[tdwg-guid] LSID metadata persistence (or lack thereof)
Richard Pyle
deepreef at bishopmuseum.org
Sun Jul 15 20:22:54 CEST 2007
I'm not sure I understand this fixation with the getData() call. Why is it
so important to use that call to retrieve bytestream information relating to
objects that are not themselevs inherently digital? Much of what we are
intereseted in within the biodiversity informatics community, in terms of
what we want to establish identifiers for, are not inherently digital
objects and therefore should NOT have any bytes returned for getData().
Some of our objects *are* inherently digital (PDFs, image files of various
formats, video clips, audio files, possibly Genbank sequences in a specified
format and encoding, etc.) To me, the distinction is very simple: is the
object that the LSID identifies a binary data file? If yes, then the binary
data become the data of the LSID. If no, then the LSID has no binary "data"
(sensu LSID Spec), and returns only metadata through getMetadata(). The
LSID spec refers to such LSIDs as "Abstract" (or sometimes "Conceptual")
LSIDs.
It's really not that complicated -- unless, as I suggested previously, I am
missing something fundamentally important.
I don't understand the advantage we gain by "force-fitting" some digitized
rendering of an otherwise non-digital object. Taxon Names (for example) have
no inherent digital manifestation. We create an artificial digital
representation of them by stringing ASCII or Unicode characters together in
a way that resembles (in principle) the characters otherwise represented by
ink on paper. But if we want to embed such a character string as "data" for
an LSID, then the LSID is teally an identifier for the *character string*
itself, NOT the "notion" or "idea" or "concept" of the taxon name. As a
taxonomist and biodiversity informatics manager, I have very little use for
LSIDs that identify specific charcter strings. I want an LSID that
itentifies the shared understanding of a taxon name -- not an
artificial/substitute rendering of the taxon name. I see no advantage to
creating one LSID for a text string that encodes a taxon name as UTF-8, and
another LSID for the same name encoded as UTF-16,and so on, and so on.
These variants are purely artificial from the perspective of what I want an
LSID for (i.e., the idea/notion/concept of a taxon name).
I do acknowledge that the idea of an "Abstract" LSID was really meant to
serve as an "umbrella" of sorts to tie together multiple data-bearing LSIDs.
The classic example is an image that can be represented as a RAW, a TIFF, or
a JPEG file format. Assuming all three image files derive from the same
shutter-release event of a camera, then the intended function of an
"Abstract" LSID is to serve to gather together the LSIDs established for
each of the three file formats of the "same" image. The images are the
"same" only in the conceptual -- i.e., that they all derive from the
shutter-release event. But the point is, the purpose of the "Abstract" LSID
is really intended to be a mechanism of organizing data-bearing LSIDs that
refer to different digital renderings of the "same thing". From the "LSID
Best Practices" website
(http://www-128.ibm.com/developerworks/opensource/library/os-lsidbp/), under
the heading "Abstract LSIDs":
"The abstract LSID provides the anchor point for software and users to
explore the metadata and obtain further pointers to all the concrete LSID
references that contain data, along with the data's exact relationship to
the abstract concept."
This implies that "Abstract" LSIDs should exist primarily to aggregate
data-bearing LSIDs.
For the most part, I don't think this is what we are really trying to do
when we want to assign LSIDs to non-digital objects like taxon names,
specimens, etc. So, in a sense, what I am advocating deviates a bit from
the intention of an "Abstract" LSID. But at least I'm not outright
violating the fundamental tenents of the LSID spec, like trying to apply a
single LSID to more than one bytestream returnable via getData().
So, again, I return to my original confusion: why all the fixation with the
getData() call?
The only reasons I can think of are:
1) Semantics (of the human communcation kind): We're uncomfortable thinking
of things like refering to the text string C-e-n-t-r-o-p-y-g-e (minus the
dashes) as being mere "metadata" for the angelfish genus described by Kaup
in 1860 -- when it just feels like the "actual" name to us (and hence should
be thought of as "data").
2) Persistence: We want to embed information as "data" for the LSID because
we want to make sure the "same information" is always there, and the LSID
spec emphasizes the permanent relationship between an LSID and its data.
The only trouble is, we want to define the word "same" in this context in a
way that is utterly incomprehensible (without all manner of comparison
algorithms) to a computer. *We* know that "Chaetodon" is the "same" as
"Chætodon", so we want a single LSID to refer to the genus name for
butterflyfishes described by Linnaeus in 1758. And we don't like being
required to always choose one rendering or the other to embed as the
bit-identical "data" for the LSID.
3) Performance(?): This is where I may be missing something fundamental.
Are there characteristics of the getData() call that are far superior to
getMetadata()?
As for number 1: all I can say is "get over it". Our unfortunate reality
in biodiversity informatics is a proponderence of homonymy -- not just in
taxon names, but in our human-mitigated communication lexicon as well.
As for number 2: We can deal with persistence through layers of standards
and convention within our community. Almost everything we talk about
involves an assumption of adherence to standards and conventions. If we
want persistent metadata, then we need to formalize a document detailing
which metadata elements should be mandatory and/or persistent and/or have
other properties that we as a community feel are important. This document
would also outline when metadata may be modified for a given LSID, vs. when
a new LSID should be generated, allowing certain metadata elements for each
to remain unchanged (e.g., perhaps one LSID for "Chaetodon" and another for
"Chætodon", for the object type "Digital Taxon Name Rendering"). The
document would also outline how multiple LSIDs should be cross-referenced to
each other (e.g., the two "DTNR" objects identified by two different LSIDs
in the previous example would both refer to the same Abstract LSID
established for the butterflyfish genus name described by Linnaeus in 1758).
As for number 3: I just hope someone can explain to me where I missed the
boat.
One final note: I do see a way that we can preserve the spirit of intent
for the "Abstract LSID" in our domain for things like Taxon Names. Rather
than explain it here, I follow up with another email describing it.
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
________________________________
From: tdwg-guid-bounces at lists.tdwg.org
[mailto:tdwg-guid-bounces at lists.tdwg.org] On Behalf Of Chuck Miller
Sent: Saturday, July 14, 2007 2:29 PM
To: Ricardo Pereira
Cc: tdwg-guid at lists.tdwg.org
Subject: RE: [tdwg-guid] LSID metadata persistence (or lack thereof)
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://
<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
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> tdwg-guid mailing list
>>>>>>> tdwg-guid at lists.tdwg.org
>>>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-guid
>>>>>>>
>>>>>>>
>>>>>>> P Think Green - don't print this email unless you really
need to
>>>>>>>
>>>>>>>
>>>>>>>
>>
******************************************************************
>>
>>>>>>> ******
>>>>>>> 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.
>>>>>>>
>>>>>>>
>>>>>>>
>>
******************************************************************
>>
>>>>>>> ********
>>>>>>> _______________________________________________
>>>>>>> tdwg-guid mailing list
>>>>>>> tdwg-guid at lists.tdwg.org
>>>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-guid
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> --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
>>>>>>
>>>>> _______________________________________________
>>>>> tdwg-guid mailing list
>>>>> tdwg-guid at lists.tdwg.org
>>>>> http://lists.tdwg.org/mailman/listinfo/tdwg-guid
>>>>>
>>> _______________________________________________
>>> tdwg-guid mailing list
>>> tdwg-guid at lists.tdwg.org
>>> http://lists.tdwg.org/mailman/listinfo/tdwg-guid
>>>
>> _______________________________________________
>> tdwg-guid mailing list
>> tdwg-guid at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-guid
>>
>
>
> _______________________________________________
> tdwg-guid mailing list
> tdwg-guid at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-guid
>
>
_______________________________________________
tdwg-guid mailing list
tdwg-guid at lists.tdwg.org
http://lists.tdwg.org/mailman/listinfo/tdwg-guid
More information about the tdwg-tag
mailing list