[Psidev-pi-dev] Release candidate 4.0.13_rc1 of psi-ms.obo

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Dear proteomics and metabolomics community,

attached there's the release candidate 4.0.13_rc1 of the psi-ms.obo file.
It contains terms for defining adduct ions and for ion mobility mass 
spectrometry (IM-MS).

New CV terms in version 4.0.13_rc1 of psi-ms.obo:
=================================================
************ new terms for adduct ions
[Term]
id: MS:1002806
name: ion
def: "An atomic or molecular species having a net positive or negative 
electric charge." [PSI:MS]
relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass 
Spectrometry Ontology

[Term]
id: MS:1002807
name: positive mode adduct ion
def: "Adduct ion with positive ionization." [PSI:MS]
is_a: MS:1000353 ! adduct ion

[Term]
id: MS:1002808
name: negative mode adduct ion
def: "Adduct ion with negative ionization." [PSI:MS]
is_a: MS:1000353 ! adduct ion

[Term]
id: MS:1002809
name: adduct ion attribute
def: "Attribute describing an adduct formation." [PSI:PI]
is_a: MS:1000547 ! object attribute

[Term]
id: MS:1002810
name: adduct ion mass
def: "Mass of an adduct formation specified by the given value." 
[DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002809 ! adduct ion attribute

[Term]
id: MS:1002811
name: adduct ion isotope
def: "Isotope of the matrix molecule M of an adduct formation." 
[PMID:18790129]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002809 ! adduct ion attribute

[Term]
id: MS:1002812
name: Regular expression for adduct ion formula
def: 
"(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])." 
[PSI:PI]
is_a: MS:1002479 ! regular expression

[Term]
id: MS:1002813
name: adduct ion formula
def: "Adduct formation formula specified by the given value." 
[PMID:22111785, DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002809 ! adduct ion attribute
relationship: has_regexp MS:1002812 ! 
(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])

************ new terms for IM-MS
[Term]
id: MS:1002814
name: volt-second per square centimeter
def: "An electrical mobility unit that equals the speed [cm/s] an ion 
reaches when pulled through a gas by a Voltage[V] over a certain 
distance [cm]." [PSI:PI]
synonym: "Vs/cm^2" EXACT []
is_a: UO:0000000 ! unit

[Term]
id: MS:1002815
name: inverse reduced ion mobility
def: "Ion mobility measurement for an ion or spectrum of ions as 
measured in an ion mobility mass spectrometer. This might refer to the 
central value of a bin into which all ions within a narrow range of 
mobilities have been aggregated." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000455 ! ion selection attribute
is_a: MS:1000503 ! scan attribute
relationship: has_units MS:1002814 ! "volt-second per square centimeter"

[Term]
id: MS:1002816
name: mean ion mobility array
def: "Array of drift times or inverse reduced ion mobilities, averaged 
from a matrix of binned m/z and ion mobility values, corresponding to a 
spectrum of individual peaks encoded with an m/z array." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000513 ! binary data array
relationship: has_units UO:0000028 ! millisecond
relationship: has_units UO:0000010 ! second
relationship: has_units MS:1002814 ! "volt-second per square centimeter"

[Term]
id: MS:1002817
name: Bruker TDF format
def: "Bruker TDF raw file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002818
name: Bruker TDF nativeID format
def: "Native format defined by frame=xsd:nonNegativeInteger 
scan=xsd:nonNegativeInteger." [PSI:MS]
is_a: MS:1000767 ! native spectrum identifier format

[Term]
id: MS:1002819
name: Bruker TDF nativeID format, combined spectra
def: "Bruker TDF comma separated list of spectra that have been combined 
prior to searching or interpretation." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002646 ! native spectrum identifier format, combined spectra

************ some concrete ion species
************ are there other concrete ions species, which should be 
included here?
[Term]
id: MS:1002820
name: M+H ion
def: "M+H ion from positive ion mode (M in the property ionMass denotes 
the mass of the neutral molecule)." [DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
property_value: ionMass: "M + 1.007276" xsd:string
is_a: MS:1002807 ! positive mode adduct ion

[Term]
id: MS:1002821
name: M-H ion
def: "M-H ion from negative ion mode (M in the property ionMass denotes 
the mass of the neutral molecule)." [DOI:10.1016/S1044-0305(99)00089-6, 
http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator]
property_value: ionMass: "M - 1.007276" xsd:string
is_a: MS:1002808 ! negative mode adduct ion

Changed CV terms in version 4.0.13_rc1 of psi-ms.obo:
=====================================================
************ Reactivated the obsolete term 'adduct ion'
[Term]
id: MS:1000353
name: adduct ion
def: "Ion formed by the interaction of an ion with one or more atoms or 
molecules to form an ion containing all the constituent atoms of the 
precursor ion as well as the additional atoms from the associated atoms 
or molecules." [PSI:MS]
is_a: MS:1002806 ! ion

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

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