psidev-ms-dev

[Psidev-ms-dev] mzML_idx's IndexType::name attribute

[Matthew C. <mat...@va...>]

Hello mzML fans,

Apparently, Mass++ is writing indexed mzML files (yay!), but it uses an 
unexpected "chroms" name to identify the chromatogram index (boo!). The 
mzML_idx XSD does not specify what are the possible values for that 
attribute. Obviously, it's impossible to write a reader that uses 
indexes if the indexes have been written with arbitrary names. It's of 
course possible to ignore the index in these cases, but we should nip 
this issue in the bud. We can release 1.1.1 to add the restriction. 
MzML.xsd wouldn't even change, just mzML_idx.xsd. Which leads to the 
question of whether we should bump mzML's version or not if only the idx 
wrapper changes...

-Matt

Re: [Psidev-ms-dev] mzML_idx's IndexType::name attribute

[Angel P. <an...@ma...>]

sounds like an issue for the validator. -a


On Fri, Dec 11, 2009 at 5:16 PM, Matthew Chambers <
mat...@va...> wrote:

> Hello mzML fans,
>
> Apparently, Mass++ is writing indexed mzML files (yay!), but it uses an
> unexpected "chroms" name to identify the chromatogram index (boo!). The
> mzML_idx XSD does not specify what are the possible values for that
> attribute. Obviously, it's impossible to write a reader that uses
> indexes if the indexes have been written with arbitrary names. It's of
> course possible to ignore the index in these cases, but we should nip
> this issue in the bud. We can release 1.1.1 to add the restriction.
> MzML.xsd wouldn't even change, just mzML_idx.xsd. Which leads to the
> question of whether we should bump mzML's version or not if only the idx
> wrapper changes...
>
> -Matt
>
>
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-- 
Angel Pizarro
Director, ITMAT Bioinformatics Facility

Re: [Psidev-ms-dev] mzML_idx's IndexType::name attribute

[Matthew C. <mat...@va...>]

What makes you say that? Can the validator even validate that attributes 
have certain string values? And as we agreed in Turku, mapping file 
changes constitute a version bump for mzML. We just never decided how to 
handle the index wrapper schema.

-Matt


Angel Pizarro wrote:
> sounds like an issue for the validator. -a
>
>
> On Fri, Dec 11, 2009 at 5:16 PM, Matthew Chambers 
> <mat...@va... 
> <mailto:mat...@va...>> wrote:
>
>     Hello mzML fans,
>
>     Apparently, Mass++ is writing indexed mzML files (yay!), but it
>     uses an
>     unexpected "chroms" name to identify the chromatogram index
>     (boo!). The
>     mzML_idx XSD does not specify what are the possible values for that
>     attribute. Obviously, it's impossible to write a reader that uses
>     indexes if the indexes have been written with arbitrary names. It's of
>     course possible to ignore the index in these cases, but we should nip
>     this issue in the bud. We can release 1.1.1 to add the restriction.
>     MzML.xsd wouldn't even change, just mzML_idx.xsd. Which leads to the
>     question of whether we should bump mzML's version or not if only
>     the idx
>     wrapper changes...
>
>     -Matt
>
>

Re: [Psidev-ms-dev] mzML_idx's IndexType::name attribute

[Angel P. <an...@ma...>]

On Mon, Dec 14, 2009 at 1:17 PM, Matthew Chambers <
mat...@va...> wrote:

> What makes you say that? Can the validator even validate that attributes
> have certain string values? And as we agreed in Turku, mapping file
> changes constitute a version bump for mzML. We just never decided how to
> handle the index wrapper schema.
>
>
Apologies I was not at Turku and admittedly did not read the summary notes
too carefully. I say it should be validator issue (in preference to a XML
schema change) to avoid a schema's version number change. In light of this
information,  it clearly will, so a schema level change is preferable.

-a



> -Matt
>
>
> Angel Pizarro wrote:
> > sounds like an issue for the validator. -a
> >
> >
> > On Fri, Dec 11, 2009 at 5:16 PM, Matthew Chambers
> > <mat...@va...
> > <mailto:mat...@va...>> wrote:
> >
> >     Hello mzML fans,
> >
> >     Apparently, Mass++ is writing indexed mzML files (yay!), but it
> >     uses an
> >     unexpected "chroms" name to identify the chromatogram index
> >     (boo!). The
> >     mzML_idx XSD does not specify what are the possible values for that
> >     attribute. Obviously, it's impossible to write a reader that uses
> >     indexes if the indexes have been written with arbitrary names. It's
> of
> >     course possible to ignore the index in these cases, but we should nip
> >     this issue in the bud. We can release 1.1.1 to add the restriction.
> >     MzML.xsd wouldn't even change, just mzML_idx.xsd. Which leads to the
> >     question of whether we should bump mzML's version or not if only
> >     the idx
> >     wrapper changes...
> >
> >     -Matt
> >
> >
>
>
> ------------------------------------------------------------------------------
> Return on Information:
> Google Enterprise Search pays you back
> Get the facts.
> http://p.sf.net/sfu/google-dev2dev
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>



-- 
Angel Pizarro
Director, ITMAT Bioinformatics Facility