[tdwg-content] most GUIDs/URIs for names/taxon stuff not ready for prime time

Tony.Rees at csiro.au Tony.Rees at csiro.au
Sun Jan 9 01:52:33 CET 2011

Steve, thanks for the reply / elaboration. I guess I am indeed talking about non-reuse of identifiers for taxon names, but at an even more basic level, is the "cure" (LSIDs) for the problem (non-unique or variably cited taxon names) actually better or worse than the original problem. I brought up the ITIS TSNs as a worked example more than a perfect model to follow and to see if there are lessons to be learned there, based on to what extent it has or has not been succesful as a numeric alternative to using taxon names for a data interchange format, as well as its degree of re-use by subsequent players in the same area (apparently zero in the LSID world at least).

>From my point of view "an" integrated taxonomic information system  is a worthwhile goal; what we actually need to discuss whether the present ITIS, CoL, uBio, ION, GNI, ZooBank etc. etc. actually have any prospect of reaching the degree of completion and responsiveness to new incoming data that such a vision requires, while eliminating the duplication of effort / proliferation of taxon IDs as indicated in my previous post, and at the same time seeing whether there is in fact a real-world need in the area of data interoperability that would use such a system of alternative identifiers if it existed. To my mind, a set of ever expanding "standards" that are only used by their respective originators are not standards at all, they are just local system identifiers and so should be relegated to that role (which is perfectly valid of course) but not promoted as being the way forward in solving biodiversity informatics data interchange issues.

Regards - Tony

From: Steve Baskauf [steve.baskauf at vanderbilt.edu]
Sent: Sunday, 9 January 2011 9:37 AM
To: Rees, Tony (CMAR, Hobart)
Cc: pete.devries at gmail.com; tdwg-content at lists.tdwg.org
Subject: Re: [tdwg-content] most GUIDs/URIs for names/taxon stuff not ready for prime time

I think that both Pete and Tony bring up good but different points.
Tony seems to be making a point about non-reuse of identifiers for taxon
names, while Pete seems to be making points about the desirability of
also having identifiers for concepts (which he might or might not intend
to be the same thing as taxon name usages) and the need for identifiers
that will work in the Linked Open Data world.

As far as Tony's point is concerned, I would like to have an answer to
the very direct question that Tony raised.  Why aren't ITIS TSNs, which
are well-known and often-used unique identifiers within their system,
being used as a part a Global Names Index GUID?  Since they are locally
unique within ITIS, they could easily be made globally unique by
concatenating them to http://gni.globalnames.org/ .  For example, if
TSN=778049, the URI would be http://gni.globalnames.org/778049 .  That
would be short, simple, globally unique, and a form that could easily be
used with content negotiation and therefore be fine for use in the LOD
world.  Databases that are already using ITIS TSNs could easily and
reliably construct the URI.  I suppose one objection to this might be
that ITIS TNS's imply TNUs and not simply names, but to my knowledge
there is only a single name/author combination per TSN and so it could
be used as part of a name identifier.  Am I correct about this?

I do not believe that the suggestion of autogenerating URIs by creating
UUIDs from the name strings is a good idea.  In the examples that Tony gave:

Physeter catodon (Linnaeus, 1758)
Physeter catodon L.
Physeter Catodon Linnaeus 1758
Physeter catodon Linnaeus, 1758
Physeter catodon Linnaeus, 1766

I'm assuming that they all (except maybe the last one) represent
formatting/spelling differences of what is actually the same name.  In
an earlier email, one of Pete's rationales for why a URI should be used
instead of an actual name string was so that the various misspellings
and differently formatted versions of the same name would be represented
by a single URI.  Yet this system of generating the URI from a UUID
through an algorithm based on the name string will allow someone who is
writing software to generate the URI based on a misspelled name without
requiring the software to check against a list of correct
names/identifiers.  How is that better than just allowing people to
enter misspelled names as string literals???  The only thing it
accomplishes is replacing something intelligible like "Junonia coenia"
with something unintelligible like 3a70f04d-fd29-5570-ba91-52dae0c3d07f

I really don't understand this infatuation with UUIDs.  I would have
thought that after the LSID debacle, this community would have learned
something the negative effect on progress of promoting an unnecessarily
complicated technical solution when one is not required to get the job
done.  Imagine you are an herbarium curator who is somewhat behind the
times technologically and a bit confused about GUIDs.   This curator has
an Excel spreadsheet with TSN IDs in it.  Do we ask him to get one of
his undergrad helpers to create a formula in an adjacent cell to the TSN
that concatenates "http://gni.globalnames.org/tsn/" to the TSN to create
the GUID that we tell him that he should be using?  Or do we ask him to
download some special software that isn't quite ready to be used that
will install a UUID generator on his computer and then spend an hour
with him on the phone walking him through the installation which won't
work because he'll have to install LUNIX, a Java virtual machine, a
MySQL database, a proxy localhost http xyz server thingamajig that he
has never heard of and doesn't understand but which seems so simple to
the TDWG tech crew?  You can ask him to use
or you can ask him to use

Which one do you think is going to confuse him?  Which one can he type?
Which one can he cite in a paper and expect people to write down?  I
complained about this in the draft of the Beginner's Guide to GUIDs
which relied heavily on UUIDs in its examples.  Let's get real here.  We
should be designing systems with the users in mind, not the programmers.


Tony.Rees at csiro.au wrote:
> Dear Pete,
> I don't think you have really addressed the question I was attempting to ask - so I will try again...
> Let's take as an example the sperm whale, Physeter macrocephalus, syn. Physeter catodon (or vice versa in some sources e.g. Mammal Species of the World 3rd edition).
> P. catodon Linnaeus 1758 is given the taxonomic serial number (TSN) of 180489 in ITIS, while P. macrocephalus has the TSN 180488. These usages are then picked up by Cat. of Life, however rather than re-using the ITIS TSNs, they are allocated the LSIDs ??? (for P. catodon) and urn:lsid:catalogueoflife.org:taxon:415df5cc-52c2-102c-b3cd-957176fb88b9:col20101221 for P. macrocephalus. (Also my understanding is that these change every year with a new release of CoL). Meanwhile over at uBio P. catodon has the LSID urn:lsid:ubio.org:namebank:105910 while P. macrocephalus has the LSID   urn:lsid:ubio.org:namebank:111731 . Of course being both Linnaean taxa, these also have ZooBank LSIDs i.e. P. catodon is urn:lsid:zoobank.org:act:046FA756-3A20-454E-8351-12EDE16574B4 while P. macrocephalus is urn:lsid:zoobank.org:act:A2F39087-C7A1-476F-88F6-B7C7B61D86AB . Meanwhile over in AFD we find the LSID urn:lsid:biodiversity.org.au:afd.taxon:587e6872-512b-402e-9c5e-f098c6495275 for P. macroceph
> a
>  lus (not sure about catodon); in ION P. catodon has the LSID urn:lsid:organismnames.com:name:553123 while P. macrocephalus has urn:lsid:organismnames.com:name:553124 and so on we go (GenBank IDs, WoRMS IDs, Fauna Europaea IDs, etc. etc.).
> Now if you look in GNI (which indexes namestrings) you will find the variants as follows:
> Physeter catodon (Linnaeus, 1758)
> Physeter catodon L.
> Physeter Catodon Linnaeus 1758
> Physeter catodon Linnaeus, 1758
> Physeter catodon Linnaeus, 1766
> (and similar for P. macrocephalus)
> each of which no doubt also has its own unique ID somewhere behind the scenes as well, all presumably awaiting reconciliation.
> My question is simply how this apparently unregulated minting of LSIDs and other unique identifiers is contributing to a solution rather than becoming a new problem requiring additional resources to reconcile (bearing in mind that we do not even have a reliable list of all named taxa at this time).
> I am sure there is an answer somewhere, it's just that I cannot see it as yet   :) - maybe someone will enlighten me however...
> Regards - Tony
> ________________________________
> From: Peter DeVries [pete.devries at gmail.com]
> Sent: Saturday, 8 January 2011 9:00 AM
> To: Rees, Tony (CMAR, Hobart)
> Cc: jsachs at csee.umbc.edu; tdwg-content at lists.tdwg.org; pmurray at anbg.gov.au; pleary at mbl.edu; dpatterson at eol.org; dmozzherin; Nathan Wilson
> Subject: Re: [tdwg-content] most GUIDs/URIs for names/taxon stuff not ready for prime time
> Hi Tony,
> That is why I think everyone should get behind the GlobalName Index which is a EoL.org / GBIF.org project. It includes the names from ITIS et al.
> The work I am doing with Dima is still experimental and in development, but it demonstrates how two independent databases can autogenerate a shared URI.
> That idea, in itself, is interesting even if you don't like UUID's etc. or the particular way the RDF is implemented now.
> I find ITIS very valuable, but it has a different ID's for the different name's for what would many would consider the same concept.
> So if a given species name changes from Aedes triseriatus to Ochlerotatus triseriatus a new ID is generated.
> This is different than how NCBI does it, but ITIS has more names.
> Also NCBI does not tell you anything about what is or is not an instance of a given species.
> Since I think ITIS and NCBI are useful resources I link to it when I find an appropriate ID to match to. You can see this in my RDF.
> I would encourage ITIS to continue and think about exposing at least some of the data as RDF using CoolURI's.
> http://www.w3.org/TR/cooluris/
> <http://www.w3.org/TR/cooluris/>http://www.w3.org/Provider/Style/URI (i.e. do the best you can :-)
> There are LOD compliant URI's for the NCBI ID's via bio2rdf and uniprot.
> One of the major advantages of the Linked Open Data approach is that there does not have to be one central place for everything.
> Data sets can be distributed and each group can focus on it's core competencies.
> Even things like species concepts could be distributed, but I think it would be best to first get a common understanding of how they will work.
> Or at least a couple different "kinds" of standard species concepts.
> I see several kinds of species-like resources out there now, some are name-based (ITIS), others are more like concepts (NCBI). Some entail
> a particular classification (NCBI, CoL, etc.). Others coin a species concept to which various classifications are associated (TaxonConcept.org)
> We are at the start of trying to untangle this mess and a good place to start is one resource that contains all the name uses.
> Besides is there any one else willing to take on the responsibility to collect and curate the 400 name variants that can exist for one species?
> >From this we can begin to connect those names to each other and as well as related data sets like publications and occurrences etc.
> I think it is good to have a diversity of projects even if there is some overlap. Each group adds some interesting ideas and perspective.
> Respectfully,
> - Pete
> P.S. Another thing we need is a shared set of URI's for attribution so that they can be easily and efficiently incorporated and tracked.
> e.g.  dataprovidedBy <http://some.shared.org/providers#ITIS>
> A simple URI rather than a huge glob of text and images for each little thing.
> Perhaps using the void vocabulary http://vocab.deri.ie/void/guide
> On Fri, Jan 7, 2011 at 2:11 PM, <Tony.Rees at csiro.au> wrote:
> Dear all,
> >From where I sit (very much on the sideline of this debate, waiting to see what happens), the main trouble I see is that (1) anyone and his dog can mint yet another unique identifier for the same taxon name, leading to uncontrolled proliferation and never ending ID reconciliation issues, and (2) there are always some names not on any particular external "identifier assigning" list which therefore lack an identifier (however have a scientific name) just when you want one. No problem, just mint your own, however that feeds back into (1) again...
> Just curious - ITIS TSNs would have to be one of the longest established and promoted systems of "non-name" identifiers for taxon names - have they been successful in anyone's view, or if not, why not...
> Any comments appreciated.
> Regards - Tony
> --
> ---------------------------------------------------------------
> 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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Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

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