[Psidev-ms-dev] New version 3.73.0 of psi-ms.obo

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Dear proteomics community,

attached you find the new version 3.73.0 of the psi-ms.obo file.

It contains new terms for localization score thresholds, added string 
value-types
for PTM location scores, and some updated definitions for PTM site 
location terms.

Changed CV terms in version 3.73.0 of psi-ms.obo:
==================================================
************ Updated the definitions of the following terms:
[Term]
id: MS:1001969
name: phosphoRS score
def: "phosphoRS score for PTM site location at the PSM-level." 
[DOI:10.1021/pr200611n, PMID:22073976]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PSM-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1001985
name: Ascore
def: "A-score for PTM site location at the PSM-level." 
[DOI:10.1038/nbt1240, PMID:16964243]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001143 ! search engine specific score for PSMs
is_a: MS:1001968 ! PSM-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002536
name: D-Score
def: "D-Score for PTM site location at the PSM-level." 
[DOI:10.1002/pmic.201200408, PMID:23307401]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PSM-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002537
name: MD-Score
def: "MD-Score for PTM site location at the PSM-level." 
[DOI:10.1074/mcp.M110.003830–1, PMID:21057138]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001968 ! PSM-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002550
name: peptide:phosphoRS score
def: "phosphoRS score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002551
name: peptide:Ascore
def: "A-score score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002553
name: peptide:D-Score
def: "D-Score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

[Term]
id: MS:1002554
name: peptide:MD-Score
def: "MD-Score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

************ Renamed from 'order' --> 'modification index'
[Term]
id: MS:1002504
name: modification index
def: "The order of modifications to be referenced elsewhere in the 
document." [PSI:PI]
xref: value-type:xsd\:integer "The allowed value-type for this CV term."
is_a: MS:1001055 ! modification parameters

************ Added string value-type\:string and
************ relationship: has_regexp MS:10012505 ! regular expression 
for modification localization scoring
************ to all PSM-level PTM localization score's and
************ to all peptide-level PTM localization score's, e.g.
[Term]
id: MS:1002551
name: peptide:Ascore
def: "A-score for PTM site location at the peptide-level." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002549 ! peptide-level PTM localization score
relationship: has_regexp MS:1002505 ! regular expression for 
modification localization scoring

New CV terms in version 3.73.0 of psi-ms.obo:
=============================================
************ New terms for PTM localization score thresholds.
[Term]
id: MS:1002555
name: PTM localization score threshold
def: "Threshold for PTM site location score." [PSI:PI]
is_a: MS:1001405 ! spectrum identification result details

[Term]
id: MS:1002556
name: Ascore threshold
def: "Threshold for Ascore PTM site location score." [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:1002557
name: D-Score threshold
def: "Threshold for D-score PTM site location score." [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:1002558
name: MD-Score threshold
def: "Threshold for MD-score PTM site location score." [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:1002559
name: H-Score threshold
def: "Threshold for H-score PTM site location score." [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:10025560
name: DeBunker:score threshold
def: "Threshold for DeBunker PTM site location score." [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:1002561
name: Mascot:PTM site assignment confidence threshold
def: "Threshold for Mascot PTM site assignment confidence." [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:1002562
name: MSQuant:PTM-score threshold
def: "Threshold for MSQuant:PTM-score." [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:1002563
name: MaxQuant:PTM Score threshold
def: "Threshold for MaxQuant:PTM Score." [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:1002564
name: MaxQuant:P-site localization probability threshold
def: "Threshold for MaxQuant:P-site localization probability." [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:1002565
name: MaxQuant:PTM Delta Score threshold
def: "Threshold for MaxQuant:PTM Delta Score." [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:1002566
name: MaxQuant:Phospho (STY) Probabilities threshold
def: "Threshold for MaxQuant:Phospho (STY) Probabilities." [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:1002567
name: phosphoRS score threshold
def: "Threshold for phosphoRS score." [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:1002568
name: phosphoRS site probability threshold
def: "Threshold for phosphoRS site probability." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002555 ! PTM localization score threshold

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Bioinformatics / Biostatistics
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I), E.049a
Universitätsstraße 150
D-44801 Bochum

Phone:	+49(0)234/32-21006
Fax:	+49(0)234/32-14554
Email:	ger...@ru...
Web:	http://www.medizinisches-proteom-center.de