[Psidev-ms-dev] Release candidate 3.42.0_rc1 of psi-ms.obo

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Dear proteomics community,

attached there's the release candidate 3.42.0_rc1 of the psi-ms.obo file.

It contains new terms for the TOPP software and added definitions for 
many terms.

Changed CV terms in version 3.42.0_rc1 of psi-ms.obo:
=====================================================
************ Changed the name from 'number of counts' --> 'number of 
detector counts'
[Term]
id: MS:1000131
name: number of detector counts
def: "The number of counted events observed in one or a group of 
elements of a detector." [PSI:MS]
is_a: MS:1000043 ! intensity unit

************ Added the data type
[Term]
id: MS:1001879
name: offset voltage
def: "The potential difference between two adjacent interface voltages 
affecting in-source collision induced dissociation." [PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000482 ! source attribute
relationship: has_units UO:0000218 ! volt

************ Added the definitions to the following terms
[Term]
id: MS:1001046
name: Sequest:sort_by_dCn
def: "Sort order of Sequest search results by the delta of the 
normalized correlation score." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001047
name: Sequest:sort_by_dM
def: "Sort order of Sequest search results by the difference between a 
theoretically calculated and the corresponding experimentally measured 
molecular mass M." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001068
name: Sequest:sort_by_Sp
def: "Sort order of Sequest search results by the Sp score." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001086
name: Sequest:sort_by_XCorr
def: "Sort order of Sequest search results by the correlation score." 
[PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001041 ! Sequest:sortCV

[Term]
id: MS:1001108
name: param: a ion
def: "Parameter information, type of product: a ion with charge on the 
N-terminal side." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001118
name: param: b ion
def: "Parameter information, type of product: b ion with charge on the 
N-terminal side." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001119
name: param: c ion
def: "Parameter information, type of product: c ion with charge on the 
N-terminal side." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001143
name: search engine specific score for peptides
def: "Search engine specific peptide scores." [PSI:PI]
is_a: MS:1001105 ! peptide result details

[Term]
id: MS:1001146
name: param: a ion-NH3
def: "Parameter information, type of product: a ion with lost ammonium." 
[PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001149
name: param: b ion-NH3
def: "Parameter information, type of product: b ion with lost ammonium." 
[PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001151
name: param: y ion-NH3
def: "Parameter information, type of product: y ion with lost ammonium." 
[PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001201
name: DB MW filter maximum
def: "Maximum value of molecular weight filter." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters
relationship: has_units UO:0000221 ! dalton
relationship: has_units UO:0000222 ! kilodalton

[Term]
id: MS:1001202
name: DB MW filter minimum
def: "Minimum value of molecular weight filter." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters
relationship: has_units UO:0000221 ! dalton
relationship: has_units UO:0000222 ! kilodalton

[Term]
id: MS:1001203
name: DB PI filter maximum
def: "Maximum value of isoelectric point filter." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters

[Term]
id: MS:1001204
name: DB PI filter minimum
def: "Minimum value of isoelectric point filter." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001512 ! Sequence database filters

[Term]
id: MS:1001245
name: PerSeptive PKS file
def: "PerSeptive peak list file format." 
[http://www.matrixscience.com/help/data_file_help.html#PKS]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1001246
name: Sciex API III file
def: "PE Sciex peak list file format." 
[http://www.matrixscience.com/help/data_file_help.html#API]
is_a: MS:1000560 ! mass spectrometer file format

[Term]
id: MS:1001249
name: search input details
def: "Details describing the search input." [PSI:PI]
relationship: part_of MS:1001000 ! spectrum interpretation

[Term]
id: MS:1001251
name: Trypsin
def: "Enzyme trypsin." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001176 ! (?<=[KR])(?!P)

[Term]
id: MS:1001252
name: DB source EBI
def: "Database source EBI." [PSI:PI]
is_a: MS:1001012 ! database source

[Term]
id: MS:1001253
name: DB source NCBI
def: "Database source NCBI." [PSI:PI]
is_a: MS:1001012 ! database source

[Term]
id: MS:1001254
name: DB source UniProt
def: "Database source UniProt." [PSI:PI]
is_a: MS:1001012 ! database source

[Term]
id: MS:1001257
name: param: v ion
def: "Parameter information, type of product: side chain loss v ion." 
[PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001258
name: param: d ion
def: "Parameter information, type of product: side chain loss d ion." 
[PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001259
name: param: immonium ion
def: "Parameter information, type of product: immonium ion." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001260
name: param: w ion
def: "Parameter information, type of product: side chain loss w ion. 
[PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001261
name: param: x ion
def: "Parameter information, type of product: x ion with charge on the 
C-terminal side." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001262
name: param: y ion
def: "Parameter information, type of product: y ion with charge on the 
C-terminal side." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001263
name: param: z ion
def: "Parameter information, type of product: z ion with charge on the 
C-terminal side." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001304
name: Asp-N
def: "Endoproteinase Asp-N." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001273 ! (?=[BD])

[Term]
id: MS:1001305
name: Asp-N_ambic
def: "Enzyme Asp-N, Ammonium Bicarbonate (AmBic)." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001274 ! (?=[DE])

[Term]
id: MS:1001306
name: Chymotrypsin
def: "Enzyme chymotrypsin." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001332 ! (?<=[FYWL])(?!P)

[Term]
id: MS:1001308
name: Formic_acid
def: "Formic acid." [PubChem_Compound:284]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001334 ! ((?<=D))|((?=D))

[Term]
id: MS:1001309
name: Lys-C
def: "Endoproteinase Lys-C." [PSI:PI]
is_a: MS:1001045 ! cleavage agent name
relationship: has_regexp MS:1001335 ! (?<=K)(?!P)

[Term]
id: MS:1001365
name: frag: internal yb ion
def: "Fragmentation information, type of product: internal yb ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001366
name: frag: internal ya ion
def: "Fragmentation information, type of product: internal ya ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001367
name: frag: z+1 ion
def: "Fragmentation information, type of product: z+1 ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001368
name: frag: z+2 ion
def: "Fragmentation information, type of product: z+2 ion." [PSI:PI]
is_a: MS:1001221 ! fragmentation information

[Term]
id: MS:1001373
name: Sequest:TIC
def: "Sequest total ion current." [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:1001406
name: param: internal yb ion
def: "Parameter information, type of product: internal yb ion." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001407
name: param: internal ya ion
def: "Parameter information, type of product: internal ya ion." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001408
name: param: z+1 ion
def: "Parameter information, type of product: z+1 ion." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001409
name: param: z+2 ion
def: "Parameter information, type of product: z+2 ion." [PSI:PI]
is_a: MS:1001066 ! ions series considered in search

[Term]
id: MS:1001463
name: Phenyx XML format
def: "Phenyx open XML file format." [PSI:PI]
is_a: MS:1000560 ! mass spectrometer file format
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001464
name: DTASelect file
def: "DTASelect file." [PMID:12643522, 
http://www.scripps.edu/cravatt/protomap/dtaselect_instructions.html]
is_a: MS:1001040 ! intermediate analysis format

[Term]
id: MS:1001466
name: MS2 file
def: "MS2 file for MS/MS spectral data." [PMID:15317041, 
DOI:10.1002/rcm.1603, http://fields.scripps.edu/sequest/SQTFormat.html]
is_a: MS:1001040 ! intermediate analysis format

New CV terms in version 3.42.0_rc1 of psi-ms.obo:
=================================================
[Term]
id: MS:1002154
name: DTAExtractor
def: "Extracts spectra of an MS run file to several files in DTA 
format." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002155
name: IDMerger
def: "Merges several protein/peptide identification files into one 
file." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002156
name: IDFileConverter
def: "Converts identification engine file formats." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002157
name: SpectraMerger
def: "Merges spectra from an LC/MS map, either by precursor or by RT 
blocks." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002158
name: MzTabExporter
def: "Exports various XML formats to an mzTab file." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002159
name: MassTraceExtractor
def: "Annotates mass traces in centroided LC/MS maps." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002160
name: PrecursorMassCorrector
def: "Correct the precursor entries of tandem MS scans." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002161
name: HighResPrecursorMassCorrector
def: "Performs precursor mz correction on centroided high resolution 
data." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002162
name: AdditiveSeries
def: "Computes an additive series to quantify a peptide in a set of 
samples." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002163
name: Decharger
def: "Decharges and merges different feature charge variants of the same 
chemical entity." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002164
name: EICExtractor
def: "Quantifies signals at given positions in (raw or picked) LC/MS 
maps." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002165
name: TOPP feature finder
def: "Feature finder component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002166
name: FeatureFinderCentroided
def: "Detects two-dimensional features in centroided LC-MS data." [PSI:PI]
is_a: MS:1002165 ! TOPP feature finder

[Term]
id: MS:1002167
name: FeatureFinderRaw
def: "Detects two-dimensional features in uncentroided LC-MS data." [PSI:PI]
is_a: MS:1002165 ! TOPP feature finder

[Term]
id: MS:1002168
name: FeatureFinderIsotopeWavelet
def: "Detects two-dimensional features in uncentroided LC-MS data with a 
wavelet algorithm." [PSI:PI]
is_a: MS:1002165 ! TOPP feature finder

[Term]
id: MS:1002169
name: FeatureFinderMetabo
def: "Detects two-dimensional features in centroided LC-MS data of 
metabolites." [PSI:PI]
is_a: MS:1002165 ! TOPP feature finder

[Term]
id: MS:1002170
name: FeatureFinderMRM
def: "Quantifies features LC-MS/MS MRM data." [PSI:PI]
is_a: MS:1002165 ! TOPP feature finder

[Term]
id: MS:1002171
name: ProteinQuantifier
def: "Computes protein abundances from annotated feature/consensus 
maps." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002172
name: ConsensusMapNormalizer
def: "Normalizes maps of one consensus XML file (after linking)." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002173
name: MapRTTransformer
def: "Applies retention time transformations to maps." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002174
name: TOPP feature linker
def: "Feature linker component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002175
name: FeatureLinkerLabeled
def: "Groups corresponding isotope-labeled features in a feature map." 
[PSI:PI]
is_a: MS:1002174 ! TOPP feature linker

[Term]
id: MS:1002176
name: FeatureLinkerUnlabeled
def: "Groups corresponding features from multiple maps." [PSI:PI]
is_a: MS:1002174 ! TOPP feature linker

[Term]
id: MS:1002177
name: FeatureLinkerUnlabeledQT
def: "Groups corresponding features from multiple maps using a quality 
threshold clustering approach." [PSI:PI]
is_a: MS:1002174 ! TOPP feature linker

[Term]
id: MS:1002178
name: CompNovo
def: "Performs a peptide/protein identification with the CompNovo 
engine." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002179
name: CompNovoCID
def: "Performs a peptide/protein identification with the CompNovo engine 
in collission-induced dissociation (CID) mode." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002180
name: TOPP software adaptor
def: "Software adaptor to an external program in the TOPP software." 
[PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002181
name: InspectAdapter
def: "Identifies MS/MS spectra using the external program Inspect." [PSI:PI]
is_a: MS:1002180 ! TOPP software adaptor

[Term]
id: MS:1002182
name: MascotAdapter
def: "Identifies MS/MS spectra using the external program Mascot." [PSI:PI]
is_a: MS:1002180 ! TOPP software adaptor

[Term]
id: MS:1002183
name: MascotAdapterOnline
def: "Identifies MS/MS spectra using the online version of the external 
program Mascot." [PSI:PI]
is_a: MS:1002180 ! TOPP software adaptor

[Term]
id: MS:1002184
name: OMSSAAdapter
def: "Identifies MS/MS spectra using the external program OMSSA." [PSI:PI]
is_a: MS:1002180 ! TOPP software adaptor

[Term]
id: MS:1002185
name: PepNovoAdapter
def: "Identifies MS/MS spectra using the external program PepNovo." [PSI:PI]
is_a: MS:1002180 ! TOPP software adaptor

[Term]
id: MS:1002186
name: XTandemAdapter
def: "Identifies MS/MS spectra using the external program XTandem." [PSI:PI]
is_a: MS:1002180 ! TOPP software adaptor

[Term]
id: MS:1002187
name: SpecLibSearcher
def: "Identifies peptide MS/MS spectra by spectral matching with a 
searchable spectral library." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002188
name: ConsensusID
def: "Computes a consensus identification from peptide identifications 
of several identification engines." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002189
name: IDConflictResolver
def: "Resolves ambiguous annotations of features with peptide 
identifications." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002190
name: IDFilter
def: "Filters results from protein or peptide identification engines 
based on different criteria." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002191
name: IDMapper
def: "Assigns protein/peptide identifications to feature or consensus 
features." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002192
name: IDPosteriorErrorProbability
def: "Estimates posterior error probabilities using a mixture model." 
[PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002193
name: IDRTCalibration
def: "Calibrate Retention times of peptide hits to standards." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002194
name: PeptideIndexer
def: "Refreshes the protein references for all peptide hits." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002195
name: PrecursorIonSelector
def: "A tool for precursor ion selection based on identification 
results." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002196
name: MRMMapper
def: "MRMMapper maps measured chromatograms (mzML) and the transitions 
used (TraML)." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002197
name: TOPP OpenSwath component
def: "OpenSwath component of the TOPP software." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002198
name: OpenSwathAnalyzer
def: "Picks peaks and finds features in an SRM experiment." [PSI:PI]
is_a: MS:1002197 ! TOPP OpenSwath component

[Term]
id: MS:1002199
name: OpenSwathChromatogramExtractor
def: "Extract chromatograms (XIC) from a MS2 map file." [PSI:PI]
is_a: MS:1002197 ! TOPP OpenSwath component

[Term]
id: MS:1002200
name: OpenSwathDecoyGenerator
def: "Generates decoys according to different models for a specific 
TraML." [PSI:PI]
is_a: MS:1002197 ! TOPP OpenSwath component

[Term]
id: MS:1002201
name: OpenSwathFeatureXMLToTSV
def: "Converts a featureXML to a mProphet tsv (tab separated values)." 
[PSI:PI]
is_a: MS:1002197 !TOPP OpenSwath component

[Term]
id: MS:1002202
name: OpenSwathRTNormalizer
def: "Generates a transformation file for retention time space into 
normalized space." [PSI:PI]
is_a: MS:1002197 ! TOPP OpenSwath component

[Term]
id: MS:1002203
name: TOPP-ProteinInference
def: "Infer proteins from a list of (high-confidence) peptides." [PSI:PI]
is_a: MS:1000752 ! TOPP software

[Term]
id: MS:1002204
name: TOPP-FalseDiscoveryRate
def: "Estimates the false discovery rate on peptide and protein level 
using decoy searches." [PSI:PI]
is_a: MS:1000752 ! TOPP software

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