[Psidev-ms-dev] Release candidate 3.40.0_rc1 of psi-ms.obo

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Dear proteomics community,

attached there's the release candidate 3.40.0_rc1 of the psi-ms.obo file.

It contains the new term 'database UniProtKB' as parent of the two terms 
'database UniProtKB/Swiss-Prot' and 'database UniProtKB/TrEMBL'.
as well as added definitions for all Phenyx - related terms (Thanks 
Pierre-Alain for providing them).

Furthermore definitions to the ProteinExtractor-related terms are now 
available.

Changed CV terms in version 3.40.0_rc1 of psi-ms.obo:
=====================================================
************ Added the definitions to the following terms
[Term]
id: MS:1001207
name: Mascot
def: "The name of the Mascot search engine." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001208
name: Sequest
def: "The name of the Sequest search engine." [PSI:PI]
is_a: MS:1001456 ! analysis software

************ Changed the is_a relationship of the following two terms 
into is_a: MS:1002126 ! database UniProtKB
[Term]
id: MS:1001104
name: database UniProtKB/Swiss-Prot
def: "The name of the UniProtKB/Swiss-Prot knowledgebase." [PSI:PI]
is_a: MS:1002126 ! database UniProtKB

[Term]
id: MS:1002060
name: database UniProtKB/TrEMBL
def: "The name of the UniProtKB/TrEMBL database." [PSI:PI]
is_a: MS:1002126 ! database UniProtKB

************ Added the definitions to the following Phenyx-related terms
[Term]
id: MS:1001209
name: Phenyx
def: "The name of the Phenyx search engine." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1001375
name: Phenyx:Instrument Type
def: "The instrument type parameter value in Phenyx." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001376
name: Phenyx:Scoring Model
def: "The selected scoring model in Phenyx." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001377
name: Phenyx:Default Parent Charge
def: "The default parent charge value in Phenyx." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001378
name: Phenyx:Trust Parent Charge
def: "The parameter in Phenyx that specifies if the experimental charge 
state is to be considered as correct." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001379
name: Phenyx:Turbo
def: "The turbo mode parameter in Phenyx." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001380
name: Phenyx:Turbo:ErrorTol
def: "The maximal allowed fragment m/z error filter considered in the 
turbo mode of Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001381
name: Phenyx:Turbo:Coverage
def: "The minimal peptide sequence coverage value, expressed in percent, 
considered in the turbo mode of Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001382
name: Phenyx:Turbo:Series
def: "The list of ion series considered in the turbo mode of Phenyx." 
[PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001383
name: Phenyx:MinPepLength
def: "The minimal number of residues for a peptide to be considered for 
a valid identification in Phenyx." [PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this 
CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001384
name: Phenyx:MinPepzscore
def: "The minimal peptide z-score for a peptide to be considered for a 
valid identification in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001385
name: Phenyx:MaxPepPvalue
def: "The maximal peptide p-value for a peptide to be considered for a 
valid identification in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001386
name: Phenyx:AC Score
def: "The minimal protein score required for a protein database entry to 
be displayed in the list of identified proteins in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001387
name: Phenyx:Conflict Resolution
def: "The parameter in Phenyx that specifies if the conflict resolution 
algorithm is to be used." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002097 ! Phenyx input parameter

[Term]
id: MS:1001388
name: Phenyx:AC
def: "The primary sequence database identifier of a protein in Phenyx." 
[PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001389
name: Phenyx:ID
xref: value-type:xsd\:string "The allowed value-type for this CV term."
def: "A secondary sequence database identifier of a protein in Phenyx." 
[PSI:PI]
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001390
name: Phenyx:Score
def: "The protein score of a protein match in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001116 ! single protein result details
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001393
name: Phenyx:Auto
def: "The value of the automatic peptide acceptance filter in Phenyx. " 
[PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001394
name: Phenyx:User
def: "The value of the user-defined peptide acceptance filter in 
Phenyx." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001395
name: Phenyx:Pepzscore
def: "The z-score value of a peptide sequence match in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001396
name: Phenyx:PepPvalue
def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score
is_a: MS:1001870 ! p-value for peptides

[Term]
id: MS:1001397
name: Phenyx:NumberOfMC
def: "The number of missed cleavages of a peptide sequence in Phenyx." 
[PSI:PI]
xref: value-type:xsd\:positiveInteger "The allowed value-type for this 
CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

[Term]
id: MS:1001398
name: Phenyx:Modif
def: "The expression of the nature and position(s) of modified 
residue(s) on a matched peptide sequence in Phenyx." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001143 ! search engine specific score for peptides
is_a: MS:1001153 ! search engine specific score

************ Added the definitions to the following 
ProteinExtractor-related terms
[Term]
id: MS:1001431
name: ProteinExtractor:MascotPeptideScoreThreshold
def: "Only peptides with scores higher than that threshold are taken 
into account in Mascot scoring for calculation of the ProteinExtractor 
metascore." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001432
name: ProteinExtractor:MascotUniqueScore
def: "In the final result each protein must have at least one peptide 
above this Mascot score threshold in ProteinExtractor metascore 
calculation." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001434
name: ProteinExtractor:MascotWeighting
def: "Influence of Mascot search engine in the process of merging the 
search engine specific protein lists into the global protein list of 
ProteinExtractor." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001436
name: ProteinExtractor:SequestPeptideScoreThreshold
def: "Only peptides with scores higher than that threshold are taken 
into account in Sequest scoring for calculation of the ProteinExtractor 
metascore." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001437
name: ProteinExtractor:SequestUniqueScore
def: "In the final result each protein must have at least one peptide 
above this Sequest score threshold in ProteinExtractor metascore 
calculation." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001438
name: ProteinExtractor:SequestWeighting
def: "Influence of Sequest search engine in the process of merging the 
search engine specific protein lists into the global protein list of 
ProteinExtractor." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001440
name: ProteinExtractor:ProteinSolverPeptideScoreThreshold
def: "Only peptides with scores higher than that threshold are taken 
into account in ProteinSolver scoring for calculation of the 
ProteinExtractor metascore." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001441
name: ProteinExtractor:ProteinSolverUniqueScore
def: "In the final result each protein must have at least one peptide 
above this ProteinSolver score threshold in ProteinExtractor metascore 
calculation." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001442
name: ProteinExtractor:ProteinSolverWeighting
def: "Influence of ProteinSolver search engine in the process of merging 
the search engine specific protein lists into the global protein list of 
ProteinExtractor." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001444
name: ProteinExtractor:PhenyxPeptideScoreThreshold
def: "Only peptides with scores higher than that threshold are taken 
into account in Phenyx scoring for calculation of the ProteinExtractor 
metascore." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001445
name: ProteinExtractor:PhenyxUniqueScore
def: "In the final result each protein must have at least one peptide 
above this Phenyx score threshold in ProteinExtractor metascore 
calculation." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001446
name: ProteinExtractor:PhenyxWeighting
def: "Influence of Phenyx search engine in the process of merging the 
search engine specific protein lists into the global protein list of 
ProteinExtractor." [DOI:10.4172/jpb.1000056]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

************ The names of the following terms were changed to begin with 
lower case letters
************ to be consistent with the 'Guidelines for the development 
of Controlled Vocabularies'
[Term]
id: MS:1001807
name: study variable attribute
def: "Attribute describing a study variable." [PSI:MS]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1001817
name: raw file attribute
def: "Attribute describing a raw file." [PSI:MS]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1001823
name: raw files group attribute
def: "Attribute describing, how raw files build a raw file group." [PSI:MS]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1001825
name: feature list attribute
def: "Attribute describing a feature list." [PSI:MS]
is_a: MS:1001806 ! quantification object attribute

************ Changed is_a: MS:1002006 ! MRM transition type --> is_a: 
MS:1002006 ! SRM transition type
[Term]
id: MS:1002008
name: decoy SRM transition
def: "A transition not expected to be present in the sample and used to 
calculate statistical confidence of target transition detections in some 
workflows." [PSI:MS]
synonym: "decoy MRM transition" EXACT []
is_a: MS:1002006 ! SRM transition type

New CV terms in version 3.40.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002126
name: database UniProtKB
def: "The name of the UniProtKB knowledgebase." [PSI:PI]
is_a: MS:1001013 ! database name

Best Regards,
Gerhard

-- 
---
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
BioInformatik
Medizinisches-Proteom-Center (MPC)
Ruhr-Universität Bochum
Zentrum für klinische Forschung I (ZKF I)
E.042
Universitätsstrasse 150
D-44801 Bochum

Phone:	+49(0)234/32-29836
Fax:	+49(0)234/32-14554
Email:	Ger...@ru...
Web:	http://www.medizinisches-proteom-center.de