Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[GO] Re: necessary & sufficient

Sean Martin sjmm at us.ibm.com
Fri Mar 12 05:51:37 PST 2004


Hi Mark,
Very late in reply, but yes!

 I believe this is exactly the sort of use intended for LSID's. Similarly 
we can have generally shared LSID's to indicate exact data format or even 
format+context as well as generally shared LSID's that indicate the 
relationship between objects.. for instance the LSID 
urn:lsid:i3c.org:predicates:IsExactlyTheSameAs could be used in RDF (for 
example) to link items in two separate databases that have different names 
(which would be LSID's issued by their respective authorities). 

As a potential user of the LSID above, I can resolve it to read a text 
description of exactly what the authority (in this case the I3C, but it 
could be anyone) meant that particular relationship to express before I 
decide to use it. If it was an LSID that defined a format, there would be 
a format spec and examples available, similarly for evidence codes, you 
would have what ever reference is appropriate for that code according to 
the "authority" for it, just one click away. By settling on a (certainly 
growing) shared set of these "defining" LSID's, interoperability and 
linkage between data items is greatly facilitated as well as reducing 
ambiguity as far as possible. One nice feature of LSID's is that the 
definition of these "defining" LSID's can be widely distributed i.e. if 
there is not yet a code/format/relationship defined for the particular 
thing you are looking at, you are able to define it under your own 
authority and anyone later coming across it in your data will immediately 
be able to resolve it to find out exactly what was meant - and then reuse 
it themselves if appropriate. This is not to say you should not be careful 
to avoid duplicate definitions - although in the cases where this happens 
you now also have a formal way for expressing the equivalence of those 
definitions.

Kindest regards, Sean

--
Sean Martin
IBM Corp.




Mark Wilkinson <markw at illuminae.com> 
02/20/2004 04:36 PM

To
Michael Ashburner <ma11 at gen.cam.ac.uk>, Sean Martin/Cambridge/IBM at IBMUS, 
Martin Senger <senger at ebi.ac.uk>
cc
gofriends <gofriends at genome.stanford.edu>, rd120 at gen.cam.ac.uk, 
SLetovsky at aol.com, djs93 at gen.cam.ac.uk
Subject
Re: [GO] Re: necessary & sufficient






Hi Michael,

It just occurred to me that this is an instance where the use of LSID's
would be **highly** appropriate - assigning an LSID to represent each
evidence code would allow external databases to add their own evidence
code terms without fear of "collisions" with each other's use of
three-letter abbreviations.  Moreover, it would allow me, as a data
consumer, to resolve a new evidence code to it's intended meaning by
discovering the assigning authority and meta-data "automatically" rather
than having to know, a priori, *both* the data provider AND their naming
system...

CA$0.03

Mark


On Thu, 2004-02-19 at 04:08, Michael Ashburner wrote:
> The GO group have discussed this at great length on many occassions
> and we are agreed that we do not, as a GO Consortium, wish to 
proliferate
> evidence terms.
>
> However, it is quite feasible for any one database to increase the 
granularity
> of their evidence codes, as indeed has been done by TAIR, for their own 
use.
> All that must happen then is for there to be a mapping of these terms
> to the accepted GO evidence codes, and for this mapping to occur at the
> time gene_association tables are given to the GO site.
>
> Michael
>
> --
> This message is from the GOFriends moderated mailing list.  A list of 
public
> announcements and discussion of the Gene Ontology (GO) project.
> Problems with the list?           E-mail: 
owner-gofriends at geneontology.org
> Subscribing   send   "subscribe"   to gofriends-request at geneontology.org
> Unsubscribing send   "unsubscribe"  to 
gofriends-request at geneontology.org
> Web:          http://www.geneontology.org/
--
Mark Wilkinson <markw at illuminae.com>
Illuminae
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/go-friends/attachments/20040312/c0d2c7a2/attachment.html>


More information about the go-friends mailing list