[Psidev-ms-dev] instrument manufacturer in CV

[Kessner, D. E. <Dar...@cs...>]

Hi all,

 

Just wanted a clarification on the encoding of the instrument
manufacturer.

 

In the example tiny*.mzML, we have:

 

<instrument>

  <cvParam cvLabel="MS" accession="MS:1000554" name="LCQ Deca"
value=""/>

  ...

</instrument>

 

In the CV we have the following branch:

- "instrument description"

  - "model by vendor"

    - "Thermo Fisher Scientific"

      - "Thermo Finnigan"

        - "LCQ Deca"

 

Is this the intended procedure for determining the instrument
manufacturer?

  1) look for a cvParam child of "model by vendor"   <find "LCQ Deca">

  2) walk up the branch until you get to the immediate child of "model
by vendor"  <walk back to "Thermo Fisher Scientific">

 

Or do we want to encode the manufacturer as a separate CV term in the
<instrument> element?

 

 

One other thing, the Thermo tree looks like:

 

- "Thermo Fisher Scientific"

  - "Finnigan MAT"

    - some instruments

  - "Thermo Electron"

    - one instrument

  - "Thermo Finnigan"

    - some instruments

  - "Thermo Scientific"

    - more instruments

 

Perhaps this tree should be flattened like the other vendors CV trees?

 

 

Darren

 

 

 

Darren Kessner

Scientific Programmer

Dar...@cs...

310-423-9538

 

Spielberg Family Center for Applied Proteomics

Cedars-Sinai Medical Center

http://www.sfcap.cshs.org/

 

 

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