There seems to be two methods to resolving this problem.
One is to change the LSID definitions to allow semantic equivalence in the data and not require exact bit stream equivalence.
The other option is to change the data representation so that it is "easily" reduced to a repeatable canonical form. For example, it is almost as easy as saying where XML ordering does not specify order of elements, elements will be ordered alphabetically. Seems stupid but it almost works.. except where you have repeating elements with the same element name where it does not work.
It seems a little odd to bend the standards for the data being delivered to fit the requirement of the LSID spec. In theory, the other standard developers who set the data being delivered did not fix order because it did not matter.
This is different from Chuck's observation that the semantics of the element within some of the standards are insufficiently specified. So, what we mean is a darwin mode species name is just a string and nothing more now.
--Bryan
On Jul 13, 2007, at 5:18 PM, Dave Vieglais wrote:
I think we are all in agreement that the data and metadata referenced by an LSID remains unchanged (in the case of the metadata, semantic equivalence is a requirement for reasons such as outlined by Matt). My question is to do purely with the data that an LSID references through the getData() operation. The form of that data could be anything really - an encrypted byte stream, digital image, Open Office document, spreadsheet, xml document...
We all know that the same data can be represented many ways that are logically, semantically and functionally equivalent yet form a different set of bytes when serialized. Data expressed in XML is one example (is <a/> = <a /> = <a></a> ?). A pallet based image is another - the order of colors in the palette may be changed, and the pixel values adjusted to match the new palette order, but the image is still the same. There are many more simple examples that can be constructed that violate the unchanged bytes rule but for all practical and functional purposes the data are unchanged.
As mentioned previously, enforcing and implementing the unchanged bytes rule is not challenging. It is however quite different from stating that the data are returned unchanged. It is this that I, and I'm sure a lot of other implementors would appreciate consensus on.
Dave V.
On Jul 14, 2007, at 09:20, Matthew Jones wrote:
In terms of the metadata returned from an LSID, or any other digital identifier, there are definite cases where metadata must be semantically persistent in order to preserve the utility of data and accuracy of scientific results.
As a trivial example, given a set of observations collected at time t, one can represent the data for those observations in dataset D and the metadata for the dataset, including the time value t, in a metadata document M. In a later event, it is discovered that t was entered incorrectly, and needs to be adjusted, creating metadata document M'. That M and M' are not congruent is critical knowledge when analyzing data from D with data from another dataset D2. In other words, because there is no true distinction between data and metadata (any given piece of information can be stored in either location), a proper archive must be able to distinguish any changes in the data and any changes in the metadata.
That said, there are some metadata that could change with little or no impact on data interpretation (e.g., the spelling of the street on which Technician Tom gets his snailmail). But at the current time its impossible to distinguish this kind of metadata from the important kind in the general case of the existing metadata standards in use (e.g., FGDC BDP, ISO 19115, EML, GML, etc).
Our process in the KNB/SEEK/NCEAS and other ecological data archives is to give persistent identifiers to both data objects and metadata objects, and provide new identifiers when either changes.
Matt
Dave Vieglais wrote:
Hi Bob, Just because a standard is published does not mean that it is practical. Requiring that a set of bytes referenced by an LSID are unchanged has a lot of implications with respect to the implementation of data services. For example, if it is agreed to abide by the rule that the blob referenced by an LSID remains forever unchanged, then that implies that the data provider stores the data as a blob, rather than risking the process of reconstructing on the fly from some database, especially for the example of data expressed in XML where functionally identical objects (constructed using different DOM libraries for example) are not identical blobs. Asserting that two instances of an object with the same LSID are semantically equivalent is a vastly more complicated processes than asserting that the canonical representation of those instances are identical. Generally there can be defined a simple set of guidelines for constructing the canonical form of an object (eg. for xml http:www.w3.org/TR/xml-c14n ) whereas asserting semantic equivalence is an ongoing topic of research. Requiring identical blobs is certainly possible, but people need to be aware of the implications of such a requirement in the early stages of designing a system to support such a specification. My preference for the canonical form relaxes the implementation requirements considerably whilst still maintaining the integrity of the data and the intent of the LSID. regards, Dave V. On Jul 14, 2007, at 08:08, Bob Morris wrote:
This entire discussion confuses me. The LSID standard is published. Why is there a discussion of what an LSID should be? The standard requires that the data, as defined by the return of getData, to be identical for all resolutions of the LSID. From page 9 of the LSID spec:
" bytes getData (LSID lsid) bytes getDataByRange (LSID lsid, integer start, integer length) Metadata_response getMetadata (LSID lsid, string[] accepted_formats) Metadata_response getMetadataSubset (LSID lsid, string[] accepted_formats, string selector) The data retrieval services may implement all of the methods, or only methods for retrieving data, or only methods for retrieving associated metadata. The same LSID named data object must be resolved always to the same set of bytes. Therefore, all of the data retrieval services return the same results for the same LSID. The user has, however, the choice of which one of these to utilize depending on its location, known quality of service and other attributes. With metadata, the situation is different. Each data retrieval service can provide different metadata for the same LSID."
This doesn't seem very ambiguous to me, and doesn't have anything to do with imperfect storage of data or anything else about the physical or electronic world. If two calls to getData() with the same argument on two occasions to possibly two different resolution services do not yield the same set of bytes, then one or the other or both of those is not executing a compliant service response. Unless this discussion is really "Shall we call something other than the return of getData by the term 'data associated with the LSID?' there seems to be nothing to discuss.
Bob
On 7/13/07, Paul Kirk p.kirk@cabi.org wrote:
In an imperfect world there is no such thing as an 'identical- byte-stream' because the technology we use is imperfect ... the disk controllers which manage our bytes and the disk we use to store our bytes have recognized error rates. Perhaps I'm being a pedant in the above analysis but I was almost persuaded that except for digital objects (images, sounds) which can be data all other 'things' (names, specimen accession numbers) had to be metadata. This to me makes no sense in the real but imperfect world we live in. An LSID assigned to a name (e.g. Homo sapiens) is assigned to the name as data, not metadata. What is 'identical' here it that if the spelling has to change for any reason the new spelling gets a new LSID and the now incorrect spelling gets deprecated (but is still resolvable) with a pointer to the correct spelling/LSID in the metadata.
OK?
Paul
From: tdwg-guid-bounces@lists.tdwg.org on behalf of Chuck Miller Sent: Fri 13/07/2007 19:03 To: Dave Vieglais Cc: tdwg-guid@lists.tdwg.org Subject: RE: [tdwg-guid] LSID metadata persistence (or lack thereof)[Scanned]
Dave, What you say is true. But, I think we already have too many variations, subtleties, and reinterpretations which are endlessly debated.
The LSID standard would be simple, clear and consistent if we used the identical-byte-stream definition. The LSID would uniquely tag a persistent byte stream. A persistent byte stream is always the same thing without any further explanation or clarification.
The provider of an LSID byte-stream would need to commit to keeping that byte-stream persistent and not represent it in multiple ways, even though technically they could. If they can't commit to that, then it can't be an LSID byte-stream.
And in the name of simplicity and clarity, if they had to provide different byte-stream representations then they would have to assign a different LSID to each and use "SameAs" metadata.
Chuck
-----Original Message----- From: Dave Vieglais [mailto:vieglais@ku.edu] Sent: Friday, July 13, 2007 12:42 PM To: Chuck Miller Cc: Ricardo Pereira; tdwg-guid@lists.tdwg.org Subject: Re: [tdwg-guid] LSID metadata persistence (or lack thereof)
Hi Ricardo, Chuck, Asserting that the byte stream returned as data associated with an LSID should never change is perhaps a bit confusing from a programmatic view. There are for example many ways to represent data in xml that are identical from an information content point of view, but the byte streams could be very different.
Perhaps it might be better to state something like "the canonical representation of the data associated with an LSID must not change", or something to that effect?
Dave V.
On Jul 14, 2007, at 05:29, Chuck Miller wrote:
Ricardo,
Looking at this definition: "Persistence of LSID Data: The data associated with an LSID (i.e, the byte stream returned by the
LSID
getData call) must never change"
Perhaps this is a more straightforward way to conceive
LSIDs. The
LSID goes with a byte stream. It's that byte stream that
must stay
the same. So, if there is a byte stream associated with a collection that needs to stay the same, then whatever that byte stream happens to be is the data that gets an LSID assigned
to it.
That sure seems a clearer definition of what is data and what is metadata, rather than the issue of primary object and all that.
So we can create a new definition in the context of LSIDs:
Data is
a byte stream that is persistent, never changes and can have an LSID. Metadata is a byte stream is non-persistent, might change and is only associated with an LSID.
The institution who assigns an LSID can make their own decision about whether the byte stream being provided is persistent or
non-
persistent. By assigning an LSID to any byte stream,
whatever it
is, the institution is declaring it to be data and persistent.
So, in the example given of an observation record with a determination that needs to remain fixed and unchanged, by assigning an LSID to that observation+determination it would be "declared to be data" and unchangeable. A different
determination
would then be different data with a different LSID. That would provide a solution for those who want to employ it. Others
could
choose not to use it.
Chuck
From: tdwg-guid-bounces@lists.tdwg.org [mailto:tdwg-guid- bounces@lists.tdwg.org] On Behalf Of Ricardo Pereira Sent: Friday, July 13, 2007 9:47 AM To: tdwg-guid@lists.tdwg.org Subject: [tdwg-guid] LSID metadata persistence (or lack thereof)
Hi there folks, As Chuck mentioned a few weeks ago, we do have a fewoutstanding issues to address regarding LSIDs. I would like to discuss those one by one, in an orderly manner, and reach
consensus
as much as we can. Then we can sum them up in a TDWG standard, possibly by or shortly after the Bratislava conference.
The first issue I would like to discuss is LSID metadatapersistence. First, let me remind you of a corollary
established by
the LSID specification:
Corollary 1: LSIDs are not guaranteed to beresolvable
indefinitely.
In other words, there is no guarantee that one willalways be
able to retrieve the data associated with an LSID as the
authority
may choose (or be forced) not to resolve an LSID anymore.
Second, let me distinguish this kind of persistence I'mtalking
about from other two related concepts (which we'll not
discuss in
this thread):
1) Persistence of Assignment: Once assigned to anobject,
an LSID is indefinitely associated with it. The same LSID
cannot be
assigned to another object. Ever! The LSID may not be resolvable anymore, but it cannot be assigned to another object. This is established by the LSID specification.
2) Persistence of LSID Data: The data associated with anLSID (i.e, the byte stream returned by the LSID getData call)
must
never change. Although the LSID may not be resolvable anymore (according to corollary 1), the data associated with an LSID
must
never ever change. That's defined by the LSID spec, too.
What I want to discuss here is the persistence of LSIDmetadata
(what is returned by the getMetadata call) or the lack thereof.
A use case associated with metadata persistence is whensomeone
collects observation records (and implicitly, their
determinations)
and runs an experiment (a model or simulation) with it. This
person
may want to record the identifiers of the points used so that someone using the results of that experiment may refer back
to the
primary data, to validate or repeat it the experiment.
The bad news is that LSID identification scheme (or anyother
GUID that I know of) was not designed to guarantee metadata persistence, and thus it cannot implement the use case above by itself. To implement that use case, the specification would
have to
guarantee that the metadata (which we are using here as data) is immutable. But it doesn't.
Most of us wish that metadata was persistent, but it isn't.Many things can change in the metadata: a new determination, a mispeling that is corrected, many things. We just cannot
guarantee
that the metadata will look like it was sometime ago.
We then reach the following conclusion. Corollary 2: LSIDs metadata is not immutable norpersistent.
The consequence of this corollary is that, if you need torefer
back to a piece of information (metadata) associated with an
LSID,
exactly as it was when you got it, you must make a copy of
it, or
arrange that someone else make that copy for you.
In other words, a client cannot assume that the metadataassociated with an LSID today will be the same tomorrow. If the client does assume that, it may be relying on a false assumption and its output may be flawed.
If we are not happy with that conclusion, we may develop anadditional component in our architecture, an archive of some
sort,
to handle (meta)data persistence. That is exactly what the
STD-DOI
project (http://www.std-doi.de/) and SEEK (http:// seek.ecoinformatics.org) have done to some extent.
While we cannot guarantee that LSID metadata ispersistent nor
immutable, we can definitely document how the metadata have
changed
through metadata versioning. That's the topic of the next
thread.
We will move on to discuss metadata versioning as soon as we are done with metadata persistence.
Cheers,Ricardo
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