[tdwg-guid] First step in implementing LSIDs
m.doering at bgbm.org
Wed Jun 6 16:31:54 CEST 2007
Finally I found some time to go through this lively thread.
I hope my post is not already outdated by someone elses ;)
Apart from the what gets an URI discussion there have been some
people expressing their doubts about LSIDs. As I have had a number of
discussions lately with people doubting that LSIDs are good for our
purposes, I would really like to question the TDWG decision to go
with LSIDs and start yet another comparison of plain http paired with
redirection, content negotiation and guidelines for using URLs. I
strongly feel that we should avoid new protocol schemes if we do not
have *very* good reasons. I will use the term URL for now to refer to
any http based identification scheme, if its PURLs, our own system or
The LSID specification already tells us how to deal with persistent
identifiers. It is an agreement that we would have to make for URLs.
As the "what gets an URI" confusion has shown those guidelines are
needed in any case, no matter if we take up LSIDs or not. Even LSIDs
can be used with or without versioning and a lot depends on
agreements in regard to the RDF behind it. So essentially we will
have to come up with our own best practices anyway.
LSID and HTTP both are based on DNS to guarantee global uniqueness
and even more important to resolve them. They both derive their
persistence from the promise of the service provider that the domain
name is kept forever and a server is running. If the domain is lost
in 50 years *both* systems are broken.
LSIDs and the semantic web dont play nicely together per se, cause
the semweb de facto requires plain http. From what I've read the
suggestion is to use an LSID proxy that maps URLs into LSIDs. The
problem then is that all RDF statements must use the proxy URL
instead of the real LSID (otherwise you/a resoner doesn't know that
the statement about the LSID and the statement about the proxyURL are
about the identical resource) so essentially noone is using the
LSIDs, they are just kept as an additional "persistent" ID. To
overcome this problem and to be able to use both, the LSID or the
proxy URL, it is suggested to use an owl:sameAs statement within the
LSID metadata to link the proxy URL with the LSID. So applications
can use this to understand we are talking about the same thing. This
gets pretty complex already and I would be surprised if there are
many applications out there that understand this.
Why not apply the owl:sameAs trick to URLs once we find that http is
dead (just in case we can't do a global search-and-replace)? We could
stay with simple URLs now, write simple software fast and get into
the complex mess at a much later stage when we know we really need to
- and not already from the start.
A very often raised requirement for the technology is also that it
should last for hundreds of years. I doubt anyone can predict in that
time period. But a very good reason to go with http is that there is
a *lot* of data bound to them and if the world decides there is
something better than http, there will be many tools to migrate your
data. I feel much more safe trusting the entire web community than
eventually getting out of the LSID trap by ourselves.
Imagine if all the different research communities decide to use their
own resource identification scheme, how bad will data integration
get? We have to deal already with DOIs, but imagine chemists,
geologists, meteorologists, physicists would all choose their own
scheme, just as we are about to issue life science identifiers? Non-
http URIs put barriers up for adoption to other communities, so I am
confident that our LSIDs will be referenced much much less than URLs.
I can see already all those proxy URLs in genebank and alike, not the
And finally yet another link to some good discussion in the W3C
semweb lifescience list:
On 06.06.2007, at 09:21, Dave Vieglais wrote:
> This discussion has been very interesting reading, and though I
> agree with Donald's comments, I find myself coming to a different
> conclusion, leaning towards HTTP URIs as a preferable scheme. The
> reasons are simple - HTTP has been around for a long time, it is
> widely implemented, and mechanisms for implementing robust services
> with that protocol are pretty well sorted out - and really there is
> nothing to stop implementation of the same functionality exhibited
> by LSIDs using HTTP. As Rod has pointed out, http is widely used
> for referencing entities within a semantic web type of context, and
> it seems foolish to ignore the momentum in those technologies as
> they provide a great deal of the desired functionality for
> interoperability and interchange of our data. As a result my
> preference is towards the use of http, primarily because my intents
> are to integrate data from a much broader community. In the end
> though, it doesn't really matter which scheme is adopted by TDWG -
> we will build http resolvers regardless, since they will be
> necessary for reasons of convenience in order to utilize LSIDs in
> all but specific, custom built applications.
> However, regardless of the scheme used to implement the GUIDs used
> by this community, it is critical that the identifiers are
> persistent and useful beyond the lives of whatever services are
> constructed to resolve them. This implies some provenance
> information may need to be captured, and I would argue that the use
> of DNS alone for handling server changes as utilized by LSIDs may
> be insufficient. The only benefit provided by DNS in this context
> is that it is acting as a single source of authority for directing
> how to locate something (in this case an ip address). What I
> suspect is really required is a more robust, and richer mechanism
> for discovering and recording provenance. The ideal would be a
> large, replicated, and distributed data store with a single service
> point which provided people and systems with a one-stop shop for
> discovering provenance for a GUID. Then if an particular GUID
> could not be directly resolved, the global provenance store could
> be consulted and the resulting information providing a pointer (or
> perhaps a series of pointers) indicating how the guid can now be
> By creating such provenance records and persisting them with as
> much care as the data, it seems that a system with stability beyond
> the vagaries of the internet could reasonably be constructed.
> Dave V.
> On Jun 6, 2007, at 00:46, Donald Hobern wrote:
>> Yesterday was a vacation here in Denmark - otherwise I'd have
>> responded a little earlier, but I'm glad to see all the comments
>> from others. I thoroughly agree with Kevin, Jason, Rich and
>> Anna. No one here believes that any particular solution is going
>> to be perfect. Our biggest need is consensus and the readiness to
>> get going with a workable solution.
>> I do recognise the strength of Rod's arguments. Indeed, if I were
>> building some system for integrating data using semantic web
>> technologies, and my only concern was ensuring the efficiency of
>> synchronous connections now, I am sure I would adopt HTTP URIs for
>> the purpose. However I remain convinced (as I've stated before)
>> that the needs of this community do subtly shift the balance in
>> another direction. We are interested in maintaining long-term
>> connections between our objects and have a perspective which goes
>> back hundreds of years. This at least should give us pause over
>> whether we want our specimens to be referenced using identifiers
>> so firmly tied to the Internet of today. More importantly, one of
>> the key drivers right at the beginning of TDWG's consideration of
>> GUIDs was that the community had plenty of experience of URL rot
>> and didn't want to rely on everyone maintaining stable virtual
>> directories on their web servers to preserve the integrity of
>> object identifiers.
>> Both LSIDs and HTTP URIs could be made to work for us. Both are
>> totally reliant on good practice on the part of data owners.
>> Personally I believe our chances of getting the community to
>> consider, define and apply such practices are enhanced by the
>> identifier technology being something a little more different and
>> distinct than just a "special URL".
>> Donald Hobern (dhobern at gbif.org)
>> Deputy Director for Informatics
>> Global Biodiversity Information Facility Secretariat
>> Universitetsparken 15, DK-2100 Copenhagen, Denmark
>> Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480
>> On Jun 6, 2007, at 12:51 AM, Kevin Richards wrote:
>>> I agree with Jason. It is not the GUID that is the cause of all
>>> the problems here - THERE IS NOTHING WRONG WITH LSIDS - we just
>>> need to move on and start using them in our own context (or any
>>> other suitable GUID - LSIDs are only the recommended GUID, NOT
>>> the only premissable GUID).
>>> If it all falls to pieces later on we could just do a search and
>>> replace to change all our GUIDs to some other scheme (to quote
>>> Bob, just serious).
>>> I agree, it is the RDF/metadata/ontologies that are the key to
>>> getting things working well.
>>>>>> "Jason Best" <jbest at brit.org> 06/06/07 8:39 AM >>>
>>> I've only had a chance to quickly skim the documents you
>>> reference, but it seems to me that the alternatives to LSIDs
>>> don't necessarily make the issues with which we are wrestling go
>>> away. We still need to decide WHAT a URI references - is it the
>>> metadata, the physical object etc? URIs don't explicitly require
>>> persistance, while LSIDs do so I see that as a positive for
>>> adopting a standard GUID that is explicit in that regard. I think
>>> the TDWG effort to spec an HTTP proxy for LSIDs makes it clear
>>> that the technical hurdles of implementing an LSID resolver (SVR
>>> records, new protocol, client limitations etc) are a bit
>>> cumbersome, but I don't think the underlying concept is fatally
>>> flawed. In reading these discussions, I'm starting to believe/
>>> understand that RDF may hold the key, regardless of the GUID that
>>> is implemented. Now I have to go read up more on RDF to see if my
>>> new-found belief has merit! ;)
>>> From: Roderic Page [mailto:r.page at bio.gla.ac.uk]
>>> Sent: Tuesday, June 05, 2007 2:10 PM
>>> To: Chuck Miller
>>> Cc: Bob Morris; Kevin Richards; tdwg-guid at lists.tdwg.org;
>>> WEITZMAN at si.edu; Jason Best
>>> Subject: Re: [tdwg-guid] First step in implementing LSIDs?[Scanned]
>>> Maybe it's time to bite the bullet and consider the elephant in
>>> the room -- LSIDs might not be what we want. Markus Döring sent
>>> some nice references to the list in April, which I've repeated
>>> below, there is also http://dx.doi.org/10.1109/MIS.2006.62 .
>>> I think the LSID debate is throwing up issues which have been
>>> addressed elsewhere (e.g., identifiers for physical things versus
>>> digital records), and some would argue have been solved to at
>>> least some people's satisfaction.
>>> LSIDs got us thinking about RDF, which is great. But otherwise I
>>> think they are making things more complicated than they need to
>>> be. I think this community is running a grave risk of committing
>>> to a technology that nobody else takes that seriously (hell, even
>>> the http://lsid.sourceforge.net/ web site is broken).
>>> The references posted by Markus Döring were:
>>> (1) http://www.dfki.uni-kl.de/dfkidok/publications/TM/07/01/
>>> "Cool URIs for the Semantic Web" by Leo Sauermann DFKI GmbH,
>>> Richard Cyganiak Freie Universität Berlin (D2R author), Max
>>> Völkel FZI Karlsruhe
>>> The authors of this document come from the semantic web community
>>> and discuss what kind of URIs should be used for RDF resources.
>>> (2) http://www.w3.org/2001/tag/doc/URNsAndRegistries-50
>>> This one here is written by the W3C and addresses the questions
>>> "When should URNs or URIs with novel URI schemes be used to name
>>> information resources for the Web?" The answers given are "Rarely
>>> if ever" and "Probably not". Common arguments in favor of such
>>> novel naming schemas are examined, and their properties compared
>>> with those of the existing http: URI scheme.
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