Re: [Psidev-ms-dev] Example files

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On Fri, 2009-06-12 at 11:34 +0200, Marc Sturm wrote: 
> Error: CV term must have a unit: MS:1000515 - intensity array
> Error: CV term must have a unit: MS:1000515 - intensity array
The PDA is measuring absorbance of light by the sample.
Our machine software reports "milli-AU". 

My first guesses do not validate:

	Semantically validating mzML file:
	Error: Unit CV term not allowed: UO:0000186 - dimensionless unit of term MS:1000515 - intensity array
	Error: Unit CV term not allowed: UO:0000157 - light unit of term MS:1000515 - intensity array
	Error: Unit CV term not allowed: UO:0000187 - percent of term MS:1000515 - intensity array
	Failed: errors are listed above!

So I propose something like:

[Term]
id: XX:XXXXXXX
name: Absorbance Units
def: "A dimensionless logarithmic unit to measure the absorbance of light transmitted through a partially absorbing substance."
is_a: UO:0000186 ! dimensionless unit
maybe
is_a: ID: PSI:1000460 Name: Unit

where I am unsure whether that should go into MS:XXXXXXX or OU:XXXXXXX.
Once I have some CV Term I can use, I'll fix the MzMLFile_PDA.xml

Yours,
Steffen

* http://en.wikipedia.org/wiki/Absorbance
  Although absorbance does not have true units, 
  it is quite often reported in "Absorbance Units" or AU

* http://www.unc.edu/~rowlett/units/dictA.html
    absorbance unit (AU)

  a logarithmic unit used to measure optical density, the absorbance of
  light transmitted through a partially absorbing substance. If T is the
  percentage of light transmitted, then the absorbance is defined to be
  -log10 T absorbance units. An increase in absorbance of 1.0 AU
  corresponds to a reduction in transmittance by a factor of 10. If the
  absorbance is 1.0 AU then 10% of the light is transmitted; at 2.0 AU
  only 1% of the light is transmitted, and so on.

BTW, there are two different "percent" in the Ontologies:
ID: PSI:1000138 Name: Percent
and ID: UO:0000187 Name: percent

Yours,
Steffen

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
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