[Open-bio-l] open-bio URNs

[Matthew Pocock]

Hi,

Some of us have been having a discussion about using
URNs for biological entities like file formats,
alphabets and applications like blast. The upshot was
that LSIDs do not seem to be a good fit to a lot of
these problems.

I've checked in version 0.1 of a spec for open-bio
URNs. It is intended as a basis for discussion, and
although probably is 90% right, nothing is set in
stone.

The draft spec is in:
  pub.open-bio.org:/home/repository/obf-common
in module:
  obda-specs
in the directory:
  naming

As we develop code that uses these URNs and register
new identifiers with CVS, I'm sure that bugs in the
spec will make themselves apparent. Hopefully by the
next hackathon, this will all be done & dusted and we
can chalk it up as a very booring, but necisary
exercise in computer science, like learning how to set
up environment variables or install emboss.

We should push these URNs through the flat file
indexing spec (replacing the hackey list of supported
file types) and think about where else it would help
to have unique and unambiguous names for things.

Brian King sent me a couple of usefull links that
interested people should probably browse:

http://www.ietf.org/rfc/rfc3406.txt 
http://www.ietf.org/rfc/rfc3121.txt

Matthew

ps 2 open issues that we could do with discussing as a
group:

1) at the moment we're prefixing these things as
urn:open-bio.org:, but perhaps urn:open-bio: would be
better. We should decide upon this before considering
official registration of the URN namespace.

2) the registration process (putting files in CVS with
names starting with the URN) doesn't work very well as
URNs contain characters of significance to file
systems (: and /). We could stick these all into a
single file, but that may become practicaly quite hard
to manage. And, then we'd fight over the file format
(+1 for xml + schema). Also, multiple people editing
one file may cause CVS to throw wobblies. Any ideas?


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