[Psidev-ms-dev] FW: PSI-MS CV updated

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________________________________

From: Eric Deutsch 
Sent: Wednesday, May 07, 2008 12:46 AM
To: psi...@li...
Cc: Eric Deutsch
Subject: PSI-MS CV updated

Hi everyone, I have just committed some changes to the psi-ms.obo file
in CVS, taking care of:

- Adding some terms from Jim S

- Adding new chromatogram tree for this new element

- A little bit of cleaning

- Took care of all open items in the term tracker, which will now be
obsoleted

- I poked around purgatory for a while and only found one term: "total
ion chromatogram ?" that I wanted to resurrect. I changed the name to
"total ion current chromatogram". There are maybe a few other nice terms
in there, but most of them aren't useful. Do we have clearance to
destroy the ones that are uncontroversially useless like "461:
additional description"? Some will definitely need some discussion if we
feel up to it.

- I would like to hand over the bear to whoever will edit it next. I
suggest:

+ Luisa delete/destroy/deprecate the units in common with the UO to
force us to start using the UO

+ Darren to start adding in the datatype and needs_units fields for
appropriate terms

Here's the diff for you to look over:

< def: "Three-character symbol m/z is used to denote the dimensionless
quantity formed by dividing the mass of an ion in unified atomic mass
units by its charge number (regardless of sign). The symbol is written
in italicized lower case letters with no spaces. Note 1: The term
mass-to-charge-ratio is deprecated. Mass-to-charge-ratio has been used
for the abscissa of a mass spectrum, although the quantity measured is
not the quotient of the ion's mass to its electric charge. The
three-character symbol m/z is recommended for the dimensionless quantity
that is the independent variable in a mass spectrum Note 2: The proposed
unit thomson (Th) is deprecated." [PSI:MS]

< synonym: "Mass To Charge Ratio" EXACT []

< synonym: "thomson" RELATED []

---

> def: "Three-character symbol m/z is used to denote the quantity formed
by dividing the mass of an ion in unified atomic mass units by its
charge number (regardless of sign). The symbol is written in italicized
lower case letters with no spaces. Note 1: The term mass-to-charge-ratio
is deprecated. Mass-to-charge ratio has been used for the abscissa of a
mass spectrum, although the quantity measured is not the quotient of the
ion's mass to its electric charge. The three-character symbol m/z is
recommended for the quantity that is the independent variable in a mass
spectrum Note 2: The proposed unit Thomson (Th) is deprecated." [PSI:MS]

> synonym: "Mass-to-charge ratio" EXACT []

> synonym: "Th" EXACT []

> synonym: "Thomson" EXACT []

257a259

> is_a: MS:1000460 ! unit

1176c1178

< name: q-tof micro

---

> name: Q-Tof micro

1182c1184

< name: q-tof ultima

---

> name: Q-Tof ultima

1329c1331

< name: dalton

---

> name: Dalton

1475c1477

< name: total ion chromatogram ?

---

> name: total ion current chromatogram

1477c1479,1481

< relationship: part_of MS:1000461 ! additional description

---

> synonym: "TIC chromatogram" EXACT []

> is_a: MS:1000524 ! data file content

> is_a: MS:1000626 ! chromatogram type

3223c3227

< def: "Binary Data Type." [PSI:MS]

---

> def: "A data array of values." [PSI:MS]

3224a3229

> relationship: part_of MS:1000625 ! chromatogram

3229c3234

< def: "M/Z Array." [PSI:MS]

---

> def: "A data array of mass divided by charge values." [PSI:MS]

3235c3240

< def: "Intensity Array." [PSI:MS]

---

> def: "A data array of intensity values." [PSI:MS]

3241c3246

< def: "Charge Array." [PSI:MS]

---

> def: "A data array of charge values." [PSI:MS]

3247c3252

< def: "Singal to Noise Array." [PSI:MS]

---

> def: "A data array of signal-to-noise values." [PSI:MS]

3254a3260

> relationship: part_of MS:1000625 ! chromatogram

3404c3410

< def: "Data processing attribute used to describe the type of data
processing performed on the data file." [PSI:MS]

---

> def: "Type of data processing performed on the data file." [PSI:MS]

3581a3588

> relationship: part_of MS:1000625 ! chromatogram

3720a3728

> synonym: "thresholding" EXACT []

3726c3734

< def: "Array of increasing time points." [PSI:MS]

---

> def: "A data array of relative time offset values from a reference
time." [PSI:MS]

3860a3869,3971

> [Term]

> id: MS:1000617

> name: wavelength array

> def: "A data array of electromagnetic radiation wavelength values."
[PSI:MS]

> is_a: MS:1000513 ! binary data array

> 

> [Term]

> id: MS:1000618

> name: highest wavelength value

> def: "Highest wavelength value observed in the uv/vis spectum."
[PSI:MS]

> is_a: MS:1000499 ! spectrum attribute

> 

> [Term]

> id: MS:1000619

> name: lowest wavelength value

> def: "Lowest wavelength value observed in the uv/vis spectrum."
[PSI:MS]

> is_a: MS:1000499 ! spectrum attribute

> 

> [Term]

> id: MS:1000620

> name: PDA spectrum

> def: "Spectrum generated from a photodiode array detector
(ultraviolet/visible spectrum)." [PSI:MS]

> is_a: MS:1000524 ! data file content

> is_a: MS:1000559 ! spectrum type

> 

> [Term]

> id: MS:1000621

> name: photodiode array detector

> def: "An array detector used to record spectra in the ultraviolet and
visable region of light." [PSI:MS]

> synonym: "PDA" EXACT []

> is_a: MS:1000026 ! detector type

> 

> [Term]

> id: MS:1000622

> name: Surveyor PDA

> def: "Surveyor PDA." [PSI:MS]

> is_a: MS:1000494 ! Thermo Scientific instrument model

> 

> [Term]

> id: MS:1000623

> name: Accela PDA

> def: "Accela PDA." [PSI:MS]

> is_a: MS:1000494 ! Thermo Scientific instrument model

> 

> [Term]

> id: MS:1000624

> name: inductive detector

> def: "Inductive detector." [PSI:MS]

> synonym: "image current detector" EXACT []

> is_a: MS:1000026 ! detector type

> 

> [Term]

> id: MS:1000625

> name: chromatogram

> def: "The representation of detector response versus time." [PSI:MS]

> relationship: part_of MS:0000000 ! Proteomics Standards Initiative
Mass Spectrometry Ontology

> 

> [Term]

> id: MS:1000626

> name: chromatogram type

> def: "Broad category or type of a chromatogram." [PSI:MS]

> relationship: part_of MS:1000625 ! chromatogram

> 

> [Term]

> id: MS:1000627

> name: selected ion current chromatogram

> def: "Chromatogram created by creating an array of the measurements of
a specific single ion current at each time point." [PSI:MS]

> synonym: "SIC chromatogram" EXACT []

> is_a: MS:1000524 ! data file content

> is_a: MS:1000559 ! spectrum type

> is_a: MS:1000626 ! chromatogram type

> 

> [Term]

> id: MS:1000628

> name: basepeak chromatogram

> def: "Chromatogram created by creating an array of the most intense
peaks at each time point." [PSI:MS]

> is_a: MS:1000524 ! data file content

> is_a: MS:1000626 ! chromatogram type

> 

> [Term]

> id: MS:1000629

> name: low intensity threshold

> def: "Threshold below which some action is taken." [PSI:MS]

> is_a: MS:1000630 ! data processing parameter

> 

> [Term]

> id: MS:1000630

> name: data processing parameter

> def: "Data processing parameter used in the data processing performed
on the data file." [PSI:MS]

> is_a: MS:1000452 ! data transformation

> 

> [Term]

> id: MS:1000631

> name: high intensity threshold

> def: "Threshold above which some action is taken." [PSI:MS]

> is_a: MS:1000630 ! data processing parameter

> 

> [Term]

> id: MS:1000632

> name: Q-Tof Premier

> def: "Waters Q-Tof Premier MS." [PSI:MS]

> is_a: MS:1000126 ! Waters instrument model

> 