[MOBY-l] I3C Life sciences identifier

[Mark Wilkinson]

Hi Michael,

Brian Gilman, a BioMOBY project member and developer, is on the Technical
Development (committee?) for I3C.  It is through him that we have an inkling of
what the I3C is doing.

<personal_gripe>
The fact that it *is* difficult to discover what the I3C is doing (and your
obvious discomfort in revealing their plans speaks to this) seems to also make
the community as a whole uncomfortable in my experience...  Given that they (we)
are the ones who will be asked put these unknown standards into practice, I can
understand that there is some objection to not being involved in the creation
process... but that is just my personal opinion;  I am not speaking for anyone
else involved in the BioMOBY project.  Certainly, this is the main reason that
all BioMOBY development is being done in the open with as much community
involvement as possible.
</personal_gripe>


Iny any case, Brian gave us an overview of the LSID at the last MOBY meeting.  We
considered it, played with it, and revamped our ideas somewhat to accomodate some
of the attributes of the LSID, but we didn't adopt it whole-sale.  As we've said
on this mailing list several times, none of us want to ignore other standards,
and it may be that we migrate closer to, or adopt wholeheartedly, the I3C's LSID
in the future, particularly if it ever does become an accepted standard.  As of
this moment, however, we have a similar identifier in the MOBY scheme that seems
sufficient to do the job at hand.

Having said that, perhaps this is a good time to revisit this issue.  We
discounted the LSID fairly quickly at the last meeting in favour of the
MOBY-Triple, and moving the AuthURI (and potentially other attributes of a
message) into the MOBY-Envelope.  Does anyone think that we should reconsider
this before we go too far?

Cheers all!

Mark


Michael Gribskov wrote:

> I have received a draft spe for a "life sciences identifier" from the
> Interoperable Informatics Infrastructure Consortium.    This seems like an
> effort similar to moby and likely to be relevant.  the proposal specifically
> mentions that it addresses a problem with the DAS standard not handling "Query
> by Identifier".  I guess my questions are:
>
> Is this group in contact with moby?
> Does this proposal work/not work with the moby idea of a service?
>
> The gist of the proposal is as follows (for the whole text I think I should
> refer you to the authors; I am uncomfortable posting the whole thing)
>
> The Life Sciences Identifier (LSID) specification defines a scheme for
> location-independent naming of distributed biologically significant data items
> such as a sequence, a clone, a gene, etc., as well as a mechanism by which the
> identity associated with the names can be authenticated without strictly
> requiring a trusted third party. A biologically significant data item is
> defined as a named data element (a file, a database row, etc.) that operates
> in a distributed, federated environment and has a defined identity. LSID's are
> not meant to identify artifacts of implementation, like a database instance,
> or a server, which should be handled by other mechanisms such as JDBC URLs or
> WSDL.
> LSID names are a type of Location-independent Object Identifier (LOID) that
> uniquely identifies a biologically significant data item. The actual location
> (address) of a data item is determined by associating the LOID with one or
> more communication protocols and network endpoints. Collectively the set of
> communication protocols and network endpoints for a data item is called its
> ServiceDescription.
>
> URN:LOID:LSID:<authority>:<namespace>:<objectID>:<securityInfo>
>
> where
> <authority>
> The name of the organization that has defined the entity.
> <namespace>
> One or more statements that constrain the scope in which this
>                  id is evaluated.
> <objectID>
> An alphanumeric sequence that uniquely defines this object
>                   within this namespace, as defined by the authority.
> <securityInfo>
> An optional field containing a cryptographic identity.
> --
> Michael Gribskov
> San Diego Supercomputer Center & Dept. of Biology
> University of California, San Diego
> 9500 Gilman Drive
> La Jolla  CA  92093-0537
> Tel:858.534.8312   Fax:858.822.0873
> Email:gribskov at sdsc.edu    http://www.sdsc.edu/~gribskov
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l

--
--------------------------------
"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada