[Psidev-ms-dev] Using mzData in Software Applications

[Per <pe...@th...>]

Dear all,

as the project manager of, Proteios (http://www.proteios.org/) - a=20
bioinformatics software project in proteomics, I strongly greet the=20
standardization work for mzData. We are currently working on integrating=20
mzData in our (Proteios) data model.

Has anyone done this before - actually used mzData in a software applicatio=
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(apart from validation and the like with standard XML tools)? Putting mzDat=
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into practical use should be very much in the interest of PSI. Unfortunatel=
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there are, in my opinion, a few things which cause (uneccessary?)=20
difficulties in an implementation.

=46irst I would suggest not using common programming language keywords (e.g=
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"float") as element/attribute names. This is a possible source of confusion=
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and makes simple mapping onto source code data structures more difficult.

Secondly, I wonder wether there is any pressing need for keeping two separa=
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arrays in cases where the apparent meaning is rather one single array of=20
pairs (e.g. "intenArray", "mzArray"). The schema does not enforce the same=
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length on these two arrays. I also wonder what the purpose of the attribute=
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length is. Can't it be removed, since the length is implicitely given by th=
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number of subelements? Consider the following excerpt from a valid(!) mzDat=
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XML-file:

        <mzArray length=3D"15">
          <float>100</float>
          <float>500</float>
        </mzArray>
        <intenArray length=3D"7">
          <float>10</float>
          <float>100</float>
          <float>20</float>
        </intenArray>

Kind Regards,
Per G=E4rd=E9n

=2D-=20
Per G=E4rd=E9n
Lund Swegene Bioinformatics Platform
Complex Systems Division
Lund University
Sweden
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phone: +46 46 2229229
fax:=20
e-mail: pe...@th...=20
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