GUIDs, LSIDs, and metadata

[Kevin Richards]

Good points.  
A few comments I have:

I think LSIDs are assumed to solve all conflicts in the various datasets of taxonomic data.  However they are JUST resolvable IDs, anything else is infrastructure surrounding the LSID mechanisms.  An LSID refers to a specific set of bytes that resides on some computer somewhere.  The assumption that an LSID will refer to, for eaxample, a global 'taxon concept' that all other taxon records should point to, is not correct.  This relies on a system to be in place that provides the functionality for this global repository.

Also I feel one argument AGAINST LSIDs is that the initial investment in infrastructure is large, ie the development and setting up of authorities, etc.  So I think this would lean people away from LSIDs, bot towards them.  The advantage with the LSID mechanism, I think, is that it is flexible enough to not rely on existing software and internet configuration.

A GUID really needs to refer to a reasonably basic record, eg a name object rather than the entire taxon concept (although you could have a GUID for either).  This allows these individual components to be referenced from other systems/datasets without having to refer to and accept the enitre concept.  It is probably a good idea to map out which sort of taxonomic objects should get GUIDs and how they relate to other objects.

Kevin Richards

>>> deepreef at BISHOPMUSEUM.ORG 09/11/05 6:50 AM >>>
Lots of good discuccion points on GUIDs -- thanks, Rod.  I need to get two
little people to two different soccer (football) games soon, so I have no
time for an elaborate response.  But I do want to comment on one point,
which I have been thinking a great deal about lately:

> 7. I think the first priority for assigning GUIDs is museum specimens.
> For taxon names (if not concepts) this is trivial, given that most name
> databases have their own, internally unique ids (but not all -- those
> databases that use names as primary keys, or which don't expose integer
> identifiers will need to rethink their design).

I think it's critical that, whatever GUID system we establish for taxon
names (and concepts), we do it in the context of the next several decades of
informatic landscape; not just in the context of immediate needs or current
political climate.

As you said at the start of your message, GUIDs by themselves are trivial.
So the only real difference between establishing a system that is intuitive
for the current needs and a system that will serve longer-term future needs,
is a little bit of careful forethought.

Official taxon name registration already exists for one of the major Codes
of Nomenclature (Bacterial), and within the next fortnight we will see a
public announcement of a plan for registration in another of the major
Codes.  I predict that all Codes of nomenclature will implement mandatory
registration for all new names by about 2010, and for all "available" names
(i.e., since Linnaeus) within five to ten years thereafter.  So the
medium-term future landscape in this case will be one in which all names are
issued a GUID through their respective Commission of Nomenclature.

Further, it's not unreasonable to predict that sometime within the next few
decades we will converge on a unified "BioCode" for all organism names,
meaning that the longer-term landscape has a single set of taxon names.
Wouldn't it be nice, after that time, if we didn't have to forever maintain
legacy GUIDs? In other words, wouldn't it be nice if the established GUID
system for all taxon names were the same *now*, at the outset, so it's a
non-issue to combine them all as one set of GUIDs later on?

I'm not entirely sold on LSIDs, but it does seem that a lot of smart and
knowledgable people are leaning that way.  My hesitation is mainly that one
of the main reasons for leaning that way is that all sorts of software
already exists for resolving them, so there is less overhead in initial
implementation.  As long as LSID meet long-term needs, that shouldn't be a
problem.  But 50 years from now, I'm not sure how wise it will seem that the
universal GUID system adopted for biological data was influenced strongly by
the available software of the time.  Imagine being locked in now to a
universal system that was designed based on software that was available in
1955!

But, not being able to predict which GUID system will be the best in the
context of 2055, we really have no choice but to go with something that
makes a lot of sense now (which is justififable, in that it's also very
important that the delicate transition from no universal GUIDs to widespread
universal GUIDs will be best supported by keeping it as painless as possible
in the context of that transition time).

But I still suggest we do things in a way that maximally keeps our options
open.  For example, in the context of LSIDs, consider different paradigms
for registring the fish name, Mygenus myspecies Hyam (Hi, Roger! :-) )

One paradigm might have each major database create its own LSID:

urn:lsid:catalogoffishes.org:SPNO:123456
urn:lsid:gbif.org:ECAT:876543
urn:lsid:itis.gov:TSN:567890

But then we're burdoned with the task of cross-mapping each of these, and
also preserving the legacy IDs into perpetuity after we've eventually
converged on a single taxon name GUID system.

I was going to illustrate several other paradigms, but soccer departure time
approaches, so I'll cut to the chase.  In the LSID paradigm, I would propose
the following system:

urn:lsid:bioregistry.org:[Data Domain]:[randomly generated 64-bit integer]

The "bioregistry.org" part represents the decoupling of the GUID from the
institution that initially created the GUID.  It encompases all domains of
biological data (taxon names, concepts, specimens, etc.).  It could be
"tdwg.org" or "gbif.org", but we're not sure those organizations will be
around 50 or 100 years from now.  I imagine that GBIF would create and
manage the bioregistry.org domain for the near-term.

The "Data Domain" represents a tag for the main domain of data (e.g.
"Specimens", or "TaxonNames", or whatever the major information domains end
up being).

The randomly generated 64-bit integer would be unique across all data
domains, so that it, by itself, is unique within bioregistry.org (no time
now to explain the rationale for this...)

Gotta run....more later.

Aloha,
Rich

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