pyopenms 2.3.0__zip

media/doc/pyenv/py27_bleeding/lib/python2.7/site-packages/pyopenms/share/OpenMS/CV/qc-cv.obo

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+format-version: 1.2
+data-version: 0.1.0
+date: 20:11:2013 11:03
+saved-by: Mathias Walzer
+remark: creator: Mathias Walzer <walzer <-at-> informatik.uni-tuebingen.de>
+import: http://unit-ontology.googlecode.com/svn/trunk/unit.obo
+import: http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo
+default-namespace: QC
+remark: namespace: QC
+remark: version: 0.1.0
+ontology: uo
+ontology: ms
+
+[Typedef]
+id: has_regexp
+name: has regexp
+
+[Typedef]
+id: has_units
+name: has_units
+
+[Typedef]
+id: part_of
+name: part_of
+is_transitive: true
+
+[Typedef]
+id: has_order
+name: has_order
+
+[Term]
+ id: QC:0000001
+ name: quality parameter
+ def: "A quality parameter of some sort." [PXS:QC]
+ 
+
+[Term]
+ id: QC:0000002
+ name: run quality parameter
+ def: "A run quality parameter of some sort." [PXS:QC]
+ is_a: QC:0000001 ! quality parameter
+ 
+
+[Term]
+ id: QC:0000003
+ name: set quality parameter
+ def: "A set quality parameter of some sort." [PXS:QC]
+ is_a: QC:0000001 ! quality parameter
+ 
+
+[Term]
+ id: QC:0000004
+ name: MS aquisition result details
+ def: "The results (e.g. counts) of the MS aquisition step of a MS experiment." [PXS:QC]
+ is_a: QC:0000001 ! quality parameter
+
+remark: run name is MS:1000577 as raw data file in [PSI:MS]
+ 
+[Term]
+ id: QC:0000005
+ name: set name
+ def: "The set name describing the set grouping." [PXS:QC]
+ is_a: QC:0000001 ! quality parameter
+
+
+[Term]
+ id: QC:0000006
+ name: MS1 spectra count
+ def: "Contains the number of MS1 spectra recorded." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+ 
+
+[Term]
+ id: QC:0000007
+ name: MS2 spectra count
+ def: "Contains the number of MS2 spectra recorded." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+ 
+
+[Term]
+ id: QC:0000008
+ name: Chromatogram count
+ def: "Contains the number of chromatograms recorded." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+
+
+[Term]
+ id: QC:0000009
+ name: MS MZ aquisition ranges
+ def: "Contains the min/max MZ range boundaries observed during MS aquisition." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+ is_a: QC:0000048 ! value table
+ 
+ 
+[Term]
+ id: QC:0000010
+ name: MS min MZ
+ def: "Contains the actual min MZ occurrence in MS aquisition." [PXS:QC]
+ is_a: QC:0000009 ! MS MZ aquisition ranges
+remark: supposed as table col
+
+
+[Term]
+ id: QC:0000011
+ name: MS max MZ
+ def: "Contains the actual max MZ occurrence in MS aquisition." [PXS:QC]
+ is_a: QC:0000009 ! MS MZ aquisition ranges
+remark: supposed as table col
+
+ 
+[Term]
+ id: QC:0000012
+ name: MS RT aquisition ranges
+ def: "Contains the min/max RT range boundaries observed during MS aquisition." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+ is_a: QC:0000048 ! value table
+
+
+[Term]
+ id: QC:0000013
+ name: MS min RT
+ def: "Contains the actual min RT occurrence in MS aquisition." [PXS:QC]
+ is_a: QC:0000012 ! MS RT aquisition ranges
+ is_a: QC:0000048 ! value table
+
+
+[Term]
+ id: QC:0000014
+ name: MS max RT
+ def: "Contains the actual max RT occurrence in MS aquisition." [PXS:QC]
+ is_a: QC:0000012 ! MS RT aquisition ranges
+remark: supposed as table col
+
+
+[Term]
+ id: QC:0000015
+ name: MS gradient settings
+ def: "Contains the min/max RT range boundaries used in machine settings during MS aquisition." [PXS:QC]
+ is_a: QC:0000012 ! MS RT aquisition ranges
+ is_a: QC:0000048 ! value table
+
+
+[Term]
+ id: QC:0000016
+ name: MS MZ detection settings
+ def: "Contains the min/max MZ range boundaries used in machine settings during MS aquisition." [PXS:QC]
+ is_a: QC:0000009 ! MS MZ aquisition ranges
+
+
+[Term]
+ id: QC:0000017
+ name: MS1 injection time
+ def: "Contains the accumulation time in the ion trap device used in machine settings during MS aquisition." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+ 
+
+[Term]
+ id: QC:0000018
+ name: MS2 injection time
+ def: "Contains the accumulation time in the ion trap device used in machine settings during MS aquisition." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+ 
+
+[Term]
+ id: QC:0000019
+ name: MS1 scan time
+ def: "Contains the	average scan time for a MS1 event used in machine settings during MS aquisition." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+
+
+[Term]
+ id: QC:0000020
+ name: MS2 scan time
+ def: "Contains the	average scan time for a MS2 event used in machine settings during MS aquisition." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+ 
+ 
+[Term]
+ id: QC:0000021
+ name: lock mass percentage
+ def: "Contains the	percentage of found lock masses during MS aquisition." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+ 
+ 
+[Term]
+ id: QC:0000022
+ name: TICs
+ def: "The total ion currents detected in each of a series of mass spectra recorded." [PXS:QC]
+ is_a: QC:0000048 ! value table
+
+ 
+[Term]
+ id: QC:0000023
+ name: TIC slump
+ def: "The percentage of tic slumps below 10k." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+
+remark: TIC plot is MS:1000235
+ 
+[Term]
+ id: QC:0000024
+ name: detector-saturation
+ def: "The average ion saturation of the detector in MS aquisition." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+ 
+
+[Term]
+ id: QC:0000025
+ name: MS identification result details
+ def: "The results (e.g. identifications) of the MS identification step of a MS experiment." [PXS:QC]
+ is_a: QC:0000001 ! quality parameter
+
+
+[Term]
+ id: QC:0000026
+ name: MS id settings
+ def: "The settings of the search engine used engine name and further parameters." [PXS:QC]
+ is_a: MS:1001249 ! search input details
+
+ 
+[Term]
+ id: QC:0000027
+ name: precursor ion tolerance 
+ def: "This paramter shows the precursor tolerance that was used for MS/MS identification." [PXS:QC]
+ is_a: MS:1001411 ! search tolerance specification
+ 
+
+[Term]
+ id: QC:0000028
+ name: product ion tolerance 
+ def: "This paramter shows the product ion tolerance that was used for MS/MS identification." [PXS:QC]
+ is_a: MS:1001411 ! search tolerance specification
+ 
+ 
+[Term]
+ id: QC:0000029
+ name: total number of PSMs
+ def: "This number indicates the number of spectra that were given peptide annotations." [PXS:QC]
+ is_a: MS:1001405 ! spectrum identification result details
+ is_a: QC:0000025 ! MS identification result details
+
+
+[Term]
+ id: QC:0000030
+ name: total number of identified peptides
+ def: "This number indicates the number peptides that were identified." [PXS:QC]
+ is_a: MS:1001405 ! spectrum identification result details
+ is_a: QC:0000025 ! MS identification result details
+
+[Term]
+ id: QC:0000031
+ name: total number of uniquely identified peptides
+ def: "This number indicates the number peptides that were uniquely identified." [PXS:QC]
+ is_a: MS:1001405 ! spectrum identification result details
+ is_a: QC:0000025 ! MS identification result details
+
+
+[Term]
+ id: QC:0000032
+ name: total number of identified proteins
+ def: "This number indicates the number proteins that were identified." [PXS:QC]
+ is_a: MS:1001405 ! spectrum identification result details
+ is_a: QC:0000025 ! MS identification result details
+ 
+
+[Term]
+ id: QC:0000033
+ name: total number of uniquely identified proteins
+ def: "This number indicates the number proteins that were uniquely identified." [PXS:QC]
+ is_a: MS:1001405 ! spectrum identification result details
+ is_a: QC:0000025 ! MS identification result details
+ 
+
+[Term]
+ id: QC:0000034
+ name: total number of modified peptides
+ def: "This number indicates the number modified peptide sequences that were identified (after FDR)." [PXS:QC]
+ is_a: MS:1001405 ! spectrum identification result details
+ is_a: QC:0000025 ! MS identification result details
+ 
+
+[Term]
+ id: QC:0000035
+ name: id ratio
+ def: "This ratio indicates the number of identified peptides vs. the number of recorded ms2 spectra." [PXS:QC]
+ is_a: MS:1001405 ! spectrum identification result details
+ is_a: QC:0000025 ! MS identification result details
+ 
+
+[Term]
+ id: QC:0000036
+ name: id coverage
+ def: "The coverages of distinct sequences for a respective engine." [PXS:QC]
+ is_a: MS:1001405 ! spectrum identification result details
+ is_a: QC:0000025 ! MS identification result details
+
+
+[Term]
+ id: QC:0000037
+ name: total number of missed cleavages
+ def: "This number indicates the number missed cleavages that were identified." [PXS:QC]
+ is_a: MS:1001405 ! spectrum identification result details
+ is_a: QC:0000025 ! MS identification result details
+ 
+
+[Term]
+ id: QC:0000038
+ name: mass accuracy
+ def: "The values of overall mass accuracy." [PXS:QC]
+ is_a: MS:1001105 ! peptide result details
+ is_a: QC:0000025 ! MS identification result details
+ is_a: QC:0000048 ! value table
+ 
+
+[Term]
+ id: QC:0000039
+ name: delta ppm
+ def: "The deviation of the precursor ion mass and the theoretical mass of the matched identification." [PXS:QC]
+ relationship: has_units UO:0000169 ! parts per million
+ is_a: QC:0000025 ! MS identification result details
+
+
+[Term]
+ id: QC:0000040
+ name: mean delta ppm
+ def: "The mean deviation of the precursor ion masses and the theoretical masses of the matched identifications." [PXS:QC]
+ relationship: has_units UO:0000169 ! parts per million
+ is_a: QC:0000025 ! MS identification result details
+
+
+[Term]
+ id: QC:0000041
+ name: median delta ppm
+ def: "The median deviation of the precursor ion masses and the theoretical masses of the matched identifications." [PXS:QC]
+ relationship: has_units UO:0000169 ! parts per million
+ is_a: QC:0000025 ! MS identification result details
+
+
+[Term]
+ id: QC:0000042
+ name: enzyme contamination
+ def: "The ratio of  the sum of chymotryptic and tryptic sequences by the number of tryptic sequences." [PXS:QC]
+ relationship: has_units UO:0000169 ! parts per million	ratio	 NA
+ is_a: QC:0000025 ! MS identification result details
+
+
+[Term]
+ id: QC:0000043
+ name: fractional masses plot
+ def: "This plot visualizes the theoretical fractional masses (e.g. from the search DB input) vs. the measured fractional masses." [PXS:QC]
+ is_a: QC:0000050 ! image plot
+ 
+
+[Term]
+ id: QC:0000044
+ name: precursors
+ def: "The table of measured precursor ions over RT/mz." [PXS:QC]
+ is_a: QC:0000048 ! value table
+ 
+
+[Term]
+ id: QC:0000045
+ name: MS quantification result details
+ def: "The results (e.g. number of features) of the MS quantification step of a MS experiment." [PXS:QC]
+ is_a: QC:0000001 ! quality parameter
+
+
+[Term]
+ id: QC:0000046
+ name: number of features
+ def: "The number of features reported." [PXS:QC]
+ is_a: QC:0000045 ! MS quantification result details
+ 
+
+[Term]
+ id: QC:0000047
+ name: features
+ def: "The tables of features over RT/mz." [PXS:QC]
+ is_a: QC:0000048 ! value table
+ is_a: QC:0000045 ! MS quantification result details
+
+
+[Term]
+ id: QC:0000048
+ name: value table
+ def: "The table contains generic information." [PXS:QC]
+
+[Term]
+ id: QC:0000049
+ name: generic table
+ def: "The table contains generic information." [PXS:QC]
+ is_a: QC:0000048 ! value table
+
+
+[Term]
+ id: QC:0000050
+ name: image plot
+ def: "The plot contains generic information." [PXS:QC]
+ 
+ 
+[Term]
+ id: QC:0000051
+ name: generic plot
+ def: "The plot contains generic information." [PXS:QC]
+ is_a: QC:0000050 ! image plot
+
+
+[Term]
+ id: QC:0000052
+ name: id ratio plot
+ def: "This plot visualizes the ratio of number of identified peptides vs. the number of recorded ms2 spectra." [PXS:QC]
+ is_a: MS:1001405 ! spectrum identification result details
+ is_a: QC:0000050 ! image plot
+ 
+ 
+[Term]
+ id: QC:0000053
+ name: mass accurracy plot
+ def: "This plot visualizes the mass accurracy of identified ms2 spectra." [PXS:QC]
+ is_a: MS:1001405 ! spectrum identification result details
+ is_a: QC:0000050 ! image plot
+  
+ 
+[Term]
+ id: QC:0000054
+ name: mass accurracy over time plot
+ def: "This plot visualizes the mass accurracy over the course of RT." [PXS:QC]
+ is_a: MS:1001405 ! spectrum identification result details
+ is_a: QC:0000050 ! image plot
+ 
+ 
+[Term]
+ id: QC:0000055
+ name: MS experiment heatmap
+ def: "This plot visualizes the intensities on RT vs mz." [PXS:QC]
+ is_a: QC:0000050 ! image plot
+ 
+
+[Term]
+ id: QC:0000056
+ name: RICs
+ def: "The reconstructed ion currents (from MS1) detected in each of a series of mass spectra recorded." [PXS:QC]
+ is_a: QC:0000048 ! value table
+
+
+[Term]
+ id: QC:0000057
+ name: RIC slump
+ def: "The percentage of ric slumps below 10k." [PXS:QC]
+ is_a: QC:0000004 ! MS aquisition result details
+
+[Term]
+ id: QC:0000058
+ name: number of identified features
+ def: "The number of identified features reported." [PXS:QC]
+ is_a: QC:0000045 ! MS quantification result details
+ is_a: QC:0000025 ! MS identification result details
+
+[Term]
+ id: QC:0000059
+ name: IS-1A
+ def: "The number of 10fold jumps in MS1 Intensity" [PXS:QC]
+ is_a: QC:0000045 ! MS quantification result details
+ is_a: QC:0000025 ! MS identification result details
+
+[Term]
+ id: QC:0000060
+ name: IS-1B
+ def: "The number of 10fold dumps in MS1 Intensity" [PXS:QC]
+ is_a: QC:0000045 ! MS quantification result details
+ is_a: QC:0000025 ! MS identification result details