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

[Eric D. <ede...@sy...>]

Hi Matt, the agree-upon rule here is that the cvParams should always
refer to the most detailed concept, and the value attribute should
*only* be filled if there is a scalar value associated with the concept
that cannot be in the CV itself.  So:

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<cvParam cvLabel=3D"MS" accession=3D"MS:1000554" name=3D"LCQ Deca" =
value=3D""/>

<cvParam cvLabel=3D"MS" accession=3D"MS:1000529" name=3D"Instrument =
Serial
Number" value=3D"23433"/>

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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".

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However, "instrument serial number" is the most specific concept in the
CV, and thus the actual SN is the value.

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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.

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Regards,

Eric

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________________________________

From: psi...@li...
[mailto:psi...@li...] On Behalf Of
Matthew Chambers
Sent: Tuesday, August 07, 2007 9:40 AM
To: psi...@li...
Subject: [Psidev-ms-dev] cvParams using name attribute as value

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I'm a little confused about the parameters which use the accession
number as a kind of value instead of the accession number identifying a
variable and then using the value attribute to assign the value.  I
don't understand why:

<cvParam cvLabel=3D"MS" accession=3D"MS:1000130" name=3D"Positive Scan"
value=3D""/> (from mzML)

Is preferable to:

<cvParam cvLabel=3D"psi" accession=3D"PSI:1000037" name=3D"Polarity"
value=3D"positive"/> (from mzData)

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There are other examples of this as well.  What's the logic here?

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-Matt Chambers