[Psidev-ms-dev] New version 3.38.0 of psi-ms.obo

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Dear proteomics community,

attached there's the new version 3.38.0 of the psi-ms.obo file.

It contains changed terms for Mascot parameters (added the missing 
definitions).
Also the definitions to database and role terms are newly added.

In addition it contains two terms proposed by Julian to specify if 
higher or lower scores are better,
which are now part_of MS:1001153 ! search engine specific score

Furthermore some new terms for mzQuantML validation and terms for the 
sofware packages XTracker and ProteoSuite are added.

The term 'tab delimited text file' is now a child of 'intermediate 
analysis format' as discussed in the last mzQuantML telco.
The 'decoy DB derived from' tree was made obsolete.

I added also the updated list of terms with lacking definitions.
Your contributions for them, are as always welcome.

Changed CV terms in version 3.38.0 of psi-ms.obo:
=================================================
************ Changes name from Feature attribute --> feature attribute 
(changed to lower case)
[Term]
id: MS:1001828
name: feature attribute
def: "Attribute describing a Feature." [PSI:MS]
is_a: MS:1001806 ! quantification object attribute

************ Added definitions to the mascot terms MS:1001316 until 
MS:1001325
************ Thanks Ville, for providing them
[Term]
id: MS:1001316
name: Mascot:SigThreshold
def: "Significance threshold below which the p-value of a peptide match 
must lie to be considered statistically significant (default 0.05)." 
[PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001317
name: Mascot:MaxProteinHits
def: "The number of protein hits to display in the report. If 'Auto', 
all protein hits that have a protein score exceeding the average peptide 
identity threshold are reported. Otherwise an integer at least 1." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001318
name: Mascot:ProteinScoringMethod
def: "Mascot protein scoring method; either 'Standard' or 'MudPIT'." 
[PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001319
name: Mascot:MinMSMSThreshold
def: "Mascot peptide match ion score threshold. If between 0 and 1, then 
peptide matches whose expect value exceeds the thresholds are 
suppressed; if at least 1, then peptide matches whose ion score is below 
the threshold are suppressed." [PSI:PI]
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001320
name: Mascot:ShowHomologousProteinsWithSamePeptides
def: "If true, show (sequence or spectrum) same-set proteins. Otherwise 
they are suppressed." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001321
name: Mascot:ShowHomologousProteinsWithSubsetOfPeptides
def: "If true, show (sequence or spectrum) sub-set and subsumable 
proteins. Otherwise they are suppressed." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001322
name: Mascot:RequireBoldRed
def: "Only used in Peptide Summary and Select Summary reports. If true, 
a peptide match must be 'bold red' to be included in the report; bold 
red means the peptide is a top ranking match in a query and appears for 
the first time (in linear order) in the list of protein hits." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001323
name: Mascot:UseUnigeneClustering
def: "If true, then the search results are against a nucleic acid 
database and Unigene clustering is enabled. Otherwise UniGene clustering 
is not in use." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001324
name: Mascot:IncludeErrorTolerantMatches
def: "If true, then the search results are error tolerant and peptide 
matches from the second pass are included in search results. Otherwise 
no error tolerant peptide matches are included." 
[http://www.matrixscience.com/help/error_tolerant_help.html]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

[Term]
id: MS:1001325
name: Mascot:ShowDecoyMatches
def: "If true, then the search results are against an automatically 
generated decoy database and the reported peptide matches and protein 
hits come from the decoy database. Otherwise peptide matches and protein 
hits come from the original database." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002095 ! Mascot input parameter

************ added the is_a relation in order to allow the use for 
mzQuantML validation
[Term]
id: MS:1000884
name: protein attribute
def: "An nonphysical attribute describing a specific protein." [PSI:MS]
relationship: part_of MS:1000882 ! protein
is_a: MS:1001806 ! quantification object attribute

************ Added definition to the following database terms
[Term]
id: MS:1001084
name: database nr
def: "Non-redundant GenBank sequence database." [PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001104
name: database UniProtKB/Swiss-Prot
def: "Swiss-Prot protein sequence database." [PSI:PI]
is_a: MS:1001013 ! UniProtKB/database name

[Term]
id: MS:1001142
name: database IPI_human
def: "International Protein Index database for Homo sapiens sequences." 
[PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001178
name: database EST
def: "Expressed sequence tag nucleotide sequence database." [PSI:PI]
is_a: MS:1001079 ! database type nucleotide

[Term]
id: MS:1001285
name: database IPI_mouse
def: "International Protein Index database for Mus musculus sequences." 
[PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001286
name: database IPI_rat
def: "International Protein Index database for Rattus norvegicus 
sequences." [PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001287
name: database IPI_zebrafish
def: "International Protein Index database for Danio rerio sequences." 
[PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001288
name: database IPI_chicken
def: "International Protein Index database for Gallus gallus sequences." 
[PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001289
name: database IPI_cow
def: "International Protein Index database for Bos taurus sequences." 
[PSI:PI]
is_a: MS:1001013 ! database name

[Term]
id: MS:1001290
name: database IPI_arabidopsis
def: "International Protein Index database for Arabidopsis thaliana 
sequences." [PSI:PI]
is_a: MS:1001013 ! database name

************ obsoleted the 'decoy DB derived from' tree
[Term]
id: MS:1001284
name: decoy DB derived from
def: "OBSOLETE The name of the database, the search database was derived 
from." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001450 ! decoy DB details
is_obsolete: true

[Term]
id: MS:1001291
name: decoy DB from nr
def: "OBSOLETE Decoy database from a non-redundant GenBank sequence 
database." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001292
name: decoy DB from IPI_rat
def: "OBSOLETE Decoy database from a International Protein Index 
database for Rattus norvegicus." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001293
name: decoy DB from IPI_mouse
def: "OBSOLETE Decoy database from a International Protein Index 
database for Mus musculus." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001294
name: decoy DB from IPI_arabidopsis
def: "OBSOLETE Decoy database from a International Protein Index 
database for Arabidopsis thaliana." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001295
name: decoy DB from EST
def: "OBSOLETE Decoy database from an expressed sequence tag nucleotide 
sequence database." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001296
name: decoy DB from IPI_zebrafish
def: "OBSOLETE Decoy database from a International Protein Index 
database for Danio rerio." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001297
name: decoy DB from UniProtKB/Swiss-Prot
def: "OBSOLETE Decoy database from a Swiss-Prot protein sequence 
database." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001298
name: decoy DB from IPI_chicken
def: "OBSOLETE Decoy database from a International Protein Index 
database for Gallus gallus." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001299
name: decoy DB from IPI_cow
def: "OBSOLETE Decoy database from a International Protein Index 
database for Bos taurus." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1001300
name: decoy DB from IPI_human
def: "OBSOLETE Decoy database from a International Protein Index 
database for Homo sapiens." [PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

[Term]
id: MS:1002060
name: database UniProtKB/TrEMBL
def: "TrEMBL protein sequence database." [PSI:PI]
is_a: MS:1001013 ! UniProtKB/database name

[Term]
id: MS:1002061
name: decoy DB from UniProtKB/TrEMBL
def: "OBSOLETE Decoy database from a TrEMBL protein sequence database." 
[PSI:PI]
comment: This term was made obsolete, because a combination of database 
name, DB composition , decoy DB type , decoy DB generation algorithm, 
decoy DB accession regexp and decoy DB details suffices.
is_a: MS:1001284 ! decoy DB derived from
is_obsolete: true

************ Added a boolean value type for the three following terms
[Term]
id: MS:1002015
name: spectral count peptide level quantitation
def: "Spectral count peptide level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001836 ! spectral counting quantitation analysis

[Term]
id: MS:1002016
name: spectral count protein level quantitation
def: "Spectral count protein level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001836 ! spectral counting quantitation analysis

[Term]
id: MS:1002017
name: spectral count proteingroup level quantitation
def: "Spectral count proteingroup level quantitation." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1001836 ! spectral counting quantitation analysis

************ Added definitions to the following five terms
[Term]
id: MS:1001267
name: software vendor
def: "Software vendor role." [PSI:PI]
is_a: MS:1001266 ! role type

[Term]
id: MS:1001268
name: programmer
def: "Programmer role." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001266 ! role type

[Term]
id: MS:1001269
name: instrument vendor
def: "Instrument vendor role." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001266 ! role type

[Term]
id: MS:1001270
name: lab personnel
def: "Lab personnel role." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001266 ! role type

[Term]
id: MS:1001271
name: researcher
def: "Researcher role." [PSI:PI]
is_a: MS:1001266 ! role type

************ Changed the name from 'quantitation software comment / 
customizations' to 'quantitation software comment or customizations'
[Term]
id: MS:1001832
name: quantitation software comment or customizations
def: "Quantitation software comment or any customizations to the default 
setup of the software." [PSI:PI]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: MS:1001129 ! quantification information

************ 'tab delimited text file' is now a child of 'intermediate 
analysis format'
[Term]
id: MS:1000914
name: tab delimited text file
def: "A file that has two or more columns of tabular data where each 
column is separated by a TAB character." [PSI:MS]
is_a: MS:1001459 ! file format
is_a: MS:1001040 ! intermediate analysis format

************ Added the definitions to the following 4 terms
[Term]
id: MS:1001430
name: ProteinExtractor:UseMascot
def: "Flag indicating to include Mascot scoring for calculation of the 
ProteinExtractor metascore." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001435
name: ProteinExtractor:UseSequest
def: "Flag indicating to include Sequest scoring for calculation of the 
ProteinExtractor metascore." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001439
name: ProteinExtractor:UseProteinSolver
def: "Flag indicating to include ProteinSolver scoring for calculation 
of the ProteinExtractor metascore." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

[Term]
id: MS:1001443
name: ProteinExtractor:UsePhenyx
def: "Flag indicating to include Phenyx scoring for calculation of the 
ProteinExtractor metascore." [PSI:PI]
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."
is_a: MS:1002098 ! ProteinExtractor input parameter

New Typedef in version 3.38.0 of psi-ms.obo:
============================================
[Typedef]
id: has_order
name: has_order

New CV terms in version 3.38.0 of psi-ms.obo:
=============================================
************ The next two terms were proposed by Julian to indicate if a 
higher or lower score is better.
************ TODO: We should later add a
************ has_order: MS:1002108 ! higher score better
************ or
************ has_order: MS:1002109 ! lower score better
************ to all peptide resp. protein scores.
************ e.g.
************
************ [Term]
************ id: MS:1001155
************ name: Sequest:xcorr
************ def: "The SEQUEST result 'XCorr'." [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
************ has_order: MS:1002108 ! higher score better

[Term]
id: MS:1002108
name: higher score better
def: "Indicates that a higher score is better." [PSI:PI]
relationship: part_of MS:1001153 ! search engine specific score

[Term]
id: MS:1002109
name: lower score better
def: "Indicates that a lower score is better." [PSI:PI]
relationship: part_of MS:1001153 ! search engine specific score

************ The following terms are intended for mzQuantML validation 
and mzQuantML MIAPE conformance checking
************ TODO: Add child terms for them later.
[Term]
id: MS:1002110
name: assay attribute
def: "Attribute describing an assay." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002111
name: assay label attribute
def: "Attribute describing an assay label." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002112
name: protein group list attribute
def: "Attribute describing a protein group list." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002113
name: protein group attribute
def: "Attribute describing a protein group." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002114
name: protein list attribute
def: "Attribute describing a protein list." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002115
name: peptide consensus list attribute
def: "Attribute describing a peptide consensus list." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002116
name: peptide consensus attribute
def: "Attribute describing a peptide consensus." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002117
name: small molecule list attribute
def: "Attribute describing a small mollecule list." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002118
name: small molecule attribute
def: "Attribute describing a small molecule." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002119
name: small molecule modification attribute
def: "Attribute describing a small molecule modification." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002120
name: experiment name
def: "The name for identifying an experiment." [PSI:PI]
is_a: MS:1001806 ! quantification object attribute

[Term]
id: MS:1002121
name: spectral count feature
def: "Dummy decribing a spectral count feature." [PSI:PI]
is_a: MS:1001828 ! feature attribute

[Term]
id: MS:1002122
name: counts reporting
def: "FeatureList of spectral counts." [PSI:PI]
is_a: MS:1001825 ! FeatureList attribute

[Term]
id: MS:1002123
name: x-Tracker
def: "x-Tracker generic tool for quantitative proteomics." 
[http://www.x-tracker.info/]
is_a: MS:1001139 ! quantitation software name

[Term]
id: MS:1002124
name: ProteoSuite
def: "ProteoSuite software for the analysis of quantitative proteomics 
data." [DOI:10.1089/omi.2012.0022, PMID:22804616, 
http://www.proteosuite.org/]
is_a: MS:1001139 ! quantitation software 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