Re: [Psidev-ms-dev] cvParams using name attribute as value

[Mike C. <tu...@gm...>]

On 8/7/07, Eric Deutsch <ede...@sy...> wrote:
> <cvParam cvLabel="MS" accession="MS:1000554" name="LCQ Deca" value=""/>
>
> <cvParam cvLabel="MS" accession="MS:1000529" name="Instrument Serial Number"
> value="23433"/>
>
>
> So for the first, the term/concept is "LCQ Deca".  For the CV, one can learn
> that an "LCQ Deca" IS A "instrument model", and so there's no need (and is
> perhaps a little dangerous) to put "LCQ Deca" as a value of "instrument
> model".
>
>
> However, "instrument serial number" is the most specific concept in the CV,
> and thus the actual SN is the value.
>
>
> This was discussed at some length and this is the new way of doing things,
> that will be uniform across all PSI and FuGE implementations. At least, that
> is my understanding. This does mean that parsers need to be a little smarter
> and be "CV-aware". The parser/interpreter can no longer assume that there
> will be a term "instrument model" and look for its value.  But rather, the
> parser/interpreter must now look to see if any of the terms provided are a
> child of "instrument model" in the CV.

Actually, the parser really should not only check whether the term
provided *is* a child in the current CV, but also whether it ever
*will be* in a future version of the CV.  Unfortunately, the
technology required to make such a check is not yet available.  :-)

I'm not very familiar with how CV is supposed to work, but from this
example it appears that the namespaces for different kinds of things
have been merged together, and that there is an assumption that there
will be no collisions.  And that anything that doesn't currently have
a name basically doesn't exist.

In the example given of writing a parser, the task of extracting the
name of the instrument, given just the mzML file, is changed from
being trivial to being essentially impossible.  The mzML file becomes
meaningless in itself, and only has meaning relative to a particular
version of the CV, which the parser must have access to.

Am I misunderstanding something?

Mike