Re: [Psidev-ms-dev] TraML 0.9.3 draft released

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

Hi Andreas, Fredrik, Steffen, et al. thank you for updating, examining,
and posting these problems.

I have just updated the various files for TraML 0.9.3 (forgive me for not
increasing the version number)

Changes:
- Added many datatype definitions to the CV
- Fixed attribute 'unitcvRef' to 'unitCvRef' for consistency
- Updated the documentation based on Steffen's comments. Note that the
documentation still has unfinished parts.

Open issues:
- Steffen mentioned retention time for inclusion lists. This may still be
a problem. Targets may refer to peptides and peptides may have retention
time information. However, the use case where one has an inclusion list
without reference to a peptide still does not allow a retention time. We
probably need to think about that some more.

So, please update and examine the latest posted files.

Thank you!
Eric


> -----Original Message-----
> From: Andreas Bertsch [mailto:be...@in...]
> Sent: Tuesday, January 05, 2010 3:58 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] TraML 0.9.3 draft released
>
> Hi Eric,
>
> > Hi everyone, TraML version 0.9.3 has been posted at the development
> web page:
> >
> > http://www.psidev.info/index.php?q=node/405
> >
> > The links to HTML documentation and examples files are all updated.
> >
> > Please examine the materials and respond.
> >
> > Major changes from 0.9.2:
> > - Elements CvList, Cv, CvParam now begin with lower case letter
> following mzIdentML
> > - Precursor and Product m/z values now specified with MS:1000827
> > - Interpretation elements no longer have primary= attribute but have
> required MS:1000926 attribute
> > - All elements now have a complexType definition
> > - I have attempted to use keys and keyRefs although they don't seem
> to be working
> >
> > Please update your implementations and example files and validators
> and report.
> I have updated the definitions of the fragmentation information terms
> and added the 'replaced_by' field to the obsoleted MaRiMba term in the
> ontology file. The OpenMS validator is also up to date. Unfortunately,
> it now reports more errors, concerning allowed values of some CV terms.
> Most of them should be added (Remember if the psi-ms.obo file contains
> a xref with the value-type the value MUST be present, and MUST NOT
> otherwise). I added value-types to the terms reported by Fredrik.
>
> - The attribute 'unitcvRef' should be 'unitCvRef', as it is in mzML and
> mzIdentML
> - Value-type fields should be added to some terms, I can fix that if
> you want.
>
> Unfortunately, I will not be able to attend the call today.
>
> Cheers,
> A.
>
>
> --
> Div. for Simulation of Biological Systems, WSI, University of Tuebingen
> Room C322, Sand 14, 72076 Tuebingen, Germany
> phone: +49-7071-29-70461 fax: +49-7071-29-5152
> http://www-bs.informatik.uni-tuebingen.de
>
>
>
>
>
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