public static ControlledVocabulary Get()
{
ControlledVocabulary vocabulary = new ControlledVocabulary("Proteomics Standards Initiative Quality Control Ontology", "https://github.com/HUPO-PSI/mzQC/raw/master/cv/qc-cv.obo", "0.1.0");
vocabulary.AddTerms(new Term[]
{
new Term(vocabulary, "QC:4000053", "Quameter metric: RT-Duration"),
new Term(vocabulary, "QC:02", "SwaMe metric: swathSizeDifference"),
new Term(vocabulary, "QC:4000060", "Quameter metric: MS2-Count"),
new Term(vocabulary, "QC:04", "SwaMe metric: NumOfSwaths"),
new Term(vocabulary, "QC:05", "SwaMe metric: Target mz"),
new Term(vocabulary, "QC:06", "SwaMe metric: TotalMS2IonCount"),
new Term(vocabulary, "QC:07", "SwaMe metric: MS2Density50"),
new Term(vocabulary, "QC:08", "SwaMe metric: MS2DensityIQR"),
new Term(vocabulary, "QC:4000059", "Quameter metric: MS1-Count"),
new Term(vocabulary, "QC:09", "SwaMe metric: scansPerSwathGroup"),
new Term(vocabulary, "QC:10", "SwaMe metric: AvgMzRange"),
new Term(vocabulary, "QC:11", "SwaMe metric: SwathProportionOfTotalTIC"),
new Term(vocabulary, "QC:12", "SwaMe metric: swDensity50"),
new Term(vocabulary, "QC:13", "SwaMe metric: swDensityIQR"),
new Term(vocabulary, "QC:14", "SwaMe metric: Peakwidths"),
new Term(vocabulary, "QC:15", "SwaMe metric: PeakCapacity"),
new Term(vocabulary, "QC:24", "SwaMe metric: TailingFactor"),
new Term(vocabulary, "QC:XXXXXXXX", "SwaMe metric: MS2PeakPrecision"),
new Term(vocabulary, "QC:16", "SwaMe metric: MS1PeakPrecision"),
new Term(vocabulary, "QC:17", "SwaMe metric: DeltaTICAverage"),
new Term(vocabulary, "QC:18", "SwaMe metric: DeltaTICIQR"),
new Term(vocabulary, "QC:19", "SwaMe metric: AvgScanTime"),
new Term(vocabulary, "QC:20", "SwaMe metric: MS2Density"),
new Term(vocabulary, "QC:21", "SwaMe metric: MS1Density"),
new Term(vocabulary, "QC:22", "SwaMe metric: MS2TICTotal"),
new Term(vocabulary, "QC:23", "SwaMe metric: MS1TICTotal"),
new Term(vocabulary, "QC:99", "Prognosticator Metric: MS1TICQuartiles"),
new Term(vocabulary, "QC:98", "Prognosticator Metric: MS2TICQuartiles"),
new Term(vocabulary, "QC:97", "Prognosticator Metric: MS1TIC"),
new Term(vocabulary, "QC:96", "Prognosticator Metric: MS2TIC"),
new Term(vocabulary, "QC:95", "Prognosticator Metric: MS1BPC"),
new Term(vocabulary, "QC:94", "Prognosticator Metric: MS2BPC"),
new Term(vocabulary, "QC:93", "Prognosticator Metric: CombinedTIC"),
new Term(vocabulary, "QC:92", "Prognosticator Metric: MS1:MS2 ratio"),
new Term(vocabulary, "QC:91", "Prognosticator Metric: MS1 weighted median skew"),
new Term(vocabulary, "QC:90", "Prognosticator Metric: MS2 weighted median skew"),
new Term(vocabulary, "QC:89", "Prognosticator Metric: MeanIrtMassError"),
new Term(vocabulary, "QC:88", "Prognosticator Metric: MaxIrtMassError"),
new Term(vocabulary, "QC:87", "Prognosticator Metric: IrtPeptideFoundProportion"),
new Term(vocabulary, "QC:86", "Prognosticator Metric: IrtPeptides"),
new Term(vocabulary, "QC:85", "Prognosticator Metric: IrtPeptidesFound"),
new Term(vocabulary, "QC:84", "Prognosticator Metric: IrtSpread"),
new Term(vocabulary, "QC:83", "Prognosticator Metric: MS1TICQuartilesByRT"),
new Term(vocabulary, "QC:82", "Prognosticator Metric: MS2TICQuartilesByRT"),
new Term(vocabulary, "QC:81", "Prognosticator Metric: IrtOrderedness")
});
return(vocabulary);
}
public static ControlledVocabulary Get()
{
ControlledVocabulary vocabulary = new ControlledVocabulary("Unit Ontology", "http://ontologies.berkeleybop.org/uo.obo", "releases/2020-03-10");
vocabulary.AddTerms(new Term[]
{
new Term(vocabulary, "UO:0000189", "count"),
new Term(vocabulary, "UO:0000010", "second"),
new Term(vocabulary, "UO:0010006", "ratio") // TODO: What's the difference between this and UO:0000190?
});
return(vocabulary);
}
public static ControlledVocabulary Get()
{
ControlledVocabulary vocabulary = new ControlledVocabulary("Proteomics Standards Initiative Mass Spectrometry Ontology", "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo", "4.1.7");
vocabulary.AddTerms(new Term[]
{
new Term(vocabulary, "XXXXXXXXXXXXXX", "SwaMe"),
new Term(vocabulary, "MS:1000040", "m/z"),
new Term(vocabulary, "MS:1000042", "Peak Intensity"),
new Term(vocabulary, "MS:1000569", "SHA-1"),
new Term(vocabulary, "MS:1000584", "mzML format"),
new Term(vocabulary, "MS:1000747", "completion time")
});
return(vocabulary);
}
public MzqcWriter()
{
uo = cvLibrary.RegisterControlledVocabulary(UnitOntology.Get(), "UO");
ms = cvLibrary.RegisterControlledVocabulary(MSVocabulary.Get(), "MS");
qc = cvLibrary.RegisterControlledVocabulary(MzQCVocabulary.Get(), "QC");
JsonClasses.Unit Count = ToUnit(uo, "UO:0000189");
JsonClasses.Unit Intensity = ToUnit(ms, "MS:1000042");
JsonClasses.Unit Mz = ToUnit(ms, "MS:1000040");
JsonClasses.Unit Ratio = ToUnit(uo, "UO:0010006"); // TODO: What's the difference between this and UO:0000190?
JsonClasses.Unit Second = ToUnit(uo, "UO:0000010");
QualityParametersByAccession = new JsonClasses.QualityParameters[]
{
ToQualityParameters(qc, "QC:4000053", Second),
ToQualityParameters(qc, "QC:02", Mz),
ToQualityParameters(qc, "QC:4000060", Count),
ToQualityParameters(qc, "QC:04", Count),
ToQualityParameters(qc, "QC:05", Mz),
ToQualityParameters(qc, "QC:06", Count),
ToQualityParameters(qc, "QC:07", Count),
ToQualityParameters(qc, "QC:08", Count),
ToQualityParameters(qc, "QC:4000059", Count),
ToQualityParameters(qc, "QC:09", Count),
ToQualityParameters(qc, "QC:10", Mz),
ToQualityParameters(qc, "QC:11", Ratio),
ToQualityParameters(qc, "QC:12", Count),
ToQualityParameters(qc, "QC:13", Count),
ToQualityParameters(qc, "QC:14", Second),
ToQualityParameters(qc, "QC:15", Count),
ToQualityParameters(qc, "QC:24", Count),
ToQualityParameters(qc, "QC:XXXXXXXX", Mz),
ToQualityParameters(qc, "QC:16", Mz),
ToQualityParameters(qc, "QC:17", Intensity),
ToQualityParameters(qc, "QC:18", Intensity),
ToQualityParameters(qc, "QC:19", Second),
ToQualityParameters(qc, "QC:20", Count),
ToQualityParameters(qc, "QC:21", Count),
ToQualityParameters(qc, "QC:22", Count),
ToQualityParameters(qc, "QC:23", Count),
ToQualityParameters(qc, "QC:99", Count),
ToQualityParameters(qc, "QC:98", Count),
ToQualityParameters(qc, "QC:97", Count),
ToQualityParameters(qc, "QC:96", Count),
ToQualityParameters(qc, "QC:95", Count),
ToQualityParameters(qc, "QC:94", Count),
ToQualityParameters(qc, "QC:93", Count),
ToQualityParameters(qc, "QC:92", Count),
ToQualityParameters(qc, "QC:91", Count),
ToQualityParameters(qc, "QC:90", Count),
ToQualityParameters(qc, "QC:89", Count),
ToQualityParameters(qc, "QC:88", Count),
ToQualityParameters(qc, "QC:87", Count),
ToQualityParameters(qc, "QC:86", Count),
ToQualityParameters(qc, "QC:85", Count),
ToQualityParameters(qc, "QC:84", Count),
ToQualityParameters(qc, "QC:83", Count),
ToQualityParameters(qc, "QC:82", Count),
ToQualityParameters(qc, "QC:81", Count)
}
.ToDictionary(qp => qp.accession);
}
private JsonClasses.QualityParameters ToQualityParameters(ControlledVocabulary cv, Term term, JsonClasses.Unit unit) => new JsonClasses.QualityParameters(cv.PrimaryNamespace, term.Id, term.Name, unit, null);
private JsonClasses.NUV ToNUV(ControlledVocabulary controlledVocabulary) => new JsonClasses.NUV()
{
name = controlledVocabulary.Name, uri = controlledVocabulary.Url, version = controlledVocabulary.Version
};
private JsonClasses.FileProperties ToFileProperties(ControlledVocabulary cv, Term term, string value) => new JsonClasses.FileProperties(cv.PrimaryNamespace, term.Id, term.Name, value);
private JsonClasses.QualityParameters ToQualityParameters(ControlledVocabulary cv, string id, JsonClasses.Unit unit) => ToQualityParameters(cv, cv.GetById(id), unit);
private JsonClasses.FileProperties ToFileProperties(ControlledVocabulary cv, string id, string value) => ToFileProperties(cv, cv.GetById(id), value);
private JsonClasses.FileFormat ToFileFormat(ControlledVocabulary cv, Term term) => new JsonClasses.FileFormat(cv.PrimaryNamespace, term.Id, term.Name);
private JsonClasses.FileFormat ToFileFormat(ControlledVocabulary cv, string id) => ToFileFormat(cv, cv.GetById(id));
private JsonClasses.Unit ToUnit(ControlledVocabulary cv, Term term) => new JsonClasses.Unit(cv.PrimaryNamespace, term.Id, term.Name);
private JsonClasses.Unit ToUnit(ControlledVocabulary cv, string id) => ToUnit(cv, cv.GetById(id));
