[tdwg-guid] First step in implementing LSIDs?[Scanned]

Roderic Page r.page at bio.gla.ac.uk
Tue Jun 5 21:09:50 CEST 2007 

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/tm-07-01.pdf
"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.


Regards

Rod

On 5 Jun 2007, at 19:40, Chuck Miller wrote:

> I just want to take the time here to say AAAAAARGGGGGH!!!  Does anyone
> else share this with me?
>
> It is clear as day that we do not have a decision on what an LSID
> specifically and exactly is (for this community), much less how to
> actually make use of an LSID, and then how in world could we reliably
> relate them together.
>
> It's difficult to accept that so much time has been spent by so many
> people discussing this at length in meetings and workshops, in Wikis,
> and in emails but still we have different opinions of what an LSID
> specifically is for biodiversity data.
>
> What mechanism can we employ that will end this LSID fuzziness once  
> and
> for all, so we can move on to making them functional?
>
> Is the official, unambiguous definition of an LSID something that  
> needs
> to be voted on and accepted at the TDWG meeting?  Perhaps several
> definitions, one for each type of LSID - concept, name, specimen,
> literature, and so on?  But a definition (right or wrong in some  
> folks'
> opinion) that will end the debate.
>
> Chuck
>
> Chuck Miller
> VP-IT & CIO
> Missouri Botanical Garden
> St. Louis, MO, USA
>
>
> -----Original Message-----
> From: tdwg-guid-bounces at lists.tdwg.org
> [mailto:tdwg-guid-bounces at lists.tdwg.org] On Behalf Of Bob Morris
> Sent: Tuesday, June 05, 2007 12:15 AM
> To: Kevin Richards
> Cc: tdwg-guid at lists.tdwg.org; WEITZMAN at si.edu; jbest at brit.org
> Subject: Re: [tdwg-guid] First step in implementing LSIDs?[Scanned]
>
> I am constantly confused in this thread by the term "use an LSID"
> seeming to mean "have an LSID".
>
> Whenever there is a "conceptual" object such as a physical object or
> an observation, there is a strong tradition that its LSID have empty
> data and meaningful metadata. In these cases, I strongly hope there
> will be such an LSID and that there be only a single one for it, which
> is not actually required by the LSID spec. Without this, for example,
> an assertion that  two different  LSID1 and LSID2 both identify the
> type specimen for Aus bus depends on good will and accurate data. On
> the other hand, if I am presented with two LSIDs that are identical,
> no reasoning on returned metadata, nor even  resolution,  is required
> to know that they are talking about the same thing. Thus, if two
> different specimen records, intending to describe the same thing,
> refer to the same LSID in their data in some attribute like
> "DESCRIBES", then those records are unambiguously describing the same
> thing. On the other hand, if the specimen records \themselves/ are to
> have LSIDs, they must NOT have the same LSID, as that violates the
> specification and purpose of LSID (or any other GUID).
>
> I think the confusion here may be some notion that an LSID inherently
> describes something. It doesn't. It only serves to distinguish its
> target  from other things that may have LSIDs.  Nothing in the LSID
> spec implies that the metadata returned by LSID resolution is a
> description, though some communities may wish to do make it so. For
> mutable electronic objects, such as a specimen record  given an LSIDs,
> it would be entirely reasonable for the resolution to return the
> current content of the record as its LSID metadata. It would be
> incorrect to return that record as data, if the content of that record
> is ever permitted to change (which specimen records usually are).
>
> On 6/5/07, Kevin Richards <richardsk at landcareresearch.co.nz> wrote:
>> I agree with Roger that LSIDs should identify the data record, not  
>> the
>> physical object.  In many cases there will not be a physical object,
>> event or whatever.  Any physical object is only really "described" by
>> the digital record (and this does not even guarantee the  
>> connection is
>> correct - due to typos etc).
>>
>> Also consider the situation where you have a single specimen and two
>> different databases that have data about that specimen - should they
> use
>> the same LSID?  I think not.  For one, when you "resolve" the LSID it
>> will only ever fetch the data for the database that is the "owner" of
>> the LSID, and is therefore handling the resolution.  It would be
> better,
>> I think, to use metadata of the objects to connect these two datasets
> -
>> eg the sameAs, replacedBy, etc RDF tags that others have mentioned on
>> this thread.  Of course it is crucial that we reuse LSIDs where
>> possible, but only if when referring to an external ID (ie not much
>> point in having the ID for "your" data being the LSID of another
> system
>> - then your data will never be uniquely identified, or retrievable).
>> Does this make sense?
>>
>> Kevin
>>
>>
>>>>> Roger Hyam <roger at tdwg.org> 06/04/07 9:31 PM >>>
>> Wow this is a big thread appears over the weekend!
>>
>> I am posting without having time to read and digest everything in its
>> entirety but only to answer Jason's original question I hope.
>>
>> Received wisdom is don't use the version part of an LSID. If you did
>> you would be creating new LSIDs anyhow so in a way it doesn't matter.
>> The identifier is supposed to be opaque so the client should never
>> break the LSID into parts anyhow and would only to byte identical
>> comparisons to the LSIDs themselves to see whether they are the same
>> things or not.
>>
>> If you want to do versioning create an LSID for the "thing that
>> changes" and an LSID for each version of that thing.
>>
>> Each of the versions are linked by dcterm:replaces and
>> dcterm:isReplacedBy.
>>
>> http://purl.org/dc/terms/isReplacedBy
>>
>> http://purl.org/dc/terms/replaces
>>
>> Each version points to the LSID for the "thing that changes" with
>> dcterm:isVersionOf
>>
>> http://purl.org/dc/terms/isVersionOf
>>
>> We have our own vocabulary item for the one link in the change that
>> isn't support by Dublin Core. tcom:versionedAs
>>
>> http://rs.tdwg.org/ontology/voc/Common#versionedAs
>>
>> This points from the "thing that changes" to the current version.
>> i.e. the version that has identical metadata to itself. Anyone who
>> caches the data for the current version of the LSID can know which
>> version they have so if it becomes retrospectively important to get
>> back to the actual version it is possible.
>>
>> Philosophically when do you version? Only the provider can say that a
>> change is significant enough to warrant a new version - but if you
>> have gone to the trouble of implementing version control you may as
>> well do it for any change. Only the data provider can say whether the
>> "thing that changes" has changed so much that it is no longer the
>> same thing.
>>
>> Personally I believe this approach nails the versioning issues.
>>
>> There is the perennial debate about whether an LSID points to a
>> physical object or not (when it doesn't have byte stream associated
>> with it). The answer is easy. It points to a digital object. If you
>> doubt this try destroying a physical specimen and then asking whether
>> you should do away with the LSID and associated data? Clearly you
>> would maintain a record of something you once had so that you could
>> still return the data. Likewise if you gave the specimen to another
>> institution you would maintain a record of having had it but would,
>> hopefully, link to the new institutions record of it.
>>
>> Hope this is helpful.
>>
>> Roger
>>
>>
>>
>> On 3 Jun 2007, at 15:08, Paul Kirk wrote:
>>
>>> Anybody got any views (strong, otherwise or proxy for others views)
>>> on whether the LSID should refer to data+metadata or just metadata?
>>>
>>> From where I sit, closer to physical objects than bits in a bit
>>> stream, I favour the former. Take names for example. Strings of
>>> characters and spaces whose form is governed by Codes and one of
>>> the means, if not the primary mean, by which we communicate
>>> (verbally, in print or electronically) about biodiversity. For
>>> LSIDs applied to names my understanding is that they must resolve
>>> to an unchanging bit stream representing the name (we implemented
>>> this in Index Fungorum 1st May 2005 when we set up the demo
>>> resolver) but the associated metadata may change. If I'm correct on
>>> this one how does it work for LSIDs only resolving metadata, which
>>> is not fixed. I know Roger tried to explain this one to me but I'm
>>> still not sure it's entirely logical.
>>>
>>> I think I'm with Rod on the LSIDs for specimens - they do not
>>> represent the physical object but are a sort of digital substitute
>>> (or substitutes) of that object.
>>>
>>> And I also support Rods view that we should as far as possible
>>> avoid the duplication of GUIDs. Thus, for names it appears logical
>>> (although I must declare an 'interest' here so others may see a
>>> conflict) that the globally recognized nomenclators (IPNI, IF,
>>> ZooBank (soon), the bacterial list, the algal list, the virus
>>> database - I forget the acronyms here) be charged with providing
>>> these GUIDs (currently as LSIDs) for all of us to use. And
>>> following on from that, the 'institution' which is charged with
>>> providing the digital representation of specimens is the
>>> institution which is the custodian of the physical object.
>>>
>>> Regards,
>>>
>>> Paul
>>>
>>> From: Roderic Page [mailto:r.page at bio.gla.ac.uk]
>>> Sent: Sun 03/06/2007 12:03
>>> To: Weitzman, Anna
>>> Cc: Richard Pyle; Paul Kirk; Jason Best; tdwg-guid at lists.tdwg.org
>>> Subject: Re: [tdwg-guid] First step in implementing LSIDs?[Scanned]
>>>
>>> I think we need to be clear what gets an LSID (or a GUID in
> general).
>>>
>>> Some of the things listed by Anna are digital records, such as an
>>> image. It seems simplest to give these GUIDs that identify the
>>> image, with metadata linking the image to the thing the image
>>> depicts (there are existing RDF vocabularies to do this).
>>>
>>> Some things listed, such as a specimen, are physical objects. These
>>> are different from digital objects, and they way in which GUIDs
>>> that identify real things are handled has caused all manner of
>>> discussion (see  http://www.w3.org/DesignIssues/HTTP-URI and
>>> related pages bookmarked at http://del.icio.us/rdmpage/303). LSIDs
>>> don't handle this well, unless we rely on metadata saying "the
>>> thing identified by."
>>>
>>> So, at least on this level to say that all seven things get the
>>> same GUID is clearly a non starter.
>>>
>>> Relationships between things can be easily specified in metadata
>>> ("is part of", "depicts", "is kind of").
>>>
>>> The final issue is GUID reuse, that is, if somebody uses a INOTAXA
>>> record, they should at a minimum refer to the INOTAXA LSID. This
>>> would particularly apply to aggregators such as GBIF, who should
>>> not present their own identifiers unless GBIF has actually created
>>> the data. You often state "presumably shortly also available to
>>> GBIF in some form". It's not clear to what that means, but if it's
>>> GBIF because INOTAXA serves it, then I think GBIF should use
>>> INOTAXA LSIDs to refer to INOTAXA records.
>>>
>>> Clearly, generating a plethora a new, effectively local ids
>>> (masquerading as global) is not a recipe for progress. If we don't
>>> reuse GUIDs we are wasting our time.
>>>
>>> Regards
>>>
>>> Rod
>>>
>>>
>>>
>>>
>>>
>>> On 2 Jun 2007, at 18:53, Weitzman, Anna wrote:
>>>
>>>> Hi Rich (et al.),
>>>> I'm going to join this particular discussion  in spite of the fact
>>>> that I have not been able to follow the entire GUID discussion
>>>> over the past couple of years and I may be repeating things that
>>>> have been resolved.
>>>>
>>>> Let's continue to investigate whether an LSID applies to the
>>>> physical specimen or the database record (or both?).
>>>>
>>>> What about the record(s) for that same physical object in the
>>>> literature?  As we mark up literature, we are going to generate
>>>> LSIDs for specimen records that will need to be resolved to be
>>>> related to the same physical object (in a collection) and the data
>>>> record (usually in that same collection's database).
>>>>
>>>> Let's look at the example that Chris Lyal and I are contemplating
>>>> as we work on implementing an INOTAXA pilot to show in Bratislava:
>>>> 1) a weevil specimen here at USNM (a type described in the BCA)
>>>> 2) a record for it in the museum's database (we do have a type
>>>> database for insects, and it will be available in a year or two),
>>>> available on the museum's website, through GBIF, and through
> INOTAXA
>>>> 3) a record from digitized and parsed BCA in INOTAXA (presumably
>>>> shortly also available to GBIF in some form)
>>>> 4) a record for the same weevil from a paper published in the
>>>> 1950s available through INOTAXA (presumably shortly also available
>>>> to GBIF in some form)
>>>> 5) a record for that weevil from a paper published in the 1990s
>>>> available through INOTAXA  (presumably shortly also available to
>>>> GBIF in some form)
>>>> 6) a published image (or series of images) in the paper from the
>>>> 1990s -- but now also digitized and made available through INOTAXA
>>>> (presumably shortly also available to GBIF in some form)
>>>> 7) a digitized image (or series of images) made in our imaging
>>>> project and made available through the museum's database, INOTAXA,
>>>> GBIF and MorphoBank
>>>>
>>>> Either each of these (1-7) will need to have its own LSID (or an
>>>> equivalent in the case of the specimen itself) or they will all
>>>> need to have the same LSID.  If the former, they will all have to
>>>> resolve to the same parent LSID--is this for the specimen or the
>>>> record in its home database?--in order for the overall
>>>> biodiversity information system to really work.
>>>>
>>>> Or let's take that a step further and make that a fish, where not
>>>> only is there a record in the museum's database with its LSID, but
>>>> that same record for the same fish that was imported some years
>>>> ago into FishBase (now out of date perhaps, but still available to
>>>> GBIF and via Fishbase).  At the time, it was imported without an
>>>> LSID and FishBase has (presumably) assigned it's own LSID...
>>>>
>>>> Or let's say that someone else digitized their copy of the same
>>>> BCA volume and followed the INOTAXA (taXMLit) and assigned yet
>>>> another LSID for the specimen record...is that really the same
>>>> 'record' or different from the one in #3?
>>>>
>>>> I would like to think that in the long run we do not need multiple
>>>> LSIDs for records that refer to the same specimen or record (as
>>>> long as we can be truly certain that they are 'the same'.  After
>>>> all, the literature markup has a whole series of unique IDs for
>>>> its various parts already, so can't we refer to 'the use of LSID
>>>> 123 in workID 987' or 'the use of LSID 123 on pageID 456 in workID
>>>> 987'?
>>>>
>>>> There are a lot of IDs here, but unless every collection database
>>>> already has an LSID that we can 'grab' and use in INOTAXA we are
>>>> going to have to create our own LSIDs and count on a community
>>>> resolver to sort it all out (and even if that were true, not all
>>>> the specimens that we are going to be referring to from INOTAXA
>>>> have been put in electronic form anyplace else, so we will have to
>>>> assign LSIDs at least temporarily--Paul did not mention how they
>>>> are going to deal with the Zoological name LSIDs as at least a
>>>> temporary solution--but I assume that they have a similar problem).
>>>>
>>>> I'm sure I don't know what the best solution is, but that's what
>>>> I'm counting on the computer scientists in this group to tell me.
>>>> I just hope they tell me soon, since we're going to need answers
>>>> soon!
>>>>
>>>> Cheers,
>>>> Anna
>>>>
>>>> Anna L. Weitzman, PhD
>>>> Botanical and Biodiversity Informatics Research
>>>> National Museum of Natural History
>>>> Smithsonian Institution
>>>>
>>>> office: 202.633.0846
>>>> mobile: 202.415.4684
>>>> weitzman at si.edu
>>>>
>>>> ________________________________
>>>>
>>>> From: tdwg-guid-bounces at lists.tdwg.org on behalf of Richard Pyle
>>>> Sent: Sat 02-Jun-07 5:08 AM
>>>> To: 'Paul Kirk'; 'Jason Best'; tdwg-guid at lists.tdwg.org
>>>> Subject: RE: [tdwg-guid] First step in implementing LSIDs?[Scanned]
>>>>
>>>>
>>>>
>>>>
>>>> Paul and List,
>>>>
>>>> First, I should clarify something about my earlier post.  I wrote
>>>> at the
>>>> start of Scenario 3:
>>>>
>>>> "3) Issue data-less LSIDs without using the revision ID feature,
>>>> and track
>>>> data change history separately from the LSIDs"
>>>>
>>>> That should have been "...and track *metadata* change history
>>>> separately
>>>> from the LSIDs" (metadata, not data).
>>>>
>>>>> So, without making things too complicated as we 'start to walk'
>>>>> in this domain of biodiversity informatics my vote is for a
>>>>> variation of scenario 3) from Rich. The reason I vote for this
>>>>> is that in the fullness of time, and the 'herb.IMI' database
>>>>> has already started this, much of the metadata with be
>>>>> LSIDs and it's correctness (i.e. sorting out typos etc) will
>>>>> be delegated to the entities who issue those LSIDs. As IPNI
>>>>> improves the quality of the metadata associated with the
>>>>> LSIDs they issue (and if I understand correctly they do use
>>>>> the scenario 3) from Rich) so the quality of the metadata
>>>>> associated with a 'herb.IMI' LSID improves. The reason I
>>>>> prefer the data + metadate 'model' is that in this instance
>>>>> the data is fixed ... who changes collection/accession
>>>>> numbers? ... so perfect for this role. Even if a collection
>>>>> moves to a new owner the original data need not 'disappear'
>>>>> in the same way that DOI's move with the objects as book and
>>>>> journal titles change from one publisher to another.
>>>>
>>>> So...if I understand correctly, you differ from my scenario 3 in
>>>> that you do
>>>> generate data-bearing LSIDs for specimens, but the data part is
>>>> limited to
>>>> only the Accession number, not the complete set of data fields
>>>> associated
>>>> with the record -- correct?  So, in effect, the object LSID
>>>> actially applies
>>>> to is the binary accession number, not the "concept" of the
>>>> specimen.  I can
>>>> imagine in this case that the LSID can be thought of as
>>>> representing the
>>>> "concept of the specimen" because the accession number itself is a
>>>> surrogate
>>>> for the physical specimen.  The only thing that concerns me about
>>>> this
>>>> approach is that there is a non-zero incidence of accidental
>>>> duplicate
>>>> catalog numbers within a given collection, and possibly errors in
>>>> associating catalog numbers.  For example, if the computer
>>>> database for a
>>>> collection had an error created by a technician who, for example,
>>>> entered
>>>> the metadata for accession number IMI1234569 by mistake, when it
>>>> should have
>>>> been IMI1234596 (and vice versa), then branding the accession
>>>> number as
>>>> "data" for the LSID means that the LSID technically *must* stay
>>>> with the
>>>> accession number (not the specimen associated with the metadata
>>>> for that
>>>> LSID), after the error is discovered.  Not a huge problem, but
> could
>>>> surprise people who had indexed the LSID before the error was
>>>> discovered,
>>>> who then came back to resolve it again after the error was fixed
>>>> (i.e., they
>>>> would get totally wrong information).  Given how rare this problem
>>>> is likely
>>>> to be (against a backdrop of many far more likely problems we will
>>>> have to
>>>> overcome), I don't see this as a strong reason not to proceed with
>>>> your
>>>> plan.
>>>>
>>>>> Final point, the 'data' is the 'herb.IMI' accession number;
>>>>> in context this is a GUI because of the existence of Index
>>>>> Herbariorum. So, our data will be 123456 not IMI123456
>>>>> because ... in the fullness of time we will include an
>>>>> Index Herbariorum LSID to 'identify' the 'institutional
>>>>> acronym' element of the metadata.
>>>>
>>>> Is the binary data for the accession number in 8-bit, or 16-bit?
> I'm
>>>> assuming 8-bit would be fine, as I suspect all collections would
> have
>>>> accession numbers that can be rendered with 256-character ASCII.
>>>> Is there
>>>> any "wrapper" to the number as binary data, or is it a straight
>>>> ASCII binary
>>>> representation (e.g.:
>>>> 001100010011001000110011001101000011010100110110 for
>>>> "12345")?
>>>>
>>>> I'm not sure I follow the logic of how embedding the accession
>>>> number as
>>>> data for the LSID allows the LSID to move to a new owner.  I would
>>>> think the
>>>> opposite. Isn't it likely that the new owner would create their own
>>>> accession number for the specimen?  In this case, they would be
>>>> forced to
>>>> generate a new LSID if they were following the same practice of
>>>> encoding the
>>>> accession number as "data", rather than metadata.
>>>>
>>>> Also, wouldn't it make more sense to include the acronym (IMI) as
>>>> part of
>>>> the data for the LSID? At least that way the "12345" would have
>>>> *some*
>>>> context.
>>>>
>>>> Finally, this approach would work only for collections where there
>>>> is a
>>>> strict 1:1 correlation between accession numbers and specimen
>>>> objects for
>>>> which an LSID is desired.
>>>>
>>>> Thanks for your comments -- this thread is already forcing me to
>>>> think about
>>>> things in a way I hadn't thought of them before.
>>>>
>>>> Aloha,
>>>> Rich
>>>>
>>>> Richard L. Pyle, PhD
>>>> Database Coordinator for Natural Sciences
>>>>   and Associate Zoologist in Ichthyology
>>>> 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
>>>>
>>>>
>>>>
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>>>
>>> ----------------------------------------
>>> Professor Roderic D. M. Page
>>> Editor, Systematic Biology
>>> DEEB, IBLS
>>> Graham Kerr Building
>>> University of Glasgow
>>> Glasgow G12 8QP
>>> United Kingdom
>>>
>>> Phone: +44 141 330 4778
>>> Fax: +44 141 330 2792
>>> email: r.page at bio.gla.ac.uk
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>>>
>>>
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----------------------------------------
Professor Roderic D. M. Page
Editor, Systematic Biology
DEEB, IBLS
Graham Kerr Building
University of Glasgow
Glasgow G12 8QP
United Kingdom

Phone: +44 141 330 4778
Fax: +44 141 330 2792
email: r.page at bio.gla.ac.uk
web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
iChat: aim://rodpage1962
reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html

Subscribe to Systematic Biology through the Society of Systematic
Biologists Website: http://systematicbiology.org
Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/
Find out what we know about a species: http://ispecies.org
Rod's rants on phyloinformatics: http://iphylo.blogspot.com
Rod's rants on ants: http://semant.blogspot.com



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