[Psidev-ms-dev] Release candidate 4.1.8_rc1 of psi-ms.obo

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Dear proteomics community,

following are new terms from the release candidate 4.1.8_rc1 of the 
psi-ms.obo file.
It contains new terms for the TopPIC and TopMG software.

New CV terms in version 4.1.8_rc1 of psi-ms.obo:
================================================
[Term]
id: MS:1002899
name: msalign format
def: "msalign file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002900
name: feature format
def: "TopFD feature file format." [PSI:MS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1002901
name: TopPIC
def: "TopPIC: a software tool for top-down mass spectrometry-based 
proteoform identification and characterization." [PMID:27423895, 
http://proteomics.informatics.iupui.edu/software/toppic/index.html]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002902
name: TopFD
def: "Top-down mass spectral feature detection." 
[http://proteomics.informatics.iupui.edu/software/toppic/index.html]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002903
name: TopMG
def: "A mass graph-based approach for the identification of modified 
proteoforms using top-down tandem mass spectra." [PMID:28453668, 
http://proteomics.informatics.iupui.edu/software/topmg/index.html]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1002904
name: proteoform-level identification attribute
def: "Proteoform level information." [PSI:PI]
is_a: MS:1002694 ! single identification result attribute

[Term]
id: MS:1002905
name: proteoform-level identification statistic
def: "Identification confidence metric for a proteoform." [PSI:PI]
is_a: MS:1002904 ! proteoform-level identification attribute

[Term]
id: MS:1002906
name: search engine specific score for proteoforms
def: "Search engine specific proteoform scores." [PSI:PI]
is_a: MS:1002905 ! proteoform-level identification statistic

[Term]
id: MS:1002907
name: proteoform-level global FDR
def: "Estimation of the global false discovery rate of proteoforms." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002905 ! proteoform-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002908
name: proteoform-level local FDR
def: "Estimation of the local false discovery rate of proteoforms." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002905 ! proteoform-level identification statistic
relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive

[Term]
id: MS:1002909
name: proteoform-level statistical threshold
def: "Estimated statistical threshold at proteoform-level." [PSI:PI]
is_a: MS:1002573 ! spectrum identification statistical threshold

[Term]
id: MS:1002910
name: proteoform-level global FDR threshold
def: "Threshold for the global false discovery rate of proteoforms." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002909 ! proteoform-level statistical threshold

[Term]
id: MS:1002911
name: proteoform-level local FDR threshold
def: "Threshold for the local false discovery rate of proteoforms." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002909 ! proteoform-level statistical threshold

[Term]
id: MS:1002912
name: TopPIC input parameter
def: "Search engine input parameters specific to TopPIC." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002913
name: TopPIC:fixed modification
def: "Fixed modifications for TopPIC searching." [PSI:PI]
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002914
name: TopPIC:N-term form
def: "N-terminal forms of proteins allowed in TopPIC searching." [PSI:PI]
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002915
name: TopPIC:error tolerance
def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002916
name: TopPIC:max shift
def: "Maximum value of the mass shift (in Dalton) of an unexpected 
modification." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002917
name: TopPIC:min shift
def: "Minimum value of the mass shift (in Dalton) of an unexpected 
modification." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002918
name: TopPIC:shift num
def: "Maximum number of unexpected modifications in a proteoform 
spectrum match." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002919
name: TopPIC:spectral cutoff type
def: "Spectrum-level cutoff type for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002920
name: TopPIC:spectral cutoff value
def: "Spectrum-level cutoff value for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002921
name: TopPIC:proteoform-level cutoff type
def: "Proteoform-level cutoff type for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002922
name: TopPIC:proteoform-level cutoff value
def: "Proteoform-level cutoff value for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002923
name: TopPIC:generating function
def: "P-value and E-value estimation using generating function." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002924
name: TopPIC:combined spectrum number
def: "Number of combined spectra." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002925
name: TopPIC:mod file
def: "The text file containing the information of common PTMs." [PSI:PI]
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002926
name: TopPIC:thread number
def: "Number of threads used in TopPIC." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002927
name: TopPIC:use TopFD feature
def: "Proteoform identification using TopFD feature file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002912 ! TopPIC input parameter

[Term]
id: MS:1002928
name: TopPIC:spectral E-value
def: "TopPIC spectrum-level E-value." [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
is_a: MS:1002353 ! PSM-level e-value
relationship: has_order MS:1002109 ! lower score better

[Term]
id: MS:1002929
name: TopPIC:spectral FDR
def: "TopPIC spectrum-level FDR." [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
is_a: MS:1002351 ! PSM-level local FDR

[Term]
id: MS:1002930
name: TopPIC:proteoform-level FDR
def: "TopPIC proteoform-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002908 ! proteoform-level local FDR
is_a: MS:1002901 ! search engine specific score for proteoforms

[Term]
id: MS:1002931
name: TopPIC:spectral p-value
def: "TopPIC spectrum-level p-value." [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
is_a: MS:1002352 ! PSM-level p-value

[Term]
id: MS:1002932
name: TopPIC:MIScore
def: "Modification identification score." [PMID:27291504]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PTM localization PSM-level statistic

[Term]
id: MS:1002933
name: TopPIC:MIScore threshold
def: "TopPIC:MIScore threshold." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

[Term]
id: MS:1002934
name: TopMG input parameter
def: "Search engine input parameters specific to TopMG." [PSI:PI]
is_a: MS:1001302 ! search engine specific input parameter

[Term]
id: MS:1002935
name: TopMG:fixed modification
def: "Fixed modifications for TopMG searching." [PSI:PI]
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002936
name: TopMG:N-term form
def: "N-terminal forms of proteins allowed in TopMG searching." [PSI:PI]
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002937
name: TopMG:error tolerance
def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002938
name: TopMG:max shift
def: "Maximum value of the mass shift (in Dalton)." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002939
name: TopMG:spectral cutoff type
def: "Spectrum-level cutoff type for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002940
name: TopMG:spectral cutoff value
def: "Spectrum-level cutoff value for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002941
name: TopMG:proteoform-level cutoff type
def: "Proteoform-level cutoff type for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002942
name: TopMG:proteoform-level cutoff value
def: "Proteoform-level cutoff value for filtering identified proteoform 
spectrum matches." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002943
name: TopMG:mod file
def: "The text file containing the information of common PTMs." [PSI:PI]
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002944
name: TopMG:thread number
def: "Number of threads used in TopMG." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002945
name: TopMG:use TopFD feature
def: "Proteoform identification using TopFD feature file." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002946
name: TopMG:proteoform graph gap size
def: "Gap size in constructing proteoform graph." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002947
name: TopMG:variable PTM number
def: "Maximum number of variable PTMs." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002948
name: TopMG:variable PTM number in proteoform graph gap
def: "Maximum number of variable PTMs in a proteoform graph gap." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002949
name: TopMG:use ASF-DIAGONAL
def: "Protein filtering using ASF-DIAGONAL method." [PMID:29327814]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002934 ! TopMG input parameter

[Term]
id: MS:1002950
name: TopMG:spectral E-value
def: "TopMG spectrum-level E-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002353 ! PSM-level e-value
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1002109 ! lower score better

[Term]
id: MS:1002951
name: TopMG:spectral FDR
def: "TopMG spectrum-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002351 ! PSM-level local FDR
is_a: MS:1001143 ! PSM-level search engine specific statistic

[Term]
id: MS:1002952
name: TopMG:proteoform-level FDR
def: "TopMG proteoform-level FDR." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002908 ! proteoform-level local FDR
is_a: MS:1002901 ! search engine specific score for proteoforms

[Term]
id: MS:1002953
name: TopMG:spectral p-value
def: "TopMG spectrum-level p-value." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002352 ! PSM-level p-value
is_a: MS:1001143 ! PSM-level search engine specific statistic

[Term]
id: MS:1002954
name: collisional cross sectional area
def: "Structural molecular descriptor for the effective interaction area 
between the ion and neutral gas measured in ion mobility mass 
spectrometry." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1000861 ! chemical compound attribute
relationship: has_units UO:0000324 ! square angstrom

Changed CV terms in version 4.1.8_rc1 of psi-ms.obo:
====================================================
No changed CV terms

Best Regards,
Gerhard

-- 

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

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

www.medizinisches-proteom-center.de 
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