[MOBY-l] I3C Life sciences identifier

[chris dagdigian]

I've seen it but the proposal was sent to me personally; not any Open 
Bio lists that I've been following. Kudos to them for showing it around.

I3C and the Open Bioinformatics Foundation are pretty close. Actually we 
host their webserver (www.i3c.org) on the same machine as bioperl.org, 
biojava.org etc. etc.

I support what they are trying to do and in fact many of the most active 
I3C'ers are also invovled or affiliated with Open Bio projects.

One problem I have which makes me concerned of their future direction is 
the recent "lying by press release" that they did. If you look at the 
front page of http://www.i3c.org you will see an official annoucement 
talking about elections etc.

The truth of the matter is that nothing resembling any sort of real 
election actually occured from what I can tell. A group of big company 
reps basically decided amongst themselves to become the governing board.

Just my $.02. I'm not speaking for the OBF.

-Chris







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.


-- 
Chris Dagdigian, <dag at sonsorol.org>
Life Science IT & Research Computing Freelancer
Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
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