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caeteracaetera
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Ontology update
1 parent 29f192f commit 7f80455

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2 files changed

+126
-8
lines changed

2 files changed

+126
-8
lines changed

‎Writer/MzMlSpectrumWriter.cs‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -119,7 +119,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
119119
URI = @"https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo",
120120
fullName = "Mass spectrometry ontology",
121121
id = "MS",
122-
version = "4.1.12"
122+
version = "4.1.38"
123123
});
124124
Serialize(serializer, new CVType
125125
{

‎Writer/OntologyMapping.cs‎

Lines changed: 125 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -227,6 +227,15 @@ public static class OntologyMapping
227227
value = ""
228228
}
229229
},
230+
{
231+
"LTQ ORBITRAP CLASSIC", new CVParamType
232+
{
233+
accession = "MS:1002835",
234+
name = "LTQ Orbitrap Classic",
235+
cvRef = "MS",
236+
value = ""
237+
}
238+
},
230239
{
231240
"LTQ ORBITRAP DISCOVERY", new CVParamType
232241
{
@@ -272,6 +281,33 @@ public static class OntologyMapping
272281
value = ""
273282
}
274283
},
284+
{
285+
"ORBITRAP VELOS", new CVParamType
286+
{
287+
accession = "MS:1001742",
288+
name = "LTQ Orbitrap Velos",
289+
cvRef = "MS",
290+
value = ""
291+
}
292+
},
293+
{
294+
"LTQ ORBITRAP VELOS PRO", new CVParamType
295+
{
296+
accession = "MS:1003096",
297+
name = "LTQ Orbitrap Velos Pro",
298+
cvRef = "MS",
299+
value = ""
300+
}
301+
},
302+
{
303+
"ORBITRAP VELOS PRO", new CVParamType
304+
{
305+
accession = "MS:1003096",
306+
name = "LTQ Orbitrap Velos Pro",
307+
cvRef = "MS",
308+
value = ""
309+
}
310+
},
275311
{
276312
"LTQ ORBITRAP ELITE", new CVParamType
277313
{
@@ -281,6 +317,15 @@ public static class OntologyMapping
281317
value = ""
282318
}
283319
},
320+
{
321+
"ORBITRAP ELITE", new CVParamType
322+
{
323+
accession = "MS:1001910",
324+
name = "LTQ Orbitrap Elite",
325+
cvRef = "MS",
326+
value = ""
327+
}
328+
},
284329
{
285330
"LTQ", new CVParamType
286331
{
@@ -299,6 +344,15 @@ public static class OntologyMapping
299344
value = ""
300345
}
301346
},
347+
{
348+
"LTQ XL", new CVParamType
349+
{
350+
accession = "MS:1000854",
351+
name = "LTQ XL",
352+
cvRef = "MS",
353+
value = ""
354+
}
355+
},
302356
{
303357
"LTQ XL ETD", new CVParamType
304358
{
@@ -326,6 +380,15 @@ public static class OntologyMapping
326380
value = ""
327381
}
328382
},
383+
{
384+
"LTQ VELOS ETD", new CVParamType
385+
{
386+
accession = "MS:1000856",
387+
name = "LTQ Velos ETD",
388+
cvRef = "MS",
389+
value = ""
390+
}
391+
},
329392
{
330393
"ORBITRAP FUSION", new CVParamType
331394
{
@@ -353,6 +416,33 @@ public static class OntologyMapping
353416
value = ""
354417
}
355418
},
419+
{
420+
"ORBITRAP ECLIPSE", new CVParamType
421+
{
422+
accession = "MS:1003029",
423+
name = "Orbitrap Eclipse",
424+
cvRef = "MS",
425+
value = ""
426+
}
427+
},
428+
{
429+
"ORBITRAP EXPLORIS 120", new CVParamType
430+
{
431+
accession = "MS:1003095",
432+
name = "Orbitrap Exploris 120",
433+
cvRef = "MS",
434+
value = ""
435+
}
436+
},
437+
{
438+
"ORBITRAP EXPLORIS 240", new CVParamType
439+
{
440+
accession = "MS:1003094",
441+
name = "Orbitrap Exploris 240",
442+
cvRef = "MS",
443+
value = ""
444+
}
445+
},
356446
{
357447
"ORBITRAP EXPLORIS 480", new CVParamType
358448
{
@@ -371,6 +461,15 @@ public static class OntologyMapping
371461
value = ""
372462
}
373463
},
464+
{
465+
"EXACTIVE PLUS", new CVParamType
466+
{
467+
accession = "MS:1002526",
468+
name = "Exactive Plus",
469+
cvRef = "MS",
470+
value = ""
471+
}
472+
},
374473
{
375474
"Q EXACTIVE", new CVParamType
376475
{
@@ -392,8 +491,8 @@ public static class OntologyMapping
392491
{
393492
"Q EXACTIVE PLUS ORBITRAP", new CVParamType
394493
{
395-
accession = "MS:1001911",
396-
name = "Q Exactive",
494+
accession = "MS:1002634",
495+
name = "Q Exactive Plus",
397496
cvRef = "MS",
398497
value = ""
399498
}
@@ -435,13 +534,14 @@ public static class OntologyMapping
435534
public static CVParamType getInstrumentModel(string instrumentName)
436535
{
437536
CVParamType instrumentModel;
537+
instrumentName = instrumentName.ToUpper();
438538
if (OntologyMapping.InstrumentModels.ContainsKey(instrumentName))
439539
{
440-
instrumentModel = OntologyMapping.InstrumentModels[instrumentName.ToUpper()];
540+
instrumentModel = OntologyMapping.InstrumentModels[instrumentName];
441541
}
442542
else
443543
{
444-
var longestMatch = InstrumentModels.Where(pair => instrumentName.ToUpper().Contains(pair.Key))
544+
var longestMatch = InstrumentModels.Where(pair => instrumentName.Contains(pair.Key))
445545
.Select(pair => pair.Key)
446546
.Aggregate("", (max, current) => max.Length > current.Length ? max : current);
447547
if (!longestMatch.IsNullOrEmpty())
@@ -477,8 +577,10 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
477577
case "MS:1000448":
478578
// LTQ FT ULTRA
479579
case "MS:1000557":
480-
// LTQ ORBITRAP
580+
// LTQ ORBITRAP
481581
case "MS:1000449":
582+
// LTQ ORBITRAP CLASSIC
583+
case "MS:1002835":
482584
// LTQ ORBITRAP DISCOVERY
483585
case "MS:1000555":
484586
// LTQ ORBITRAP XL
@@ -489,6 +591,8 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
489591
case "MS:1000643":
490592
// LTQ ORBITRAP VELOS
491593
case "MS:1001742":
594+
// LTQ ORBITRAP VELOS PRO
595+
case "MS:1003096":
492596
// LTQ ORBITRAP ELITE
493597
case "MS:1001910":
494598
// ORBITRAP FUSION
@@ -497,7 +601,13 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
497601
case "MS:1002417":
498602
// ORBITRAP FUSION LUMOS
499603
case "MS:1002732":
500-
// ORBITRAP EXPLORIS 480
604+
// ORBITRAP ECLIPSE
605+
case "MS:1003029":
606+
// ORBITRAP EXPLORIS 120
607+
case "MS:1003095":
608+
// ORBITRAP EXPLORIS 240
609+
case "MS:1003094":
610+
// ORBITRAP EXPLORIS 480
501611
case "MS:1003028":
502612
detectors = new List<CVParamType>
503613
{
@@ -519,6 +629,8 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
519629
break;
520630
// EXACTIVE
521631
case "MS:1000649":
632+
// EXACTIVE PLUS
633+
case "MS:1002526":
522634
// Q EXACTIVE
523635
case "MS:1001911":
524636
// Q EXACTIVE HF
@@ -540,9 +652,15 @@ public static List<CVParamType> GetDetectors(string instrumentAccession)
540652
break;
541653
// LTQ
542654
case "MS:1000447":
655+
// LTQ VELOS
656+
case "MS:1000855":
657+
// LTQ VELOS ETD
658+
case "MS:1000856":
543659
// LXQ
544660
case "MS:1000450":
545-
// LTQ XL ETD
661+
// LTQ XL
662+
case "MS:1000854":
663+
// LTQ XL ETD
546664
case "MS:1000638":
547665
// MALDI LTQ XL
548666
case "MS:1000642":

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