format-version: 1.2
data-version: 0.1.0
date: 27:09:2018 16:05
saved-by: julianu
import: http://ontologies.berkeleybop.org/uo.obo
import: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
import: https://raw.githubusercontent.com/HUPO-PSI/qcML-development/master/cv/qc-cv-legacy-0.0.8.obo
default-namespace: QC
namespace-id-rule: * MS:$sequence(7,0,9999999)$
namespace-id-rule: * QC:$sequence(7,0,9999999)$
remark: namespace: MS
remark: namespace: QC
remark: coverage: Mass spectrometer quality control metrics
remark: creator: Martin Eisenacher <martin.eisenacher <-at-> ruhr-uni-bochum.de>
remark: creator: Julian Uszkoreit <julian.uszkoreit <-at-> ruhr-uni-bochum.de>
ontology: qc

[Term]
id: MS:1009001
name: quality control metrics generating software
def: "Quality control metrics generating softwares are special types of analysis softwares, which are capable to generate QC metrics." [PSI:PI]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1009002
name: QuaMeter IDFree
def: "QuaMeter IDFree is a QC metrics generating software." [PSI:PI]
is_a: MS:1009001 ! quality control metrics generating software

[Term]
id: MS:1009003
name: iMonDB
def: "iMonDB is a QC metrics generating software." [PSI:PI]
is_a: MS:1009001 ! quality control metrics generating software

[Term]
id: QC:4000001
name: QC metric
def: "Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations." [PSI:QC]

[Term]
id: QC:4000002
name: QC metric type
def: "the QC metric type describes what type the respective metric is, like e.g. single value, n-tuple or table" [PSI:QC]

[Term]
id: QC:4000003
name: single value
def: "metrics consisting of a single value (in contrast to n-tuple or table)." [PSI:QC]
is_a: QC:4000002 ! QC metric type

[Term]
id: QC:4000004
name: n-tuple
def: "Metrics consisting of n values (in contrast to single_value or table), n specified by the CV param value, e.g. n=4 for quartiles." [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000002 ! QC metric type

[Term]
id: QC:4000005
name: corresponding lists
def: "Metrics consisting of a variable number of lists with n elements each, n specified by the CV param value. The k-th elements of the lists correspond to each other (as RT and intensity lists for a chromatogram)." [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000002 ! QC metric type

[Term]
id: QC:4000006
name: table
def: "metrics consisting of a table or data frame (in contrast to single_value or n-tuple), the values of the table may have different types in each column (in contrast to a matrix). The actual structure of the matrix is defined in the QC document." [PSI:QC]
is_a: QC:4000002 ! QC metric type

[Term]
id: QC:4000007
name: matrix
def: "A matrix is a rectangular array of values of the same type (in contrast to a table). The actual structure of the matrix is defined in the QC document." [PSI:QC]
is_a: QC:4000002 ! QC metric type

[Term]
id: QC:4000008
name: QC metric basis
def: "The basis for this QC metric, like ID based, ID free, quant based..." [PSI:QC]

[Term]
id: QC:4000009
name: ID based
def: "metrics based on a previous identification run (in contrast to ID_free, Quant_based)" [PSI:QC]
is_a: QC:4000008 ! QC metric basis

[Term]
id: QC:4000010
name: ID free
def: "metrics not based on a previous identification run (in contrast to ID_based, quant_based)" [PSI:QC]
is_a: QC:4000008 ! QC metric basis

[Term]
id: QC:4000011
name: Quantification based
def: "metrics based on a previous quantification run (in contrast to ID_free, ID_based)" [PSI:QC]
is_a: QC:4000008 ! QC metric basis

[Term]
id: QC:4000012
name: QC metric relation
def: "A QC metric describes the basis for the metric calculation like \"one MS run\" or \"one spectrum\"" [PSI:QC]

[Term]
id: QC:4000013
name: QC metric relation: one run
def: "describes a metric which is calculated on one run (e.g. one .raw file)" [PSI:QC]
is_a: QC:4000012 ! QC metric relation

[Term]
id: QC:4000014
name: QC metric relation: multiple runs
def: "a metric which is calculated on multiple runs / a set of runs (e.g. multiple .raw files)" [PSI:QC]
is_a: QC:4000012 ! QC metric relation

[Term]
id: QC:4000015
name: QC metric relation: one spectrum
def: "a metric which is calculated on one spectrum" [PSI:QC]
is_a: QC:4000012 ! QC metric relation

[Term]
id: QC:4000016
name: QC metric relation: multiple spectra
def: "a metric which is calculated on multiple spectra" [PSI:QC]
is_a: QC:4000012 ! QC metric relation

[Term]
id: QC:4000020
name: XIC metric
def: "a metric based on extracted ion chromatograms" [PSI:QC]
is_a: QC:4000022 ! chromatogram metric

[Term]
id: QC:4000021
name: retention time metric
def: "a metric based on the retention time" [PSI:QC]
is_a: QC:4000001 ! QC metric

[Term]
id: QC:4000022
name: chromatogram metric
def: "a metric based on the chromatogram" [PSI:QC]
is_a: QC:4000001 ! QC metric

[Term]
id: QC:4000023
name: MS1 metric
def: "a metric based on MS1 events" [PSI:QC]
is_a: QC:4000001 ! QC metric

[Term]
id: QC:4000024
name: MS2 metric
def: "a metric based on MS2 events" [PSI:QC]
is_a: QC:4000001 ! QC metric

[Term]
id: QC:4000025
name: ion source metric
def: "a metric related to events in the ions source" [PSI:QC]
is_a: QC:4000001 ! QC metric

[Term]
id: QC:4000026
name: environment metric
def: "a metric related to measurements of the environment" [PSI:QC]
is_a: QC:4000001 ! QC metric

[Term]
id: QC:4000050
name: XIC-WideFrac
def: "The fraction of precursor ions accounting for the top half of all peak widths" [PSI:QC]
is_a: QC:4000003 ! single value
is_a: QC:4000010 ! ID free
is_a: QC:4000020 ! XIC metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000086 ! full width at half-maximum

[Term]
id: QC:4000051
name: XIC-FWHM quantiles
def: "The first to n-th quantile of peak widths for the wide XICs. The cvParam value defines the number of given quantiles n." [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000004 ! n-tuple
is_a: QC:4000010 ! ID free
is_a: QC:4000020 ! XIC metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000086 ! full width at half-maximum

[Term]
id: QC:4000052
name: XIC-Height quantiles ratio to Q1
def: "The log ratio for second to n-th quantile of wide XIC heights over first quantile of heights. The cvParam value defines the number of given quantiles n (the corresponding tuple of the metric has n-1 values)." [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000004 ! n-tuple
is_a: QC:4000010 ! ID free
is_a: QC:4000020 ! XIC metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000627 ! selected ion current chromatogram
relationship: has_relation MS:1000042 ! peak intensity

[Term]
id: QC:4000053
name: RT duration
def: "The retention time duration of the MS run, similar to the highest scan time minus the lowest scan time." [PSI:QC]
is_a: QC:4000003 ! single value
is_a: QC:4000010 ! ID free
is_a: QC:4000021 ! retention time metric
relationship: has_relation QC:4000013 ! QC metric relation: one run

[Term]
id: QC:4000054
name: RT of TIC quantile
def: "The interval when the respective quantile of the TIC accumulates divided by retention time duration. The number of quantiles n is is defined by the cvParam value." [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000004 ! n-tuple
is_a: QC:4000010 ! ID free
is_a: QC:4000021 ! retention time metric
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000235 ! total ion current chromatogram

[Term]
id: QC:4000055
name: MS1 quantiles RT fraction
def: "The interval for the first to n-th quantile of all MS1 events divided by RT-Duration. The number of quantiles n is is defined by the cvParam value." [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000004 ! n-tuple
is_a: QC:4000010 ! ID free
is_a: QC:4000021 ! retention time metric
is_a: QC:4000023 ! MS1 metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000579 ! MS1 spectrum

[Term]
id: QC:4000056
name: MS2 quantiles RT fraction
def: "The interval for the first to n-th quantile of all MS2 events divided by RT-Duration. The number of quantiles n is is defined by the cvParam value." [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000004 ! n-tuple
is_a: QC:4000010 ! ID free
is_a: QC:4000021 ! retention time metric
is_a: QC:4000024 ! MS2 metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000580 ! MSn spectrum

[Term]
id: QC:4000057
name: MS1 quantile TIC change ratio to Q1
def: "The log ratio for the second to n-th quantile of TIC changes over first quantile of TIC changes. The cvParam value defines the number of given quantiles n (the corresponding tuple of the metric has n-1 values)." [PSI:QC]
is_a: QC:4000004 ! n-tuple
is_a: QC:4000010 ! ID free
is_a: QC:4000022 ! chromatogram metric
is_a: QC:4000023 ! MS1 metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000235 ! total ion current chromatogram

[Term]
id: QC:4000058
name: MS1 quantile TIC ratio to Q1
def: "The log ratio for the second to n-th quantile of TIC over first quantile of TIC. The cvParam value defines the number of given quantiles n (the corresponding tuple of the metric has n-1 values)." [PSI:QC]
is_a: QC:4000004 ! n-tuple
is_a: QC:4000010 ! ID free
is_a: QC:4000022 ! chromatogram metric
is_a: QC:4000023 ! MS1 metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000235 ! total ion current chromatogram

[Term]
id: QC:4000059
name: MS1 count
def: "The number of MS1 events in the run." [PSI:QC]
is_a: QC:4000003 ! single value
is_a: QC:4000010 ! ID free
is_a: QC:4000023 ! MS1 metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000579 ! MS1 spectrum

[Term]
id: QC:4000060
name: MS2 count
def: "The number of MS2 events in the run." [PSI:QC]
is_a: QC:4000003 ! single value
is_a: QC:4000010 ! ID free
is_a: QC:4000023 ! MS1 metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000580 ! MSn spectrum

[Term]
id: QC:4000061
name: maximal MS2 frequency
def: "The fastest frequency for MS/MS collection in any minute over the complete run" [PSI:QC]
is_a: QC:4000003 ! single value
is_a: QC:4000010 ! ID free
is_a: QC:4000024 ! MS2 metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000580 ! MSn spectrum
relationship: has_relation MS:1000029 ! sampling frequency

[Term]
id: QC:4000062
name: MS2 density per quantile
def: "The was the first to n-th quantile of MS2 scan peak counts. The cvParam value defines the number of given quantiles n." [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000004 ! n-tuple
is_a: QC:4000010 ! ID free
is_a: QC:4000024 ! MS2 metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000035 ! peak picking

[Term]
id: QC:4000063
name: MS2 known precursor charges fractions
def: "The fraction of MS/MS precursors of the corresponding charge. The fractions are given in the first list, charges in the second list. The cvParam value defines the number of entries in both lists." [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000005 ! corresponding lists
is_a: QC:4000010 ! ID free
is_a: QC:4000024 ! MS2 metric
is_a: QC:4000025 ! ion source metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000041 ! charge state

[Term]
id: QC:4000064
name: MS2 unknown and likely precursor charges fractions
def: "The fraction of MS/MS precursors of unknown, but possible likely charges. The fractions are given in the first list, the likely charges in the second list, charge 0 stands for unknown. The cvParam value defines the number of entries in both lists." [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000005 ! corresponding lists
is_a: QC:4000010 ! ID free
is_a: QC:4000024 ! MS2 metric
is_a: QC:4000025 ! ion source metric
relationship: has_relation QC:4000013 ! QC metric relation: one run
relationship: has_relation MS:1000041 ! charge state

[Term]
id: QC:4000065
name: Precursor median m/z for IDs
def: "Median m/z value for all identified peptides (unique ions)." [PSI:QC]
is_a: QC:4000003 ! single value
is_a: QC:4000009 ! ID based
is_a: QC:4000023 ! MS1 metric
is_a: QC:4000025 ! ion source metric
relationship: has_relation QC:4000013 ! QC metric relation: one run

[Term]
id: QC:4000066
name: Fraction of MS2 identified at different MS1 quantiles
def: "Fraction of total MS2 scans identified in the respective quantile of peptides sorted by MS1 maximum intensity. The cvParam value defines the number of given quantiles n." [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000004 ! n-tuple
is_a: QC:4000009 ! ID based
is_a: QC:4000023 ! MS1 metric
is_a: QC:4000024 ! MS2 metric
relationship: has_relation QC:4000013 ! QC metric relation: one run

[Term]
id: QC:4000067
name: Total ion current chromatogram
def: "The (centroided) total ion current chromatogram. The first list contains the m/z values, the second list the corresponding abundancies. The cvParam value defines the number of entries in both lists." [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000005 ! corresponding lists
is_a: QC:4000010 ! ID free
is_a: QC:4000022 ! chromatogram metric
relationship: has_relation QC:4000013 ! QC metric relation: one run

[Term]
id: QC:4000068
name: Ambient humidity
def: "The Ambient humidity. The cvParam value defines the number of values. TODO: why is this an n-tuple?" [PSI:QC]
xref: value-type:xsd\:int "The allowed value-type for this CV term."
is_a: QC:4000004 ! n-tuple
is_a: QC:4000010 ! ID free
is_a: QC:4000026 ! environment metric
relationship: has_relation QC:4000013 ! QC metric relation: one run

[Typedef]
id: has_relation
name: has_relation

[Typedef]
id: has_type
name: has_type

[Typedef]
id: has_units
name: has_units