forked from PRIDE-Archive/pride-ontology
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathpride_cv.obo
4141 lines (3473 loc) · 134 KB
/
pride_cv.obo
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
format-version: 1.4
date: 12:11:2024 11:31
data-version: 2.1.7
saved-by: Deepti Jaiswal Kundu
auto-generated-by: OBO-Edit 2.3.1
default-namespace: PRIDE
remark: I would set treat-xrefs-as-equivalent but there are some weird xrefs that would break that behaviour (PRIDE:PRIDE, value-type:xsd\:string, ...)
import: http://purl.obolibrary.org/obo/chmo.owl
import: http://www.ebi.ac.uk/efo/efo.owl
ontology: pride
[Typedef]
id: part_of
name: part_of
is_transitive: true
[Term]
id: PRIDE:0000000
name: Reference additional parameter
def: "Root node for terms relating to Reference additional parameters, in the context of ExperimentCollection/Experiment/Reference/additional/CvParam" [PRIDE:PRIDE]
[Term]
id: PRIDE:0000001
name: Protocol step description additional parameter
def: "Root node for terms relating to the description of a protocol as ordered steps, in relation to the PRIDE.xml element ExperimentCollection/Experiment/Protocol/ProtocolSteps/StepDescription" [PRIDE:PRIDE]
[Term]
id: PRIDE:0000002
name: ModificationItem additional parameter
def: "Root node for terms relating to the description of a ModificationItem (post translational modification or artifactual modification) in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/PeptideItem/ModificationItem/additional/cvParam" [PRIDE:PRIDE]
[Term]
id: PRIDE:0000003
name: Peptide item additional parameter
def: "Root node for terms relating to the description of a PeptideItem in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/PeptideItem/additional/cvParam" [PRIDE:PRIDE]
[Term]
id: PRIDE:0000004
name: Identification additional parameter
def: "Root node for terms relating to the description of an Identification in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/additional/cvParam" [PRIDE:PRIDE]
[Term]
id: PRIDE:0000005
name: Gel additional parameter
def: "Root node for terms relating to the description of a Gel in relation to the PRIDE.xml element ExperimentCollection/Experiment/TwoDimensionalIdentification/Gel/additional/cvParam" [PRIDE:PRIDE]
[Term]
id: PRIDE:0000006
name: Experiment additional parameter
def: "Root node for terms relating to the description of an Experiment in relation to the PRIDE.xml element ExperimentCollection/Experiment/additional/cvParam" [PRIDE:PRIDE]
[Term]
id: PRIDE:0000007
name: SearchEngineVersion
def: "Version number / identifier for search engine."[PRIDE:PRIDE]
is_obsolete: true
[Term]
id: PRIDE:0000008
name: Protein search engine output parameter
def: "Protein search engine output parameters are critical for analyzing and validating the results of peptide and protein identification." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000009
name: Ion mass tolerance
def: "Ion mass tolerence refers to the permissible deviation between the measured mass of an ion and its theoretical mass" [PRIDE:PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
is_a: PRIDE:0000049 ! Peptide search engine output parameter
[Term]
id: PRIDE:0000010
name: Precursor ion mass tolerance
def: "Precursor ion mass tolerance efines the acceptable range of deviation between the experimental mass-to-charge ratio (𝑚/𝑧)of a precursor ion and its theoretical (m/z) value during database searches" [PRIDE:PRIDE]
is_a: PRIDE:0000009 ! Ion mass tolerance
[Term]
id: PRIDE:0000011
name: MS2 ion mass tolerance
def: "MS2 ion mass tolerance refers to the acceptable deviation range between the experimentally measured fragment ion masses and their theoretical values during the identification of peptides and proteins in tandem mass spectrometry (MS/MS)" [PRIDE:PRIDE]
is_a: PRIDE:0000009 ! Ion mass tolerance
[Term]
id: PRIDE:0000012
name: Delta Cn
def: "1.0 - normalized correlation score." [PRIDE:PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest
[Term]
id: PRIDE:0000013
name: X correlation
def: "A statistical measure used in proteomics to evaluate the quality of peptide-spectrum matches (PSMs) in tandem mass spectrometry (MS/MS) data" [PRIDE:PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
is_a: PRIDE:0000049 ! Peptide search engine output parameter
[Term]
id: PRIDE:0000014
name: X correlation (+1)
def: "XCorrelation (+1) refers to the cross-correlation score adjustment applied during peptide-spectrum matching (PSM) in search engines like SEQUEST" [PRIDE:PRIDE]
is_a: PRIDE:0000013 ! X correlation
[Term]
id: PRIDE:0000015
name: X correlation (+2)
def: "XCorrelation (+2) refers to the cross-correlation (XCorr) scores for peptide-spectrum matches (PSMs) associated with doubly charged precursor ions (𝑧=2) in proteomics" [PRIDE:PRIDE]
is_a: PRIDE:0000013 ! X correlation
[Term]
id: PRIDE:0000016
name: X correlation (+3)
def: "XCorrelation (+3) refers to the cross-correlation (XCorr) scores associated with triply charged precursor ions (z=3) in proteomics data analysis" [PRIDE:PRIDE]
is_a: PRIDE:0000013 ! X correlation
[Term]
id: PRIDE:0000017
name: Sample description additional parameter
def: "Root term for parameters in the context of ExperimentCollection/Experiment/mzData/description/admin/sampleDescription/cvParam" [PRIDE:PRIDE]
[Term]
id: PRIDE:0000018
name: Disease free
def: "Term to describe the fact that the sample derives from an organism which has been positively shown to be free of disease, e.g. as the consequence of a broad-spectrum screen. NOTE: A request has been made to have this concept added to MeSH. Once this has been achieved, this term will be dropped from the PRIDE CV and all uses of the this term will be updated to the appropriate MeSH concept." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
[Term]
id: PRIDE:0000019
name: Solubilization
def: "To make something soluble or more soluble, especially in water, by the action of a detergent or other agent." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
[Term]
id: PRIDE:0000020
name: Depletion
def: "The removal of specific components of a complex mixture of proteins or peptides on the basis of some specific property of those components." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
[Term]
id: PRIDE:0000021
name: Fractionation
def: "Process of classification of an analyte or a group of analytes from a sample according to physical (e.g., size) or chemical (e.g., bonding, reactivity) properties. (from https://doi.org/10.1351/goldbook.FT06825)" [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
[Term]
id: PRIDE:0000022
name: Separation
def: "To separate a complex mixture of proteins or peptides based on molecular characteristics and interaction type over a given amount of time." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
[Term]
id: PRIDE:0000023
name: Band excision
def: "The removal of a region of a gel which contains protein(s) of interest." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
[Term]
id: PRIDE:0000024
name: Enzyme digestion
def: "The fragmentation of proteins into peptides through the use of an enzyme such as trypsin." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
[Term]
id: PRIDE:0000025
name: Reduction
def: "reduction generally refers to the chemical process used to break disulfide bonds between cysteine residues in proteins" [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
[Term]
id: PRIDE:0000026
name: Alkylation
def: "The transfer of an alkyl group from one molecule to another." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
[Term]
id: PRIDE:0000027
name: Mass spectrometry
def: "This is a measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
[Term]
id: PRIDE:0000028
name: Cv Label
def: "Valid values for cvLabel entries referencing external database / CV / ontology." [PRIDE:PRIDE]
[Term]
id: PRIDE:0000029
name: PubMed
def: "PubMed is a free resource developed by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM)" [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label
[Term]
id: PRIDE:0000030
name: PRIDE
def: "Valid value for the cvLabel entry referencing PRIDE" [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label
[Term]
id: PRIDE:0000031
name: GO
def: "Valid value for the cvLabel entry referencing GO." [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label
[Term]
id: PRIDE:0000032
name: MeSH
def: "Valid value for the cvLabel entry referencing Medical Subject Headings (MeSH)" [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label
[Term]
id: PRIDE:0000033
name: NEWT
def: "Valid value for the cvLabel entry referencing NEWT or the NCBI taxonomy." [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label
[Term]
id: PRIDE:0000034
name: PSI
def: "Valid value for the cvLabel entry referencing the PSI ontology" [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label
[Term]
id: PRIDE:0000035
name: UNIMOD
def: "Valid value for the cvLabel entry referencing UNIMOD" [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label
[Term]
id: PRIDE:0000036
name: RESID
def: "Valid value for the cvLabel entry referencing RESID." [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label
[Term]
id: PRIDE:0000037
name: Staining
def: "A technique used in biology, histology, and microscopy to enhance contrast in samples, making structures or components visible under a microscope" [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
[Term]
id: PRIDE:0000038
name: ISBN
def: "Valid value for the cvLabel entry referencing ISBN" [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label
[Term]
id: PRIDE:0000039
name: Organelle isolation
def: "Any technique which separates differentiated structures from the cell." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
[Term]
id: PRIDE:0000040
name: Experiment description
def: "This CV term should be used in association with a value that is a free-text description of the experiment." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter
[Term]
id: PRIDE:0000041
name: Search database protein sequence
def: "Database used to search the protein sequence" [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000042
name: DOI
def: "The DOI system provides a persistent link to the journal's location on the internet, even if the URL changes." [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label
[Term]
id: PRIDE:0000043
name: FIX
is_a: PRIDE:0000028 ! Cv Label
[Term]
id: PRIDE:0000044
name: Search algorithm
def: "A method used to retrieve specific data from a collection of data, based on a given criterion" [PRIDE:PRIDE]
[Term]
id: PRIDE:0000045
name: Sequest
def: "Sequest is one of the earliest and most widely used search engines for protein identification in mass spectrometry-based proteomics" [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm
is_a: PRIDE:0000573 ! Identification software
[Term]
id: PRIDE:0000046
name: Mascot
def: "Mascot is a widely used search engine for protein identification in mass spectrometry-based proteomics" [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm
is_a: PRIDE:0000571 ! Quantification Software
is_a: PRIDE:0000573 ! Identification software
[Term]
id: PRIDE:0000047
name: XTandem
def: "X!Tandem is an open-source search engine for protein identification in mass spectrometry-based proteomics" [PRIDE:PRIDE]
comment: Really X
is_a: PRIDE:0000044 ! Search algorithm
is_a: PRIDE:0000573 ! Identification software
[Term]
id: PRIDE:0000048
name: Output parameter
def: "Output parameters in mass spectrometry search engines refer to the results and metrics provided after analyzing the experimental MS/MS spectra and comparing them to theoretical spectra from a protein database" [PRIDE:PRIDE]
is_obsolete: true
[Term]
id: PRIDE:0000049
name: Peptide search engine output parameter
def: "The output parameters of a peptide search engine refer to the key metrics, scores, and information that describe the results of matching experimental mass spectra (MS/MS) to theoretical spectra from a protein sequence database" [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
[Term]
id: PRIDE:0000050
name: Rank/Sp
def: "Final correlation score rank and preliminary score rank." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest
[Term]
id: PRIDE:0000051
name: (M+H)+
def: "m/z of the singly-charged precursor (precursor mass + mass of hydrogen atom)." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest
[Term]
id: PRIDE:0000052
name: Cn
def: "normalized correlation score." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest
[Term]
id: PRIDE:0000053
name: Sequest score
def: "raw correlation score (Sequest)." [PRIDE:PRIDE]
synonym: "C*10^4" RELATED []
is_a: PRIDE:0000008 ! Protein search engine output parameter
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest
[Term]
id: PRIDE:0000054
name: Sp
def: "preliminary score." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest
[Term]
id: PRIDE:0000055
name: Ions
def: "the number of frament ions matched (in the preliminary scoring process) out of the total number of fragment masses for the peptide." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest
[Term]
id: PRIDE:0000056
name: Bioworks
def: "A companion tool often used for processing and analyzing mass spectrometry data" [PRIDE:PRIDE]
is_a: PRIDE:0000045 ! Sequest
is_a: PRIDE:0000573 ! Identification software
[Term]
id: PRIDE:0000057
name: Molecular weight
def: "Molecular weight of a protein." [PRIDE:PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
relationship: part_of PRIDE:0000056 ! Bioworks
[Term]
id: PRIDE:0000058
name: z
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000056 ! Bioworks
[Term]
id: PRIDE:0000059
name: File
def: "File is a digital container used to store information on a computer or other electronic device" [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
[Term]
id: PRIDE:0000060
name: Scan
def: "The scan refers to a unique identifier for a specific mass spectrum acquired during the experiment. Each scan corresponds to a particular fragmentation event in the mass spectrometer." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
[Term]
id: PRIDE:0000061
name: Coverage
def: "coverage refers to the proportion of a protein sequence that is represented by identified peptides in a given experiment" [PRIDE:PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
relationship: part_of PRIDE:0000056 ! Bioworks
[Term]
id: PRIDE:0000062
name: rsp
def: "It is used as a measure to assess the confidence of peptide identifications based on the output of peptide search engines such as Mascot, SEQUEST, X! Tandem, and others." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000056 ! Bioworks
[Term]
id: PRIDE:0000063
name: Protein description line
def: "A protein description line typically refers to a concise textual entry or annotation that provides information about a specific protein, such as its function, molecular characteristics, or role in biological processes" [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000064
name: Secondary accession
def: "A secondary accession refers to an additional identifier assigned to a protein entry in databases like UniProt" [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000065
name: Upstream flanking sequence
def: "Any sequence reported before the start of the peptide." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
[Term]
id: PRIDE:0000066
name: Downstream flanking seqeuence
def: "Any sequence reported after the end of the peptide sequence." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
[Term]
id: PRIDE:0000067
name: Reference reporting this experiment
def: "referencing an experiment in scientific contexts, it's important to cite the original publication that reports the methods, results, or analysis involved in the experiment. Typically, this will involve citing the DOI (Digital Object Identifier), journal title, and other relevant details." [PRIDE:PRIDE]
is_a: PRIDE:0000000 ! Reference additional parameter
[Term]
id: PRIDE:0000068
name: Reference describing sample preparation
def: "referencing sample preparation for mass spectrometry or proteomics, the specific protocols and methods can vary depending on the type of analysis being conducted (e.g., quantitative proteomics, post-translational modification analysis, etc.)." [PRIDE:PRIDE]
is_a: PRIDE:0000000 ! Reference additional parameter
[Term]
id: PRIDE:0000069
name: Mascot score
def: "Score as defined for the Mascot search algorithm." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000046 ! Mascot
[Term]
id: PRIDE:0000070
name: Peptide cleavage
def: "Cleavage of the peptide bond." [PRIDE:PRIDE]
is_a: PRIDE:0000024 ! Enzyme digestion
[Term]
id: PRIDE:0000071
name: Search engine setting
def: "Search engine settings refer to the specific parameters and configurations that are used to optimize how a peptide or protein search engine identifies and matches experimental data (e.g., MS/MS spectra) to theoretical peptide sequences in a database. " [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
is_a: PRIDE:0000003 ! Peptide item additional parameter
[Term]
id: PRIDE:0000072
name: Fixed modification setting
def: "fixed modifications refer to chemical modifications that are consistently present in all peptides of a given experiment, typically due to a sample preparation step or reagent used." [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting
[Term]
id: PRIDE:0000073
name: Variable modification setting
def: "variable modifications refer to post-translational modifications (PTMs) or other chemical changes that can occur at specific amino acid residues but do not necessarily occur in every peptide or protein" [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting
[Term]
id: PRIDE:0000074
name: Maximum Missed Cleavages Setting
def: "The maximum missed cleavages setting refers to the number of missed enzyme cleavages allowed during peptide digestion" [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting
[Term]
id: PRIDE:0000075
name: Mass value type setting
def: "It refers to how the mass of peptides, ions, or proteins is represented during a search or analysis" [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting
[Term]
id: PRIDE:0000076
name: Mass value type setting monoisotopic
def: "The monoisotopic mass setting refers to the mass of a molecule based on the lightest isotope of each element, typically the most abundant isotope, like carbon-12 (12C) for carbon, hydrogen-1 (1H) for hydrogen, and oxygen-16 (16O) for oxygen." [PRIDE:PRIDE]
is_a: PRIDE:0000075 ! Mass value type setting
[Term]
id: PRIDE:0000077
name: Mass value type setting average
def: "The average mass setting refers to the weighted average mass of all isotopes of each element present in a molecule." [PRIDE:PRIDE]
is_a: PRIDE:0000075 ! Mass value type setting
[Term]
id: PRIDE:0000078
name: Peptide mass tolerance setting
def: "The peptide mass tolerance setting is a critical parameter used to define how much variation is acceptable between the observed mass of a peptide in the mass spectrum and the theoretical mass calculated from a database search. " [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting
[Term]
id: PRIDE:0000079
name: Accurate mass mode setting
def: "The Accurate Mass Mode setting refers to a mode of operation where the mass spectrometer is configured to measure the mass of ions with a higher degree of precision than in standard scanning modes." [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting
[Term]
id: PRIDE:0000080
name: Accurate mass mode setting true
def: "Accurate mass mode setting typically refers to configuring the instrument to measure ion masses with high precision" [PRIDE:PRIDE]
is_a: PRIDE:0000079 ! Accurate mass mode setting
[Term]
id: PRIDE:0000081
name: Accurate mass mode setting false
def: "Accurate mass mode setting is set to false in mass spectrometry, it means that the instrument will not prioritize high-resolution mass measurements." [PRIDE:PRIDE]
is_a: PRIDE:0000079 ! Accurate mass mode setting
[Term]
id: PRIDE:0000082
name: Mass error type setting
def: "The mass error type setting refers to how mass errors are reported and interpreted during data acquisition and analysis." [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting
[Term]
id: PRIDE:0000083
name: mass error type setting ppm
def: "the mass error type is set to ppm (parts per million), it specifies that the acceptable mass error is calculated relative to the theoretical mass of the ion, and it is expressed as parts per million (ppm). " [PRIDE:PRIDE]
is_a: PRIDE:0000082 ! Mass error type setting
[Term]
id: PRIDE:0000084
name: mass error type setting mmu
def: "mass errors refer to discrepancies in the measured mass of ions compared to their theoretical or expected mass values." [PRIDE:PRIDE]
is_a: PRIDE:0000082 ! Mass error type setting
[Term]
id: PRIDE:0000085
name: mass error type setting percent
def: "mass error type setting percent refers to the percentage of mass error in the measured mass-to-charge ratio (m/z) compared to the expected or theoretical value." [PRIDE:PRIDE]
is_a: PRIDE:0000082 ! Mass error type setting
[Term]
id: PRIDE:0000086
name: mass error type setting Daltons
def: "mass error type daltons, how the discrepancy between the measured and expected mass is expressed in absolute units of mass (daltons), rather than as a percentage." [PRIDE:PRIDE]
is_a: PRIDE:0000082 ! Mass error type setting
[Term]
id: PRIDE:0000087
name: Protonated setting
def: "protonated setting refers to the protonation of a molecule or ion during the ionization process, particularly in positive ion mode." [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting
[Term]
id: PRIDE:0000088
name: Protonated setting MH+
def: "protonated setting MH⁺ refers to the protonated molecular ion of a compound, where M represents the neutral molecule, and the H⁺ signifies the added proton." [PRIDE;PRIDE]
is_a: PRIDE:0000087 ! Protonated setting
[Term]
id: PRIDE:0000089
name: Protonated setting Mr
is_a: PRIDE:0000087 ! Protonated setting
[Term]
id: PRIDE:0000090
name: Protonated setting M-H-
def: "protonated setting M-H⁻ refers to the deprotonated molecular ion (also known as the negative ion form), where M represents the neutral molecule, and H⁻ signifies the loss of a proton (H⁺), resulting in a negatively charged ion." [PRIDE:PRIDE]
is_a: PRIDE:0000087 ! Protonated setting
[Term]
id: PRIDE:0000091
name: Rank
def: "rank represents the quality or confidence of the peptide-spectrum match (PSM), with the rank value showing the best match and progressively lower-ranked results indicating less confident identifications." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
[Term]
id: PRIDE:0000092
name: All peptides matched
def: "the output of a peptide search engine where every peptide in a sample has been identified and matched against a database." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
[Term]
id: PRIDE:0000093
name: All peptides matched true
def: "All peptides matched true is in a peptide search engine output (like Mascot, SEQUEST, X! Tandem, or Andromeda), it generally means that all detected peptide spectra were successfully matched to corresponding peptides in the protein database." [PRIDE:PRIDE]
is_a: PRIDE:0000092 ! All peptides matched
[Term]
id: PRIDE:0000094
name: All peptides matched false
def: "some mass spectra from the experiment could not be linked to a known peptide sequence from the protein database." [PRIDE:PRIDE]
is_a: PRIDE:0000092 ! All peptides matched
[Term]
id: PRIDE:0000095
name: Masses matched
def: "Masses matched refers to the number (or percentage) of experimental mass-to-charge ratios (m/z) from a mass spectrum that were successfully matched to theoretical peptide masses in a protein database" [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
[Term]
id: PRIDE:0000096
name: Reported Chromosome
def: "Reported chromosome is the chromosomal location of the protein or peptide that has been identified." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000097
name: Project
def: "Allows experiments to be grouped or organised under projects. Experiments may be grouped under more than one project." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter
[Term]
id: PRIDE:0000098
name: Indistinguishable alternative protein accession
def: "A qualifier is mandatory when using this term. The qualifier is an alternative protein accession that is indistinguishable from the primary protein accession based upon observed peptide sequences only." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000099
name: PeptideProphet probability score
def: "The probability score for this peptide assignment to be correct, as calculated by PeptideProphet." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000101 ! PeptideProphet
[Term]
id: PRIDE:0000100
name: ProteinProphet probability score
def: "The probability score for this protein identification to be correct, as calculated by ProteinProphet." [PRIDE:PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
relationship: part_of PRIDE:0000102 ! ProteinProphet
[Term]
id: PRIDE:0000101
name: PeptideProphet
def: "The PeptideProphet algorithm." [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm
[Term]
id: PRIDE:0000102
name: ProteinProphet
def: "The ProteinProphet algorithm." [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm
[Term]
id: PRIDE:0000103
name: Gel run date
def: "The date upon which the gel was run. A value is mandatory - must be formatted as xsd:dateTime." [PRIDE:PRIDE]
is_a: PRIDE:0000005 ! Gel additional parameter
[Term]
id: PRIDE:0000104
name: Sample volume loaded
def: "The volume of sample loaded on to the gel measured in micro litres. Mandatory value must be formatted as xsd:Double." [PRIDE:PRIDE]
is_a: PRIDE:0000005 ! Gel additional parameter
[Term]
id: PRIDE:0000105
name: Width in pixels
def: "The width of the referenced gel image in pixels. Mandatory value of type xsd:int." [PRIDE:PRIDE]
is_a: PRIDE:0000005 ! Gel additional parameter
[Term]
id: PRIDE:0000106
name: Height in pixels
def: "The height of the referenced gel image in pixels. Mandatory value of type xsd:int." [PRIDE:PRIDE]
is_a: PRIDE:0000005 ! Gel additional parameter
[Term]
id: PRIDE:0000107
name: Gel spot parameter
def: "Parameters describing the spot on a gel that has been analysed resulting in the annotated protein identification." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000108
name: Gel spot intensity
def: "The intensity of the spot on the gel. Mandatory value of type xsd:double." [PRIDE:PRIDE]
is_a: PRIDE:0000107 ! Gel spot parameter
[Term]
id: PRIDE:0000109
name: Gel spot area
def: "The area of the spot on the gel measured in millimetres squared. Mandatory value of type xsd:double." [PRIDE:PRIDE]
is_a: PRIDE:0000107 ! Gel spot parameter
[Term]
id: PRIDE:0000110
name: Gel spot volume
def: "The volume of the spot on the gel measured in millimetres cubed. Mandatory value of type xsd:double." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000131 ! Spot normalized volume
[Term]
id: PRIDE:0000111
name: Reference describing data analysis
def: "A reference annotated with this term describes analysis of the data presented in the enclosing PRIDE experiment." [PRIDE:PRIDE]
is_a: PRIDE:0000000 ! Reference additional parameter
[Term]
id: PRIDE:0000112
name: Identified by peptide mass fingerprint
def: "The annotated protein identification arises from peptide mass fingerprinting. Peptide identifications may or may not be included." [PRIDE:PRIDE]
synonym: "PMF" EXACT []
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000113
name: Identified by peptide fragmentation
def: "The protein identification annotated with this term has been identified by peptide fragmentation and subsequent database searching." [PRIDE:PRIDE]
synonym: "PFF" EXACT []
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000114
name: iTRAQ reagent 114
def: "The name of the sample labelled with iTRAQ reagent 114." [PRIDE:PRIDE]
is_a: PRIDE:0000329 ! iTRAQ reagent
[Term]
id: PRIDE:0000115
name: iTRAQ reagent 115
def: "The name of the sample labelled with iTRAQ reagent 115." [PRIDE:PRIDE]
is_a: PRIDE:0000329 ! iTRAQ reagent
[Term]
id: PRIDE:0000116
name: iTRAQ reagent 116
def: "The name of the sample labelled with iTRAQ reagent 116." [PRIDE:PRIDE]
is_a: PRIDE:0000329 ! iTRAQ reagent
[Term]
id: PRIDE:0000117
name: iTRAQ reagent 117
def: "The name of the sample labelled with iTRAQ reagent 117." [PRIDE:PRIDE]
is_a: PRIDE:0000329 ! iTRAQ reagent
[Term]
id: PRIDE:0000118
name: iTRAQ intensity 114
def: "The intensity of the sample labelled with iTRAQ reagent 114." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000119
name: iTRAQ intensity 115
def: "The intensity of the sample labelled with iTRAQ reagent 115." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000120
name: iTRAQ intensity 116
def: "The intensity of the sample labelled with iTRAQ reagent 116." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000121
name: iTRAQ intensity 117
def: "The intensity of the sample labelled with iTRAQ reagent 117." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000122
name: Two Dimensional Polyacrylamide Gel Electrophoresis
def: "A type of gel electrophoresis in which proteins are first separated by charge and then by molecular weight, enabling the analysis of complex protein mixtures." [PRIDE:PRIDE]
is_a: PRIDE:0000022 ! Separation
[Term]
id: PRIDE:0000123
name: Immobilized pH Gradient Electrophoresis
def: "Electrophoresis using an gel which has a pH gradient along its length." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000122 ! Two Dimensional Polyacrylamide Gel Electrophoresis
is_a: PRIDE:0000568 ! 2D PAGE
[Term]
id: PRIDE:0000124
name: Sodium dodecyl sulfate polyacrylamide gel electrophoresis
def: "A type of polyacrylamide gel electrophoresis in which the anionic detergent sodium dodecyl sulfate (SDS) is used to denature the sample proteins into linear monomers, rendering their charge proportional to their length so that migration is a function of size. Abbreviated SDS-polyacrylamide gel electrophoresis or SDS-PAGE." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000122 ! Two Dimensional Polyacrylamide Gel Electrophoresis
is_a: PRIDE:0000568 ! 2D PAGE
[Term]
id: PRIDE:0000125
name: pH low value
def: "The lowest pH of an immobilised pH gradient gel." [PRIDE:PRIDE]
is_a: PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis
[Term]
id: PRIDE:0000126
name: pH high value
def: "The highest pH of an immobilised pH gradient gel." [PRIDE:PRIDE]
is_a: PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis
[Term]
id: PRIDE:0000127
name: IPG strip length cm
def: "The length in centimeters of an immobilised pH gradient gel." [PRIDE:PRIDE]
comment: This value associated with this CV term should always be in centimeters.
is_a: PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis
[Term]
id: PRIDE:0000128
name: First dimension details
def: "Details of immobilised pH gradient gel electrophoresis which exclude the pH range of the gel and strip length parameters." [PRIDE:PRIDE]
comment: This CV term should be used in association with a value that is a free-text description of the first dimension details
relationship: part_of PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis
[Term]
id: PRIDE:0000129
name: Second dimension details
def: "Details of sodium dodecyl sulfate polyacrylamide gel electrophoresis." [PRIDE:PRIDE]
comment: This CV term should be used in association with a value that is a free-text description of the second dimension details
is_a: PRIDE:0000124 ! Sodium dodecyl sulfate polyacrylamide gel electrophoresis
[Term]
id: PRIDE:0000130
name: Obsoleted parameters
def: "Obsoleted terms." [Curator:Rc]
is_obsolete: true
[Term]
id: PRIDE:0000131
name: Spot normalized volume
def: "A value for spot volume which is standardized across gels and is derived from the individual gel spot volume values." [PRIDE:PRIDE]
is_a: PRIDE:0000107 ! Gel spot parameter
[Term]
id: PRIDE:0000132
name: Spot normalized volume method
def: "The method by which the normalized value for spot volume is derived from the individual gel spot volume values." [PRIDE:PRIDE]
is_a: PRIDE:0000107 ! Gel spot parameter
[Term]
id: PRIDE:0000133
name: Isobaric residue K/Q
def: "The amino acids glutamine (Q) (mol wt = 146) cannot be distinguished from lysine (K) (mol wt = 146)." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
[Term]
id: PRIDE:0000134
name: Anticoagulant
def: "A substance that prevents coagulation; that is, it stops blood from clotting." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
[Term]
id: PRIDE:0000135
name: Mapping date
def: "Date of last mapping of given identifier to current UniProt accession number." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000136
name: Mapping status
def: "Status of last mapping of given identifier to current UniProt accession number. Valid values are 'mappingAllOK', 'not mapped peptide mismatch', 'not mapped accession not found' and 'not mapped taxon not found' ." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000137
name: Mapping history
def: "Status of last mapping of given identifier to current UniProt accession number. Valid values are 'unchanged since last mapping', 'changed accession' and 'changed version of accession' ." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
[Term]
id: PRIDE:0000138
name: Discriminant score
def: "PeptideProphet discriminant score fval." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000101 ! PeptideProphet
[Term]
id: PRIDE:0000139
name: Not Mapped SOAP Error
def: "Error message: SOAP protocol failed." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status
[Term]
id: PRIDE:0000140
name: Not Mapped Database Error
def: "Error message: Error with queried database." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status
[Term]
id: PRIDE:0000141
name: Not Mapped No Mapping Found
def: "Error message: Unable to match given identifier." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status
[Term]
id: PRIDE:0000142
name: Not Mapped Peptide Mismatch
def: "Error message: One or more peptide sequences did not match query sequence." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status
[Term]
id: PRIDE:0000143
name: Mapped Taxon Not Found
def: "Error message: No mapping to proteins from defined taxon." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status
[Term]
id: PRIDE:0000144
name: Mapped All Ok
def: "Sucessful completion of operation message." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status
[Term]
id: PRIDE:0000145
name: PepSplice
def: "The PepSplice algorithm." [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm
is_a: PRIDE:0000573 ! Identification software
[Term]
id: PRIDE:0000146
name: PepSplice precision
def: "PepSplice precision refers to the accuracy of peptide-spectrum matches (PSMs) produced by the PepSplice search engine, a specialized tool used for the identification of peptides, particularly for novel or unexpected peptide sequences. Precision is a key metric used to assess the quality and reliability of search results in proteomics." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice
[Term]
id: PRIDE:0000147
name: PepSplice false discovery rate
def:"PepSlice false discovery rate is a critical metric used to control the number of false positives (incorrect peptide-spectrum matches or PSMs) in the search results" [PRIDE:PRIDE]
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice
[Term]
id: PRIDE:0000148
name: PepSplice P-value
def: "A Score based on the hypergeometric model." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice
[Term]
id: PRIDE:0000149
name: PepSplice Deltascore
def: "The Difference between the pvalues of the 1st and the 2nd best peptide; if two peptides have the same pvalue, they are taken together." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice
[Term]
id: PRIDE:0000150
name: PepSplice Score Count
def: "The score count." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice
[Term]
id: PRIDE:0000151
name: PepSplice Penalty
def: "The Sum of all penalties for the peptide assignment." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice
[Term]
id: PRIDE:0000152
name: PepSplice Read Direction
def: "The reading direction on the DNA." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice
[Term]
id: PRIDE:0000153
name: PepSplice Forward Read Direction
def: "The reading direction on the DNA is 5' to 3'." [PRIDE:PRIDE]
is_a: PRIDE:0000152 ! PepSplice Read Direction
[Term]
id: PRIDE:0000154
name: PepSplice Reverse Read Direction
def: "The reading direction on the DNA 3' to 5'." [PRIDE:PRIDE]
is_a: PRIDE:0000152 ! PepSplice Read Direction
is_a: PRIDE:0000145 ! PepSplice
[Term]
id: PRIDE:0000155
name: Unmappable
def: "unsucessful mapping." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status
[Term]
id: PRIDE:0000156
name: Project identifier
def: "unique identifier of project." [PRIDE:PRIDE]
synonym: "Project ID" EXACT []
relationship: part_of PRIDE:0000097 ! Project
[Term]
id: PRIDE:0000157
name: Search type