[tdwg-guid] LSID metadata persistence (or lack thereof)
Dave Vieglais
vieglais at ku.edu
Sun Jul 15 07:50:54 CEST 2007
Hi Chuck,
if XML is disallowed as a data format that can be returned using
getData() operation, then should we also disallow any data format
where the same information can be represented in alternate byte
streams (images, documents, source code, etc.)? Perhaps a better
option is to create a new method getDataRepr() (get data
representation) or perhaps getDataInstance() or something like that
where the data is guaranteed to be be consistent between calls even
if the byte stream can not. This would allow sufficient flexibility
for implementors to be less concerned with the very low level details
of the implementation and not reduce the actual utility of the LSID
system since the referenced data can still be guaranteed to be
consistent.
Just a reminder as well, thus far the discussions about LSIDs seem to
have been very focussed on the specific requirements of GBIF, which
is all good but there are other systems which are currently using
LSIDs (as mentioned by Matt) or can benefit greatly from a consistent
GUID scheme. It would be great if the LSID use guidelines that are
derived during the TDWG process also remain relevant and useful to
the broader community.
Dave V.
On Jul 15, 2007, at 12:28, Chuck Miller wrote:
> Ricardo,
> I disagree on your assertion of consensus on a couple of points.
>
> On 2) there is no consensus/decision on whether XML can be returned
> from a getData call. I asked this question and it has not been
> answered. We could disallow XML as an allowed format for getData
> and allow it only for getMetadata.
>
> We do not have consensus and actually have disagreement on "We
> shouldn't for example return the bare scientific
> name of a species in the getData() call just because that can be
> immutable" because "the name itself is in the metadata" I for
> one believe that we cannot avoid returning a scientific name byte
> stream in the getData for an LSID for a scientific name. That
> requirement is fundamental to what we need for biodiversity data.
> Pragmatically and empirically, names and specimens/observations are
> THE most fundamental data objects existing today in the databases
> published by GBIF. So if we can't put LSIDs on names, we have
> failed to enable one of the most fundamental needs of this
> community. If the definition of LSIDs needs to be amended to
> enable that, then so be it.
>
> Chuck
>
> From: tdwg-guid-bounces at lists.tdwg.org on behalf of Ricardo Pereira
> Sent: Fri 7/13/2007 8:12 PM
> Cc: tdwg-guid at lists.tdwg.org
> Subject: Re: [tdwg-guid] LSID metadata persistence (or lack thereof)
>
> Folks,
>
> Thanks much to all of you who replied to my post. All the posts
> were
> really relevant to our discussion.
>
> Before we go ahead, however, let us stop for a minute to try and
> summarize the points we agree upon and the points in which there is
> still significant controversy.
>
> I believe that we reached consensus in the following issues:
>
> 1) We do agree that *LSID metadata is not required to be persistent*
> (i.e. clients cannot assume it is immutable). See note [1].
>
> 2) We should not force XML representations of data to be byte
> identical
> just to return that in the LSID getData() call. We must find
> another way
> to fulfill this requirement.
>
> 3) We should not try to return something in the LSID getData() call
> just
> for the sake of it. We shouldn't for example return the bare
> scientific
> name of a species in the getData() call just because that can be
> immutable and thus fulfill the requirement from the LSID spec. This is
> counterproductive because the name itself is in the metadata
> already and
> no client would gain anything from calling getData() in this case.
>
>
> We have also raised new issues that may be worth discussing (in
> their own separate thread if possible):
>
> 4) We "may" bend the immutability rule of LSID getData() to our
> benefit
> and accept data that is not byte stream identical, but only
> "semantically" identical (depending on content type maybe). If we do
> this, we may use the LSID getData() call more effectively to identify
> real datasets such as matrices, identification keys, etc.
>
> 5) As Brian pointed out, we may need to revisit what we call data and
> metadata. We have been using the LSID getMetadata() call to return
> what
> some people may call data (taxon names, specimens, collections).
> And we
> forgot completely that there may be other kinds of data out there that
> may be returned in the getData() call and that those still need
> metadata
> to describe them. I think this may be worth discussing in a
> separate thread.
>
> Did I leave anything out? If so, please let us know by replying to
> my post and adding a short entry to either list above.
>
> Cheers,
>
> Ricardo
>
>
>
> Notes:
> -------
>
> [1] Matt may disagree with me here, but my point is that we can't
> force
> all authorities (i.e. data providers) to keep perfect archives of all
> versions of their databases given a heterogeneous and distributed
> environment we operate in. While some may want to provide this
> feature,
> other providers may not want or be able to.
>
>
> Richard Pyle wrote:
> > It seems to me that there is a third method to resolving the
> problem:
> >
> > When we want to identify an object that is itself digital in
> nature (e.g., a
> > database record, or a binary data file such as a PDF, JPG, ASCII,
> Unicode,
> > or whatever), we resolve said binary object via getData(). If,
> for some
> > reason, we change the exact bit-sequence of that digital/binary
> object
> > (e.g., color-correct an image, change a text string from ASII to
> Unicode, or
> > whatever...), we assign a new LSID to it (whether that "new" LSID
> differs
> > from the "old" LSID only via the optional "Revision" part of the
> LSID, or
> > via a new Object Identification part, is a topic for another
> debate).
> >
> > When we want to identify an object that does not itself have a
> digital
> > manifestation -- like a physical object (e.g., specimen or a
> particular
> > printed copy of a publication) or an abstract/conceptual object
> (e.g., a
> > taxon name, a taxon concept, a geographica place, or a cited
> publication) --
> > then we return *nothing* in response to getData(), and we treat
> all the
> > attributes of said physical/abstract/conceptual object of
> interest to us as
> > metadata.
> >
> > If there are cases where certain metadata elements of an object
> without an
> > inherent digital existence need to persists (and there are), yet
> we also
> > want to allow modifications to metadata elements without the need to
> > generate new identifiers for the underlying object (and we do) --
> then we
> > deal with those within our own community via adopted standards
> and best
> > practices.
> >
> > I would disagree strongly with bending the existing LSID
> standard, and would
> > just as strongly favor working within its existing framework
> (which, I
> > think, we can). I would also disagree with the practice of
> embedding XML
> > documents as "data" for an LSID, unless the LSID is intended to
> represent
> > the XML document itself (in which case there might be a different
> LSID to
> > represent the database record that was used to generate the XML
> document;
> > and yet another LSID to represent the abstract concept that the
> database
> > record was created to represent -- like a taxon name, for example).
> >
> > If we want to use LSIDs to pass around XML packages (that are not
> rendered
> > as RDF) about abstract objects (e.g., taxon names), why doesn't our
> > community define within our semantic vocabulary something along
> the lines of
> > "TCS_XML", which can be established as a standard metadata
> component for
> > LSIDs assigned to taxon concepts (i.e., abstract objects,
> identified by
> > "data-less" LSIDs). The exact bytestream of the content of that
> metadata
> > element can change, without changing its canonical rendering.
> >
> > I'm beginning to suspect (strongly) that I am completely missing
> some
> > fundamental point here -- and perhaps is is the same point that
> underlies
> > the apparent antagonism towards LSIDs in general (which I do not
> yet share).
> > But I am fairly certain we are dealing with some level of
> miscommunication
> > here.
> >
> > Aloha,
> > Rich
> >
> >
> >> -----Original Message-----
> >> From: tdwg-guid-bounces at lists.tdwg.org
> >> [mailto:tdwg-guid-bounces at lists.tdwg.org] On Behalf Of P.
> >> Bryan Heidorn
> >> Sent: Friday, July 13, 2007 12:48 PM
> >> To: Dave Vieglais
> >> Cc: tdwg-guid at lists.tdwg.org
> >> Subject: Re: [tdwg-guid] LSID metadata persistence (or lack
> >> thereof)[Scanned]
> >>
> >> 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 at 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 at lists.tdwg.org on behalf of
> >>>>>>>
> >> Chuck Miller
> >>
> >>>>>>> Sent: Fri 13/07/2007 19:03
> >>>>>>> To: Dave Vieglais
> >>>>>>> Cc: tdwg-guid at 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 at ku.edu]
> >>>>>>> Sent: Friday, July 13, 2007 12:42 PM
> >>>>>>> To: Chuck Miller
> >>>>>>> Cc: Ricardo Pereira; tdwg-guid at 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 at lists.tdwg.org [mailto:tdwg-guid-
> >>>>>>>> bounces at lists.tdwg.org] On Behalf Of Ricardo Pereira
> >>>>>>>> Sent: Friday, July 13, 2007 9:47 AM
> >>>>>>>> To: tdwg-guid at 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 few
> >>>>>>>> outstanding 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 metadata
> >>>>>>>> persistence. First, let me remind you of a corollary
> >>>>>>>>
> >>>>>>> established by
> >>>>>>>
> >>>>>>>> the LSID specification:
> >>>>>>>>
> >>>>>>>> Corollary 1: LSIDs are not guaranteed to be
> >>>>>>>>
> >>>>>>> resolvable
> >>>>>>>
> >>>>>>>> indefinitely.
> >>>>>>>>
> >>>>>>>> In other words, there is no guarantee that one will
> >>>>>>>>
> >>>>>>> always 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'm
> >>>>>>>>
> >>>>>>> talking
> >>>>>>>
> >>>>>>>> about from other two related concepts (which we'll not
> >>>>>>>>
> >>>>>>> discuss in
> >>>>>>>
> >>>>>>>> this thread):
> >>>>>>>>
> >>>>>>>> 1) Persistence of Assignment: Once assigned to an
> >>>>>>>>
> >>>>>>> object,
> >>>>>>>
> >>>>>>>> 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 an
> >>
> >>>>>>>> LSID (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 LSID
> >>>>>>>>
> >>>>>>> metadata
> >>>>>>>
> >>>>>>>> (what is returned by the getMetadata call) or the
> >>>>>>>>
> >> lack thereof.
> >>
> >>>>>>>> A use case associated with metadata persistence is when
> >>>>>>>>
> >>>>>>> someone
> >>>>>>>
> >>>>>>>> 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 any
> >>>>>>>>
> >>>>>>> other
> >>>>>>>
> >>>>>>>> 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 nor
> >>>>>>>> persistent.
> >>>>>>>>
> >>>>>>>> The consequence of this corollary is that, if you need to
> >>>>>>>>
> >>>>>>> refer
> >>>>>>>
> >>>>>>>> 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 metadata
> >>>>>>>> associated 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 an
> >>
> >>>>>>>> additional 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 is
> >>>>>>>>
> >>>>>>> persistent 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
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> tdwg-guid mailing list
> >>>>>>>> tdwg-guid at lists.tdwg.org
> >>>>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-guid
> >>>>>>>>
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> >>>>>>> P Think Green - don't print this email unless you really
> need to
> >>>>>>>
> >>>>>>>
> >>>>>>>
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> >>>>>>>
> >>>>>> --Robert A. Morris
> >>>>>> Professor of Computer Science
> >>>>>> UMASS-Boston
> >>>>>> ram at cs.umb.edu
> >>>>>> http://bdei.cs.umb.edu/
> >>>>>> http://www.cs.umb.edu/~ram
> >>>>>> http://www.cs.umb.edu/~ram/calendar.html
> >>>>>> phone (+1)617 287 6466
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