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Some more files to Update CV

Steffen Neumann authored on 15/10/2019 12:00:14
Showing 4 changed files

... ...
@@ -1,5 +1,5 @@
1 1
 //
2
-// $Id: CVTranslator.cpp 7331 2015-03-24 16:11:12Z chambm $
2
+// $Id$
3 3
 //
4 4
 //
5 5
 // Original author: Darren Kessner <darren@proteowizard.org>
... ...
@@ -133,7 +133,8 @@ bool shouldIgnore(const string& key, CVID value, CVID cvid)
133 133
     return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit ||
134 134
             key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14
135 135
             key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point
136
-            key=="de_" && value==MS_DE && cvid==1001274); // conflict between 1000246 and 1001274
136
+            key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274
137
+            cvid == UO_volt_second_per_square_centimeter); // conflict between 1002814 200010007 (volt-second per square centimeter) 
137 138
 }
138 139
 
139 140
 
... ...
@@ -1,5 +1,5 @@
1 1
 //
2
-// $Id: CVTranslator.hpp 1656 2009-12-30 20:54:17Z chambm $
2
+// $Id$
3 3
 //
4 4
 //
5 5
 // Original author: Darren Kessner <darren@proteowizard.org>
... ...
@@ -1,5 +1,5 @@
1 1
 //
2
-// $Id: CVTranslatorTest.cpp 4129 2012-11-20 00:05:37Z chambm $
2
+// $Id$
3 3
 //
4 4
 //
5 5
 // Original author: Darren Kessner <darren@proteowizard.org>
... ...
@@ -1,15 +1,15 @@
1 1
 format-version: 1.2
2
-data-version: 4.0.1
3
-date: 15:07:2016 14:16
2
+data-version: 4.1.30
3
+date: 30:08:2019 16:10
4 4
 saved-by: Gerhard Mayer
5
-auto-generated-by: OBO-Edit 2.3
6
-import: http://www.berkeleybop.org/ontologies/pato/pato.obo
7
-import: http://www.berkeleybop.org/ontologies/uo/uo.obo
5
+auto-generated-by: OBO-Edit 2.3.1
6
+import: http://ontologies.berkeleybop.org/pato.obo
7
+import: http://ontologies.berkeleybop.org/uo.obo
8 8
 default-namespace: MS
9 9
 namespace-id-rule: * MS:$sequence(7,0,9999999)$
10
+namespace-id-rule: * PEFF:$sequence(7,0,9999999)$
10 11
 remark: namespace: MS
11
-remark: version: 4.0.1
12
-remark: release date: 2016-07-15
12
+remark: namespace: PEFF
13 13
 remark: coverage: Mass spectrometer output files and spectra interpretation
14 14
 remark: creator: Matt Chambers <matt.chambers <-at-> vanderbilt.edu>
15 15
 remark: creator: Andreas Bertsch <bertsch <-at-> informatik.uni-tuebingen.de>
... ...
@@ -22,8 +22,8 @@ remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standa
22 22
 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
23 23
 remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net
24 24
 remark: URL: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
25
-remark: This work is licensed under the Creative Commons Attribution 3.0 Unported License.
26
-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.
25
+remark: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.
26
+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.
27 27
 ontology: ms
28 28
 
29 29
 [Typedef]
... ...
@@ -930,7 +930,6 @@ is_a: MS:1000525 ! spectrum representation
930 930
 id: MS:1000129
931 931
 name: negative scan
932 932
 def: "Polarity of the scan is negative." [PSI:MS]
933
-is_a: PATO:0002186 ! polarity
934 933
 is_a: MS:1000465 ! scan polarity
935 934
 is_a: MS:1000808 ! chromatogram attribute
936 935
 
... ...
@@ -938,7 +937,6 @@ is_a: MS:1000808 ! chromatogram attribute
938 937
 id: MS:1000130
939 938
 name: positive scan
940 939
 def: "Polarity of the scan is positive." [PSI:MS]
941
-is_a: PATO:0002186 ! polarity
942 940
 is_a: MS:1000465 ! scan polarity
943 941
 is_a: MS:1000808 ! chromatogram attribute
944 942
 
... ...
@@ -990,7 +988,6 @@ id: MS:1000137
990 988
 name: electron volt
991 989
 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]
992 990
 comment: This term was made obsolete because it was redundant with the Unit Ontology term electron volt (UO:0000266).
993
-synonym: "eV" EXACT []
994 991
 is_obsolete: true
995 992
 
996 993
 [Term]
... ...
@@ -1070,7 +1067,7 @@ is_a: MS:1001534 ! Bruker Daltonics flex series
1070 1067
 [Term]
1071 1068
 id: MS:1000150
1072 1069
 name: Auto Spec Ultima NT
1073
-def: "Waters AutoSpec Ultima NT MS." [PSI:MS]
1070
+def: "Waters magnetic sector based AutoSpec Ultima NT MS." [PSI:MS]
1074 1071
 is_a: MS:1000126 ! Waters instrument model
1075 1072
 
1076 1073
 [Term]
... ...
@@ -1304,7 +1301,7 @@ is_a: MS:1000126 ! Waters instrument model
1304 1301
 
1305 1302
 [Term]
1306 1303
 id: MS:1000189
1307
-name: Q-Tof ultima
1304
+name: Q-Tof Ultima
1308 1305
 def: "Waters oa-ToF based Q-Tof Ultima." [PSI:MS]
1309 1306
 is_a: MS:1000126 ! Waters instrument model
1310 1307
 
... ...
@@ -1317,13 +1314,13 @@ is_a: MS:1000121 ! SCIEX instrument model
1317 1314
 [Term]
1318 1315
 id: MS:1000191
1319 1316
 name: quattro micro
1320
-def: "Waters oa-ToF based micro." [PSI:MS]
1317
+def: "Waters (triple) quadrupole based micro." [PSI:MS]
1321 1318
 is_a: MS:1000126 ! Waters instrument model
1322 1319
 
1323 1320
 [Term]
1324 1321
 id: MS:1000192
1325
-name: Quattro UItima
1326
-def: "Waters oa-ToF based Ultima." [PSI:MS]
1322
+name: Quattro Ultima
1323
+def: "Waters (triple) quadrupole based Ultima." [PSI:MS]
1327 1324
 is_a: MS:1000126 ! Waters instrument model
1328 1325
 
1329 1326
 [Term]
... ...
@@ -1455,7 +1452,6 @@ is_a: MS:1000231 ! peak
1455 1452
 id: MS:1000211
1456 1453
 name: OBSOLETE charge number
1457 1454
 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]
1458
-synonym: "z" EXACT []
1459 1455
 xref: value-type:xsd\:int "The allowed value-type for this CV term."
1460 1456
 is_obsolete: true
1461 1457
 
... ...
@@ -1464,7 +1460,6 @@ id: MS:1000212
1464 1460
 name: dalton
1465 1461
 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]
1466 1462
 comment: This term was made obsolete because it was redundant with the Unit Ontology term dalton (UO:0000221).
1467
-synonym: "Da" EXACT []
1468 1463
 is_obsolete: true
1469 1464
 
1470 1465
 [Term]
... ...
@@ -1644,10 +1639,9 @@ is_obsolete: true
1644 1639
 [Term]
1645 1640
 id: MS:1000235
1646 1641
 name: total ion current chromatogram
1647
-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]
1642
+def: "Representation of the total ion current detected in each of a series of mass spectra versus time." [PSI:MS]
1648 1643
 synonym: "TIC chromatogram" EXACT []
1649
-is_a: MS:1000524 ! data file content
1650
-is_a: MS:1000810 ! mass chromatogram
1644
+is_a: MS:1000810 ! ion current chromatogram
1651 1645
 
1652 1646
 [Term]
1653 1647
 id: MS:1000236
... ...
@@ -2274,7 +2268,6 @@ id: MS:1000322
2274 2268
 name: charge inversion mass spectrum
2275 2269
 def: "The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z." [PSI:MS]
2276 2270
 is_a: MS:1000294 ! mass spectrum
2277
-is_a: MS:1000524 ! data file content
2278 2271
 
2279 2272
 [Term]
2280 2273
 id: MS:1000323
... ...
@@ -2299,7 +2292,6 @@ name: constant neutral gain spectrum
2299 2292
 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]
2300 2293
 synonym: "constant neutral mass gain spectrum" EXACT []
2301 2294
 is_a: MS:1000294 ! mass spectrum
2302
-is_a: MS:1000524 ! data file content
2303 2295
 
2304 2296
 [Term]
2305 2297
 id: MS:1000326
... ...
@@ -2307,7 +2299,6 @@ name: constant neutral loss spectrum
2307 2299
 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]
2308 2300
 synonym: "constant neutral mass loss spectrum" EXACT []
2309 2301
 is_a: MS:1000294 ! mass spectrum
2310
-is_a: MS:1000524 ! data file content
2311 2302
 
2312 2303
 [Term]
2313 2304
 id: MS:1000327
... ...
@@ -2413,7 +2404,6 @@ id: MS:1000341
2413 2404
 name: precursor ion spectrum
2414 2405
 def: "Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z." [PSI:MS]
2415 2406
 is_a: MS:1000294 ! mass spectrum
2416
-is_a: MS:1000524 ! data file content
2417 2407
 
2418 2408
 [Term]
2419 2409
 id: MS:1000342
... ...
@@ -2429,7 +2419,6 @@ name: product ion spectrum
2429 2419
 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]
2430 2420
 comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580).
2431 2421
 is_a: MS:1000294 ! mass spectrum
2432
-is_a: MS:1000524 ! data file content
2433 2422
 is_obsolete: true
2434 2423
 
2435 2424
 [Term]
... ...
@@ -2492,9 +2481,8 @@ is_obsolete: true
2492 2481
 [Term]
2493 2482
 id: MS:1000353
2494 2483
 name: adduct ion
2495
-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]
2496
-comment: This child of the former purgatory term ion chemical type was made obsolete.
2497
-is_obsolete: true
2484
+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]
2485
+is_a: MS:1002806 ! ion
2498 2486
 
2499 2487
 [Term]
2500 2488
 id: MS:1000354
... ...
@@ -3053,7 +3041,7 @@ is_obsolete: true
3053 3041
 id: MS:1000437
3054 3042
 name: ion reaction
3055 3043
 def: "OBSOLETE Chemical transformation involving an ion." [PSI:MS]
3056
-comment: This child of the former purgatory term ion? was made obsolete.
3044
+comment: This child of the former purgatory term ion was made obsolete.
3057 3045
 is_obsolete: true
3058 3046
 
3059 3047
 [Term]
... ...
@@ -3238,7 +3226,7 @@ is_obsolete: true
3238 3226
 [Term]
3239 3227
 id: MS:1000465
3240 3228
 name: scan polarity
3241
-def: "An acquisition mode to which specifies weather polarity is negative, positive or alternating." [PSI:MS]
3229
+def: "Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer." [PSI:MS]
3242 3230
 relationship: part_of MS:1000441 ! scan
3243 3231
 
3244 3232
 [Term]
... ...
@@ -3262,8 +3250,8 @@ is_a: MS:1000490 ! Agilent instrument model
3262 3250
 
3263 3251
 [Term]
3264 3252
 id: MS:1000469
3265
-name: 6120 Quadrupole LC/MS
3266
-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]
3253
+name: 6120A Quadrupole LC/MS
3254
+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]
3267 3255
 is_a: MS:1000490 ! Agilent instrument model
3268 3256
 
3269 3257
 [Term]
... ...
@@ -3515,21 +3503,21 @@ relationship: has_units UO:0000269 ! absorbance unit
3515 3503
 id: MS:1000506
3516 3504
 name: ion role
3517 3505
 def: "OBSOLETE Ion Role." [PSI:MS]
3518
-comment: This child of the former purgatory term ion? was made obsolete.
3506
+comment: This child of the former purgatory term ion was made obsolete.
3519 3507
 is_obsolete: true
3520 3508
 
3521 3509
 [Term]
3522 3510
 id: MS:1000507
3523 3511
 name: ion attribute
3524 3512
 def: "OBSOLETE Ion properties that are associated with a value." [PSI:MS]
3525
-comment: This child of the former purgatory term ion? was made obsolete.
3513
+comment: This child of the former purgatory term ion was made obsolete.
3526 3514
 is_obsolete: true
3527 3515
 
3528 3516
 [Term]
3529 3517
 id: MS:1000508
3530 3518
 name: ion chemical type
3531 3519
 def: "OBSOLETE Ion Type." [PSI:MS]
3532
-comment: This child of the former purgatory term ion? was made obsolete.
3520
+comment: This child of the former purgatory term ion was made obsolete.
3533 3521
 is_obsolete: true
3534 3522
 
3535 3523
 [Term]
... ...
@@ -4021,7 +4009,6 @@ synonym: "Q1 spectrum" EXACT []
4021 4009
 synonym: "Q3 spectrum" EXACT []
4022 4010
 synonym: "Single-Stage Mass Spectrometry" EXACT []
4023 4011
 is_a: MS:1000294 ! mass spectrum
4024
-is_a: MS:1000524 ! data file content
4025 4012
 
4026 4013
 [Term]
4027 4014
 id: MS:1000580
... ...
@@ -4031,14 +4018,12 @@ synonym: "multiple-stage mass spectrometry spectrum" EXACT []
4031 4018
 synonym: "nth generation product ion spectrum" EXACT []
4032 4019
 synonym: "product ion spectrum" EXACT []
4033 4020
 is_a: MS:1000294 ! mass spectrum
4034
-is_a: MS:1000524 ! data file content
4035 4021
 
4036 4022
 [Term]
4037 4023
 id: MS:1000581
4038 4024
 name: CRM spectrum
4039 4025
 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]
4040 4026
 is_a: MS:1000294 ! mass spectrum
4041
-is_a: MS:1000524 ! data file content
4042 4027
 
4043 4028
 [Term]
4044 4029
 id: MS:1000582
... ...
@@ -4048,7 +4033,6 @@ synonym: "MIM spectrum" EXACT []
4048 4033
 synonym: "multiple ion monitoring spectrum" EXACT []
4049 4034
 synonym: "selected ion monitoring spectrum" EXACT []
4050 4035
 is_a: MS:1000294 ! mass spectrum
4051
-is_a: MS:1000524 ! data file content
4052 4036
 
4053 4037
 [Term]
4054 4038
 id: MS:1000583
... ...
@@ -4058,7 +4042,6 @@ synonym: "MRM spectrum" EXACT []
4058 4042
 synonym: "multiple reaction monitoring spectrum" EXACT []
4059 4043
 synonym: "selected reaction monitoring spectrum" EXACT []
4060 4044
 is_a: MS:1000294 ! mass spectrum
4061
-is_a: MS:1000524 ! data file content
4062 4045
 
4063 4046
 [Term]
4064 4047
 id: MS:1000584
... ...
@@ -4342,29 +4325,27 @@ is_a: MS:1000026 ! detector type
4342 4325
 [Term]
4343 4326
 id: MS:1000625
4344 4327
 name: chromatogram
4345
-def: "The representation of detector response versus time." [PSI:MS]
4328
+def: "Representation of a chromatographic separation attribute measurement versus time." [PSI:MS]
4346 4329
 relationship: part_of MS:1001458 ! spectrum generation information
4347 4330
 
4348 4331
 [Term]
4349 4332
 id: MS:1000626
4350 4333
 name: chromatogram type
4351
-def: "Broad category or type of a chromatogram." [PSI:MS]
4334
+def: "Type of chromatogram measurement being represented." [PSI:MS]
4352 4335
 relationship: part_of MS:1000625 ! chromatogram
4353 4336
 
4354 4337
 [Term]
4355 4338
 id: MS:1000627
4356 4339
 name: selected ion current chromatogram
4357
-def: "Chromatogram created by creating an array of the measurements of a specific single ion current at each time point." [PSI:MS]
4340
+def: "Representation of an array of the measurements of a specific single ion current versus time." [PSI:MS]
4358 4341
 synonym: "SIC chromatogram" EXACT []
4359
-is_a: MS:1000524 ! data file content
4360
-is_a: MS:1000810 ! mass chromatogram
4342
+is_a: MS:1000810 ! ion current chromatogram
4361 4343
 
4362 4344
 [Term]
4363 4345
 id: MS:1000628
4364 4346
 name: basepeak chromatogram
4365
-def: "Chromatogram created by creating an array of the most intense peaks at each time point." [PSI:MS]
4366
-is_a: MS:1000524 ! data file content
4367
-is_a: MS:1000810 ! mass chromatogram
4347
+def: "Representation of an array of the most intense peaks versus time." [PSI:MS]
4348
+is_a: MS:1000810 ! ion current chromatogram
4368 4349
 
4369 4350
 [Term]
4370 4351
 id: MS:1000629
... ...
@@ -4693,8 +4674,8 @@ is_a: MS:1000490 ! Agilent instrument model
4693 4674
 
4694 4675
 [Term]
4695 4676
 id: MS:1000677
4696
-name: 6520 Quadrupole Time-of-Flight LC/MS
4697
-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]
4677
+name: 6520A Quadrupole Time-of-Flight LC/MS
4678
+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]
4698 4679
 is_a: MS:1000490 ! Agilent instrument model
4699 4680
 
4700 4681
 [Term]
... ...
@@ -5172,7 +5153,7 @@ is_a: MS:1001486 ! data filtering
5172 5153
 id: MS:1000747
5173 5154
 name: completion time
5174 5155
 def: "The time that a data processing action was finished." [PSI:MS]
5175
-xref: value-type:xsd\:date "The allowed value-type for this CV term."
5156
+xref: value-type:xsd\:dateTime "The allowed value-type for this CV term."
5176 5157
 is_a: MS:1000630 ! data processing parameter
5177 5158
 
5178 5159
 [Term]
... ...
@@ -5463,14 +5444,12 @@ relationship: has_units UO:0000269 ! absorbance unit
5463 5444
 id: MS:1000789
5464 5445
 name: enhanced multiply charged spectrum
5465 5446
 def: "MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions." [PSI:MS]
5466
-is_a: MS:1000524 ! data file content
5467 5447
 is_a: MS:1000579 ! MS1 spectrum
5468 5448
 
5469 5449
 [Term]
5470 5450
 id: MS:1000790
5471 5451
 name: time-delayed fragmentation spectrum
5472 5452
 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]
5473
-is_a: MS:1000524 ! data file content
5474 5453
 is_a: MS:1000580 ! MSn spectrum
5475 5454
 
5476 5455
 [Term]
... ...
@@ -5621,15 +5600,15 @@ is_a: MS:1000808 ! chromatogram attribute
5621 5600
 
5622 5601
 [Term]
5623 5602
 id: MS:1000810
5624
-name: mass chromatogram
5625
-def: "A plot of the relative abundance of a beam or other collection of ions as a function of the retention time." [PSI:MS]
5603
+name: ion current chromatogram
5604
+def: "Representation of the current of ions versus time." [PSI:MS]
5626 5605
 is_a: MS:1000524 ! data file content
5627 5606
 is_a: MS:1000626 ! chromatogram type
5628 5607
 
5629 5608
 [Term]
5630 5609
 id: MS:1000811
5631 5610
 name: electromagnetic radiation chromatogram
5632
-def: "The measurement of electromagnetic properties as a function of the retention time." [PSI:MS]
5611
+def: "Representation of electromagnetic properties versus time." [PSI:MS]
5633 5612
 synonym: "EMR radiation chromatogram" EXACT []
5634 5613
 is_a: MS:1000524 ! data file content
5635 5614
 is_a: MS:1000626 ! chromatogram type
... ...
@@ -5637,15 +5616,13 @@ is_a: MS:1000626 ! chromatogram type
5637 5616
 [Term]
5638 5617
 id: MS:1000812
5639 5618
 name: absorption chromatogram
5640
-def: "The measurement of light absorbed by the sample as a function of the retention time." [PSI:MS]
5641
-is_a: MS:1000524 ! data file content
5619
+def: "Representation of light absorbed by the sample versus time." [PSI:MS]
5642 5620
 is_a: MS:1000811 ! electromagnetic radiation chromatogram
5643 5621
 
5644 5622
 [Term]
5645 5623
 id: MS:1000813
5646 5624
 name: emission chromatogram
5647
-def: "The measurement of light emitted by the sample as a function of the retention time." [PSI:MS]
5648
-is_a: MS:1000524 ! data file content
5625
+def: "Representation of light emitted by the sample versus time." [PSI:MS]
5649 5626
 is_a: MS:1000811 ! electromagnetic radiation chromatogram
5650 5627
 
5651 5628
 [Term]
... ...
@@ -5693,6 +5670,7 @@ def: "A data array of flow rate measurements." [PSI:MS]
5693 5670
 xref: binary-data-type:MS\:1000521 "32-bit float"
5694 5671
 xref: binary-data-type:MS\:1000523 "64-bit float"
5695 5672
 is_a: MS:1000513 ! binary data array
5673
+relationship: has_units UO:0000271 ! microliters per minute
5696 5674
 
5697 5675
 [Term]
5698 5676
 id: MS:1000821
... ...
@@ -6089,7 +6067,7 @@ relationship: has_units UO:0000218 ! volt
6089 6067
 id: MS:1000878
6090 6068
 name: external reference identifier
6091 6069
 def: "An identifier/accession number to an external reference database." [PSI:MS]
6092
-relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies
6070
+is_a: MS:1002840 ! external reference data
6093 6071
 
6094 6072
 [Term]
6095 6073
 id: MS:1000879
... ...
@@ -6548,9 +6526,9 @@ is_a: MS:1001011 ! search database details
6548 6526
 [Term]
6549 6527
 id: MS:1001016
6550 6528
 name: database version
6551
-def: "OBSOLETE: Use attribute in mzIdentML instead. Version of the search database." [PSI:PI]
6529
+def: "Version of the search database. In mzIdentML use the attribute instead." [PSI:PI]
6530
+xref: value-type:xsd\:string "The allowed value-type for this CV term."
6552 6531
 is_a: MS:1001011 ! search database details
6553
-is_obsolete: true
6554 6532
 
6555 6533
 [Term]
6556 6534
 id: MS:1001017
... ...
@@ -7116,8 +7094,7 @@ name: retention time(s)
7116 7094
 def: "OBSOLETE Retention time of the spectrum from the source file." [PSI:PI]
7117 7095
 comment: This term was made obsolete because scan start time (MS:1000016) should be used instead.
7118 7096
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
7119
-is_a: MS:1001105 ! peptide result details
7120
-is_a: MS:1001405 ! spectrum identification result details
7097
+is_a: MS:1001105 ! peptide sequence-level identification attribute
7121 7098
 relationship: has_units UO:0000010 ! second
7122 7099
 relationship: has_units UO:0000031 ! minute
7123 7100
 is_obsolete: true
... ...
@@ -7226,7 +7203,7 @@ name: peptide raw area
7226 7203
 def: "OBSOLETE Peptide raw area." [PSI:PI]
7227 7204
 comment: This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844).
7228 7205
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
7229
-is_a: MS:1001805 ! quantification datatype
7206
+is_a: MS:1002737 ! peptide-level quantification datatype
7230 7207
 is_obsolete: true
7231 7208
 
7232 7209
 [Term]
... ...
@@ -7234,35 +7211,35 @@ id: MS:1001131
7234 7211
 name: error on peptide area
7235 7212
 def: "Error on peptide area." [PSI:PI]
7236 7213
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
7237
-is_a: MS:1001805 ! quantification datatype
7214
+is_a: MS:1002737 ! peptide-level quantification datatype
7238 7215
 
7239 7216
 [Term]
7240 7217
 id: MS:1001132
7241 7218
 name: peptide ratio
7242 7219
 def: "Peptide ratio." [PSI:PI]
7243 7220
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
7244
-is_a: MS:1001805 ! quantification datatype
7221
+is_a: MS:1002737 ! peptide-level quantification datatype
7245 7222
 
7246 7223
 [Term]
7247 7224
 id: MS:1001133
7248 7225
 name: error on peptide ratio
7249 7226
 def: "Error on peptide ratio." [PSI:PI]
7250 7227
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
7251
-is_a: MS:1001805 ! quantification datatype
7228
+is_a: MS:1002737 ! peptide-level quantification datatype
7252 7229
 
7253 7230
 [Term]
7254 7231
 id: MS:1001134
7255 7232
 name: protein ratio
7256 7233
 def: "Protein ratio." [PSI:PI]
7257 7234
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
7258
-is_a: MS:1001805 ! quantification datatype
7235
+is_a: MS:1002738 ! protein-level quantification datatype
7259 7236
 
7260 7237
 [Term]
7261 7238
 id: MS:1001135
7262 7239
 name: error on protein ratio
7263 7240
 def: "Error on protein ratio." [PSI:PI]
7264 7241
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
7265
-is_a: MS:1001805 ! quantification datatype
7242
+is_a: MS:1002738 ! protein-level quantification datatype
7266 7243
 
7267 7244
 [Term]
7268 7245
 id: MS:1001136
... ...
@@ -7270,7 +7247,7 @@ name: p-value (protein diff from 1 randomly)
7270 7247
 def: "OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI]
7271 7248
 comment: This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855).
7272 7249
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
7273
-is_a: MS:1001805 ! quantification datatype
7250
+is_a: MS:1002738 ! protein-level quantification datatype
7274 7251
 is_obsolete: true
7275 7252
 
7276 7253
 [Term]
... ...
@@ -7585,7 +7562,7 @@ name: p-value
7585 7562
 def: "OBSOLETE Quality estimation by p-value." [PSI:PI]
7586 7563
 comment: This term was made obsolete because now is split into peptide and protein terms.
7587 7564
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
7588
-is_a: MS:1001092 ! peptide identification confidence metric
7565
+is_a: MS:1001092 ! peptide sequence-level identification statistic
7589 7566
 is_a: MS:1001198 ! protein identification confidence metric
7590 7567
 is_obsolete: true
7591 7568
 
... ...
@@ -7634,7 +7611,7 @@ is_a: MS:1001450 ! decoy DB details
7634 7611
 id: MS:1001198
7635 7612
 name: protein identification confidence metric
7636 7613
 def: "Identification confidence metric for a protein." [PSI:PI]
7637
-is_a: MS:1001116 ! single protein result details
7614
+is_a: MS:1001116 ! single protein identification statistic
7638 7615
 
7639 7616
 [Term]
7640 7617
 id: MS:1001199
... ...
@@ -8230,6 +8207,7 @@ is_a: MS:1002093 ! search engine input parameter
8230 8207
 id: MS:1001303
8231 8208
 name: Arg-C
8232 8209
 def: "Endoproteinase Arg-C." [PSI:PI]
8210
+synonym: "Trypsin/R" EXACT []
8233 8211
 synonym: "Clostripain" EXACT []
8234 8212
 is_a: MS:1001045 ! cleavage agent name
8235 8213
 relationship: has_regexp MS:1001272 ! (?<=R)(?!P)
... ...
@@ -8273,6 +8251,7 @@ relationship: has_regexp MS:1001334 ! ((?<=D))|((?=D))
8273 8251
 id: MS:1001309
8274 8252
 name: Lys-C
8275 8253
 def: "Endoproteinase Lys-C." [PSI:PI]
8254
+synonym: "Trypsin/K" EXACT []
8276 8255
 is_a: MS:1001045 ! cleavage agent name
8277 8256
 relationship: has_regexp MS:1001335 ! (?<=K)(?!P)
8278 8257
 
... ...
@@ -9001,13 +8980,13 @@ is_a: MS:1001143 ! PSM-level search engine specific statistic
9001 8980
 [Term]
9002 8981
 id: MS:1001421
9003 8982
 name: pepXML format
9004
-def: "Source file for this mzIdentML was in a pepXML file format." [PSI:PI]
8983
+def: "The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI]
9005 8984
 is_a: MS:1001040 ! intermediate analysis format
9006 8985
 
9007 8986
 [Term]
9008 8987
 id: MS:1001422
9009 8988
 name: protXML format
9010
-def: "Source file for this mzIdentML was in protXML file format." [PSI:PI]
8989
+def: "The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI]
9011 8990
 is_a: MS:1001040 ! intermediate analysis format
9012 8991
 
9013 8992
 [Term]
... ...
@@ -9333,27 +9312,24 @@ relationship: part_of MS:1001000 ! spectrum interpretation
9333 9312
 [Term]
9334 9313
 id: MS:1001472
9335 9314
 name: selected ion monitoring chromatogram
9336
-def: "Chromatogram created by creating an array of the measurements of a selectively monitored ion at each time point." [PSI:MS]
9315
+def: "Representation of an array of the measurements of a selectively monitored ion versus time." [PSI:MS]
9337 9316
 synonym: "SIM chromatogram" EXACT []
9338
-is_a: MS:1000524 ! data file content
9339
-is_a: MS:1000810 ! mass chromatogram
9317
+is_a: MS:1000810 ! ion current chromatogram
9340 9318
 
9341 9319
 [Term]
9342 9320
 id: MS:1001473
9343 9321
 name: selected reaction monitoring chromatogram
9344
-def: "Chromatogram created by creating an array of the measurements of a selectively monitored reaction at each time point." [PSI:MS]
9322
+def: "Representation of an array of the measurements of a selectively monitored reaction versus time." [PSI:MS]
9345 9323
 synonym: "SRM chromatogram" EXACT []
9346
-is_a: MS:1000524 ! data file content
9347
-is_a: MS:1000810 ! mass chromatogram
9324
+is_a: MS:1000810 ! ion current chromatogram
9348 9325
 
9349 9326
 [Term]
9350 9327
 id: MS:1001474
9351 9328
 name: consecutive reaction monitoring chromatogram
9352
-def: "OBSOLETE Chromatogram created by creating an array of the measurements of a series of monitored reactions at each time point." [PSI:MS]
9329
+def: "OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time." [PSI:MS]
9353 9330
 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.
9354 9331
 synonym: "CRM chromatogram" EXACT []
9355
-is_a: MS:1000524 ! data file content
9356
-is_a: MS:1000810 ! mass chromatogram
9332
+is_a: MS:1000810 ! ion current chromatogram
9357 9333
 is_obsolete: true
9358 9334
 
9359 9335
 [Term]
... ...
@@ -10035,7 +10011,7 @@ id: MS:1001581
10035 10011
 name: FAIMS compensation voltage
10036 10012
 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]
10037 10013
 synonym: "FAIMS CV" EXACT []
10038
-is_a: MS:1000503 ! scan attribute
10014
+is_a: MS:1002892 ! ion mobility attribute
10039 10015
 
10040 10016
 [Term]
10041 10017
 id: MS:1001582
... ...
@@ -11385,8 +11361,8 @@ is_a: MS:1000126 ! Waters instrument model
11385 11361
 
11386 11362
 [Term]
11387 11363
 id: MS:1001767
11388
-name: nanoACQUITY UPLC System with Technology
11389
-def: "Waters LC-system nanoACQUITY UPLC System with Technology." [PSI:MS]
11364
+name: nanoACQUITY UPLC System with 1D Technology
11365
+def: "Waters LC-system nanoACQUITY UPLC System with 1D Technology." [PSI:MS]
11390 11366
 is_a: MS:1000126 ! Waters instrument model
11391 11367
 
11392 11368
 [Term]
... ...
@@ -11518,7 +11494,7 @@ is_a: MS:1000126 ! Waters instrument model
11518 11494
 [Term]
11519 11495
 id: MS:1001789
11520 11496
 name: Quattro micro GC
11521
-def: "Waters quadrupole based Quattro micro GC." [PSI:MS]
11497
+def: "Waters (triple) quadrupole based Quattro micro GC." [PSI:MS]
11522 11498
 is_a: MS:1000126 ! Waters instrument model
11523 11499
 
11524 11500
 [Term]
... ...
@@ -11556,8 +11532,8 @@ is_a: MS:1001457 ! data processing software
11556 11532
 
11557 11533
 [Term]
11558 11534
 id: MS:1001796
11559
-name: Unify
11560
-def: "Waters Unify software for liquid chromatography and mass spectrometry acquisition." [PSI:MS]
11535
+name: UNIFY
11536
+def: "Waters UNIFY software for liquid chromatography and mass spectrometry acquisition." [PSI:MS]
11561 11537
 is_a: MS:1000694 ! Waters software
11562 11538
 is_a: MS:1001456 ! analysis software
11563 11539
 is_a: MS:1001457 ! data processing software
... ...
@@ -11618,7 +11594,7 @@ is_a: MS:1001800 ! LECO instrument model
11618 11594
 [Term]
11619 11595
 id: MS:1001805
11620 11596
 name: quantification datatype
11621
-def: "The data type of the value reported in a QuantLayer for a feature, peptide, protein, protein group." [PSI:MS]
11597
+def: "The data type of the value reported in a QuantLayer." [PSI:MS]
11622 11598
 is_a: MS:1001129 ! quantification information
11623 11599
 
11624 11600
 [Term]
... ...
@@ -11817,7 +11793,7 @@ is_a: MS:1001833 ! quantitation analysis summary
11817 11793
 [Term]
11818 11794
 id: MS:1001837
11819 11795
 name: iTRAQ quantitation analysis
11820
-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]
11796
+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]
11821 11797
 is_a: MS:1002009 ! isobaric label quantitation analysis
11822 11798
 
11823 11799
 [Term]
... ...
@@ -11837,35 +11813,35 @@ id: MS:1001840
11837 11813
 name: LC-MS feature intensity
11838 11814
 def: "Maximum peak intensity of the LC-MS feature." [PSI:PI]
11839 11815
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
11840
-is_a: MS:1001805 ! quantification datatype
11816
+is_a: MS:1002735 ! feature-level quantification datatype
11841 11817
 
11842 11818
 [Term]
11843 11819
 id: MS:1001841
11844 11820
 name: LC-MS feature volume
11845 11821
 def: "Real (intensity times area) volume of the LC-MS feature." [PSI:PI]
11846 11822
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
11847
-is_a: MS:1001805 ! quantification datatype
11823
+is_a: MS:1002735 ! feature-level quantification datatype
11848 11824
 
11849 11825
 [Term]
11850 11826
 id: MS:1001842
11851
-name: peptide PSM count
11852
-def: "The number of MS2 spectra identified for this peptide in spectral counting." [PSI:PI]
11827
+name: sequence-level spectral count
11828
+def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI]
11853 11829
 xref: value-type:xsd\:int "The allowed value-type for this CV term."
11854
-is_a: MS:1001805 ! quantification datatype
11830
+is_a: MS:1002737 ! peptide-level quantification datatype
11855 11831
 
11856 11832
 [Term]
11857 11833
 id: MS:1001843
11858 11834
 name: MS1 feature maximum intensity
11859 11835
 def: "Maximum intensity of MS1 feature." [PSI:PI]
11860 11836
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
11861
-is_a: MS:1001805 ! quantification datatype
11837
+is_a: MS:1002735 ! feature-level quantification datatype
11862 11838
 
11863 11839
 [Term]
11864 11840
 id: MS:1001844
11865 11841
 name: MS1 feature area
11866 11842
 def: "Area of MS1 feature." [PSI:PI]
11867 11843
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
11868
-is_a: MS:1001805 ! quantification datatype
11844
+is_a: MS:1002735 ! feature-level quantification datatype
11869 11845
 
11870 11846
 [Term]
11871 11847
 id: MS:1001845
... ...
@@ -11902,7 +11878,7 @@ name: sum of MatchedFeature values
11902 11878
 def: "OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values." [PSI:PI]
11903 11879
 comment: This term was made obsolete because the concept MatchedFeature was dropped.
11904 11880
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
11905
-is_a: MS:1001805 ! quantification datatype
11881
+is_a: MS:1002735 ! feature-level quantification datatype
11906 11882
 is_obsolete: true
11907 11883
 
11908 11884
 [Term]
... ...
@@ -11910,21 +11886,21 @@ id: MS:1001850
11910 11886
 name: normalized peptide value
11911 11887
 def: "Normalized peptide value." [PSI:PI]
11912 11888
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
11913
-is_a: MS:1001805 ! quantification datatype
11889
+is_a: MS:1002737 ! peptide-level quantification datatype
11914 11890
 
11915 11891
 [Term]
11916 11892
 id: MS:1001851
11917 11893
 name: protein value: sum of peptide values
11918 11894
 def: "Protein quantification value calculated as sum of peptide values." [PSI:PI]
11919 11895
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
11920
-is_a: MS:1001805 ! quantification datatype
11896
+is_a: MS:1002738 ! protein-level quantification datatype
11921 11897
 
11922 11898
 [Term]
11923 11899
 id: MS:1001852
11924 11900
 name: normalized protein value
11925 11901
 def: "Normalized protein value." [PSI:PI]
11926 11902
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
11927
-is_a: MS:1001805 ! quantification datatype
11903
+is_a: MS:1002738 ! protein-level quantification datatype
11928 11904
 
11929 11905
 [Term]
11930 11906
 id: MS:1001853
... ...
@@ -11980,7 +11956,7 @@ id: MS:1001860
11980 11956
 name: protein value: mean of peptide ratios
11981 11957
 def: "Protein quantification value calculated as mean of peptide ratios." [PSI:PI]
11982 11958
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
11983
-is_a: MS:1001805 ! quantification datatype
11959
+is_a: MS:1002738 ! protein-level quantification datatype
11984 11960
 
11985 11961
 [Term]
11986 11962
 id: MS:1001861
... ...
@@ -12078,7 +12054,7 @@ name: FDRScore
12078 12054
 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]
12079 12055
 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).
12080 12056
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
12081
-is_a: MS:1001143 ! search engine specific score for PSMs
12057
+is_a: MS:1001143 ! PSM-level search engine specific statistic
12082 12058
 is_a: MS:1001153 ! search engine specific score
12083 12059
 is_obsolete: true
12084 12060
 
... ...
@@ -12108,9 +12084,6 @@ is_a: MS:1001798 ! LECO software
12108 12084
 id: MS:1001878
12109 12085
 name: MALDI Solutions Microbial Identification
12110 12086
 def: "Shimadzu Biotech software for data acquisition, processing, and analysis." [PSI:MS]
12111
-is_a: MS:1001455 ! acquisition software
12112
-is_a: MS:1001456 ! analysis software
12113
-is_a: MS:1001457 ! data processing software
12114 12087
 is_a: MS:1001558 ! MALDI Solutions
12115 12088
 
12116 12089
 [Term]
... ...
@@ -12190,28 +12163,28 @@ id: MS:1001890
12190 12163
 name: Progenesis:protein normalised abundance
12191 12164
 def: "The data type normalised abundance for proteins produced by Progenesis LC-MS." [PSI:MS]
12192 12165
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
12193
-is_a: MS:1001805 ! quantification datatype
12166
+is_a: MS:1002738 ! protein-level quantification datatype
12194 12167
 
12195 12168
 [Term]
12196 12169
 id: MS:1001891
12197 12170
 name: Progenesis:peptide normalised abundance
12198 12171
 def: "The data type normalised abundance for peptides produced by Progenesis LC-MS." [PSI:MS]
12199 12172
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
12200
-is_a: MS:1001805 ! quantification datatype
12173
+is_a: MS:1002737 ! peptide-level quantification datatype
12201 12174
 
12202 12175
 [Term]
12203 12176
 id: MS:1001892
12204 12177
 name: Progenesis:protein raw abundance
12205 12178
 def: "The data type raw abundance for proteins produced by Progenesis LC-MS." [PSI:MS]
12206 12179
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
12207
-is_a: MS:1001805 ! quantification datatype
12180
+is_a: MS:1002738 ! protein-level quantification datatype
12208 12181
 
12209 12182
 [Term]
12210 12183
 id: MS:1001893
12211 12184
 name: Progenesis:peptide raw abundance
12212 12185
 def: "The data type raw abundance for peptide produced by Progenesis LC-MS." [PSI:MS]
12213 12186
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
12214
-is_a: MS:1001805 ! quantification datatype
12187
+is_a: MS:1002737 ! peptide-level quantification datatype
12215 12188
 
12216 12189
 [Term]
12217 12190
 id: MS:1001894
... ...
@@ -12225,42 +12198,42 @@ id: MS:1001895
12225 12198
 name: Progenesis:peptide count
12226 12199
 def: "The data type peptide count produced by Progenesis LC-MS." [PSI:MS]
12227 12200
 xref: value-type:xsd\:int "The allowed value-type for this CV term."
12228
-is_a: MS:1001805 ! quantification datatype
12201
+is_a: MS:1002737 ! peptide-level quantification datatype
12229 12202
 
12230 12203
 [Term]
12231 12204
 id: MS:1001896
12232 12205
 name: Progenesis:feature intensity
12233 12206
 def: "The data type feature intensity produced by Progenesis LC-MS." [PSI:MS]
12234 12207
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
12235
-is_a: MS:1001805 ! quantification datatype
12208
+is_a: MS:1002735 ! feature-level quantification datatype
12236 12209
 
12237 12210
 [Term]
12238 12211
 id: MS:1001897
12239 12212
 name: MaxQuant:peptide counts (unique)
12240 12213
 def: "The data type peptide counts (unique) produced by MaxQuant." [PSI:MS]
12241 12214
 xref: value-type:xsd\:int "The allowed value-type for this CV term."
12242
-is_a: MS:1001805 ! quantification datatype
12215
+is_a: MS:1002737 ! peptide-level quantification datatype
12243 12216
 
12244 12217
 [Term]
12245 12218
 id: MS:1001898
12246 12219
 name: MaxQuant:peptide counts (all)
12247 12220
 def: "The data type peptide counts (all) produced by MaxQuant." [PSI:MS]
12248 12221
 xref: value-type:xsd\:int "The allowed value-type for this CV term."
12249
-is_a: MS:1001805 ! quantification datatype
12222
+is_a: MS:1002737 ! peptide-level quantification datatype
12250 12223
 
12251 12224
 [Term]
12252 12225
 id: MS:1001899
12253 12226
 name: MaxQuant:peptide counts (razor+unique)
12254 12227
 def: "The data type peptide counts (razor+unique) produced by MaxQuant." [PSI:MS]
12255 12228
 xref: value-type:xsd\:int "The allowed value-type for this CV term."
12256
-is_a: MS:1001805 ! quantification datatype
12229
+is_a: MS:1002737 ! peptide-level quantification datatype
12257 12230
 
12258 12231
 [Term]
12259 12232
 id: MS:1001900
12260 12233
 name: MaxQuant:sequence length
12261 12234
 def: "The data type sequence length produced by MaxQuant." [PSI:MS]
12262 12235
 xref: value-type:xsd\:int "The allowed value-type for this CV term."
12263
-is_a: MS:1001805 ! quantification datatype
12236
+is_a: MS:1002737 ! peptide-level quantification datatype
12264 12237
 
12265 12238
 [Term]
12266 12239
 id: MS:1001901
... ...
@@ -12281,7 +12254,7 @@ id: MS:1001903
12281 12254
 name: MaxQuant:feature intensity
12282 12255
 def: "The data type feature intensity produced by MaxQuant." [PSI:MS]
12283 12256
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
12284
-is_a: MS:1001805 ! quantification datatype
12257
+is_a: MS:1002735 ! feature-level quantification datatype
12285 12258
 
12286 12259
 [Term]
12287 12260
 id: MS:1001904
... ...
@@ -12295,14 +12268,14 @@ id: MS:1001905
12295 12268
 name: emPAI value
12296 12269
 def: "The emPAI value of protein abundance, produced from the emPAI algorithm." [PSI:MS]
12297 12270
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
12298
-is_a: MS:1001805 ! quantification datatype
12271
+is_a: MS:1002738 ! protein-level quantification datatype
12299 12272
 
12300 12273
 [Term]
12301 12274
 id: MS:1001906
12302 12275
 name: APEX value
12303 12276
 def: "The APEX value of protein abundance, produced from the APEX software." [PSI:MS]
12304 12277
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
12305
-is_a: MS:1001805 ! quantification datatype
12278
+is_a: MS:1002738 ! protein-level quantification datatype
12306 12279
 
12307 12280
 [Term]
12308 12281
 id: MS:1001907
... ...
@@ -12417,7 +12390,7 @@ id: MS:1001923
12417 12390
 name: external reference keyword
12418 12391
 def: "Free text attribute that can enrich the information about an entity." [PSI:PI]
12419 12392
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
12420
-is_a: MS:1000878 ! external reference identifier
12393
+is_a: MS:1002840 ! external reference data
12421 12394
 
12422 12395
 [Term]
12423 12396
 id: MS:1001924
... ...
@@ -13015,8 +12988,7 @@ is_a: MS:1001833 ! quantitation analysis summary
13015 12988
 [Term]
13016 12989
 id: MS:1002010
13017 12990
 name: TMT quantitation analysis
13018
-def: "Quantitation analysis using the Thermo Fisher tandem mass tag (TMT) labelling workflow." [PSI:PI]
13019
-is_a: MS:1001833 ! quantitation analysis summary
12991
+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]
13020 12992
 is_a: MS:1002009 ! isobaric label quantitation analysis
13021 12993
 
13022 12994
 [Term]
... ...
@@ -13206,9 +13178,9 @@ is_a: MS:1002033 ! contact role
13206 13178
 
13207 13179
 [Term]
13208 13180
 id: MS:1002038
13209
-name: unlabeled sample
13181
+name: label free sample
13210 13182
 def: "A sample that has not been labelled or modified. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:PI]
13211
-synonym: "light labeled sample" EXACT []
13183
+synonym: "light sample" EXACT []
13212 13184
 is_a: MS:1000548 ! sample attribute
13213 13185
 
13214 13186
 [Term]
... ...
@@ -13395,14 +13367,14 @@ id: MS:1002064
13395 13367
 name: peptide consensus RT
13396 13368
 def: "Peptide consensus retention time." [PSI:PI]
13397 13369
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
13398
-is_a: MS:1001805 ! quantification datatype
13370
+is_a: MS:1002737 ! peptide-level quantification datatype
13399 13371
 
13400 13372
 [Term]
13401 13373
 id: MS:1002065
13402 13374
 name: peptide consensus m/z
13403 13375
 def: "Peptide consensus mass/charge ratio." [PSI:PI]
13404 13376
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
13405
-is_a: MS:1001805 ! quantification datatype
13377
+is_a: MS:1002737 ! peptide-level quantification datatype
13406 13378
 
13407 13379
 [Term]
13408 13380
 id: MS:1002066
... ...
@@ -13416,7 +13388,7 @@ id: MS:1002067
13416 13388
 name: protein value: median of peptide ratios
13417 13389
 def: "Protein quantification value calculated as median of peptide ratios." [PSI:PI]
13418 13390
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
13419
-is_a: MS:1001805 ! quantification datatype
13391
+is_a: MS:1002738 ! protein-level quantification datatype
13420 13392
 
13421 13393
 [Term]
13422 13394
 id: MS:1002068
... ...
@@ -13957,7 +13929,7 @@ id: MS:1002153
13957 13929
 name: protein level PSM counts
13958 13930
 def: "The number of spectra identified for this protein in spectral counting." [PSI:PI]
13959 13931
 xref: value-type:xsd\:int "The allowed value-type for this CV term."
13960
-is_a: MS:1001805 ! quantification datatype
13932
+is_a: MS:1002738 ! protein-level quantification datatype
13961 13933
 
13962 13934
 [Term]
13963 13935
 id: MS:1002154
... ...
@@ -14311,7 +14283,7 @@ is_a: MS:1001861 ! quantification data processing
14311 14283
 [Term]
14312 14284
 id: MS:1002212
14313 14285
 name: IPTL quantitation analysis
14314
-def: "Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric." [PSI:PI]
14286
+def: "Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric." [PSI:PI, PMID:19655813]
14315 14287
 is_a: MS:1002009 ! isobaric label quantitation analysis
14316 14288
 
14317 14289
 [Term]
... ...
@@ -14707,7 +14679,7 @@ id: MS:1002268
14707 14679
 name: Byonic:Best LogProb
14708 14680
 def: "Best (most negative) log p-value of an individual PSM." [PSI:PI]
14709 14681
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
14710
-is_a: MS:1001116 ! single protein result details
14682
+is_a: MS:1001116 ! single protein identification statistic
14711 14683
 is_a: MS:1001153 ! search engine specific score
14712 14684
 relationship: has_order MS:1002109 ! lower score better
14713 14685
 
... ...
@@ -14766,7 +14738,7 @@ is_a: MS:1000126 ! Waters instrument model
14766 14738
 [Term]
14767 14739
 id: MS:1002277
14768 14740
 name: AutoSpec Premier
14769
-def: "Waters AutoSpec Premier." [PSI:MS]
14741
+def: "Waters AutoSpec Premier magnetic sector instrument." [PSI:MS]
14770 14742
 is_a: MS:1000126 ! Waters instrument model
14771 14743
 
14772 14744
 [Term]
... ...
@@ -14835,6 +14807,7 @@ is_a: MS:1002286 ! Trans-Proteomic Pipeline software
14835 14807
 id: MS:1002288
14836 14808
 name: iProphet
14837 14809
 def: "A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format." [PMID:21876204]
14810
+synonym: "InterProphet" EXACT []
14838 14811
 is_a: MS:1002286 ! Trans-Proteomic Pipeline software
14839 14812
 
14840 14813
 [Term]
... ...
@@ -14985,19 +14958,19 @@ relationship: has_order MS:1002108 ! higher score better
14985 14958
 [Term]
14986 14959
 id: MS:1002312
14987 14960
 name: MS-Numpress linear prediction compression
14988
-def: "Compression using MS-Numpress linear prediction compression." [https://github.com/fickludd/ms-numpress]
14961
+def: "Compression using MS-Numpress linear prediction compression." [https://github.com/ms-numpress/ms-numpress]
14989 14962
 is_a: MS:1000572 ! binary data compression type
14990 14963
 
14991 14964
 [Term]
14992 14965
 id: MS:1002313
14993 14966
 name: MS-Numpress positive integer compression
14994
-def: "Compression using MS-Numpress positive integer compression." [https://github.com/fickludd/ms-numpress]
14967
+def: "Compression using MS-Numpress positive integer compression." [https://github.com/ms-numpress/ms-numpress]
14995 14968
 is_a: MS:1000572 ! binary data compression type
14996 14969
 
14997 14970
 [Term]
14998 14971
 id: MS:1002314
14999 14972
 name: MS-Numpress short logged float compression
15000
-def: "Compression using MS-Numpress short logged float compression." [https://github.com/fickludd/ms-numpress]
14973
+def: "Compression using MS-Numpress short logged float compression." [https://github.com/ms-numpress/ms-numpress]
15001 14974
 is_a: MS:1000572 ! binary data compression type
15002 14975
 
15003 14976
 [Term]
... ...
@@ -15139,14 +15112,12 @@ id: MS:1002334
15139 15112
 name: ProCon
15140 15113
 def: "Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML." [PSI:PI, http://www.medizinisches-proteom-center.de/procon]
15141 15114
 is_a: MS:1002333 ! conversion software
15142
-is_a: MS:1001457 ! data processing software
15143 15115
 
15144 15116
 [Term]
15145 15117
 id: MS:1002335
15146 15118
 name: PRIDE Converter2
15147 15119
 def: "Java software designed to convert one of several proteomics identification results formats into PRIDE XML." [PMID:22949509]
15148 15120
 is_a: MS:1002333 ! conversion software
15149
-is_a: MS:1001457 ! data processing software
15150 15121
 
15151 15122
 [Term]
15152 15123
 id: MS:1002336
... ...
@@ -15200,7 +15171,7 @@ is_a: MS:1001457 ! data processing software
15200 15171
 id: MS:1002343
15201 15172
 name: ion stability type
15202 15173
 def: "OBSOLETE Stability type of the ion." [PSI:PI]
15203
-comment: This child of the former purgatory term ion? was made obsolete.
15174
+comment: This child of the former purgatory term ion was made obsolete.
15204 15175
 is_obsolete: true
15205 15176
 
15206 15177
 [Term]
... ...
@@ -15323,7 +15294,7 @@ relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
15323 15294
 [Term]
15324 15295
 id: MS:1002360
15325 15296
 name: distinct peptide-level FDRScore
15326
-def: "mzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
15297
+def: "MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI]
15327 15298
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
15328 15299
 is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic
15329 15300
 is_a: MS:1002363 ! search engine specific score for proteins
... ...
@@ -15362,7 +15333,7 @@ is_a: MS:1001116 ! single protein identification statistic
15362 15333
 [Term]
15363 15334
 id: MS:1002365
15364 15335
 name: FDRScore for proteins
15365
-def: "mzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI]
15336
+def: "MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI]
15366 15337
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
15367 15338
 is_a: MS:1002363 ! search engine specific score for proteins
15368 15339
 relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one
... ...
@@ -15370,7 +15341,7 @@ relationship: has_domain MS:1002349 ! value greater than zero but less than or e
15370 15341
 [Term]
15371 15342
 id: MS:1002366
15372 15343
 name: combined FDRScore for proteins
15373
-def: "mzidLibrary Combined FDRScore for proteins." [PSI:PI]
15344
+def: "MzidLibrary Combined FDRScore for proteins." [PSI:PI]
15374 15345
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
15375 15346
 is_a: MS:1002363 ! search engine specific score for proteins
15376 15347
 relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one
... ...
@@ -15526,7 +15497,6 @@ name: PIA
15526 15497
 def: "PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis." [PSI:PI, http://www.medizinisches-proteom-center.de/pia]
15527 15498
 is_a: MS:1002414 ! postprocessing software
15528 15499
 is_a: MS:1001456 ! analysis software
15529
-is_a: MS:1001457 ! data processing software
15530 15500
 
15531 15501
 [Term]
15532 15502
 id: MS:1002388
... ...
@@ -15669,7 +15639,7 @@ id: MS:1002408
15669 15639
 name: number of distinct protein sequences
15670 15640
 def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [PSI:PI]
15671 15641
 xref: value-type:xsd\:int "The allowed value-type for this CV term."
15672
-is_a: MS:1002405 ! protein cluster details
15642
+is_a: MS:1002405 ! protein group-level result list attribute
15673 15643
 
15674 15644
 [Term]
15675 15645
 id: MS:1002409
... ...
@@ -15695,7 +15665,7 @@ id: MS:1002412
15695 15665
 name: total XIC area
15696 15666
 def: "Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM)." [PSI:PI]
15697 15667
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
15698
-is_a: MS:1001805 ! quantification datatype
15668
+is_a: MS:1002737 ! peptide-level quantification datatype
15699 15669
 
15700 15670
 [Term]
15701 15671
 id: MS:1002413
... ...
@@ -15848,7 +15818,7 @@ is_a: MS:1001249 ! search input details
15848 15818
 id: MS:1002435
15849 15819
 name: data processing start time
15850 15820
 def: "The time that a data processing action was started." [PSI:MS]
15851
-xref: value-type:xsd\:date "The allowed value-type for this CV term."
15821
+xref: value-type:xsd\:dateTime "The allowed value-type for this CV term."
15852 15822
 is_a: MS:1000630 ! data processing parameter
15853 15823
 
15854 15824
 [Term]
... ...
@@ -16132,6 +16102,7 @@ name: ion mobility drift time
16132 16102
 def: "Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated." [PSI:MS]
16133 16103
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
16134 16104
 is_a: MS:1000455 ! ion selection attribute
16105
+is_a: MS:1002892 ! ion mobility attribute
16135 16106
 relationship: has_units UO:0000028 ! millisecond
16136 16107
 
16137 16108
 [Term]
... ...
@@ -16139,7 +16110,7 @@ id: MS:1002477
16139 16110
 name: mean drift time array
16140 16111
 def: "Array of drift times, averaged from a matrix of binned m/z and drift time values, corresponding to spectrum of individual peaks encoded with an m/z array." [PSI:MS]
16141 16112
 xref: value-type:xsd\:float "The allowed value-type for this CV term."
16142
-is_a: MS:1000513 ! binary data array
16113
+is_a: MS:1002893 ! ion mobility array
16143 16114
 relationship: has_units UO:0000028 ! millisecond
16144 16115
 relationship: has_units UO:0000010 ! second
16145 16116
 
... ...
@@ -16159,7 +16130,7 @@ relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrom
16159 16130
 [Term]
16160 16131
 id: MS:1002480
16161 16132
 name: regular expression for a digital object identifier (DOI)
16162
-def: "(10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+)" [PSI:PI, http://dx.doi.org/]
16133
+def: "(10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+)." [PSI:PI, http://dx.doi.org/]
16163 16134
 is_a: MS:1002479 ! regular expression
16164 16135
 
16165 16136
 [Term]
... ...
@@ -16278,7 +16249,7 @@ id: MS:1002499
16278 16249
 name: peptide level score
16279 16250
 def: "OBSOLETE Peptide level score." [PSI:PI]
16280 16251
 comment: This term was obsoleted because it was never intended to go in the CV.
16281
-is_a: MS:1002358 ! search engine specific score for distinct peptides
16252
+is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic
16282 16253
 is_obsolete: true
16283 16254
 
16284 16255
 [Term]
... ...
@@ -16316,7 +16287,7 @@ is_a: MS:1001055 ! modification parameters
16316 16287
 [Term]
16317 16288
 id: MS:1002505
16318 16289
 name: regular expression for modification localization scoring
16319
-def: "([:digit:]+:[0|1]\{1\}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]*:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})" [PSI:PI]
16290
+def: "([:digit:]+:[0|1]\{1\}.[:digit:]+[Ee]{0,1}[+-]{0,1}[:digit:]*:[:digit:]+[|]\{1\}[:digit:]+:(true|false)\{1\})." [PSI:PI]
16320 16291
 is_a: MS:1002479 ! regular expression
16321 16292
 
16322 16293
 [Term]
... ...
@@ -16406,14 +16377,14 @@ id: MS:1002518
16406 16377
 name: Progenesis:protein group normalised abundance
16407 16378
 def: "The data type normalised abundance for protein groups produced by Progenesis LC-MS." [PSI:PI]
16408 16379
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
16409
-is_a: MS:1001805 ! quantification datatype
16380
+is_a: MS:1002739 ! protein group-level quantification datatype
16410 16381
 
16411 16382
 [Term]
16412 16383
 id: MS:1002519
16413 16384
 name: Progenesis:protein group raw abundance
16414 16385
 def: "The data type raw abundance for protein groups produced by Progenesis LC-MS." [PSI:PI]
16415 16386
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
16416
-is_a: MS:1001805 ! quantification datatype
16387
+is_a: MS:1002739 ! protein group-level quantification datatype
16417 16388
 
16418 16389
 [Term]
16419 16390
 id: MS:1002520
... ...
@@ -16524,7 +16495,7 @@ is_a: MS:1001143 ! PSM-level search engine specific statistic
16524 16495
 [Term]
16525 16496
 id: MS:1002536
16526 16497
 name: D-Score
16527
-def: "D-Score for PTM site location at the PSM-level." [DOI:10.1002/pmic.201200408, PMID:23307401]
16498
+def: "D-Score for PTM site location at the PSM-level." [PMID:23307401]
16528 16499
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
16529 16500
 is_a: MS:1001968 ! PTM localization PSM-level statistic
16530 16501
 relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
... ...
@@ -16532,7 +16503,7 @@ relationship: has_regexp MS:1002505 ! regular expression for modification locali
16532 16503
 [Term]
16533 16504
 id: MS:1002537
16534 16505
 name: MD-Score
16535
-def: "MD-Score for PTM site location at the PSM-level." [DOI:10.1074/mcp.M110.003830–1, PMID:21057138]
16506
+def: "MD-Score for PTM site location at the PSM-level." [PMID:21057138]
16536 16507
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
16537 16508
 is_a: MS:1001968 ! PTM localization PSM-level statistic
16538 16509
 relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring
... ...
@@ -16608,7 +16579,7 @@ is_a: MS:1001805 ! quantification datatype
16608 16579
 [Term]
16609 16580
 id: MS:1002548
16610 16581
 name: distributed normalized spectral abundance factor
16611
-def: "A distributed normalized spectral abundance factor (dNSAF." [DOI:10.1021/ac9023999, PMID:20166708] 
16582
+def: "A distributed normalized spectral abundance factor (dNSAF)." [DOI:10.1021/ac9023999, PMID:20166708] 
16612 16583
 is_a: MS:1001805 ! quantification datatype
16613 16584
 
16614 16585
 [Term]
... ...
@@ -16801,7 +16772,7 @@ is_a: MS:1001456 ! analysis software
16801 16772
 
16802 16773
 [Term]
16803 16774
 id: MS:1002576
16804
-name: Andromeda result file
16775
+name: Andromeda result format
16805 16776
 def: "Andromeda result file output format." [PSI:PI]
16806 16777
 is_a: MS:1001040 ! intermediate analysis format
16807 16778
 
... ...
@@ -16940,7 +16911,7 @@ is_a: MS:1001456 ! analysis software
16940 16911
 [Term]
16941 16912
 id: MS:1002599
16942 16913
 name: splash key
16943
-def: "The Splash, is an unique identifier for Spectra, as the InChI Key is an unique identifier for chemical compounds." [http://splash.fiehnlab.ucdavis.edu/]
16914
+def: "Spectral Hash key, an unique identifier for spectra." [PMID:27824832]
16944 16915
 xref: value-type:xsd\:string "The allowed value-type for this CV term."
16945 16916
 is_a: MS:1001405 ! spectrum identification result details
16946 16917
 
... ...
@@ -16959,7 +16930,7 @@ is_a: MS:1000914 ! tab delimited text format
16959 16930
 
16960 16931
 [Term]
16961 16932
 id: MS:1002602
16962
-name: quantification reagent
16933
+name: sample label
16963 16934
 def: "Reagent used in labeled quantification methods." [PSI:PI]
16964 16935
 is_a: MS:1002111 ! assay label attribute
16965 16936
 is_a: MS:1000548 ! sample attribute
... ...
@@ -16968,7 +16939,7 @@ is_a: MS:1000548 ! sample attribute
16968 16939
 id: MS:1002603
16969 16940
 name: ICAT reagent
16970 16941
 def: "Isotope coded affinity tag reagent." [PSI:PI]
16971
-is_a: MS:1002602 ! quantification reagent
16942
+is_a: MS:1002602 ! sample label
16972 16943
 
16973 16944
 [Term]
16974 16945
 id: MS:1002604
... ...
@@ -16986,7 +16957,7 @@ is_a: MS:1002603 ! ICAT reagent
16986 16957
 id: MS:1002606
16987 16958
 name: ICPL reagent
16988 16959
 def: "Isotope coded protein labeling reagent." [PSI:PI]
16989
-is_a: MS:1002602 ! quantification reagent
16960
+is_a: MS:1002602 ! sample label
16990 16961
 
16991 16962
 [Term]
16992 16963
 id: MS:1002607
... ...
@@ -17016,7 +16987,7 @@ is_a: MS:1002606 ! ICPL reagent
17016 16987
 id: MS:1002611
17017 16988
 name: SILAC reagent
17018 16989
 def: "Stable isotope labeling with amino acids in cell culture reagent." [PSI:PI]
17019
-is_a: MS:1002602 ! quantification reagent
16990
+is_a: MS:1002602 ! sample label
17020 16991
 
17021 16992
 [Term]
17022 16993
 id: MS:1002612
... ...
@@ -17039,8 +17010,8 @@ is_a: MS:1002611 ! SILAC reagent
17039 17010
 [Term]
17040 17011
 id: MS:1002615
17041 17012
 name: TMT reagent
17042
-def: "Tandem mass tag reagent." [PSI:PI]
17043
-is_a: MS:1002602 ! quantification reagent
17013
+def: "Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT or hydrazideTMT isobaric labeling." [PSI:PI]
17014
+is_a: MS:1002602 ! sample label
17044 17015
 
17045 17016
 [Term]
17046 17017
 id: MS:1002616
... ...
@@ -17081,8 +17052,8 @@ is_a: MS:1002615 ! TMT reagent
17081 17052
 [Term]
17082 17053
 id: MS:1002622
17083 17054
 name: iTRAQ reagent
17084
-def: "Isobaric tag for relative and absolute quantitation reagent." [PSI:PI]
17085
-is_a: MS:1002602 ! quantification reagent
17055
+def: "Isobaric tag for relative and absolute quantitation (iTRAQ or iTRAQH) reagent." [PSI:PI]
17056
+is_a: MS:1002602 ! sample label
17086 17057
 
17087 17058
 [Term]
17088 17059
 id: MS:1002623
... ...
@@ -17378,7 +17349,7 @@ relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[
17378 17349
 [Term]
17379 17350
 id: MS:1002665
17380 17351
 name: regular expression for interaction scores derived from cross-linking
17381
-def: "([:digit:]+[.][a|b]:([:digit:]+|null):[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\}))" [PSI:PI]
17352
+def: "([:digit:]+[.][a|b]:([:digit:]+|null):[:digit:]+[.][:digit:]+([Ee][+-][0-9]+)*:(true|false]\{1\}))." [PSI:PI]
17382 17353
 is_a: MS:1002479 ! regular expression
17383 17354
 
17384 17355
 [Term]
... ...
@@ -17465,15 +17436,15 @@ relationship: has_regexp MS:1002665 ! ([:digit:]+[.][a|b]:[:digit:]+:[:digit:]+[
17465 17436
 
17466 17437
 [Term]
17467 17438
 id: MS:1002678
17468
-name: supplemental higher energy beam-type collision-induced dissociation
17469
-def: "A supplemental collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV." [PSI:MS]
17439
+name: supplemental beam-type collision-induced dissociation
17440
+def: "A supplemental collision-induced dissociation process that occurs in a beam-type collision cell in addition to another primary type of dissociation." [PSI:MS]
17470 17441
 is_a: MS:1000422 ! beam-type collision-induced dissociation
17471 17442
 
17472 17443
 [Term]
17473 17444
 id: MS:1002679
17474 17445
 name: supplemental collision-induced dissociation
17475 17446
 def: "The dissociation of an ion after supplemental collisional excitation." [PSI:MS]
17476
-is_a: MS:1000044 ! dissociation method
17447
+is_a: MS:1000133 ! collision-induced dissociation
17477 17448
 
17478 17449
 [Term]
17479 17450
 id: MS:1002680
... ...
@@ -17488,7 +17459,7 @@ id: MS:1002681
17488 17459
 name: OpenXQuest:combined score
17489 17460
 def: "OpenXQuest's combined score for a cross-link spectrum match." [PSI:PI]
17490 17461
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
17491
-is_a: MS:1001143 ! search engine specific score for PSMs
17462
+is_a: MS:1001143 ! PSM-level search engine specific statistic
17492 17463
 is_a: MS:1001153 ! search engine specific score
17493 17464
 relationship: has_order MS:1002108 ! higher score better
17494 17465
 
... ...
@@ -17497,7 +17468,7 @@ id: MS:1002682
17497 17468
 name: OpenXQuest:xcorr xlink
17498 17469
 def: "OpenXQuest's cross-correlation of cross-linked ions subscore." [PSI:PI]
17499 17470
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
17500
-is_a: MS:1001143 ! search engine specific score for PSMs
17471
+is_a: MS:1001143 ! PSM-level search engine specific statistic
17501 17472
 is_a: MS:1001153 ! search engine specific score
17502 17473
 relationship: has_order MS:1002108 ! higher score better
17503 17474
 
... ...
@@ -17506,7 +17477,7 @@ id: MS:1002683
17506 17477
 name: OpenXQuest:xcorr common
17507 17478
 def: "OpenXQuest's cross-correlation of unlinked ions subscore." [PSI:PI]
17508 17479
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
17509
-is_a: MS:1001143 ! search engine specific score for PSMs
17480
+is_a: MS:1001143 ! PSM-level search engine specific statistic
17510 17481
 is_a: MS:1001153 ! search engine specific score
17511 17482
 relationship: has_order MS:1002108 ! higher score better
17512 17483
 
... ...
@@ -17515,7 +17486,7 @@ id: MS:1002684
17515 17486
 name: OpenXQuest:match-odds
17516 17487
 def: "OpenXQuest's match-odds subscore." [PSI:PI]
17517 17488
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
17518
-is_a: MS:1001143 ! search engine specific score for PSMs
17489
+is_a: MS:1001143 ! PSM-level search engine specific statistic
17519 17490
 is_a: MS:1001153 ! search engine specific score
17520 17491
 relationship: has_order MS:1002108 ! higher score better
17521 17492
 relationship: has_domain MS:1002306 ! value greater than zero
... ...
@@ -17525,7 +17496,7 @@ id: MS:1002685
17525 17496
 name: OpenXQuest:intsum
17526 17497
 def: "OpenXQuest's sum of matched peak intensity subscore." [PSI:PI]
17527 17498
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
17528
-is_a: MS:1001143 ! search engine specific score for PSMs
17499
+is_a: MS:1001143 ! PSM-level search engine specific statistic
17529 17500
 is_a: MS:1001153 ! search engine specific score
17530 17501
 relationship: has_order MS:1002108 ! higher score better
17531 17502
 relationship: has_domain MS:1002306 ! value greater than zero
... ...
@@ -17535,7 +17506,7 @@ id: MS:1002686
17535 17506
 name: OpenXQuest:wTIC
17536 17507
 def: "OpenXQuest's weighted percent of total ion current subscore." [PSI:PI]
17537 17508
 xref: value-type:xsd\:double "The allowed value-type for this CV term."
17538
-is_a: MS:1001143 ! search engine specific score for PSMs
17509
+is_a: MS:1001143 ! PSM-level search engine specific statistic
17539 17510
 is_a: MS:1001153 ! search engine specific score
17540 17511
 relationship: has_order MS:1002108 ! higher score better
17541 17512
 relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive
... ...
@@ -17654,3 +17625,2463 @@ name: protein group-level result list statistic
17654 17625
 def: "Attrbiute of an entire list of protein groups." [PSI:PI]
17655 17626
 is_a: MS:1002405 ! protein group-level result list attribute
17656 17627
 
17628
+[Term]
17629
+id: MS:1002719
17630
+name: Pegasus BT
17631
+def: "LECO bench-top GC time-of-flight mass spectrometer." [PSI:PI]
17632
+is_a: MS:1001800 ! LECO instrument model
17633
+
17634
+[Term]
17635
+id: MS:1002720
17636
+name: MSPathFinder
17637
+def: "PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra." [PSI:PI]
17638
+is_a: MS:1001456 ! analysis software
17639
+
17640
+[Term]
17641
+id: MS:1002721
17642
+name: MSPathFinder:SpecEValue
17643
+def: "MSPathFinder spectral E-value." [PSI:PI]
17644
+xref: value-type:xsd\:double "The allowed value-type for this CV term."
17645
+is_a: MS:1002353 ! PSM-level e-value
17646
+is_a: MS:1001143 ! PSM-level search engine specific statistic
17647
+relationship: has_order MS:1002109 ! lower score better
17648
+
17649
+[Term]
17650
+id: MS:1002722
17651
+name: MSPathFinder:EValue
17652
+def: "MSPathFinder E-value." [PSI:PI]
17653
+xref: value-type:xsd\:double "The allowed value-type for this CV term."
17654
+is_a: MS:1002353 ! PSM-level e-value
17655
+is_a: MS:1001143 ! PSM-level search engine specific statistic
17656
+relationship: has_order MS:1002109 ! lower score better
17657
+
17658
+[Term]
17659
+id: MS:1002723
17660
+name: MSPathFinder:QValue
17661
+def: "MSPathFinder Q-value." [PSI:PI]
17662
+xref: value-type:xsd\:double "The allowed value-type for this CV term."
17663
+is_a: MS:1002354 ! PSM-level q-value
17664
+is_a: MS:1001143 ! PSM-level search engine specific statistic
17665
+
17666
+[Term]
17667
+id: MS:1002724
17668
+name: MSPathFinder:PepQValue
17669
+def: "MSPathFinder peptide-level Q-value." [PSI:PI]
17670
+xref: value-type:xsd\:double "The allowed value-type for this CV term."
17671
+is_a: MS:1001143 ! PSM-level search engine specific statistic
17672
+
17673
+[Term]
17674
+id: MS:1002725
17675
+name: MSPathFinder:RawScore
17676
+def: "MSPathFinder raw score." [PSI:PI]
17677
+xref: value-type:xsd\:double "The allowed value-type for this CV term."
17678
+is_a: MS:1001143 ! PSM-level search engine specific statistic
17679
+
17680
+[Term]
17681
+id: MS:1002726
17682
+name: SYNAPT G2-Si
17683
+def: "Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI]
17684
+is_a: MS:1000126 ! Waters instrument model
17685
+
17686
+[Term]
17687
+id: MS:1002727
17688
+name: MALDI SYNAPT G2-Si
17689
+def: "Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI]
17690
+is_a: MS:1000126 ! Waters instrument model
17691
+
17692
+[Term]
17693
+id: MS:1002728
17694
+name: Vion IMS QTof
17695
+def: "Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI]
17696
+is_a: MS:1000126 ! Waters instrument model
17697
+
17698
+[Term]
17699
+id: MS:1002729
17700
+name: Xevo G2 XS Tof
17701
+def: "Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI]
17702
+is_a: MS:1000126 ! Waters instrument model
17703
+
17704
+[Term]
17705
+id: MS:1002730
17706
+name: Xevo TQ-XS
17707
+def: "Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer." [PSI:PI]
17708
+is_a: MS:1000126 ! Waters instrument model
17709
+
17710
+[Term]
17711
+id: MS:1002731
17712
+name: Xevo TQ-S micro
17713
+def: "Waters Corporation Xevo TQ-S micro triple quadrupole mass spectrometer." [PSI:PI]
17714
+is_a: MS:1000126 ! Waters instrument model
17715
+
17716
+[Term]
17717
+id: MS:1002732
17718
+name: Orbitrap Fusion Lumos
17719
+def: "Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI]
17720
+is_a: MS:1000494 ! Thermo Scientific instrument model
17721
+