Globally Unique Identifier
deepreef at BISHOPMUSEUM.ORG
Thu Sep 23 13:29:26 CEST 2004
I want to start by wholeheartedly endorsing Wouter's plea for
non-information-bearing (meaningless) GUIDs. This feature is CRITICAL to
the long-term success of any GUID system. It is absolutely imperative that
there NEVER be any motivation to change the content of a GUID (i.e., it
should be permanent). If the GUID itself contains any information
whatsoever, there may be motivation to change that information at a later
For this reason, I had initially preferred the DOI approach, but over time,
I am gradually warming up to the LSID approach. While components of an LSID
do, indeed, represent information, they represent the one piece of
information that I think may legitimately belong embedded within a GUID:
context. That is, the context, or domain, of the GUID itself. The context
in this case would be the "issuer" of the GUID -- not necessarily the
current "owner" of the GUID (see more discussion on this below). Though the
organization that issued a GUID may eventually disappear, the fact that the
organization was the one to issue the GUID in the first place will never
change, and thus represents a permanent and unchanging component of the
GUID. Without the context portion, the GUID itself is really nothing more
than a random string of characters. In summary, I'm warming up to the LSID
approach because it represents embedded context, without the risk of
temptation to change the content of a GUID after it has been issued.
Regarding Donald's PPT file, I have a couple of comments and questions:
(Assumes Title slide is "Slide 1")
You note there is "No reliable mechanism" to relate the same record from
different providers to each other. But in the context of DarwinCore, the
combination of [InstitutionCode]+[CollectionCode]+[CatalogNumber] should
represent a virtual GUID (provided that the Global Provider Registry ensures
no duplication of [InstitutionCode]). I do realize that words like "should"
and "reliable" are critical here. Perhaps the DarwinCore implementation
should enforce the requirement of uniqueness of
[CollectionCode]+[CatalogNumber] within a single [InstitutionCode], and
further ensure globally unique [InstitutionCode] values via the Global
Wouldn't most of the problems indicated in the first four bulleted points be
largely solved by the Global Provider Registry? Using the [InstitutionCode]
would allow lookup in the registry for a (current/active) metadata URL, and
the metadata URL would provide information on where to access a particular
[CollectionCode]+[CatalogNumber] piece of data.
The issue of specimens changing numbers and/or collections is problematic,
The issue of versioning is a bit dicey, in my mind (e.g., at what resolution
of information change)? Some things, like changing taxonomic determinations
(i.e., "real" changes) need to be handled in a robust way. Other things,
like the correction of typos and different styles of representing the exact
same information (e.g., R.L. Pile==>R.L. Pyle; or R.L. Pyle==>Pyle, R.L.)
probably don't need to be versioned. Other sorts of changes (e.g., the
elaboration of previously existing information, such as the addition of
retroactively-generated georeference coordinates) fall somewhere in-between.
We should all get behind SEEK in addressing these issues (Taxon concept
mapping). Ultimately, we minimally need a GUID pool for References
(inclusive of unpublished works), and a GUID pool for what I call
"Protonyms" (original creations of IC_N Code-compliant names). The union of
these two GUIDs (what I would call "Assertions") would itself represent a
GUID to a "potential concept" (Berendsohn). (Note: my preference would be to
define Protonyms as a subtype of Assertions, and therefore Protonym GUIDs
would be a subset drawn from the same pool as Assertion GUIDs -- but this is
a technical discussion for another time).
Good stuff here, but I'll respond with some of my personal opinions:
- RevisionID: see points of concern already expressed above
- Specimen Record LSIDs: I gather from subsequent slides that you recognize
two alternative approaches: having the "owner" of a specimen assign the LSID
within the context of their own <domainName>, or adopting GBIF as the
international standard issuer for ALL specimen GUID. In other words, GBIF
would represent the centralized issuer of GUIDs for all biological
specimens, and the biological specimen community would/should rally around
GBIF for thus purpose, and adopt GBIF specimen GUIDs as their own. I
personally have no problem with this (I do not live in fear of "Big Brother"
centralization when it serves the benefit of all, as I believe it would in
this case) -- but I know there are many who might have a problem with it,
and therefore it might not garner widespread adoption without large volumes
If, on the other hand, each organization issues its own GUIDs for its own
set of specimens, then the question is when, if ever, GBIF would assign a
specimen GUID? Perhaps as a surrogate for institutions that lack the
technological ability to assign their own LSIDs? But I wonder, how many
institutions that could server electronic data of their holdings to the
internet would lack the ability to assign their own LSIDs?
As you've outlined in subsequent slides, I see two alternative paths: A)
Get the biological world to rally around GBIF as the centralized provider of
GUIDs for specimens for all collections; or B) Have each
collection/institution issue its own set of LSIDs for its own specimens, and
have GBIF adopt those LSIDs for its own internal purposes. I could get
behind either approach, but I see danger in the adoption of a mixture of
these two approaches. I'll defer elaboration, but a lot of it has to do with
potential confusion about whether the GUID applies fundamentally to the
physical specimen, or the electronic conglomeration of data associated with
the specimen. Also, I think we should avoid the risk of assigning two
separate GUIDs for the same "single data element" (sensu your Slide 5).
- Name record LSIDs: I understand the example of an IPNI LSID for a plant
name, and presumably there would be analogous "Catalog of Fishes" LSIDs for
each fish name, etc. But I don't think that would be a wise approach.
Unlike specimen records, where there are fairly unambiguous "owner"
institutions (or at least "original owner" institutions that issued a GUID),
taxonomic aggregators (IPNI, ITIS, Species2000, GBIF, uBio, etc.) are most
certainly not owners of the taxonomic names that they include in their
databases. We would want to avoid the risk of duplicate GUIDs for the same
name, and thus the need for mapping, e.g., an IPNI GUID for a name to its
ITIS equivalent. Again, I can't help but think that the world will be a
better place if we can avoid assigning multiple GUIDs to the same "single
One approach would be to rally around GBIF, and rely on them to issue GUIDs
for all taxon names. However, I also recognize that we do not exist in a
political/personality vacuum with regards to "ownership" of taxonomic names,
or the electronic representations thereof. Therefore, the closest thing
that exists to an "owner" of a taxonomic name is the Commission of
Nomenclature (and it's respective Code of Nomenclature) under which the name
was established. Thus, when it comes to assigning GUIDs for names (not
concepts), I would propose the following:
urn:lsid:ICZN.org:TaxonName:XXXXXX (all zoological names)
urn:lsid:ICBN.org:TaxonName:XXXXXX (all botanical names)
urn:lsid:ICNB[or LBSN??].org:TaxonName:XXXXXX (all bacteriological names)
urn:lsid:ICTV[or ICVCN??].org:TaxonName:XXXXXX (all virus names)
In an ideal world, we'd get to the point where there would be a need for
only one registrar of nomenclature, e.g.:
But I don't think we're quite there yet.
In any case, the idea would be for the taxon name aggregators to adopt the
unambiguously unique GUID for each taxon name.
Taxonomic concepts are a whole 'nother ball of wax....
I actually prefer this approach (GBIF as the central issuer of specimen
GUIDs), for a variety of reasons. One of the main reasons is that it would
assure uniqueness of an integer within a given <namespace> (e.g.,
Specimens), which would make things a bit easier for those of us who like to
use integers as primary keys in databases. In other words, it avoids the
possibility of urn:lsid:bishopmuseum.org:Specimen:1234567 colliding with
urn:lsid:usnm.gov:Specimen:1234567, when reducing the GUID to just its
integer component for local application purposes (where context can be
enforced by other means). However, I should point something out regarding
the "Advantage" part of this slide, which is that the "problem" of
transferring record locations doesn't exist, provided that the <domainName>
component of the LSID is taken as the issuer of the GUID, not as the current
owner of the specimen. In other words, if Bishop Museum assigned GUID
urn:lsid:bishopmuseum.org:Specimen:1234567 to a specimen, and then gave that
specimen to Smithsonian, then Smithsonian would retain the complete GUID
intact as: urn:lsid:bishopmuseum.org:Specimen:1234567.
The danger comes when you try to use the <domainName> component as metadata
to represent the current location of the specimen and/or its electronically
represented data. This is where Wouter's original point about 'meaningless'
GUIDs comes into play. If the whole point of using LSIDs is to embed the
"current location" information within the ID itself so that applications can
retrieve additional data associated with the GUID directly, then I have some
concerns (mostly address already).
Why there is a reference to urn:lsid:gbif.net:TaxonConcept:106734 at the top
of this slide???
Again, I'm not sure I understand on this slide why there is a reference to
Also, in this model, what function does the LSID serve that is not met by
the concatenated [InstitutionCode]+[CollectionCode]+[CatalogNumber] (in the
context of Global Provider Registry).
Slide 10 (taxon concepts and literature):
This message is already getting too long... :-)
I already touched on this above under "Slide 4". I definitely agree that we
need a GUID system for References. This should include more than just
published references. It doesn't quite exist yet among the existing
Reference registrars (as far as I can tell) to accommodate the specific
needs of taxonomists (e.g. referring to a subsection of a reference as
representing an original taxonomic description), so I do see a need to
create a Reference GUID system specific to biology. I could rant for pages
on this, but I'll summarize simply with a plea to *DEFINE* a Concept GUID as
an intersection between an Name GUID and a Reference GUID (i.e., what I
would call an "Assertion"). Not all Name-Reference combinations will be
worthy of recognition as a distinct "Concept", but all are *potentially*
representative of a concept (Berendsohn), and thus all should be drawn from
the same pool of GUIDs as Concept GUIDs. In other words, "Concepts" should
be thought of as a subtype of Name-Reference instances. I would go further
to suggest (as I did above) that "Name" GUIDs should also be a subtype of
Name-Reference instances (non-exclusive of Concept subtype instances), using
the Name-Reference instance that represents the Code-recognized original
description of the name as the "handle" to the Name.
By this approach, you need only two GUID object classes <objectClass>: one
for References, and one for Name-Reference intersections (Assertions). The
latter of these could serve as the source for both Concept GUIDs and Name
My own answers to your questions:
1) Are LSIDs the most appropriate technology?
I'm increasingly coming to that conclusion.
2) Should identifiers be assigned and resolved centrally or via a fully
distributed model (or should providers have the option of using either
I think the best option would be central. The next option would be full
distributed. Leaving it as an option would, in my opinion, be a BIG
3) Which objects should receive identifiers?
Specimens, References, Name-Reference intersections (Assertions), and
perhaps Agents. [TaxonNames and Concepts can be subsets of Name-Reference
3a) Should we develop a set of object classes for biodiversity informatics
and assign identifiers to instances of all of these?
I think so, yes. Of course, it depends a bit on who you mean by "we". I'm
thinking sensu lato.
3b) Should identifiers be associated with real world objects (e.g.
specimens), or with digitised records representing them (e.g. perhaps
multiple records representing different digitisation attempts by different
researchers for the same specimen), or both?
I would say definitely real-world objects (treating things like
Code-recognized original descriptions of taxon names, and citable references
as "real-world objects"). I do NOT think we should have separate GUIDs for
digital representations thereof. Alternative digital representations are
simply clutter that will eventually be weeded out of the system, once we all
get organized on this stuff, and harness the power of the internet to
implement a global editing/QA system.
4) What should be done about existing records without identifiers?
As far as I know, ALL records are currently without identifiers (unless
someone established a widely accepted GUID system and I missed the
4a) Should they be left alone?
4b) Should they all be updated with identifiers?
4c) Should the provider software be modified to generate "soft" identifiers
(ones which we cannot guarantee in all cases to be unique) based e.g. on the
combination of InstitutionCode, CollectionCode and CatalogNumber?
As an interim solution, perhaps. See my comments under "Slide 2" above.
5) Are revision identifiers a useful feature?
I would like to think not. If the information is truly dynamic over time
(e.g., re-determinations of taxonomic identity of specimens), then
individual instances should probably receive their own set of GUIDs (as
opposed to versions of the "parent" GUID). If the information is static
over time, and changes represent objective corrections, then I don't see a
real need to track that within the context of a GUID (record edit history
may or may not need to be tracked, but this seems to me to be a separate
issue from GUIDs).
5b) How many providers will be able to provide and handle them?
If versioning is incorporated, then it should be designed such that a
"default" version is provided automatically when versioning is not handled.
Sorry for the long post, but I feel that this issue is extremely important
at this point in bioinformatics history.
Richard L. Pyle, PhD
Natural Sciences Database Coordinator, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org
> -----Original Message-----
> From: TDWG - Structure of Descriptive Data
> [mailto:TDWG-SDD at LISTSERV.NHM.KU.EDU]On Behalf Of Donald Hobern
> Sent: Thursday, September 23, 2004 6:22 AM
> To: TDWG-SDD at LISTSERV.NHM.KU.EDU
> Subject: Re: Globally Unique Identifier
> This is precisely one of the key questions we need to address with any
> identifier framework we adopt. I think we could easily use LSIDs in a
> way that should overcome your concerns, and I think that the built-in
> mechanisms for discovery and metadata access within the LSID model are
> really exciting.
> I have just put together a PowerPoint presentation to explain some of
> what I think we could achieve with globally unique identifiers and
> particularly with LSIDS. It can be downloaded from:
> It may be clearest if you go through it as a slide show rather than in
> edit mode.
> Donald Hobern (dhobern at gbif.org)
> Programme Officer for Data Access and Database Interoperability
> Global Biodiversity Information Facility Secretariat
> Universitetsparken 15, DK-2100 Copenhagen, Denmark
> Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480
> -----Original Message-----
> From: TDWG - Structure of Descriptive Data
> [mailto:TDWG-SDD at LISTSERV.NHM.KU.EDU] On Behalf Of Wouter Addink
> Sent: 23. september 2004 17:38
> To: TDWG-SDD at LISTSERV.NHM.KU.EDU
> Subject: Re: Globally Unique Identifier
> It seems that DOI allows for any existing IDs to be used as part of the
> unique identifier. That seems to me as a fast to adopt short term
> but not a good idea for the long term. At first sight I very much liked
> LSID specification, but the longer I think about it, the less I like
> parts. What I think is missing in the LSID specification is that the
> identifier should be 'meaningless' apart from being an identifier to
> time independent (and to avoid possible political problems). Any
> with a URN I can think of has some meaning, which makes solutions like a
> MAC-address generated GUID favorable in my opinion. And any meaning you
> (like an authority of an object) can be specified in metadata instead of
> using it in the identifier. What is not very clear to me in the LSID
> specification is where the LSID generated by a LSIDAssigningService is
> actually stored.
> Wouter Addink
> ----- Original Message -----
> From: "Gregor Hagedorn" <G.Hagedorn at BBA.DE>
> To: <TDWG-SDD at LISTSERV.NHM.KU.EDU>
> Sent: Wednesday, September 08, 2004 6:20 PM
> Subject: Re: Globally Unique Identifier
> >I am not quite sure, but to me it seems with "GUID" you refer to the
> > numeric, MAC-address generated GUID type. I have nothing against
> > these. However, any URN in my view is a GUID that has most of the
> > properties you mention:
> >> - it is guaranteed to be unique globally, and can be created
> >> anytime by any server or client machine - it has no meaning as to
> >> where the data is physically located and will there not confuse any
> >> user about this
> >> - most id
> >> mechanisms, especially URI/URN ids require a 'governing body' to
> >> handle namespaces/urls to ensure every URN is unique, whereas a GUID
> >> is always unique
> > The governing body is restricted to the primary web address, and in
> > most cases such an address is already available. Being a member of a
> > governmental institution that explicitly forbids the use without
> > prior consent, and forbids the use of its domain name once you are no
> > longer working for them, I realize some potential for problem.
> >> I do think a URL of some kind would be useful for things such as
> >> global searches of multiple databases, as this will allow the search
> >> to go directly to the data source where the name, referene, etc comes
> >> from. But this should not be part of its ID. Maybe a name/id should
> >> have several foms, a GUID for an ID and a URL + a GUID for a fully
> >> specified name.
> >> What are the current thoughts on these ideas?
> > A GUID is only part of the problem. The other half of the problem is
> > actually getting at the resource. URN schemes like DOI or LSID (I
> > prefer the latter) intend to define resolution mechanisms. That make
> > the URN not yet a URL - in my view the good comes with the good,
> > location and reorganization independence.
> > I believe GBIF should install such an LSID resolver, which is why in
> > the UBIF proxy model, under Links, I propose to support a general URL
> > (including potentially URNS), a typed LSID and a typed DOI. This
> > could be simplified to have just a URN (LSID and DOI are URNs), but
> > that would then require string parsing to determine and recognize the
> > preferred resolvable GUID types. Comments on splitting/not splitting
> > this are welcome!
> > There may be some need to define a non-resolvable URN/numeric GUID as
> > well. However, that would not be under the linking question. Is it
> > correct that linking requires resolvability, or am I thinking into a
> > wrong direction?
> > Gregor
> > ----------------------------------------------------------
> > Gregor Hagedorn (G.Hagedorn at bba.de)
> > Institute for Plant Virology, Microbiology, and Biosafety
> > Federal Research Center for Agriculture and Forestry (BBA)
> > Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220
> > 14195 Berlin, Germany Fax: +49-30-8304-2203
> > Often wrong but never in doubt!
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