[Psidev-ms-dev] Difference between purgatory / obsolete

[Steffen N. <sne...@ip...>]

Hi,

I didn't come across a halfway formal definition / distinction between 
OBSOLETE'ing stuff, and moving it to purgatory, although we had 
a thread on this here last year ("Marking CV terms obsolete")

Also I'd expect some process to make sure that stuff 
shoved into purgatory really should be obsoleted at some stage.

This has also implications on the validity of instance documents, 
because files which have some cvParam which IS_A "something" 
(where "something" is a MUST) are invalid once the cvParam 
is moved from "something" to "purgatory", *unless it also retains*
the original IS_A "something".

I found (grep -B 1 -A 1 "MS:1000479 ! purgatory" psi-ms.obo)
that there are Terms with a mix of:

	relationship: part_of MS:1000479 ! purgatory
	is_obsolete: true

	relationship: part_of MS:1000479 ! purgatory
	without is_obsolete

	is_a: MS:1000479 ! purgatory
	without is_obsolete

So: 

1) Why do we use purgatory in first place ?

2) Do we want a policy whether and how the CV is cleansed 
   and purgatory stuff marked OBSOLETE ?

3) How do we handle documents which become invalid 
   with these changes ?

4) Should these definitions/processes 
   become part of the spec documents ?

Yours,
Steffen

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
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