[Psidev-ms-dev] Release candidate 3.46.0_rc3 of psi-ms.obo

[Gerhard M. <Ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 3.46.0_rc3 of the psi-ms.obo file.

As I notticed now, we have already a term (MS:1000138) for the 'percent 
collision energy'.
Also some new terms for describing SRM transitions are added now.


Changed CV terms in version 3.46.0_rc3 of psi-ms.obo:
=====================================================
************ 1) Changed the definition from
************    "Collision energy required to fragment an ion 
represented as a percent value." to
************    "Energy for an ion experiencing collision with a 
stationary gas particle resulting in dissociation of the ion in percent, 
normalized to the mass of the ion."
************ 2) Added the has_units relationship
[Term]
id: MS:1000138
name: percent collision energy
def: "Energy for an ion experiencing collision with a stationary gas 
particle resulting in dissociation of the ion in percent, normalized to 
the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000045 ! collision energy
relationship: has_units UO:0000187 ! percent


************ Changed name from "selected ion m/z" to "selected peptide 
ion m/z" (to make it more clear for use in SRM)
[Term]
id: MS:1000744
name: selected peptide ion m/z
def: "Mass-to-charge ratio of the ion selected for fragmentation." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
relationship: has_units MS:1000040 ! m/z


************ 1) Changed the definition from
************    "The intensity of the product ion." to
************    "The intensity of a single product ion."
************    to make clear the difference to the new term "average 
product ion intensity" (MS:1002226)
************ 2) Added the float value type
[Term]
id: MS:1001226
name: product ion intensity
def: "The intensity of a single product ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
synonym: "fragment ion intensity" EXACT []
is_a: MS:1001221 ! fragmentation information
relationship: has_units MS:1000131 ! number of detector counts
relationship: has_units MS:1000132 ! percent of base peak
relationship: has_units MS:1000814 ! counts per second
relationship: has_units MS:1000905 ! percent of base peak times 100



New CV terms in version 3.46.0_rc3 of psi-ms.obo:
=================================================
[Term]
id: MS:1002218
name: percent collision energy ramp start
def: "Collision energy at the start of the collision energy ramp in 
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! percent collision energy
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002219
name: percent collision energy ramp end
def: "Collision energy at the end of the collision energy ramp in 
percent, normalized to the mass of the ion." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000138 ! percent collision energy
relationship: has_units UO:0000187 ! percent

[Term]
id: MS:1002220
name: MRMaid
def: "A web-based SRM assay design tool whose transitions are generated 
by mining the millions of identified peptide spectra held in the EBI's 
PRIDE database." [PSI:PI]
is_a: MS:1000871 ! SRM software

[Term]
id: MS:1002221
name: MRMaid:peptide score
def: "Score in MRMaid to indicate the expected performance of the 
peptide in SRM." [PSI:PI]
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1002222
name: transition attribute
def: "Attribute associated with a SRM transition." [PSI:MS]
is_a: MS:1000547 ! object attribute
relationship: part_of MS:1000908 ! transition

[Term]
id: MS:1002223
name: peptide ion probability
def: "Probability of detecting peptide when parent protein is present." 
[PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! transition attribute

[Term]
id: MS:1002224
name: product ion probability
def: "Probability of detecting product ion when parental peptide ion is 
present." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1002222 ! transition attribute

[Term]
id: MS:1002225
name: product ion observed times
def: "The times the specific product ion has been observed in a series 
of experiments." [PSI:PI]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: MS:1002222 ! transition attribute

[Term]
id: MS:1002226
name: average product ion intensity
def: "Average value of product ion intensity in a collection of 
identified spectra." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001226 ! product ion intensity

[Term]
id: MS:1002227
name: product ion intensity standard deviation
def: "Standard deviation of product ion intensity in a collection of 
identified spectra." [PSI:PI]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001226 ! product ion intensity

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
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Phone:	+49(0)234/32-21006
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Email:	Ger...@ru...
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