[Psidev-ms-dev] Release candidate 4.0.15_rc3 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics community,

attached there's the release candidate 4.0.15_rc3 of the psi-ms.obo file.

It contains new terms for the MetaMorpheus search engine,
new terms for the metabolomics software package XCMS,
a new term for 'alternating polarity mode' and two new
cleavage agent terms:


New CV terms in version 4.0.15_rc3 of psi-ms.obo:
=================================================
************ new terms for the MetaMorpheus search engine
[Term]
id: MS:1002826
name: MetaMorpheus
def: "MetaMorpheus search engine." 
[https://github.com/smith-chem-wisc/MetaMorpheus]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002827
name: MetaMorpheus:score
def: "MetaMorpheus score for PSMs." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002108 ! higher score better

[Term]
id: MS:1002828
name: MetaMorpheus:protein score
def: "MetaMorpheus score for protein groups." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002368 ! search engine specific score for protein groups
relationship: has_order MS:1002108 ! higher score better

************ new terms for XCMS
[Term]
id: MS:1002829
name: XCMS:into
def: "Feature intensity produced by XCMS findPeaks() from integrated 
peak intensity." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

[Term]
id: MS:1002830
name: XCMS:intf
def: "Feature intensity produced by XCMS findPeaks() from baseline 
corrected integrated peak intensity." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

[Term]
id: MS:1002831
name: XCMS:maxo
def: "Feature intensity produced by XCMS findPeaks() from maximum peak 
intensity." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

[Term]
id: MS:1002832
name: XCMS:area
def: "Feature intensity produced by XCMS findPeaks() from feature area 
that is not normalized by the scan rate." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002735 ! feature-level quantification datatype

************ new term 'alternating polarity mode'
[Term]
id: MS:1002833
name: alternating polarity mode
def: "Polarities of the scans of a run are alternating, i.e. both 
positive and negative mode scans are acquired." [PSI:PI]
is_a: MS:1000857 ! run attribute

************ new cleavage agent terms
[Term]
id: MS:1002834
name: (?<=[K])(?\!P)
def: "Regular expression for Trypsin/K." [PSI:PI]
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1002835
name: Trypsin/K
def: "Cleavage agent Trypsin/K." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1002834 ! (?<=[K])(?\!P)

[Term]
id: MS:1002836
name: (?<=[R])(?\!P)
def: "Regular expression for Trypsin/R." [PSI:PI]
is_a: MS:1001180 ! Cleavage agent regular expression

[Term]
id: MS:1002837
name: Trypsin/R
def: "Cleavage agent Trypsin/R." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1002834 ! (?<=[R])(?\!P)


Changed CV terms in version 4.0.15_rc3 of psi-ms.obo:
=====================================================
************ Changed the definition
[Term]
id: MS:1000465
name: scan polarity
def: "Relative orientation of the electromagnetic field during the 
selection and detection of ions in the mass spectrometer." [PSI:MS]
relationship: part_of MS:1000441 ! scan


Best Regards,
Gerhard

-- 

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*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

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