@@ -1,5 +1,5 @@

 //

-// $Id: CVTranslator.cpp 7331 2015-03-24 16:11:12Z chambm $

+// $Id$

 //

 //

 // Original author: Darren Kessner <darren@proteowizard.org>

@@ -133,7 +133,8 @@ bool shouldIgnore(const string& key, CVID value, CVID cvid)

     return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||

             key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14

             key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point

-            key=="de_" && value==MS_DE && cvid==1001274); // conflict between 1000246 and 1001274

+            key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274

+            cvid == UO_volt_second_per_square_centimeter); // conflict between 1002814 200010007 (volt-second per square centimeter) 

 }

@@ -1,5 +1,5 @@

 //

-// $Id: CVTranslator.hpp 1656 2009-12-30 20:54:17Z chambm $

+// $Id$

 //

 //

 // Original author: Darren Kessner <darren@proteowizard.org>

@@ -1,5 +1,5 @@

 //

-// $Id: CVTranslatorTest.cpp 4129 2012-11-20 00:05:37Z chambm $

+// $Id$

 //

 //

 // Original author: Darren Kessner <darren@proteowizard.org>

@@ -1,15 +1,15 @@

 format-version: 1.2

-data-version: 4.0.1

-date: 15:07:2016 14:16

+data-version: 4.1.30

+date: 30:08:2019 16:10

 saved-by: Gerhard Mayer

-auto-generated-by: OBO-Edit 2.3

-import: http://www.berkeleybop.org/ontologies/pato/pato.obo

-import: http://www.berkeleybop.org/ontologies/uo/uo.obo

+auto-generated-by: OBO-Edit 2.3.1

+import: http://ontologies.berkeleybop.org/pato.obo

+import: http://ontologies.berkeleybop.org/uo.obo

 default-namespace: MS

 namespace-id-rule: * MS:$sequence(7,0,9999999)$

+namespace-id-rule: * PEFF:$sequence(7,0,9999999)$

 remark: namespace: MS

-remark: version: 4.0.1

-remark: release date: 2016-07-15

+remark: namespace: PEFF

 remark: coverage: Mass spectrometer output files and spectra interpretation

 remark: creator: Matt Chambers <matt.chambers <-at-> vanderbilt.edu>

 remark: creator: Andreas Bertsch <bertsch <-at-> informatik.uni-tuebingen.de>

@@ -22,8 +22,8 @@ remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standa

 remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page

 remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net

 remark: URL: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

-remark: This work is licensed under the Creative Commons Attribution 3.0 Unported License.

-remark: To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.

+remark: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.

+remark: To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.

 ontology: ms

 [Typedef]

@@ -930,7 +930,6 @@ is_a: MS:1000525 ! spectrum representation

 id: MS:1000129

 name: negative scan

 def: "Polarity of the scan is negative." [PSI:MS]

-is_a: PATO:0002186 ! polarity

 is_a: MS:1000465 ! scan polarity

 is_a: MS:1000808 ! chromatogram attribute

@@ -938,7 +937,6 @@ is_a: MS:1000808 ! chromatogram attribute

 id: MS:1000130

 name: positive scan

 def: "Polarity of the scan is positive." [PSI:MS]

-is_a: PATO:0002186 ! polarity

 is_a: MS:1000465 ! scan polarity

 is_a: MS:1000808 ! chromatogram attribute

@@ -990,7 +988,6 @@ id: MS:1000137

 name: electron volt

 def: "OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J." [PSI:MS]

 comment: This term was made obsolete because it was redundant with the Unit Ontology term electron volt (UO:0000266).

-synonym: "eV" EXACT []

 is_obsolete: true

 [Term]

@@ -1070,7 +1067,7 @@ is_a: MS:1001534 ! Bruker Daltonics flex series

 [Term]

 id: MS:1000150

 name: Auto Spec Ultima NT

-def: "Waters AutoSpec Ultima NT MS." [PSI:MS]

+def: "Waters magnetic sector based AutoSpec Ultima NT MS." [PSI:MS]

 is_a: MS:1000126 ! Waters instrument model

 [Term]

@@ -1304,7 +1301,7 @@ is_a: MS:1000126 ! Waters instrument model

 [Term]

 id: MS:1000189

-name: Q-Tof ultima

+name: Q-Tof Ultima

 def: "Waters oa-ToF based Q-Tof Ultima." [PSI:MS]

 is_a: MS:1000126 ! Waters instrument model

@@ -1317,13 +1314,13 @@ is_a: MS:1000121 ! SCIEX instrument model

 [Term]

 id: MS:1000191

 name: quattro micro

-def: "Waters oa-ToF based micro." [PSI:MS]

+def: "Waters (triple) quadrupole based micro." [PSI:MS]

 is_a: MS:1000126 ! Waters instrument model

 [Term]

 id: MS:1000192

-name: Quattro UItima

-def: "Waters oa-ToF based Ultima." [PSI:MS]

+name: Quattro Ultima

+def: "Waters (triple) quadrupole based Ultima." [PSI:MS]

 is_a: MS:1000126 ! Waters instrument model

 [Term]

@@ -1455,7 +1452,6 @@ is_a: MS:1000231 ! peak

 id: MS:1000211

 name: OBSOLETE charge number

 def: "OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state." [PSI:MS]

-synonym: "z" EXACT []

 xref: value-type:xsd\:int "The allowed value-type for this CV term."

 is_obsolete: true

@@ -1464,7 +1460,6 @@ id: MS:1000212

 name: dalton

 def: "OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg." [PSI:MS]

 comment: This term was made obsolete because it was redundant with the Unit Ontology term dalton (UO:0000221).

-synonym: "Da" EXACT []

 is_obsolete: true

 [Term]

@@ -1644,10 +1639,9 @@ is_obsolete: true

 [Term]

 id: MS:1000235

 name: total ion current chromatogram

-def: "Chromatogram obtained by plotting the total ion current detected in each of a series of mass spectra recorded as a function of retention time." [PSI:MS]

+def: "Representation of the total ion current detected in each of a series of mass spectra versus time." [PSI:MS]

 synonym: "TIC chromatogram" EXACT []

-is_a: MS:1000524 ! data file content

-is_a: MS:1000810 ! mass chromatogram

+is_a: MS:1000810 ! ion current chromatogram

 [Term]

 id: MS:1000236

@@ -2274,7 +2268,6 @@ id: MS:1000322

 name: charge inversion mass spectrum

 def: "The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z." [PSI:MS]

 is_a: MS:1000294 ! mass spectrum

-is_a: MS:1000524 ! data file content

 [Term]

 id: MS:1000323

@@ -2299,7 +2292,6 @@ name: constant neutral gain spectrum

 def: "A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell." [PSI:MS]

 synonym: "constant neutral mass gain spectrum" EXACT []

 is_a: MS:1000294 ! mass spectrum

-is_a: MS:1000524 ! data file content

 [Term]

 id: MS:1000326

@@ -2307,7 +2299,6 @@ name: constant neutral loss spectrum

 def: "A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum." [PSI:MS]

 synonym: "constant neutral mass loss spectrum" EXACT []

 is_a: MS:1000294 ! mass spectrum

-is_a: MS:1000524 ! data file content

 [Term]

 id: MS:1000327

@@ -2413,7 +2404,6 @@ id: MS:1000341

 name: precursor ion spectrum

 def: "Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z." [PSI:MS]

 is_a: MS:1000294 ! mass spectrum

-is_a: MS:1000524 ! data file content

 [Term]

 id: MS:1000342

@@ -2429,7 +2419,6 @@ name: product ion spectrum

 def: "OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions." [PSI:MS]

 comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580).

 is_a: MS:1000294 ! mass spectrum

-is_a: MS:1000524 ! data file content

 is_obsolete: true

 [Term]

@@ -2492,9 +2481,8 @@ is_obsolete: true

 [Term]

 id: MS:1000353

 name: adduct ion

-def: "OBSOLETE Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules." [PSI:MS]

-comment: This child of the former purgatory term ion chemical type was made obsolete.

-is_obsolete: true

+def: "Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules." [PSI:MS]

+is_a: MS:1002806 ! ion

 [Term]

 id: MS:1000354

@@ -3053,7 +3041,7 @@ is_obsolete: true

 id: MS:1000437

 name: ion reaction

 def: "OBSOLETE Chemical transformation involving an ion." [PSI:MS]

-comment: This child of the former purgatory term ion? was made obsolete.

+comment: This child of the former purgatory term ion was made obsolete.

 is_obsolete: true

 [Term]

@@ -3238,7 +3226,7 @@ is_obsolete: true

 [Term]

 id: MS:1000465

 name: scan polarity

-def: "An acquisition mode to which specifies weather polarity is negative, positive or alternating." [PSI:MS]

+def: "Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer." [PSI:MS]

 relationship: part_of MS:1000441 ! scan

 [Term]

@@ -3262,8 +3250,8 @@ is_a: MS:1000490 ! Agilent instrument model

 [Term]

 id: MS:1000469

-name: 6120 Quadrupole LC/MS

-def: "The 6120 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition." [PSI:MS]

+name: 6120A Quadrupole LC/MS

+def: "The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition." [PSI:MS]

 is_a: MS:1000490 ! Agilent instrument model

 [Term]

@@ -3515,21 +3503,21 @@ relationship: has_units UO:0000269 ! absorbance unit

 id: MS:1000506

 name: ion role

 def: "OBSOLETE Ion Role." [PSI:MS]

-comment: This child of the former purgatory term ion? was made obsolete.

+comment: This child of the former purgatory term ion was made obsolete.

 is_obsolete: true

 [Term]

 id: MS:1000507

 name: ion attribute

 def: "OBSOLETE Ion properties that are associated with a value." [PSI:MS]

-comment: This child of the former purgatory term ion? was made obsolete.

+comment: This child of the former purgatory term ion was made obsolete.

 is_obsolete: true

 [Term]

 id: MS:1000508

 name: ion chemical type

 def: "OBSOLETE Ion Type." [PSI:MS]

-comment: This child of the former purgatory term ion? was made obsolete.

+comment: This child of the former purgatory term ion was made obsolete.

 is_obsolete: true

 [Term]

@@ -4021,7 +4009,6 @@ synonym: "Q1 spectrum" EXACT []

 synonym: "Q3 spectrum" EXACT []

 synonym: "Single-Stage Mass Spectrometry" EXACT []

 is_a: MS:1000294 ! mass spectrum

-is_a: MS:1000524 ! data file content

 [Term]

 id: MS:1000580

@@ -4031,14 +4018,12 @@ synonym: "multiple-stage mass spectrometry spectrum" EXACT []

 synonym: "nth generation product ion spectrum" EXACT []

 synonym: "product ion spectrum" EXACT []

 is_a: MS:1000294 ! mass spectrum

-is_a: MS:1000524 ! data file content

 [Term]

 id: MS:1000581

 name: CRM spectrum

 def: "Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS]

 is_a: MS:1000294 ! mass spectrum

-is_a: MS:1000524 ! data file content

 [Term]

 id: MS:1000582

@@ -4048,7 +4033,6 @@ synonym: "MIM spectrum" EXACT []

 synonym: "multiple ion monitoring spectrum" EXACT []

 synonym: "selected ion monitoring spectrum" EXACT []

 is_a: MS:1000294 ! mass spectrum

-is_a: MS:1000524 ! data file content

 [Term]

 id: MS:1000583

@@ -4058,7 +4042,6 @@ synonym: "MRM spectrum" EXACT []

 synonym: "multiple reaction monitoring spectrum" EXACT []

 synonym: "selected reaction monitoring spectrum" EXACT []

 is_a: MS:1000294 ! mass spectrum

-is_a: MS:1000524 ! data file content

 [Term]

 id: MS:1000584

@@ -4342,29 +4325,27 @@ is_a: MS:1000026 ! detector type

 [Term]

 id: MS:1000625

 name: chromatogram

-def: "The representation of detector response versus time." [PSI:MS]

+def: "Representation of a chromatographic separation attribute measurement versus time." [PSI:MS]

 relationship: part_of MS:1001458 ! spectrum generation information

 [Term]

 id: MS:1000626

 name: chromatogram type

-def: "Broad category or type of a chromatogram." [PSI:MS]

+def: "Type of chromatogram measurement being represented." [PSI:MS]

 relationship: part_of MS:1000625 ! chromatogram

 [Term]

 id: MS:1000627

 name: selected ion current chromatogram

-def: "Chromatogram created by creating an array of the measurements of a specific single ion current at each time point." [PSI:MS]

+def: "Representation of an array of the measurements of a specific single ion current versus time." [PSI:MS]

 synonym: "SIC chromatogram" EXACT []

-is_a: MS:1000524 ! data file content

-is_a: MS:1000810 ! mass chromatogram

+is_a: MS:1000810 ! ion current chromatogram

 [Term]

 id: MS:1000628

 name: basepeak chromatogram

-def: "Chromatogram created by creating an array of the most intense peaks at each time point." [PSI:MS]

-is_a: MS:1000524 ! data file content

-is_a: MS:1000810 ! mass chromatogram

+def: "Representation of an array of the most intense peaks versus time." [PSI:MS]

+is_a: MS:1000810 ! ion current chromatogram

 [Term]

 id: MS:1000629

@@ -4693,8 +4674,8 @@ is_a: MS:1000490 ! Agilent instrument model

 [Term]

 id: MS:1000677

-name: 6520 Quadrupole Time-of-Flight LC/MS

-def: "The 6520 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS]

+name: 6520A Quadrupole Time-of-Flight LC/MS

+def: "The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS]

 is_a: MS:1000490 ! Agilent instrument model

 [Term]

@@ -5172,7 +5153,7 @@ is_a: MS:1001486 ! data filtering

 id: MS:1000747

 name: completion time

 def: "The time that a data processing action was finished." [PSI:MS]

-xref: value-type:xsd\:date "The allowed value-type for this CV term."

+xref: value-type:xsd\:dateTime "The allowed value-type for this CV term."

 is_a: MS:1000630 ! data processing parameter

 [Term]

@@ -5463,14 +5444,12 @@ relationship: has_units UO:0000269 ! absorbance unit

 id: MS:1000789

 name: enhanced multiply charged spectrum

 def: "MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions." [PSI:MS]

-is_a: MS:1000524 ! data file content

 is_a: MS:1000579 ! MS1 spectrum

 [Term]

 id: MS:1000790

 name: time-delayed fragmentation spectrum

 def: "MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation." [PSI:MS]

-is_a: MS:1000524 ! data file content

 is_a: MS:1000580 ! MSn spectrum

 [Term]

@@ -5621,15 +5600,15 @@ is_a: MS:1000808 ! chromatogram attribute

 [Term]

 id: MS:1000810

-name: mass chromatogram

-def: "A plot of the relative abundance of a beam or other collection of ions as a function of the retention time." [PSI:MS]

+name: ion current chromatogram

+def: "Representation of the current of ions versus time." [PSI:MS]

 is_a: MS:1000524 ! data file content

 is_a: MS:1000626 ! chromatogram type

 [Term]

 id: MS:1000811

 name: electromagnetic radiation chromatogram

-def: "The measurement of electromagnetic properties as a function of the retention time." [PSI:MS]

+def: "Representation of electromagnetic properties versus time." [PSI:MS]

 synonym: "EMR radiation chromatogram" EXACT []

 is_a: MS:1000524 ! data file content

 is_a: MS:1000626 ! chromatogram type

@@ -5637,15 +5616,13 @@ is_a: MS:1000626 ! chromatogram type

 [Term]

 id: MS:1000812

 name: absorption chromatogram

-def: "The measurement of light absorbed by the sample as a function of the retention time." [PSI:MS]

-is_a: MS:1000524 ! data file content

+def: "Representation of light absorbed by the sample versus time." [PSI:MS]

 is_a: MS:1000811 ! electromagnetic radiation chromatogram

 [Term]

 id: MS:1000813

 name: emission chromatogram

-def: "The measurement of light emitted by the sample as a function of the retention time." [PSI:MS]

-is_a: MS:1000524 ! data file content

+def: "Representation of light emitted by the sample versus time." [PSI:MS]

 is_a: MS:1000811 ! electromagnetic radiation chromatogram

 [Term]

@@ -5693,6 +5670,7 @@ def: "A data array of flow rate measurements." [PSI:MS]

 xref: binary-data-type:MS\:1000521 "32-bit float"

 xref: binary-data-type:MS\:1000523 "64-bit float"

 is_a: MS:1000513 ! binary data array

+relationship: has_units UO:0000271 ! microliters per minute

 [Term]

 id: MS:1000821

@@ -6089,7 +6067,7 @@ relationship: has_units UO:0000218 ! volt

 id: MS:1000878

 name: external reference identifier

 def: "An identifier/accession number to an external reference database." [PSI:MS]

-relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies

+is_a: MS:1002840 ! external reference data

 [Term]

 id: MS:1000879

@@ -6548,9 +6526,9 @@ is_a: MS:1001011 ! search database details

 [Term]

 id: MS:1001016

 name: database version

-def: "OBSOLETE: Use attribute in mzIdentML instead. Version of the search database." [PSI:PI]

+def: "Version of the search database. In mzIdentML use the attribute instead." [PSI:PI]

+xref: value-type:xsd\:string "The allowed value-type for this CV term."

 is_a: MS:1001011 ! search database details

-is_obsolete: true

 [Term]

 id: MS:1001017

@@ -7116,8 +7094,7 @@ name: retention time(s)

 def: "OBSOLETE Retention time of the spectrum from the source file." [PSI:PI]

 comment: This term was made obsolete because scan start time (MS:1000016) should be used instead.

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001105 ! peptide result details

-is_a: MS:1001405 ! spectrum identification result details

+is_a: MS:1001105 ! peptide sequence-level identification attribute

 relationship: has_units UO:0000010 ! second

 relationship: has_units UO:0000031 ! minute

 is_obsolete: true

@@ -7226,7 +7203,7 @@ name: peptide raw area

 def: "OBSOLETE Peptide raw area." [PSI:PI]

 comment: This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844).

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 is_obsolete: true

 [Term]

@@ -7234,35 +7211,35 @@ id: MS:1001131

 name: error on peptide area

 def: "Error on peptide area." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1001132

 name: peptide ratio

 def: "Peptide ratio." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1001133

 name: error on peptide ratio

 def: "Error on peptide ratio." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1001134

 name: protein ratio

 def: "Protein ratio." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002738 ! protein-level quantification datatype

 [Term]

 id: MS:1001135

 name: error on protein ratio

 def: "Error on protein ratio." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002738 ! protein-level quantification datatype

 [Term]

 id: MS:1001136

@@ -7270,7 +7247,7 @@ name: p-value (protein diff from 1 randomly)

 def: "OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI]

 comment: This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855).

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002738 ! protein-level quantification datatype

 is_obsolete: true

 [Term]

@@ -7585,7 +7562,7 @@ name: p-value

 def: "OBSOLETE Quality estimation by p-value." [PSI:PI]

 comment: This term was made obsolete because now is split into peptide and protein terms.

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001092 ! peptide identification confidence metric

+is_a: MS:1001092 ! peptide sequence-level identification statistic

 is_a: MS:1001198 ! protein identification confidence metric

 is_obsolete: true

@@ -7634,7 +7611,7 @@ is_a: MS:1001450 ! decoy DB details

 id: MS:1001198

 name: protein identification confidence metric

 def: "Identification confidence metric for a protein." [PSI:PI]

-is_a: MS:1001116 ! single protein result details

+is_a: MS:1001116 ! single protein identification statistic

 [Term]

 id: MS:1001199

@@ -8230,6 +8207,7 @@ is_a: MS:1002093 ! search engine input parameter

 id: MS:1001303

 name: Arg-C

 def: "Endoproteinase Arg-C." [PSI:PI]

+synonym: "Trypsin/R" EXACT []

 synonym: "Clostripain" EXACT []

 is_a: MS:1001045 ! cleavage agent name

 relationship: has_regexp MS:1001272 ! (?<=R)(?!P)

@@ -8273,6 +8251,7 @@ relationship: has_regexp MS:1001334 ! ((?<=D))|((?=D))

 id: MS:1001309

 name: Lys-C

 def: "Endoproteinase Lys-C." [PSI:PI]

+synonym: "Trypsin/K" EXACT []

 is_a: MS:1001045 ! cleavage agent name

 relationship: has_regexp MS:1001335 ! (?<=K)(?!P)

@@ -9001,13 +8980,13 @@ is_a: MS:1001143 ! PSM-level search engine specific statistic

 [Term]

 id: MS:1001421

 name: pepXML format

-def: "Source file for this mzIdentML was in a pepXML file format." [PSI:PI]

+def: "The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI]

 is_a: MS:1001040 ! intermediate analysis format

 [Term]

 id: MS:1001422

 name: protXML format

-def: "Source file for this mzIdentML was in protXML file format." [PSI:PI]

+def: "The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI]

 is_a: MS:1001040 ! intermediate analysis format

 [Term]

@@ -9333,27 +9312,24 @@ relationship: part_of MS:1001000 ! spectrum interpretation

 [Term]

 id: MS:1001472

 name: selected ion monitoring chromatogram

-def: "Chromatogram created by creating an array of the measurements of a selectively monitored ion at each time point." [PSI:MS]

+def: "Representation of an array of the measurements of a selectively monitored ion versus time." [PSI:MS]

 synonym: "SIM chromatogram" EXACT []

-is_a: MS:1000524 ! data file content

-is_a: MS:1000810 ! mass chromatogram

+is_a: MS:1000810 ! ion current chromatogram

 [Term]

 id: MS:1001473

 name: selected reaction monitoring chromatogram

-def: "Chromatogram created by creating an array of the measurements of a selectively monitored reaction at each time point." [PSI:MS]

+def: "Representation of an array of the measurements of a selectively monitored reaction versus time." [PSI:MS]

 synonym: "SRM chromatogram" EXACT []

-is_a: MS:1000524 ! data file content

-is_a: MS:1000810 ! mass chromatogram

+is_a: MS:1000810 ! ion current chromatogram

 [Term]

 id: MS:1001474

 name: consecutive reaction monitoring chromatogram

-def: "OBSOLETE Chromatogram created by creating an array of the measurements of a series of monitored reactions at each time point." [PSI:MS]

+def: "OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time." [PSI:MS]

 comment: This term was made obsolete because, by design, it can't be properly represented in mzML 1.1. CRM experiments must be represented in a spectrum-centric way.

 synonym: "CRM chromatogram" EXACT []

-is_a: MS:1000524 ! data file content

-is_a: MS:1000810 ! mass chromatogram

+is_a: MS:1000810 ! ion current chromatogram

 is_obsolete: true

 [Term]

@@ -10035,7 +10011,7 @@ id: MS:1001581

 name: FAIMS compensation voltage

 def: "The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion." [PSI:MS]

 synonym: "FAIMS CV" EXACT []

-is_a: MS:1000503 ! scan attribute

+is_a: MS:1002892 ! ion mobility attribute

 [Term]

 id: MS:1001582

@@ -11385,8 +11361,8 @@ is_a: MS:1000126 ! Waters instrument model

 [Term]

 id: MS:1001767

-name: nanoACQUITY UPLC System with Technology

-def: "Waters LC-system nanoACQUITY UPLC System with Technology." [PSI:MS]

+name: nanoACQUITY UPLC System with 1D Technology

+def: "Waters LC-system nanoACQUITY UPLC System with 1D Technology." [PSI:MS]

 is_a: MS:1000126 ! Waters instrument model

 [Term]

@@ -11518,7 +11494,7 @@ is_a: MS:1000126 ! Waters instrument model

 [Term]

 id: MS:1001789

 name: Quattro micro GC

-def: "Waters quadrupole based Quattro micro GC." [PSI:MS]

+def: "Waters (triple) quadrupole based Quattro micro GC." [PSI:MS]

 is_a: MS:1000126 ! Waters instrument model

 [Term]

@@ -11556,8 +11532,8 @@ is_a: MS:1001457 ! data processing software

 [Term]

 id: MS:1001796

-name: Unify

-def: "Waters Unify software for liquid chromatography and mass spectrometry acquisition." [PSI:MS]

+name: UNIFY

+def: "Waters UNIFY software for liquid chromatography and mass spectrometry acquisition." [PSI:MS]

 is_a: MS:1000694 ! Waters software

 is_a: MS:1001456 ! analysis software

 is_a: MS:1001457 ! data processing software

@@ -11618,7 +11594,7 @@ is_a: MS:1001800 ! LECO instrument model

 [Term]

 id: MS:1001805

 name: quantification datatype

-def: "The data type of the value reported in a QuantLayer for a feature, peptide, protein, protein group." [PSI:MS]

+def: "The data type of the value reported in a QuantLayer." [PSI:MS]

 is_a: MS:1001129 ! quantification information

 [Term]

@@ -11817,7 +11793,7 @@ is_a: MS:1001833 ! quantitation analysis summary

 [Term]

 id: MS:1001837

 name: iTRAQ quantitation analysis

-def: "Quantification analysis using the SCIEX iTRAQ isobaric labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near 114 m/z." [PSI:PI]

+def: "Quantification analysis using the SCIEX amine-reactive isobaric tags for relative and absolute quantification (iTRAQ) labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in the 114-121 m/z range." [PSI:PI, PMID:15385600]

 is_a: MS:1002009 ! isobaric label quantitation analysis

 [Term]

@@ -11837,35 +11813,35 @@ id: MS:1001840

 name: LC-MS feature intensity

 def: "Maximum peak intensity of the LC-MS feature." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002735 ! feature-level quantification datatype

 [Term]

 id: MS:1001841

 name: LC-MS feature volume

 def: "Real (intensity times area) volume of the LC-MS feature." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002735 ! feature-level quantification datatype

 [Term]

 id: MS:1001842

-name: peptide PSM count

-def: "The number of MS2 spectra identified for this peptide in spectral counting." [PSI:PI]

+name: sequence-level spectral count

+def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI]

 xref: value-type:xsd\:int "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1001843

 name: MS1 feature maximum intensity

 def: "Maximum intensity of MS1 feature." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002735 ! feature-level quantification datatype

 [Term]

 id: MS:1001844

 name: MS1 feature area

 def: "Area of MS1 feature." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002735 ! feature-level quantification datatype

 [Term]

 id: MS:1001845

@@ -11902,7 +11878,7 @@ name: sum of MatchedFeature values

 def: "OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values." [PSI:PI]

 comment: This term was made obsolete because the concept MatchedFeature was dropped.

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002735 ! feature-level quantification datatype

 is_obsolete: true

 [Term]

@@ -11910,21 +11886,21 @@ id: MS:1001850

 name: normalized peptide value

 def: "Normalized peptide value." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1001851

 name: protein value: sum of peptide values

 def: "Protein quantification value calculated as sum of peptide values." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002738 ! protein-level quantification datatype

 [Term]

 id: MS:1001852

 name: normalized protein value

 def: "Normalized protein value." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002738 ! protein-level quantification datatype

 [Term]

 id: MS:1001853

@@ -11980,7 +11956,7 @@ id: MS:1001860

 name: protein value: mean of peptide ratios

 def: "Protein quantification value calculated as mean of peptide ratios." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002738 ! protein-level quantification datatype

 [Term]

 id: MS:1001861

@@ -12078,7 +12054,7 @@ name: FDRScore

 def: "OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0." [PMID:19253293]

 comment: This term was made obsolete because it was split into the more specific terms for PSM-level FDRScore (1002355), distinct peptide-level FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein group-level FDRScore (MS:1002374).

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001143 ! search engine specific score for PSMs

+is_a: MS:1001143 ! PSM-level search engine specific statistic

 is_a: MS:1001153 ! search engine specific score

 is_obsolete: true

@@ -12108,9 +12084,6 @@ is_a: MS:1001798 ! LECO software

 id: MS:1001878

 name: MALDI Solutions Microbial Identification

 def: "Shimadzu Biotech software for data acquisition, processing, and analysis." [PSI:MS]

-is_a: MS:1001455 ! acquisition software

-is_a: MS:1001456 ! analysis software

-is_a: MS:1001457 ! data processing software

 is_a: MS:1001558 ! MALDI Solutions

 [Term]

@@ -12190,28 +12163,28 @@ id: MS:1001890

 name: Progenesis:protein normalised abundance

 def: "The data type normalised abundance for proteins produced by Progenesis LC-MS." [PSI:MS]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002738 ! protein-level quantification datatype

 [Term]

 id: MS:1001891

 name: Progenesis:peptide normalised abundance

 def: "The data type normalised abundance for peptides produced by Progenesis LC-MS." [PSI:MS]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1001892

 name: Progenesis:protein raw abundance

 def: "The data type raw abundance for proteins produced by Progenesis LC-MS." [PSI:MS]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002738 ! protein-level quantification datatype

 [Term]

 id: MS:1001893

 name: Progenesis:peptide raw abundance

 def: "The data type raw abundance for peptide produced by Progenesis LC-MS." [PSI:MS]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1001894

@@ -12225,42 +12198,42 @@ id: MS:1001895

 name: Progenesis:peptide count

 def: "The data type peptide count produced by Progenesis LC-MS." [PSI:MS]

 xref: value-type:xsd\:int "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1001896

 name: Progenesis:feature intensity

 def: "The data type feature intensity produced by Progenesis LC-MS." [PSI:MS]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002735 ! feature-level quantification datatype

 [Term]

 id: MS:1001897

 name: MaxQuant:peptide counts (unique)

 def: "The data type peptide counts (unique) produced by MaxQuant." [PSI:MS]

 xref: value-type:xsd\:int "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1001898

 name: MaxQuant:peptide counts (all)

 def: "The data type peptide counts (all) produced by MaxQuant." [PSI:MS]

 xref: value-type:xsd\:int "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1001899

 name: MaxQuant:peptide counts (razor+unique)

 def: "The data type peptide counts (razor+unique) produced by MaxQuant." [PSI:MS]

 xref: value-type:xsd\:int "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1001900

 name: MaxQuant:sequence length

 def: "The data type sequence length produced by MaxQuant." [PSI:MS]

 xref: value-type:xsd\:int "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1001901

@@ -12281,7 +12254,7 @@ id: MS:1001903

 name: MaxQuant:feature intensity

 def: "The data type feature intensity produced by MaxQuant." [PSI:MS]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002735 ! feature-level quantification datatype

 [Term]

 id: MS:1001904

@@ -12295,14 +12268,14 @@ id: MS:1001905

 name: emPAI value

 def: "The emPAI value of protein abundance, produced from the emPAI algorithm." [PSI:MS]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002738 ! protein-level quantification datatype

 [Term]

 id: MS:1001906

 name: APEX value

 def: "The APEX value of protein abundance, produced from the APEX software." [PSI:MS]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002738 ! protein-level quantification datatype

 [Term]

 id: MS:1001907

@@ -12417,7 +12390,7 @@ id: MS:1001923

 name: external reference keyword

 def: "Free text attribute that can enrich the information about an entity." [PSI:PI]

 xref: value-type:xsd\:string "The allowed value-type for this CV term."

-is_a: MS:1000878 ! external reference identifier

+is_a: MS:1002840 ! external reference data

 [Term]

 id: MS:1001924

@@ -13015,8 +12988,7 @@ is_a: MS:1001833 ! quantitation analysis summary

 [Term]

 id: MS:1002010

 name: TMT quantitation analysis

-def: "Quantitation analysis using the Thermo Fisher tandem mass tag (TMT) labelling workflow." [PSI:PI]

-is_a: MS:1001833 ! quantitation analysis summary

+def: "Quantitation analysis using the Thermo Fisher amine-reactive tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are measured in MS2 spectra in the 126-131 m/z." [PSI:PI, PMID:12713048]

 is_a: MS:1002009 ! isobaric label quantitation analysis

 [Term]

@@ -13206,9 +13178,9 @@ is_a: MS:1002033 ! contact role

 [Term]

 id: MS:1002038

-name: unlabeled sample

+name: label free sample

 def: "A sample that has not been labelled or modified. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:PI]

-synonym: "light labeled sample" EXACT []

+synonym: "light sample" EXACT []

 is_a: MS:1000548 ! sample attribute

 [Term]

@@ -13395,14 +13367,14 @@ id: MS:1002064

 name: peptide consensus RT

 def: "Peptide consensus retention time." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1002065

 name: peptide consensus m/z

 def: "Peptide consensus mass/charge ratio." [PSI:PI]

 xref: value-type:xsd\:double "The allowed value-type for this CV term."

-is_a: MS:1001805 ! quantification datatype

+is_a: MS:1002737 ! peptide-level quantification datatype

 [Term]

 id: MS:1002066

@@ -13416,7 +13388,7 @@ id: MS:1002067