psidev-ms-dev

[Psidev-ms-dev] FW: PSI-MSS WG call Monday

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

Hi everyone, the PSI Mass Spectrometry Standards Working Group call is
Monday July 21 at 9am PDT:

 

http://www.timeanddate.com/worldclock/fixedtime.html?day=21&month=7&year
=2008&hour=17&min=0&sec=0&p1=136

 

+ Germany: 08001012079

+ Switzerland: 0800000860

+ UK: 08081095644

+ USA: 1-866-314-3683

+ Generic international: +44 2083222500 (UK number)

access code: 297427

 

The agenda will be to review some recent discussions, the mzML
implementers table and other items about the CV and such.

 

Topics:

 

- MIAPE example document

- Other example documents

- CV

- CV template updates to vendors

- Documentation

- Web site

- mzML support information table

- Validator

- Amsterdam

- Next call

 

Thanks,

Eric

 

[Psidev-ms-dev] Current mapping file

[Marc S. <st...@in...>]

Hi all,

i was looking for the mapping file (CV to XML schema) and did not find 
it on the website.
Is this intended or was it simply forgotten? I think it should be easily 
available.

I did find several differing  versions of the mapping file in the CVS 
and SVN.
Now i'm not sure which one to use. Can you please point me to the most 
recent one?

Thanks,
  Marc

Re: [Psidev-ms-dev] Current mapping file

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

This is the only version I'm aware of and it was updated to the latest 
syntax last week:
https://psidev.svn.sourceforge.net/svnroot/psidev/psi/mzml/validator/ms-mapping.xml

I volunteered to go through and flesh out the rules but haven't gotten 
to it yet; this is partly because there are many terms in the CV that I 
don't know where they belong!

-Matt


Marc Sturm wrote:
> Hi all,
>
> i was looking for the mapping file (CV to XML schema) and did not find 
> it on the website.
> Is this intended or was it simply forgotten? I think it should be easily 
> available.
>
> I did find several differing  versions of the mapping file in the CVS 
> and SVN.
> Now i'm not sure which one to use. Can you please point me to the most 
> recent one?
>
> Thanks,
>   Marc
>
>   

Re: [Psidev-ms-dev] Current mapping file

[Marc S. <st...@in...>]

Hi Matt and all others,

thanks for the up-to-date link.
The other version I found is at: 
http://psidev.cvs.sourceforge.net/psidev/psi/psi-ms/mzML/schema/ms-mapping.xml?view=log

I have several questions/comments regarding the mapping file.

Comment 1:
There is no mapping for the "/mzML/run" tag

Comment 2:
There is no mapping for the 
"/mzML/run/spectrumList/spectrum/spectrumDescription/precursorList/precursor/isolationWindow" 
tag

Comment 3:
There is no mapping for the "data processing parameter" terms (MS:1000630)

Question 1:
According to the mapping file the "ms level" term (MS:1000511) should be 
under "spectrumDescription", but is under "spectrum" in the tiny1 example.
Which one is right?

Best,
  Marc


P.S.:
I attached a small XSL script I use to visualize the mapping file.
Perhaps it it useful for others as well.
You simply have to add the absolute path to the XSL script to the 
mapping, then you can visualize the file in a web browser:

<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" 
href="file:///C:/Desktop/Projekte/OpenMS/PSI - 
mzML/Mapping/ms-mapping.xsl"?>
...

Re: [Psidev-ms-dev] Current mapping file

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

Hi Marc, thanks for the feedback. I have added a direct link to this
file on the mzML information page, so it is easier to find. Thanks for
send the XSL file. We'll add that, too.

Lennart has reported that they have built a working validator at the
EBI, using their other new development, a stand-alone jmzML component
(minimal memory footprint Java object model for reading mzML), and that
they will soon release both, and he will email the list at that point.

Hopefully your comments and questions will be addressed as the new
version is released.

Thanks!
Eric


> -----Original Message-----
> From: psi...@li...
[mailto:psidev-ms-dev-
> bo...@li...] On Behalf Of Marc Sturm
> Sent: Monday, July 21, 2008 6:50 AM
> To: Mass spectrometry standard development
> Subject: Re: [Psidev-ms-dev] Current mapping file
> 
> Hi Matt and all others,
> 
> thanks for the up-to-date link.
> The other version I found is at:
> http://psidev.cvs.sourceforge.net/psidev/psi/psi-ms/mzML/schema/ms-
> mapping.xml?view=log
> 
> I have several questions/comments regarding the mapping file.
> 
> Comment 1:
> There is no mapping for the "/mzML/run" tag
> 
> Comment 2:
> There is no mapping for the
>
"/mzML/run/spectrumList/spectrum/spectrumDescription/precursorList/precu
rs
> or/isolationWindow"
> tag
> 
> Comment 3:
> There is no mapping for the "data processing parameter" terms
(MS:1000630)
> 
> Question 1:
> According to the mapping file the "ms level" term (MS:1000511) should
be
> under "spectrumDescription", but is under "spectrum" in the tiny1
example.
> Which one is right?
> 
> Best,
>   Marc
> 
> 
> P.S.:
> I attached a small XSL script I use to visualize the mapping file.
> Perhaps it it useful for others as well.
> You simply have to add the absolute path to the XSL script to the
> mapping, then you can visualize the file in a web browser:
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <?xml-stylesheet type="text/xsl"
> href="file:///C:/Desktop/Projekte/OpenMS/PSI -
> mzML/Mapping/ms-mapping.xsl"?>
> ...

Re: [Psidev-ms-dev] Current mapping file

[Lennart M. <len...@eb...>]

Hi Marc,


> thanks for the up-to-date link.
> The other version I found is at: 
> http://psidev.cvs.sourceforge.net/psidev/psi/psi-ms/mzML/schema/ms-mapping.xml?view=log 

Well spotted. I have now deleted this from CVS, and remarked in the log 
comment of the commit that the files should be obtained from the psidev 
SVN instead, along with the path to the validator configuration files.


> I have several questions/comments regarding the mapping file.
> 
> Comment 1:
> There is no mapping for the "/mzML/run" tag

Correct, I couldn't easily find anything that we require or expect 
there, so I let the rule out. Maybe there should be one or more rules 
added for this location, but fleshing out the mapping file is still a 
work in progress. You're very welcome to make suggestions, actually.


> Comment 2:
> There is no mapping for the 
> "/mzML/run/spectrumList/spectrum/spectrumDescription/precursorList/precursor/isolationWindow" 
> tag

Correct, we should add a meaningful rule here.


> Comment 3:
> There is no mapping for the "data processing parameter" terms (MS:1000630)

Correct again; needs to be added.


> Question 1:
> According to the mapping file the "ms level" term (MS:1000511) should be 
> under "spectrumDescription", but is under "spectrum" in the tiny1 example.
> Which one is right?

Good question. Can't remember off the top of my head what this should 
be. So you can see: there's work yet to be done on the mapping file!


Essentially, my main effort in these matters right now is spent on 
getting our reference validator up and running. Once that is achieved, 
the mapping file can be refined as we go along (the whole thing is 
descriptively configured from the XML file, so no code needs changing).

I think we should probably have a conference call dedicated to the 
mapping file at a point in the near future, but that is open to discussion.

Regardless, it would be good to have the reference validator out there 
first, so people are free to play with the mapping rules and instance 
documents. At the EBI, we're ironing out the last bugs in the validator 
now (while the mzML validator itself is simple and consists of nearly 
trivial code, this is only because (i) we have this rather complex but 
minimal memory footprint jmzML component that effectively uses an mzML 
file as a cache file, and (ii) we build the entire back-end on the 
generic PSI validator framework, which is a very complicated suite of 
modules that are high-tech codepieces in their own right -- this 
framework is also used by the PSI-MI people, for instance).


Cheers,

lnnrt.

Re: [Psidev-ms-dev] Current mapping file

[Marc S. <stu...@gm...>]

Hi Lennart,

i'll inform you if i find other dangling ends in the mapping file.
i'm only 70% through with out mzML implementation.

Best,
  Marc

Lennart Martens wrote:
> Hi Marc,
>
>
>   
>> thanks for the up-to-date link.
>> The other version I found is at: 
>> http://psidev.cvs.sourceforge.net/psidev/psi/psi-ms/mzML/schema/ms-mapping.xml?view=log 
>>     
>
> Well spotted. I have now deleted this from CVS, and remarked in the log 
> comment of the commit that the files should be obtained from the psidev 
> SVN instead, along with the path to the validator configuration files.
>
>
>   
>> I have several questions/comments regarding the mapping file.
>>
>> Comment 1:
>> There is no mapping for the "/mzML/run" tag
>>     
>
> Correct, I couldn't easily find anything that we require or expect 
> there, so I let the rule out. Maybe there should be one or more rules 
> added for this location, but fleshing out the mapping file is still a 
> work in progress. You're very welcome to make suggestions, actually.
>
>
>   
>> Comment 2:
>> There is no mapping for the 
>> "/mzML/run/spectrumList/spectrum/spectrumDescription/precursorList/precursor/isolationWindow" 
>> tag
>>     
>
> Correct, we should add a meaningful rule here.
>
>
>   
>> Comment 3:
>> There is no mapping for the "data processing parameter" terms (MS:1000630)
>>     
>
> Correct again; needs to be added.
>
>
>   
>> Question 1:
>> According to the mapping file the "ms level" term (MS:1000511) should be 
>> under "spectrumDescription", but is under "spectrum" in the tiny1 example.
>> Which one is right?
>>     
>
> Good question. Can't remember off the top of my head what this should 
> be. So you can see: there's work yet to be done on the mapping file!
>
>
> Essentially, my main effort in these matters right now is spent on 
> getting our reference validator up and running. Once that is achieved, 
> the mapping file can be refined as we go along (the whole thing is 
> descriptively configured from the XML file, so no code needs changing).
>
> I think we should probably have a conference call dedicated to the 
> mapping file at a point in the near future, but that is open to discussion.
>
> Regardless, it would be good to have the reference validator out there 
> first, so people are free to play with the mapping rules and instance 
> documents. At the EBI, we're ironing out the last bugs in the validator 
> now (while the mzML validator itself is simple and consists of nearly 
> trivial code, this is only because (i) we have this rather complex but 
> minimal memory footprint jmzML component that effectively uses an mzML 
> file as a cache file, and (ii) we build the entire back-end on the 
> generic PSI validator framework, which is a very complicated suite of 
> modules that are high-tech codepieces in their own right -- this 
> framework is also used by the PSI-MI people, for instance).
>
>
> Cheers,
>
> lnnrt.
>
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