientific Name", as you hopefully see in the above document, the term in ITIS generally corresponds to what I see from the ICBN use (Art. 16-24) and the ICZN use (Art. 4-5 in particular, as the "combination" formation, rather than the more atomized uses like "specific name" which is like "epithet"). There are of course other thing in ITIS with TSNs, like database artifacts, that are labeled as such and retained but hidden from most users to avoid confusion and not strand any user that might already have the TSN.
>
> By way of an example of the use of "name" fields.... Just recently I was given a nice "finished" world dataset for a modest animal-family-that-shall-remain-nameless, and the "name" fields were in some cases just as ITIS uses them, and in others there were additional things like authorship and so on lumped in with the name parts in those fields, though there were no years provided even then. So, usable, but the amount of work to essentially re-parse the data was surprising for just a couple hundred names, and even then they were inconsistent and incomplete, so someone now has to go collect all the missing details and go over it all again, and it clearly needs some smoothing around the edges as well. That was for just 200+ names from a single source. Ugh, thanks....
>
> As to the relationship to taxon concept, if you squinted your eyes "just so" you could qualify as Rich did above and suggest that those TSNs that happen to represent names with usage=valid/accepted (and preferably those with some level of verification indicated, vs. the legacy data we're still dealing with!) "essentially represent a taxon concept", but I don't really think that is appropriate at this point.... actually the closest thing in ITIS to a "taxon concept" would be certain entries in the reference_links table (the intersection between the scientific names entries and the reference entries), but even that is too abstract in my view. Since any number of references may be linked to a single TSN, that TSN won't necessarily yield something that maps to "a taxon concept" unless you're thinking "sensu ITIS v2011-05-31" or something of that ilk, which is I guess another way to think about it, with its own pros/cons.
>
> And I agree with Rich's warnings of many pitfalls below (dragons and such).
>
> I'll leave it there. Oops. So much for the "quick" comment....
>
> Best,
> Dave
>
> David Nicolson
> Data Development Coordinator, Integrated Taxonomic Information System
> Biologist, USGS Core Science Systems, Biological Informatics Program
> nicolsod at si.edu Office 202-633-2149 Fax 202-786-2934
> http://www.itis.gov/
> http://www.cbif.gc.ca/itis/
> "Nihil sumas necesse est..."
>
>
> -----Original Message-----
> From: Richard Pyle [mailto:deepreef at bishopmuseum.org]
> Sent: Friday, June 03, 2011 3:16 PM
> To: 'Steven J. Baskauf'; 'Kevin Richards'
> Cc: tdwg-content at lists.tdwg.org; Orrell, Thomas; 'Alan J Hampson'; Nicolson, David; 'Gerald Guala'
> Subject: RE: [tdwg-content] ITIS TSNID to uBio NamebankIDs mapping
>
> Hi All,
>
> I'm just catching up on email now, after a series of other work-related
> obligations and virtual attendance at a cybertaxonomy/e-literature meeting
> in Chicago this week. I do not now have time to review the entire thread,
> so I'll jump into the stream with Steve's recent post.
>
>
>> I think that one reason why this question has been on my mind is that I've
>>
> been waiting for
>
>> GNUB (Global Name Use Bank) to come out.
>>
>
> Just a quick update, due to budgetary woes in the U.S. Federal Government,
> NSF funding for awarded proposals has been pushed every further back. If
> I'm not mistaken, something like 18 months passed between proposal
> submission and availability of funds for the BiSciCol grant, which our
> institution was only able to (finally!) start processing within the past few
> months. Why is this relevant to GNUB? Because the BiSciCol grant includes
> the most substantial funding yet for implementation of GNUB (indeed, the
> only funding for GNUB by name). The good news is that, now that funding is
> in hand and money (finally) flowing, development & implementation of GNUB is
> ramping up quickly. And the promise of more (and more substantial) funding
> is just around the corner (watch this space).
>
>
>> I'm not really up on how it is going to work, but my impression is that it
>>
> was going
>
>> to be based on the Global Name Index (GNI) which was mentioned in that
>>
> earlier
>
>> January thread.
>>
>
> Not exactly. GNI and GNUB represent two ends of a spectrum. GNI is at the
> "minimal metadata/maximal content" end of the spectrum -- basically a
> repository of any text-string purported to represent a taxon name that can
> be linked via a resolvable identifier. GNUB is at the "richly
> metadata'd/carefully curated" end of the spectrum, representing a highly
> normalized structure with permanent resolvable GUIDs and the potential for
> robust information/data services. In the vernacular, GNI is the "dirty
> bucket", and GNUB is the "clean bucket". At the moment, the connection
> between GNUB and GNI is unidirectional, in that the content of the
> progenitor of GNUB has been indexed in GNI, but there is no mechanism (yet)
> for GNI content to feed into GNUB. The reason for this is fairly
> straightforward: it's very easy to flatten out normalized content into
> simple text strings (GNUB-->GNI), but it's much more difficult (impossible?)
> to migrate metadata-poor, moderately parsed content into a highly structured
> system.
>
>
>> At that point, the GNI names didn't have any identifiers that were exposed
>>
> to
>
>> the public as permanent GUIDs. I'm assuming that if GNUB refers to GNI
>>
> names,
>
>> they will have some kind of identifiers. So if that happens how is the
>>
> GUID
>
>> recommendation 8 going to be followed? As Kevin said in
>> http://lists.tdwg.org/pipermail/tdwg-content/2011-June/002499.html "What I
>>
> take
>
>> from recommendation 8 of the GUID applicability guide ... is that if you
>>
> DON'T
>
>> already have a record in your own database for a taxon name/concept, then
>> reuse an existing one. " What we have here with GNI is a situation where
>>
> none
>
>> of the records have identifiers. In my mind, the "best practice"
>>
> according to
>
>> recommendation 8 would be for the GNI to reuse existing identifiers where
>> they exist and NOT make up new ones. This is a bit more complicated
>>
> because the
>
>> ITIS identifiers (which are in common use) don't have an http URI version
>>
> that is
>
>> resolvable, and while the uBio identifiers have a resolvable http URI,
>>
> it's in the
>
>> form of a proxied LSID, which I've already complained is very ugly. So
>>
> I'd like to
>
>> hear some ideas about how to have "reused" identifiers in the GNI.
>>
>
> In terms of GUIDs, the objects in GNUB and the objects in GNI are not the
> same, and therefore cannot share identifiers. The core object in GNI is a
> text-string. Indeed, the text string itself can be the actual identifier,
> because it *is* the thing being identified. In other words, because the
> essential uniqueness of an instance (record) in GNI by definition *is* the
> text string (i.e., the series of UTF-8-encoded characters), then that text
> string represents a perfectly suitable unique identifier. There is no need
> to generate a surrogate identifier like an integer number or UUID or LSID or
> whatever (except, perhaps, for internal use as a primary key for joining
> tables; but those identifiers need not/should not be exposed to the outside
> world).
>
> By contrast, the core object in GNUB is a taxon name usage instance -- which
> is a purely abstract notion of the usage of a taxon name within some
> documentation source (like a publication). In this case, the text-string
> name is merely a property of the GUID-identified object, and would be an
> extremely BAD choice to use as a unique identifier. This is why GNUB needs
> to generate a unique identifier to represent this core data object. The
> form that identifier takes (UUID, LSID, integer, DOI, whatever) from the
> perspective of the end user should be completely irrelevant, because the
> user should rarely (if ever) see it, and should certainly *never* be in a
> position to type it on a keyboard (we can discuss the appearance of ZooBank
> LSIDs on printed pages separately). All that matters is that it is
> persistent, globally unique identifier that can be used to cross-link
> information and can be conveniently resolved to the metadata of the object
> it represents.
>
> But the point is, recommendation 8 of the GUID applicability guide is not
> being violated in the context of GNI and GNUB.
>
> The real problem in all of this is the inconsistent meaning people apply to
> the notion of a "taxon name". In GNI-space, the name is simply a text
> string. In GNUB-space, the "name-object" is a code-compliant Protonym that
> serves to cross-link Name-usages to each other. ITIS is different still.
> My understanding (David N.: correct me if I'm wrong), is that all TSNs that
> correspond to "valid/accepted" names (where
> [taxonomic_units].[usage]='valid'|'accepted') essentially represent a taxon
> concept. The rest of the TSNs (where
> [taxonomic_units].[usage]='invalid'|'not accepted') represent a variety of
> things, ranging from different combinations to alternate spellings to
> subjective synonyms, each of which is referable to one of the
> "valid/accepted" names. CoL uses names as proxies to taxon concepts (not
> sure how they handle synonyms vs. misspellings, etc.) And there are other
> variations as well -- to most botanists, "Aus bus L." and "Xus bus (L.)
> Smith" represent "different names", whereas to most zoologists (who would
> not bother to include the "Smith"), regard them as the "different
> combinations of the same name" (zoologists are less consistent than
> botanists in this regard).
>
> The point is, this inconsistency and heterogeneity of what is meant by a
> "name" in taxonomy is, in my opinion, the single GREATEST obstacle in
> achieving informatics harmony among biodiversity datsets.
>
>
>> One thing that comes to my mind would be to have a "domain name" like
>> "http://purl.org/gni/" or "http://purl.org/tn/" ("tn" for "taxon name")
>>
> and
>
>> to follow it with a namespace/id combination similar to what is done with
>>
> lsids.
>
>> So for example "itis/19408" and "ubio/448439" could be appended,
>> creating http://purl.org/gni/itis/19408 and
>>
> http://purl.org/gni/ubio/448439 for "
>
>> Quercus rubra L." Both URIs could point to the same RDF and that RDF
>>
> could
>
>> indicate that the two identifiers are owl:sameAs .
>>
>
> This syntax is basically what ZooBank does (and GNUB will do), within their
> own domain name. But I like the idea of a common URL domain that allows
> these qualified identifiers to be appended.
>
> The real problem is what you describe next:
>
>
>> I realize from what Bob Morris has cautioned in the past that there are
>>
> problems
>
>> with owl:sameAs when the two things aren't actually the same thing
>> (e.g. if the uBio ID refers to a name string only but the ITIS TSN refers
>>
> to the name
>
>> plus an "accepted" status and a relationship to parent taxa).
>>
>
> Do NOT underestimate the significance of this point.
>
>
>> However, if there were an understanding that the GNI only refers to name
>>
> strings,
>
>> then one could still refer to http://purl.org/gni/itis/19408 as an
>>
> identifier for the
>
>> name string of the thing (whatever it is) that is referred to by an ITIS
>>
> TSN of 19408.
>
> Here be dragons -- for lots of reasons. At this point, you might as well
> just do a text-string match on the name. The problem is, you'll miss the
> match if authorship is not identical, but you risk homonymy mis-match if
> authorship is not included.
>
>
>> I have no idea whether this would be a good idea or not, but I was really
>>
> cringing
>
>> to think about 19 million newly minted UUIDs appended to
>>
> "http://gni.globalnames.org/"
>
>> and figuring out how to connect those horrid things to the names and ITIS
>>
> TSNs
>
>> that I'm already using. I think that I said this before, but using the
>>
> purl.org domain
>
>> rather than one like http://gni.globalnames.org/ would in the future allow
>>
>
>
>> somebody else to take over management of providing the metadata when the
>> GUIDs are resolved without having to deal with issues of who "owns" the
>>
> domain name.
>
> As I said before, I think it's perfectly fine to generate UUIDs for internal
> purposes within GNI for varius performance reasons (or whatever), but I
> don't think it's wise to expose those UUIDs externally. Because the
> uniqueness of a GNI record *is* the text string, then it makes more sense to
> me to simply use the text string. However, that only works for
> GNI/uBio/NameBank, where the essence of the record *is* the text string.
> It's a non-starter for other datasets like GNUB, ITIS, CoL, and most others,
> where the essence of the record is something altogether different.
>
> Aloha,
> Rich
>
>
> Richard L. Pyle, PhD
> Database Coordinator for Natural Sciences
> Associate Zoologist in Ichthyology
> Dive Safety Officer
> Department of Natural Sciences, Bishop Museum
> 1525 Bernice St., Honolulu, HI 96817
> Ph: (808)848-4115, Fax: (808)847-8252
> email: deepreef at bishopmuseum.org
> http://hbs.bishopmuseum.org/staff/pylerichard.html
>
>
>
>
>
>
> .
>
>
--
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) 343-6707
http://bioimages.vanderbilt.edu
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