Re: [Psidev-ms-dev] Errors in example files

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

Hi Marc,

I'm afraid you're jumping the gun a bit here. The documents you mention 
used older versions of the CV. It seems to be:
http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo?revision=1.84&view=markup
for PLGS and
http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo?revision=1.75&view=markup
for tiny.pwiz

This version difference explains the validation problems you're seeing. 
The integer value types were then obsoleted and the intensity term 
hadn't been renamed. It's up for debate whether these examples should be 
updated to use the newest CV, but the files are valid the way they are 
now. It's good to catch this though because it's something a validator 
will have to deal with. You can't validate a file using an old CV 
against the newest CV and expect it to be error-free. At the same time, 
I expect you use some compile-time magic for the CV like we do in pwiz 
so supporting older versions of the CV could be troublesome. I'm not 
sure how to fix the problem, but I can diagnose it. :)

On another note, it was a pain in the ass to link up the CV version to 
the CVS version. We should definitely, definitely, definitely put RCS 
keywords in the OBO and mapping files so that we can match up the 
CVS/SVN revision to the OBO/mapping file itself. This will add a line like:
remark: $Id: psi-ms.obo 1.42 2009-08-14 22:12:04Z chambm $
to the OBO file and
<-- $Id: ms-mapping.xml 142 2009-08-14 22:12:04Z chambm $ -->
to the mapping file.

Are there any objections to the RCS keywords?

-Matt


Marc Sturm wrote:
> Hi all,
>
> I updated our semantic validator and found that two example files are 
> not entirely valid:
>
> 1) plgs_example.mzML
>
> Error: CV term must have a unit: MS:1000042 - intensity
> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
> 'peak intensity'
> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
> the value type 'MS:1000521 ! 32-bit float'.
> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
> the value type 'MS:1000521 ! 32-bit float'.
> Error: CV term must have a unit: MS:1000042 - intensity
> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
> 'peak intensity'
> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
> the value type 'MS:1000521 ! 32-bit float'.
> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
> the value type 'MS:1000521 ! 32-bit float'.
> Error: CV term must have a unit: MS:1000042 - intensity
> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
> 'peak intensity'
> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
> the value type 'MS:1000521 ! 32-bit float'.
> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
> the value type 'MS:1000521 ! 32-bit float'.
> Error: CV term must have a unit: MS:1000042 - intensity
> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
> 'peak intensity'
> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
> the value type 'MS:1000521 ! 32-bit float'.
> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
> the value type 'MS:1000521 ! 32-bit float'.
> Error: CV term must have a unit: MS:1000042 - intensity
> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
> 'peak intensity'
> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
> the value type 'MS:1000521 ! 32-bit float'.
> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
> the value type 'MS:1000521 ! 32-bit float'.
> Error: CV term must have a unit: MS:1000042 - intensity
> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
> 'peak intensity'
> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
> the value type 'MS:1000521 ! 32-bit float'.
> Error: Binary data array of type 'MS:1000516 ! charge array' cannot have 
> the value type 'MS:1000521 ! 32-bit float'.
>
> 2) tiny.pwiz.1.1.mzML
>
> Error: CV term must have a unit: MS:1000042 - intensity
> Error: Name of CV term not correct: 'MS:1000042 - intensity' should be 
> 'peak intensity'
>
> Best,
>   Marc
>
>
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