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

[pierre-alain b. <pie...@is...>]

Thanks Gerhard
Pierre-Alain

On 21.11.2012 16:37, Gerhard Mayer wrote:
> 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
>
>
>
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