mzQuant new terms - Githubissues

Changed and new terms in psi-ms.obo based on version 3.7.3 (release date: 2011-07-13)

Existing terms with modifications (mainly in is_a, but also in name, xref and / or def lines):

[xref lines allowing values are deleted to avoid reporting values in CV terms; they should be given in the data matrix of mzQuantML]

[Term] id: MS:1001130 name: peptide raw area def: "Peptide raw area. TODO: clarify!" [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001131 name: error on peptide area def: "Error on peptide area." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001132 name: peptide ratio def: "Peptide ratio." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001133 name: error on peptide ratio def: "Error on peptide ratio." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001134 name: protein ratio def: "Protein ratio." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001135 name: error on protein ratio def: "Error on protein ratio." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001136 name: p-value (protein diff from 1 randomly) def: "P-value (protein diff from 1 randomly). TODO: clarify!" [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001137 name: absolute quantity def: "Absolute quantity in terms of real concentration or molecule copy number in sample." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001138 name: error on absolute quantity def: "Error on absolute quantity." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001140 name: quantitation software version def: "Quantitation software version. TODO: OBSOLETE, because part of mzQuantML schema!" [PSI:PI] is_a: MS:1001129 ! quantification information

[Term] id: MS:1001141 name: intensity of precursor ion def: "The intensity of the precursor ion." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001488 name: Mascot Distiller def: "Mascot Distiller." [PSI:PI] is_a: MS:1001456 ! analysis software is_a: MS:1001139 ! quantitation software name

[Term] id: MS:1000739 name: WARP-LC def: "Bruker WARP-LC software." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001139 ! quantitation software name

New terms:

[Term] id: MS:1001798 name: quantification datatype def: "The data type of the value reported in a QuantLayer for a feature, matchedfeature, peptide, protein, protein group." [PSI:MS] is_a: MS:1001129 ! quantification information

[Term] id: MS:1001799 name: quantification object attribute def: "Attributes describing the details of an object relevant for reporting quantification workflows or values." [PSI:MS] is_a: MS:1001129 ! quantification information

[Term] id: MS:1001800 name: StudyVariable attribute def: "Attribute describing a study variable." [PSI:MS] is_a: MS:1001799 ! quantification object attribute

[Term] id: MS:1001801 name: technical replicate def: "The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'" [PSI:MS] xref: value-type:xsd:string "The allowed value-type for this CV term." is_a: MS:1001800 ! StudyVariable attribute

[Term] id: MS:1001802 name: biological replicate def: "The study variable is 'biological replicate'. This means, the run was generated from another individuum or sample." [PSI:MS] is_a: MS:1001800 ! StudyVariable attribute

[Term] id: MS:1001803 name: experimental condition 'case' def: "The experimental condition is 'case' in contrast to 'control'." [PSI:MS] is_a: MS:1001800 ! StudyVariable attribute

[Term] id: MS:1001804 name: experimental condition 'control' def: "The experimental condition is 'control' in contrast to 'case'." [PSI:MS] is_a: MS:1001800 ! StudyVariable attribute

[Term] id: MS:1001805 name: experimental condition 'disease' def: "The experimental condition is 'disease' in contrast to 'healthy'." [PSI:MS] is_a: MS:1001800 ! StudyVariable attribute

[Term] id: MS:1001806 name: experimental condition 'healthy' def: "The experimental condition is 'healthy' in contrast to 'disease'." [PSI:MS] is_a: MS:1001800 ! StudyVariable attribute

[Term] id: MS:1001807 name: generic experimental condition def: "The experimental condition is given in the value of this term." [PSI:MS] xref: value-type:xsd:string "The allowed value-type for this CV term." is_a: MS:1001800 ! StudyVariable attribute

[Term] id: MS:1001808 name: time series, time point X def: "The experimental design followed a time series design. The time point of this run is given in the value of this term." [PSI:MS] xref: value-type:xsd:int "The allowed value-type for this CV term." is_a: MS:1001800 ! StudyVariable attribute

[Term] id: MS:1001809 name: dilution series, concentration X def: "The experimental design followed a dilution series design. The concentration of this run is given in the value of this term." [PSI:MS] xref: value-type:xsd:double "The allowed value-type for this CV term." is_a: MS:1001800 ! StudyVariable attribute

[Term] id: MS:1001810 name: RawFile attribute def: "Attribute describing a raw file." [PSI:MS] is_a: MS:1001799 ! quantification object attribute

[Term] id: MS:1001811 name: one sample run def: "The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free)." [PSI:MS] is_a: MS:1001810 ! RawFile attribute

[Term] id: MS:1001812 name: two sample run def: "The raw file contains the run of two samples (e.g. SILAC, metabolic labeling)." [PSI:MS] is_a: MS:1001810 ! RawFile attribute

[Term] id: MS:1001813 name: three sample run def: "The raw file contains the run of three samples (e.g. 3-plex SILAC)." [PSI:MS] is_a: MS:1001810 ! RawFile attribute

[Term] id: MS:1001814 name: four sample run def: "The raw file contains the run of four samples (e.g. 4-plex iTraq)." [PSI:MS] is_a: MS:1001810 ! RawFile attribute

[Term] id: MS:1001815 name: eight sample run def: "The raw file contains the run of eight samples (e.g. 8-plex iTraq)." [PSI:MS] is_a: MS:1001810 ! RawFile attribute

[Term] id: MS:1001816 name: RawFilesGroup attribute def: "Attribute describing, how raw files build a raw file group." [PSI:MS] is_a: MS:1001799 ! quantification object attribute

[Term] id: MS:1001817 name: merge of runs of 1D gel bands def: "Attribute describing, how raw files build a raw file group." [PSI:MS] is_a: MS:1001816 ! RawFilesGroup attribute

[Term] id: MS:1001818 name: FeatureList attribute def: "Attribute describing a FeatureList." [PSI:MS] is_a: MS:1001799 ! quantification object attribute

[Term] id: MS:1001819 name: mass trace reporting: rectangles def: "The mass trace of the features of this feature list specifies rectangles. Each mass trace has the syntax (RT_start,MZ_start,RT_end,MZ_end), i.e. opposite corners are given." [PSI:MS] is_a: MS:1001818 ! FeatureList attribute

[Term] id: MS:1001820 name: mass trace reporting: polygons def: "The mass trace of the features of this feature list specifies polygons. Each mass trace has the syntax (RT_1,MZ_1,RT_2,MZ_2,...,RT_i,MZ_i,...,RT_n,MZ_n), where the line (RT_n,MZ_n)->(RT_1,MZ_1) is implicite." [PSI:MS] is_a: MS:1001818 ! FeatureList attribute

[Term] id: MS:1001821 name: Feature attribute def: "Attribute describing a Feature." [PSI:MS] is_a: MS:1001799 ! quantification object attribute

[Term] id: MS:1001822 name: SRM transition ID def: "SRM transition ID. TODO: clarify!" [PSI:MS] is_a: MS:1001821 ! Feature attribute

[Term] id: MS:1001823 name: Progenesis LC-MS def: "Software from Nonlinear Dynamics for LC-MS label-free workflow" [PSI:MS] is_a: MS:1001139 ! quantitation software name

[Term] id: MS:1001824 name: SILACAnalyzer def: "Software for SILAC workflow" [PSI:MS] is_a: MS:1001139 ! quantitation software name

[Term] id: MS:1001827 name: quantitation software comment / customizations def: "Quantitation software comment or any customizations to the default setup of the software." [PSI:PI] is_a: MS:1001129 ! quantification information

[Term] id: MS:1001828 name: quantitation analysis summary def: "The overall workflow of this quantitation report." [PSI:PI] is_a: MS:1001129 ! quantification information

[Term] id: MS:1001829 name: LC-MS label-free def: "LC-MS label-free workflow (RT m/z map)." [PSI:PI] is_a: MS:1001828 ! quantitation analysis summary

[Term] id: MS:1001830 name: SILAC def: "SILAC workflow (heavy, light, and sometimes medium peak)." [PSI:PI] is_a: MS:1001828 ! quantitation analysis summary

[Term] id: MS:1001831 name: spectral counting def: "Spectral counting workflow (number of identified MS/MS spectra as approximation of peptide / protein quant.)." [PSI:PI] is_a: MS:1001828 ! quantitation analysis summary

[Term] id: MS:1001832 name: iTraq def: "iTraq workflow (reporter ions on MS/MS level)." [PSI:PI] is_a: MS:1001828 ! quantitation analysis summary

[Term] id: MS:1001833 name: SRM def: "Selected Reaction Monitoring workflow (XIC quant. of precursor / fragment mass pair)." [PSI:PI] is_a: MS:1001828 ! quantitation analysis summary

[Term] id: MS:1001834 name: metabolic labeling 14N / 15N def: "Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens)." [PSI:PI] is_a: MS:1001828 ! quantitation analysis summary

[Term] id: MS:1001835 name: LC-MS feature intensity def: "Maximum peak intensity of the LC-MS feature." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001836 name: LC-MS feature volume def: "Real (intensity times area) volume of the LC-MS feature." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001836 name: peptide PSM count def: "The number of MS/MS spectra identified for this peptide in spectral counting." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001837 name: peak intensity def: "Maximum intensity of MS1 peak (e.g. SILAC, 15N)." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001838 name: peak area def: "Area of MS1 peak (e.g. SILAC, 15N)." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001839 name: peak area def: "Area of MS1 peak (e.g. SILAC, 15N)." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001840 name: isotopic pattern area def: "Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N)." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001841 name: reporter ion intensity def: "Intensity of MS/MS reporter ion (e.g. iTraq)." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001842 name: simple ratio of two value def: "Simple ratio of two values (enumerator and denominator). TODO: clarify: correct place in obo?" [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001843 name: sum of MatchedFeature values def: "Peptide quantification value calculated as sum of MatchedFeature quantification values." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001844 name: normalized peptide value def: "Normalized peptide value. TODO: How to code normalization method, only as dataprocessing or here?" [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001845 name: protein value: sum of peptide values def: "Protein quantification value calculated as sum of peptide values." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001846 name: normalized protein value def: "Normalized protein value. TODO: How to code normalization method, only as dataprocessing or here?" [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001847 name: max fold change def: "Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis)." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001848 name: ANOVA p-value def: "Global datatype: p-value of ANOVA of group means (e.g. Progenesis)." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001849 name: t-test p-value def: "P-value of t-Test of two groups. TODO clarify how to specify the two groups!" [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001850 name: reporter ion raw value def: "Intensity (or area) of MS/MS reporter ion (e.g. iTraq)." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001851 name: reporter ion normalized value def: "Normalized value of MS/MS reporter ion (e.g. iTraq)." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001852 name: XIC area def: "Area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001853 name: normalized XIC area def: "Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001854 name: protein value: mean of peptide ratios def: "Protein quantification value calculated as mean of peptide ratios." [PSI:PI] is_a: MS:1001798 ! quantification datatype

[Term] id: MS:1001855 name: quant. data processing def: "Terms used to describe types of quant. data processing." [PSI:MS] relationship: part_of MS:1001000 ! spectrum interpretation

[Term] id: MS:1001856 name: normalization to mean of sum of all proteins def: "Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting)." [PSI:MS] is_a: MS:1001855 ! quant. data processing

[Term] id: MS:1001857 name: quantile normalization, proteins def: "Normalization of protein values to approach the same distribution." [PSI:MS] is_a: MS:1001855 ! quant. data processing

[Term] id: MS:1001858 name: quantile normalization, peptides def: "Normalization of peptide values to approach the same distribution." [PSI:MS] is_a: MS:1001855 ! quant. data processing

[Term] id: MS:1001859 name: Progenesis automatic alignment def: "Automatic RT alignment of Progenesis software." [PSI:MS] is_a: MS:1001855 ! quant. data processing

[Term] id: MS:1001860 name: Progenesis manual alignment def: "RT alignment of Progenesis software using automatic and manual vectors." [PSI:MS] is_a: MS:1001855 ! quant. data processing

[Term] id: MS:1001861 name: Progenesis normalization def: "Normalization as performed by Progenesis LC-MS." [PSI:MS] is_a: MS:1001855 ! quant. data processing

Reported by: dovelleiro

MICommunity / psidev

mzQuant new terms #556

Existing terms with modifications (mainly in is_a, but also in name, xref and / or def lines):

New terms: