[Psidev-ms-dev] Release candidate 3.35.0_rc1 of psi-ms.obo

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Dear proteomics community,

attached there's the release candidate 3.35.0_rc1 of the psi-ms.obo.

It contains new terms for first and second column elution times, the
terms for the multidimensional chromatography modulation description
and 4 new terms for ProteomeDiscoverer input parameters.
In addition the missing def items to some terms were added.

@Steve Robles: please check, if the new terms are appropriate for your need.

Changed CV terms in version 3.35.0_rc1 of psi-ms.obo:
=====================================================
************ Changed the definition from
************ The time of elution from a chromatographic column, relative 
to the start of the chromatography. -->
************ The time of elution from all used chromatographic columns 
(one or more) in the chromatographic separation step, relative to the 
start of the chromatography.
[Term]
id: MS:1000826
name: elution time
def: "The time of elution from all used chromatographic columns (one or 
more) in the chromatographic separation step, relative to the start of 
the chromatography." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

************ Added the def: item
[Term]
id: MS:1001007
name: Sequest:OutputLines
def: "Number of peptide results to show." [PSI:MS]
xref: value-type:xsd\:nonNegativeInteger "The allowed value-type for 
this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Added the def: item
[Term]
id: MS:1001009
name: Sequest:DescriptionLines
def: "Number of full protein descriptions to show for top N peptides." 
[PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Added the def: item
[Term]
id: MS:1001028
name: Sequest:SequenceHeaderFilter
def: "String in the header of a sequence entry for that entry to be 
searched." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Added the def: item
[Term]
id: MS:1001037
name: Sequest:ShowFragmentIons
def: "Flag indicating that fragment ions should be shown" [PSI:MS]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

************ Added the def: item
[Term]
id: MS:1001062
name: Mascot MGF file
def: "Mascot MGF file." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

************ Added the def: item
[Term]
id: MS:1001513
name: DB sequence filter pattern
def: "DB sequence filter pattern." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters

************ Added the def: item
[Term]
id: MS:1001514
name: DB accession filter string
def: "DB accession filter string." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters

New CV terms in version 3.35.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002082
name: first column elution time
def: "The time of elution from the first chromatographic column in the 
chromatographic separation step, relative to the start of the 
chromatography." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1002083
name: second column elution time
def: "The time of elution from the second chromatographic column in the 
chromatographic separation step, relative to the start of the 
chromatography." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000010 ! second
relationship: has_units UO:0000031 ! minute

[Term]
id: MS:1002084
name: multidimensional chromatography modulation description
def: "Multidimensional chromatography modulation description." [PSI:MS]
is_a: MS:1000857 ! run attribute

[Term]
id: MS:1002085
name: two-dimensional gas chromatography with fixed modulation time
def: "Two-dimensional gas chromatography where a single modulation time 
is used throughout the acquisition." [PSI:MS]
is_a: MS:1002084 ! multidimensional chromatography modulation description

[Term]
id: MS:1002086
name: two-dimensional gas chromatography with discrete modulation time steps
def: "Two-dimensional gas chromatography where the acquisition is 
divided into steps, each with a different modulation time." [PSI:MS]
is_a: MS:1002084 ! multidimensional chromatography modulation description

[Term]
id: MS:1002087
name: two-dimensional liquid chromatography with fixed modulation time
def: "Two-dimensional liquid chromatography where a single modulation 
time is used throughout the acquisition." [PSI:MS]
is_a: MS:1002084 ! multidimensional chromatography modulation description

[Term]
id: MS:1002088
name: two-dimensional liquid chromatography with discrete modulation 
time steps
def: "Two-dimensional liquid chromatography where the acquisition is 
divided into steps, each with a different modulation time." [PSI:MS]
is_a: MS:1002084 ! multidimensional chromatography modulation description

[Term]
id: MS:1002089
name: ProteomeDiscoverer:Peptide Without Protein XCorr Threshold
def: "XCorr threshold for storing peptides that do not belong to a 
protein." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002090
name: Calculate Probability Scores
def: "Flag indicating that a probability score for the assessment that a 
reported peptide match is a random occurence is calculated." [PSI:MS]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002091
name: ProteomeDiscoverer:Maximum Delta Cn
def: "Delta Cn threshold for filtering out PSM's." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002092
name: Percolator:Validation based on
def: "Algorithm (e.g. q-value or PEP) used for calculation of the 
validation score using Percolator." [PSI:MS]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

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)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de