Re: [Psidev-ms-dev] TraML::Interpretation and Modification: - attributes as cvParams?

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

Hi Matt, comments/questions below...



> From: Matthew Chambers [mailto:mat...@va...]

>

> I suggest the Interpretation::primary and Modification::*MassDelta

> attributes be changed to cvParams.

>

> The primary attribute could still be

> a boolean, but I also suggest that it change to a rank. If it was a

> rank, multiple interpretations could be rank 1, which seems to me to be

> a reasonable use case (it's a reason NOT to use a transition).



Okay, I'm fine with changing this to a CvParam. Instead of:

  <Interpretation primary="true">

    <CvParam cvRef="MS" accession="MS:1001220" name="frag: y ion"/>

    <CvParam cvRef="MS" accession="MS:1000903" name="product ion series
ordinal" value="8"/>

    <CvParam cvRef="MS" accession="MS:1000904" name="product ion m/z delta"
value="0.03"/>

  </Interpretation>

We'll have:

  <Interpretation>

    <CvParam cvRef="MS" accession="MS:100xxxx" name="fragment interpretation
rank" value="1"/>

    <CvParam cvRef="MS" accession="MS:1001220" name="frag: y ion"/>

    <CvParam cvRef="MS" accession="MS:1000903" name="product ion series
ordinal" value="8"/>

    <CvParam cvRef="MS" accession="MS:1000904" name="product ion m/z delta"
value="0.03"/>

  </Interpretation>

Yes?





> For modification, I think that optional double-valued attributes are

> very annoying for an object model. How does a program test if the value

> is not set? It either needs a reference-centric implementation

> (Java/.NET but not C/C++) with null testing, or it needs an extra

> boolean attribute like "hasSomeValue".



I’m not sure I understand the problem here.  Is the problem that the
datatype is <double> and it’s optional? OR is it that it can be either
monoisotopicMassDelta or averageMassDelta and really should have one of the
two, although maybe that information is not known. So either one or the
other could be present. Or neither. But preferably not both. Although no
major reason why not both...



So taking a stab..



Instead of:

  <Modification location="1" monoisotopicMassDelta="15.994919">

    <CvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/>

  </Modification>

You want:

  <Modification location="1">

    <CvParam cvRef="MS" accession="MS:1000xxx" name="monoisotopic mass
delta" value="15.994919"/>

    <CvParam cvRef="UNIMOD" accession="UNIMOD:35" name="Oxidation"/>

  </Modification>



??



> Modification's optional location attribute could probably be mandatory.

> Or is it supposed to be omitted for terminal mods?



As far as I can see from the xsd and docs <Modification>’s location
attribute is a required attribute. Am I misunderstanding?





> -Matt

>

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