[Psidev-pi-dev] New version 4.1.9 of psi-ms.obo

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

Dear proteomics/metabolomics community,

the new version 4.1.9 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains new terms for isomer, isotopomer, isotopologue and their peaks
as well as name changes for the PEFF regular expression terms.


New CV terms in version 4.1.9 of psi-ms.obo:
============================================
[Term]
id: MS:1002955
name: hr-ms compound identification confidence level
def: "Refined High Resolution mass spectrometry confidence level for 
annotation of identified compounds as proposed by Schymanski et al. The 
value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 
2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540]
xref: value-type:xsd:string "The allowed value-type for this CV term."
is_a: MS:1002895 ! small molecule identification attribute

[Term]
id: MS:1002956
name: isotopic ion MS peak
def: "A mass spectrometry peak that represents one or more isotopic 
ions. The value slot contains a description of the represented isotope 
set, e.g. 'M+1 peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1000231 ! peak

[Term]
id: MS:1002957
name: isotopomer MS peak
def: "The described isotopomer mass spectrometric signal. The value slot 
contains a description of the represented isotopomer, e.g. '13C peak', 
'15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002956 ! isotopic ion MS peak

[Term]
id: MS:1002958
name: isotopologue MS peak
def: "The described isotopologue mass spectrometric signal. The value 
slot contains a description of the represented isotopologue, e.g. '13C1 
peak' or '15N1 peak'." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002956 ! isotopic ion MS peak

[Term]
id: MS:1002959
name: isomer
def: "One of several species (or molecular entities) that have the same 
atomic composition (molecular formula) but different line formulae or 
different stereochemical formulae." 
[https://goldbook.iupac.org/html/I/I03289.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Ontology

[Term]
id: MS:1002960
name: isotopomer
def: "An isomer that differs from another only in the spatial 
distribution of the constitutive isotopic atoms." 
[https://goldbook.iupac.org/html/I/I03352.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002959 ! isomer

[Term]
id: MS:1002961
name: isotopologue
def: "A molecular entity that differs only in isotopic composition 
(number of isotopic substitutions)." 
[https://goldbook.iupac.org/html/I/I03351.html]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002959 ! isomer



Changed CV terms in version 4.1.9 of psi-ms.obo:
================================================
************ Obsoleted the following term
[Term]
id: MS:1002897
name: isotopomer peak
def: "OBSOLETE Identifies a peak when no de-isotoping has been 
performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', 
'15N', '18O', '31P'." [PSI:PI]
comment: This term was obsoleted because it was replaced by the more 
exact terms terms MS:1002956 'isotopic ion MS peak', MS:1002957 
'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead.
xref: value-type:xsd:string "The allowed value-type for this CV term."
is_a: MS:1000231 ! peak
is_obsolete: true

************ Exchanged the name and definition for the PEFF regular 
expression
************ terms PEFF:1002001, PEFF:1002002 and PEFF:1002003 in order 
to make
************ the psi-ms.obo file loadable in OBO-Edit again (currently the
************ validator exits with an error message special characters 
are not
************ allowed in names).
[Term]
id: PEFF:1002001
name: regular expression for PEFF description line
def: "([0-9]+|[0-9]+|[a-zA-Z0-9]*)." [PSI:PEFF]
is_a: MS:1002479 ! regular expression

[Term]
id: PEFF:1002002
name: regular expression for PEFF molecular sequence type
def: 
"(AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)." 
[PSI:PEFF]
is_a: MS:1002479 ! regular expression

[Term]
id: PEFF:1002003
name: regular expression for PEFF sequence status
def: "(Complete|Fragment|[a-z0-9A-Z]+)." [PSI:PEFF]
is_a: MS:1002479 ! regular expression

Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

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