From: Gerhard M. <Ger...@ru...> - 2012-11-28 12:08:49
Attachments:
psi-ms_3.41.0.zip
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Dear proteomics community, attached there's the new version 3.41.0 of the psi-ms.obo file. To the CV terms used in <AnalysisSummary> of mzQuantML, the datatype xsd\:boolean was added. In addition it contains some new terms (identification file format attribute, numerator data type attribute and denominator data type attribute) for mzQuantML validation and the replacement of some 'TOPP software'-related terms by newer terms. Some Remarks: ============= 1) The term MS:1000131 (number of counts) is a parent term only Therefore it has no data type. 2) The term MS:1001842 (peptide PSM count) now has an integer data type 3) The new term MS:1002153 (protein level PSM counts) can now be used to specify the number of counts on the protein level Changed CV terms in version 3.41.0 of psi-ms.obo: ================================================= ************ Added a xsd\:double data type to all 'quantification datatype' (MS:1001805) childs, ************ except for spectral count values, which now have a xsd\:integer data type ************ Changed the name from 'protein group/subset relationship' --> 'protein group or subset relationship' [Term] id: MS:1001101 name: protein group or subset relationship def: "Protein group or subset relationships." [PSI:PI] is_a: MS:1001085 ! protein result details ************ Added a xsd\:boolean data type to the following terms [Term] id: MS:1002001 name: MS1 label-based raw feature quantitation def: "MS1 label-based raw feature quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002018 ! MS1 label-based analysis [Term] id: MS:1002002 name: MS1 label-based peptide level quantitation def: "MS1 label-based peptide level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002018 ! MS1 label-based analysis [Term] id: MS:1002003 name: MS1 label-based protein level quantitation def: "MS1 label-based protein level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002018 ! MS1 label-based analysis [Term] id: MS:1002004 name: MS1 label-based proteingroup level quantitation def: "MS1 label-based proteingroup level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002018 ! MS1 label-based analysis [Term] id: MS:1002019 name: label-free raw feature quantitation def: "Label-free raw feature quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001834 ! LC-MS label-free quantitation analysis [Term] id: MS:1002020 name: label-free peptide level quantitation def: "Label-free peptide level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001834 ! LC-MS label-free quantitation analysis [Term] id: MS:1002021 name: label-free protein level quantitation def: "Label-free protein level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001834 ! LC-MS label-free quantitation analysis [Term] id: MS:1002022 name: label-free proteingroup level quantitation def: "Label-free proteingroup level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001834 ! LC-MS label-free quantitation analysis [Term] id: MS:1002024 name: MS2 tag-based feature level quantitation def: "MS2 tag-based feature level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002023 ! MS2 tag-based analysis [Term] id: MS:1002025 name: MS2 tag-based peptide level quantitation def: "MS2 tag-based peptide level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002023 ! MS2 tag-based analysis [Term] id: MS:1002026 name: MS2 tag-based protein level quantitation def: "MS2 tag-based protein level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002023 ! MS2 tag-based analysis [Term] id: MS:1002027 name: MS2 tag-based proteingroup level quantitation def: "MS2 tag-based proteingroup level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002023 ! MS2 tag-based analysis ************ Added an integer data type to the next term [Term] id: MS:1001842 name: peptide PSM count def: "The number of MS/MS spectra identified for this peptide in spectral counting." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype ************ Renamed from 'method file attribute' --> 'method file format attribute' [Term] id: MS:1002128 name: method file format attribute def: "Attribute describing a method file format." [PSI:PI] is_a: MS:1001806 ! quantification object attribute ************ Changed the definition for the next term [Term] id: MS:1002129 name: ITRAQAnalyzer def: "Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment." [http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/OpenMS-release/html/TOPP__ITRAQAnalyzer.html] is_a: MS:1001139 ! quantitation software name is_a: MS:1000752 ! TOPP software ************ The following four terms for the TOPP software are made obsolete, because the were replaced by new terms: [Term] id: MS:1000760 name: MapAligner def: "OBSOLETE Corrects retention time distortions between maps." [PSI:MS] comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP map aligner' (MS:1002147) branch. is_a: MS:1000752 ! TOPP software is_obsolete: true [Term] id: MS:1000762 name: NoiseFilter def: "OBSOLETE Removes noise from profile spectra by using different smoothing techniques." [PSI:MS] comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP noise filter' (MS:1002131) branch. is_a: MS:1000752 ! TOPP software is_obsolete: true [Term] id: MS:1000763 name: PeakPicker def: "OBSOLETE Finds mass spectrometric peaks in profile mass spectra." [PSI:MS] comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP peak picker' (MS:1002134) branch. is_a: MS:1000752 ! TOPP software is_obsolete: true [Term] id: MS:1000765 name: SpectraFilter def: "OBSOLETE Applies a filter to peak spectra." [PSI:MS] comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP spectra filter' (MS:1002137) branch. is_a: MS:1000752 ! TOPP software is_obsolete: true New CV terms in version 3.41.0 of psi-ms.obo: ============================================= [Term] id: MS:1002130 name: identification file format attribute def: "Attribute describing an identification file format." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002131 name: TOPP noise filter def: "Noise filter component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002132 name: NoiseFilterGaussian def: "Removes noise from profile spectra by using gaussian filter smoothing techniques." [PSI:PI] is_a: MS:1002131 ! TOPP noise filter [Term] id: MS:1002133 name: NoiseFilterSGolay def: "Removes noise from profile spectra by using golay filter smoothing techniques." [PSI:PI] is_a: MS:1002131 ! TOPP noise filter [Term] id: MS:1002134 name: TOPP peak picker def: "Peak picker component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002135 name: PeakPickerHiRes def: "Finds mass spectrometric peaks in profile mass spectra." [PSI:PI] is_a: MS:1002134 ! TOPP peak picker [Term] id: MS:1002136 name: PeakPickerWavelet def: "Finds mass spectrometric peaks in profile mass spectra." [PSI:PI] is_a: MS:1002134 ! TOPP peak picker [Term] id: MS:1002137 name: TOPP spectra filter def: "Spectra filter component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002138 name: SpectraFilterBernNorm def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002139 name: SpectraFilterMarkerMower def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002140 name: SpectraFilterNLargest def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002141 name: SpectraFilterNormalizer def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002142 name: SpectraFilterParentPeakMower def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002143 name: SpectraFilterScaler def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002144 name: SpectraFilterSqrtMower def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002145 name: SpectraFilterThresholdMower def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002146 name: SpectraFilterWindowMower def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002147 name: TOPP map aligner def: "Map aligner component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002148 name: MapAlignerIdentification def: "Corrects retention time distortions between maps based on common peptide identifications." [PSI:PI] is_a: MS:1002147 ! TOPP map aligner [Term] id: MS:1002149 name: MapAlignerPoseClustering def: "Corrects retention time distortions between maps using a pose clustering approach." [PSI:PI] is_a: MS:1002147 ! TOPP map aligner [Term] id: MS:1002150 name: MapAlignerSpectrum def: "Corrects retention time distortions between maps by spectrum alignment." [PSI:PI] is_a: MS:1002147 ! TOPP map aligner [Term] id: MS:1002151 name: numerator data type attribute def: "Attribute describing the data type of the numerator of a ratio." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002152 name: denominator data type attribute def: "Attribute describing the data type of the denominator of a ratio." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002153 name: protein level PSM counts def: "The number of spectra identified for this protein in spectral counting." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype Best Regards, Gerhard -- --- Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.042 Universitätsstrasse 150 D-44801 Bochum Phone: +49(0)234/32-29836 Fax: +49(0)234/32-14554 Email: Ger...@ru... Web: http://www.medizinisches-proteom-center.de |
From: Eric D. <ede...@sy...> - 2012-11-28 16:03:02
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Hi Gerhard, many thanks for your continued work on this. If I recall correctly, "number of counts" is a *unit* term. The unit ontology doesn't contain such a unit, so we added this to our ontology to serve as a unit. It should be analogous to 'number of electrons' in a detector, but for a case where we don't know that the unit is electrons, but just "counts". Maybe we should change it to "number of detector counts". This is primarily used to specify the units of intensities of spectra. I think to be semantically correct, this term should not have any child terms except for ones directly related to this concept. Regards, Eric -----Original Message----- From: Gerhard Mayer [mailto:Ger...@ru...] Sent: Wednesday, November 28, 2012 4:09 AM To: psi...@li...; psi...@li...; Mass spectrometry standard development Subject: [Psidev-ms-vocab] New version 3.41.0 of psi-ms-obo Dear proteomics community, attached there's the new version 3.41.0 of the psi-ms.obo file. To the CV terms used in <AnalysisSummary> of mzQuantML, the datatype xsd\:boolean was added. In addition it contains some new terms (identification file format attribute, numerator data type attribute and denominator data type attribute) for mzQuantML validation and the replacement of some 'TOPP software'-related terms by newer terms. Some Remarks: ============= 1) The term MS:1000131 (number of counts) is a parent term only Therefore it has no data type. 2) The term MS:1001842 (peptide PSM count) now has an integer data type 3) The new term MS:1002153 (protein level PSM counts) can now be used to specify the number of counts on the protein level Changed CV terms in version 3.41.0 of psi-ms.obo: ================================================= ************ Added a xsd\:double data type to all 'quantification datatype' (MS:1001805) childs, ************ except for spectral count values, which now have a xsd\:integer data type ************ Changed the name from 'protein group/subset relationship' --> 'protein group or subset relationship' [Term] id: MS:1001101 name: protein group or subset relationship def: "Protein group or subset relationships." [PSI:PI] is_a: MS:1001085 ! protein result details ************ Added a xsd\:boolean data type to the following terms [Term] id: MS:1002001 name: MS1 label-based raw feature quantitation def: "MS1 label-based raw feature quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002018 ! MS1 label-based analysis [Term] id: MS:1002002 name: MS1 label-based peptide level quantitation def: "MS1 label-based peptide level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002018 ! MS1 label-based analysis [Term] id: MS:1002003 name: MS1 label-based protein level quantitation def: "MS1 label-based protein level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002018 ! MS1 label-based analysis [Term] id: MS:1002004 name: MS1 label-based proteingroup level quantitation def: "MS1 label-based proteingroup level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002018 ! MS1 label-based analysis [Term] id: MS:1002019 name: label-free raw feature quantitation def: "Label-free raw feature quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001834 ! LC-MS label-free quantitation analysis [Term] id: MS:1002020 name: label-free peptide level quantitation def: "Label-free peptide level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001834 ! LC-MS label-free quantitation analysis [Term] id: MS:1002021 name: label-free protein level quantitation def: "Label-free protein level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001834 ! LC-MS label-free quantitation analysis [Term] id: MS:1002022 name: label-free proteingroup level quantitation def: "Label-free proteingroup level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1001834 ! LC-MS label-free quantitation analysis [Term] id: MS:1002024 name: MS2 tag-based feature level quantitation def: "MS2 tag-based feature level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002023 ! MS2 tag-based analysis [Term] id: MS:1002025 name: MS2 tag-based peptide level quantitation def: "MS2 tag-based peptide level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002023 ! MS2 tag-based analysis [Term] id: MS:1002026 name: MS2 tag-based protein level quantitation def: "MS2 tag-based protein level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002023 ! MS2 tag-based analysis [Term] id: MS:1002027 name: MS2 tag-based proteingroup level quantitation def: "MS2 tag-based proteingroup level quantitation." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002023 ! MS2 tag-based analysis ************ Added an integer data type to the next term [Term] id: MS:1001842 name: peptide PSM count def: "The number of MS/MS spectra identified for this peptide in spectral counting." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype ************ Renamed from 'method file attribute' --> 'method file format attribute' [Term] id: MS:1002128 name: method file format attribute def: "Attribute describing a method file format." [PSI:PI] is_a: MS:1001806 ! quantification object attribute ************ Changed the definition for the next term [Term] id: MS:1002129 name: ITRAQAnalyzer def: "Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment." [http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/OpenMS-release /html/TOPP__ITRAQAnalyzer.html] is_a: MS:1001139 ! quantitation software name is_a: MS:1000752 ! TOPP software ************ The following four terms for the TOPP software are made obsolete, because the were replaced by new terms: [Term] id: MS:1000760 name: MapAligner def: "OBSOLETE Corrects retention time distortions between maps." [PSI:MS] comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP map aligner' (MS:1002147) branch. is_a: MS:1000752 ! TOPP software is_obsolete: true [Term] id: MS:1000762 name: NoiseFilter def: "OBSOLETE Removes noise from profile spectra by using different smoothing techniques." [PSI:MS] comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP noise filter' (MS:1002131) branch. is_a: MS:1000752 ! TOPP software is_obsolete: true [Term] id: MS:1000763 name: PeakPicker def: "OBSOLETE Finds mass spectrometric peaks in profile mass spectra." [PSI:MS] comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP peak picker' (MS:1002134) branch. is_a: MS:1000752 ! TOPP software is_obsolete: true [Term] id: MS:1000765 name: SpectraFilter def: "OBSOLETE Applies a filter to peak spectra." [PSI:MS] comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP spectra filter' (MS:1002137) branch. is_a: MS:1000752 ! TOPP software is_obsolete: true New CV terms in version 3.41.0 of psi-ms.obo: ============================================= [Term] id: MS:1002130 name: identification file format attribute def: "Attribute describing an identification file format." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002131 name: TOPP noise filter def: "Noise filter component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002132 name: NoiseFilterGaussian def: "Removes noise from profile spectra by using gaussian filter smoothing techniques." [PSI:PI] is_a: MS:1002131 ! TOPP noise filter [Term] id: MS:1002133 name: NoiseFilterSGolay def: "Removes noise from profile spectra by using golay filter smoothing techniques." [PSI:PI] is_a: MS:1002131 ! TOPP noise filter [Term] id: MS:1002134 name: TOPP peak picker def: "Peak picker component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002135 name: PeakPickerHiRes def: "Finds mass spectrometric peaks in profile mass spectra." [PSI:PI] is_a: MS:1002134 ! TOPP peak picker [Term] id: MS:1002136 name: PeakPickerWavelet def: "Finds mass spectrometric peaks in profile mass spectra." [PSI:PI] is_a: MS:1002134 ! TOPP peak picker [Term] id: MS:1002137 name: TOPP spectra filter def: "Spectra filter component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002138 name: SpectraFilterBernNorm def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002139 name: SpectraFilterMarkerMower def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002140 name: SpectraFilterNLargest def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002141 name: SpectraFilterNormalizer def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002142 name: SpectraFilterParentPeakMower def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002143 name: SpectraFilterScaler def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002144 name: SpectraFilterSqrtMower def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002145 name: SpectraFilterThresholdMower def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002146 name: SpectraFilterWindowMower def: "Applies a filter to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002147 name: TOPP map aligner def: "Map aligner component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002148 name: MapAlignerIdentification def: "Corrects retention time distortions between maps based on common peptide identifications." [PSI:PI] is_a: MS:1002147 ! TOPP map aligner [Term] id: MS:1002149 name: MapAlignerPoseClustering def: "Corrects retention time distortions between maps using a pose clustering approach." [PSI:PI] is_a: MS:1002147 ! TOPP map aligner [Term] id: MS:1002150 name: MapAlignerSpectrum def: "Corrects retention time distortions between maps by spectrum alignment." [PSI:PI] is_a: MS:1002147 ! TOPP map aligner [Term] id: MS:1002151 name: numerator data type attribute def: "Attribute describing the data type of the numerator of a ratio." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002152 name: denominator data type attribute def: "Attribute describing the data type of the denominator of a ratio." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002153 name: protein level PSM counts def: "The number of spectra identified for this protein in spectral counting." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1001805 ! quantification datatype Best Regards, Gerhard -- --- Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer BioInformatik Medizinisches-Proteom-Center (MPC) Ruhr-Universität Bochum Zentrum für klinische Forschung I (ZKF I) E.042 Universitätsstrasse 150 D-44801 Bochum Phone: +49(0)234/32-29836 Fax: +49(0)234/32-14554 Email: Ger...@ru... Web: http://www.medizinisches-proteom-center.de |