psidev-ms-dev

[Psidev-ms-dev] TraML 0.9.3 draft released

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

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.

 

Thanks,

Eric

----------------------------------

Eric Deutsch, Ph.D.
Institute for Systems Biology
1441 North 34th Street
Seattle WA 98103
Tel: 206-732-1397
Fax: 206-732-1260
Email: ede...@sy...
WWW: http://www.systemsbiology.org/Senior_Research_Scientists/Eric_Deutsch

 

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

[Fredrik L. <Fre...@im...>]

Hi,

I've updated the inclusion list example, found at the same URL as 
before. For some reason the openMS validator complains about protein 
accession (MS:1000885) and local retention time (MS:1000895) having 
values. Is this due to some mapping file or ontology issues? I cannot 
spot anything strange, but maybe someone else can explain this?

Thanks

Fredrik

Eric Deutsch wrote:
>
> 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.
>
> Thanks,
>
> Eric
>
> ----------------------------------
>
> Eric Deutsch, Ph.D.
> Institute for Systems Biology
> 1441 North 34th Street
> Seattle WA 98103
> Tel: 206-732-1397
> Fax: 206-732-1260
> Email: ede...@sy... <mailto:ede...@sy...>
> WWW: http://www.systemsbiology.org/Senior_Research_Scientists/Eric_Deutsch
>

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

[Andreas B. <be...@in...>]

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

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

[Steffen N. <sne...@ip...>]

On Tue, 2010-01-05 at 00:12 -0800, Eric Deutsch wrote:

> Please examine the materials and respond.

- The header line still refers to 0.9.2
- The documents mentions analysisXML in 2.2, 
  with an invalid URL.

- <Target> (include and exclude, for that matter) 
  doesn't have the notion of an m/z window:
  1) You might be not interested in everything below 200Da
  2) Depending on the instrument it might be necessary 
  to use broader isolation windows for sufficient 
  product ion intensities.
  
- <Target> (include and exclude, for that matter) 
  doesn't have the notion of <RetentionTime> to 
  (optionally) restrict a RT (window)

- 3.30 says "Precursor (Q1) of the transition" should add "target"

- <configuration> could allow an isolation width, 
  as an alternative to the mz min/max I mentioned above.
  mzML had some lengthy min/max vs. width discussions last year ...

- The name "Tra(nsition)ML" suggests that the format is 
  for (TripleQuad) MRM experiments. For "1.3 Use Cases" I'd like to add
  more explicitly the description of a tandemMS (and MS^n) run.

  To me, TraML can also describe a "method" for an MS run.
  For Bruker QTof, such a description lives in files such as 
  method.m/microTOFQAcquisition.method, but they're (so far)
  quite undocumented.

Yours,
Steffen

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409