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

Paul Kirk p.kirk at cabi.org
Sun Jun 3 16:08:25 CEST 2007

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.


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.



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!


	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

		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

	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*

	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.


	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

	tdwg-guid mailing list
	tdwg-guid at lists.tdwg.org

	tdwg-guid mailing list
	tdwg-guid at lists.tdwg.org

Professor Roderic D. M. Page
Editor, Systematic Biology
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 <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 <http://ispecies.org/> 
Rod's rants on phyloinformatics: http://iphylo.blogspot.com <http://iphylo.blogspot.com/> 
Rod's rants on ants: http://semant.blogspot.com <http://semant.blogspot.com/> 

The information contained in this e-mail and any files transmitted with it is confidential and is for the exclusive use of the intended recipient. If you are not the intended recipient please note that any distribution, copying or use of this communication or the information in it is prohibited. 

Whilst CAB International trading as CABI takes steps to prevent the transmission of viruses via e-mail, we cannot guarantee that any e-mail or attachment is free from computer viruses and you are strongly advised to undertake your own anti-virus precautions.

If you have received this communication in error, please notify us by e-mail at cabi at cabi.org or by telephone on +44 (0)1491 829199 and then delete the e-mail and any copies of it.

CABI is an International Organization recognised by the UK Government under Statutory Instrument 1982 No. 1071.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.tdwg.org/pipermail/tdwg-tag/attachments/20070603/c354bda4/attachment.html 

More information about the tdwg-tag mailing list