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From: mayerg97 <ger...@ru...> - 2018-06-19 09:09:07
|
Dear proteomics/metabolomics community, the new version 4.1.9 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains new terms for isomer, isotopomer, isotopologue and their peaks as well as name changes for the PEFF regular expression terms. New CV terms in version 4.1.9 of psi-ms.obo: ============================================ [Term] id: MS:1002955 name: hr-ms compound identification confidence level def: "Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540] xref: value-type:xsd:string "The allowed value-type for this CV term." is_a: MS:1002895 ! small molecule identification attribute [Term] id: MS:1002956 name: isotopic ion MS peak def: "A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000231 ! peak [Term] id: MS:1002957 name: isotopomer MS peak def: "The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002956 ! isotopic ion MS peak [Term] id: MS:1002958 name: isotopologue MS peak def: "The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002956 ! isotopic ion MS peak [Term] id: MS:1002959 name: isomer def: "One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae." [https://goldbook.iupac.org/html/I/I03289.html] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1002960 name: isotopomer def: "An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms." [https://goldbook.iupac.org/html/I/I03352.html] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002959 ! isomer [Term] id: MS:1002961 name: isotopologue def: "A molecular entity that differs only in isotopic composition (number of isotopic substitutions)." [https://goldbook.iupac.org/html/I/I03351.html] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002959 ! isomer Changed CV terms in version 4.1.9 of psi-ms.obo: ================================================ ************ Obsoleted the following term [Term] id: MS:1002897 name: isotopomer peak def: "OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'." [PSI:PI] comment: This term was obsoleted because it was replaced by the more exact terms terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead. xref: value-type:xsd:string "The allowed value-type for this CV term." is_a: MS:1000231 ! peak is_obsolete: true ************ Exchanged the name and definition for the PEFF regular expression ************ terms PEFF:1002001, PEFF:1002002 and PEFF:1002003 in order to make ************ the psi-ms.obo file loadable in OBO-Edit again (currently the ************ validator exits with an error message special characters are not ************ allowed in names). [Term] id: PEFF:1002001 name: regular expression for PEFF description line def: "([0-9]+|[0-9]+|[a-zA-Z0-9]*)." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: PEFF:1002002 name: regular expression for PEFF molecular sequence type def: "(AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: PEFF:1002003 name: regular expression for PEFF sequence status def: "(Complete|Fragment|[a-z0-9A-Z]+)." [PSI:PEFF] is_a: MS:1002479 ! regular expression Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-06-15 13:29:12
|
Dear proteomics/metabolomics community, following are new terms from the release candidate 4.1.9_rc2 of the psi-ms.obo file. It contains new terms for isomer, isotopomer, isotopologue and their peaks as well as name changes for the PEFF regular expression terms. New CV terms in version 4.1.9_rc2 of psi-ms.obo: ================================================ [Term] id: MS:1002955 name: hr-ms compound identification confidence level def: "Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540] xref: value-type:xsd:string "The allowed value-type for this CV term." is_a: MS:1002895 ! small molecule identification attribute [Term] id: MS:1002956 name: isotopic ion MS peak def: "A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000231 ! peak [Term] id: MS:1002957 name: isotopomer MS peak def: "The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002956 ! isotopic ion MS peak [Term] id: MS:1002958 name: isotopologue MS peak def: "The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002956 ! isotopic ion MS peak [Term] id: MS:1002959 name: isomer def: "One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae." [https://goldbook.iupac.org/html/I/I03289.html] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1002960 name: isotopomer def: "An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms." [https://goldbook.iupac.org/html/I/I03352.html] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002959 ! isomer [Term] id: MS:1002961 name: isotopologue def: "A molecular entity that differs only in isotopic composition (number of isotopic substitutions)." [https://goldbook.iupac.org/html/I/I03351.html] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002959 ! isomer Changed CV terms in version 4.1.9_rc2 of psi-ms.obo: ==================================================== ************ Obsoleted the following term [Term] id: MS:1002897 name: isotopomer peak def: "OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'." [PSI:PI] comment: This term was obsoleted because it was replaced by the more exact terms terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead. xref: value-type:xsd:string "The allowed value-type for this CV term." is_a: MS:1000231 ! peak is_obsolete: true ************ Exchanged the name and definition for the PEFF regular expression ************ terms PEFF:1002001, PEFF:1002002 and PEFF:1002003 in order to make ************ the psi-ms.obo file loadable in OBO-Edit again (currently the ************ validator exits with an error message special characters are not ************ allowed in names). [Term] id: PEFF:1002001 name: regular expression for PEFF description line def: "([0-9]+|[0-9]+|[a-zA-Z0-9]*)." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: PEFF:1002002 name: regular expression for PEFF molecular sequence type def: "(AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: PEFF:1002003 name: regular expression for PEFF sequence status def: "(Complete|Fragment|[a-z0-9A-Z]+)." [PSI:PEFF] is_a: MS:1002479 ! regular expression Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-06-14 10:40:07
|
Dear proteomics/metabolomics community, following are new terms from the release candidate 4.1.9_rc1 of the psi-ms.obo file. It contains new terms for isomer, isotopomer, isotopologue and their peaks. New CV terms in version 4.1.9_rc1 of psi-ms.obo: ================================================ [Term] id: MS:1002955 name: hr-ms compound identification confidence level def: "Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540] xref: value-type:xsd:string "The allowed value-type for this CV term." is_a: MS:1002895 ! small molecule identification attribute [Term] id: MS:1002956 name: isotopic ion MS peak def: "A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000231 ! peak [Term] id: MS:1002957 name: isotopomer MS peak def: "The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002956 ! isotopic ion MS peak [Term] id: MS:1002958 name: isotopologue MS peak def: "The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002956 ! isotopic ion MS peak [Term] id: MS:1002959 name: isomer def: "One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae." [https://goldbook.iupac.org/html/I/I03289.html] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology [Term] id: MS:1002960 name: isotopomer def: "An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms." [https://goldbook.iupac.org/html/I/I03352.html] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002959 ! isomer [Term] id: MS:1002961 name: isotopologue def: "A molecular entity that differs only in isotopic composition (number of isotopic substitutions)." [https://goldbook.iupac.org/html/I/I03351.html] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002959 ! isomer Changed CV terms in version 4.1.9_rc1 of psi-ms.obo: ==================================================== ************ Obsoleted the following term [Term] id: MS:1002897 name: isotopomer peak def: "OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'." [PSI:PI] comment: This term was obsoleted because it was replaced by the more exact terms terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead. xref: value-type:xsd:string "The allowed value-type for this CV term." is_a: MS:1000231 ! peak is_obsolete: true Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-06-08 10:32:31
|
Hi all, I would propose to add a generic term with a string value like e.g. [Term] id: MS:1002955 name: isotopomer def: "The quantified isotopomer. The value slot contains the quantified peak, e.g. '13C peak' or '15N peak'." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Ontology Cheers, Gerhard Am 06.06.2018 um 17:21 schrieb Jones, Andy: > > Hi all, > > I have a potential term request for mzTab-M in this section, where we > allow the exporter to state if quant is being provided for an assumed > peak other than the monoisotopic one (for quant approaches that are > not de-isotoping features). I don’t see any such term already in > PSI-MS, does this seem sensible to add, or should we just add a > specification for a number e.g. +1, +2 (relative to the monoisotopic > peak). I recognize that for very-high res instruments one might be > able to resolve separately a 13C and a 15N peak, I think this is done > here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838547/ > <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838547/>. For these > kinds of approaches, it would seem useful to be able to state some > other knowledge about the peak being quantified. > > Let me know any thoughts! > > Best wishes > > Andy > > 6.4.5. isotopomer > > *Description:* > > > > If de-isotoping has not been performed, then the isotopomer quantified > MUST be reported here e.g. “+1”, “+2”, “13C peak” using cvParams, > otherwise (i.e. for approaches where SMF rows are de-isotoped > features) this MUST be null. > > *Type:* > > > > Parameter > > *Is Nullable:* > > > > *TRUE* > > *Example:* > > > > SFH SMF_ID … isotopomer … > > SMF 1 … *[MS,MS:1000XX,”13C peak”, ]…* > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > Psidev-ms-vocab mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-06-06 07:25:37
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Dear proteomics/metabolomics community, the new version 4.1.8 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains new terms for the TopPIC and TopMG software. New CV terms in version 4.1.8 of psi-ms.obo: ============================================ [Term] id: MS:1002899 name: msalign format def: "msalign file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002900 name: feature format def: "TopFD feature file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002901 name: TopPIC def: "TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization." [PMID:27423895, http://proteomics.informatics.iupui.edu/software/toppic/index.html] is_a: MS:1001456 ! analysis software [Term] id: MS:1002902 name: TopFD def: "Top-down mass spectral feature detection." [http://proteomics.informatics.iupui.edu/software/toppic/index.html] is_a: MS:1001456 ! analysis software [Term] id: MS:1002903 name: TopMG def: "A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra." [PMID:28453668, http://proteomics.informatics.iupui.edu/software/topmg/index.html] is_a: MS:1001456 ! analysis software [Term] id: MS:1002904 name: proteoform-level identification attribute def: "Proteoform level information." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002905 name: proteoform-level identification statistic def: "Identification confidence metric for a proteoform." [PSI:PI] is_a: MS:1002904 ! proteoform-level identification attribute [Term] id: MS:1002906 name: search engine specific score for proteoforms def: "Search engine specific proteoform scores." [PSI:PI] is_a: MS:1002905 ! proteoform-level identification statistic [Term] id: MS:1002907 name: proteoform-level global FDR def: "Estimation of the global false discovery rate of proteoforms." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002905 ! proteoform-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1002908 name: proteoform-level local FDR def: "Estimation of the local false discovery rate of proteoforms." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002905 ! proteoform-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1002909 name: proteoform-level statistical threshold def: "Estimated statistical threshold at proteoform-level." [PSI:PI] is_a: MS:1002573 ! spectrum identification statistical threshold [Term] id: MS:1002910 name: proteoform-level global FDR threshold def: "Threshold for the global false discovery rate of proteoforms." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002909 ! proteoform-level statistical threshold [Term] id: MS:1002911 name: proteoform-level local FDR threshold def: "Threshold for the local false discovery rate of proteoforms." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002909 ! proteoform-level statistical threshold [Term] id: MS:1002912 name: TopPIC input parameter def: "Search engine input parameters specific to TopPIC." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002913 name: TopPIC:fixed modification def: "Fixed modifications for TopPIC searching." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002914 name: TopPIC:N-term form def: "N-terminal forms of proteins allowed in TopPIC searching." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002915 name: TopPIC:error tolerance def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002916 name: TopPIC:max shift def: "Maximum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002917 name: TopPIC:min shift def: "Minimum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002918 name: TopPIC:shift num def: "Maximum number of unexpected modifications in a proteoform spectrum match." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002919 name: TopPIC:spectral cutoff type def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002920 name: TopPIC:spectral cutoff value def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002921 name: TopPIC:proteoform-level cutoff type def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002922 name: TopPIC:proteoform-level cutoff value def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002923 name: TopPIC:generating function def: "P-value and E-value estimation using generating function." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002924 name: TopPIC:combined spectrum number def: "Number of combined spectra." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002925 name: TopPIC:mod file def: "The text file containing the information of common PTMs." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002926 name: TopPIC:thread number def: "Number of threads used in TopPIC." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002927 name: TopPIC:use TopFD feature def: "Proteoform identification using TopFD feature file." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002928 name: TopPIC:spectral E-value def: "TopPIC spectrum-level E-value." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002353 ! PSM-level e-value relationship: has_order MS:1002109 ! lower score better [Term] id: MS:1002929 name: TopPIC:spectral FDR def: "TopPIC spectrum-level FDR." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002351 ! PSM-level local FDR [Term] id: MS:1002930 name: TopPIC:proteoform-level FDR def: "TopPIC proteoform-level FDR." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002908 ! proteoform-level local FDR is_a: MS:1002901 ! search engine specific score for proteoforms [Term] id: MS:1002931 name: TopPIC:spectral p-value def: "TopPIC spectrum-level p-value." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002352 ! PSM-level p-value [Term] id: MS:1002932 name: TopPIC:MIScore def: "Modification identification score." [PMID:27291504] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic [Term] id: MS:1002933 name: TopPIC:MIScore threshold def: "TopPIC:MIScore threshold." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold [Term] id: MS:1002934 name: TopMG input parameter def: "Search engine input parameters specific to TopMG." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002935 name: TopMG:fixed modification def: "Fixed modifications for TopMG searching." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002936 name: TopMG:N-term form def: "N-terminal forms of proteins allowed in TopMG searching." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002937 name: TopMG:error tolerance def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002938 name: TopMG:max shift def: "Maximum value of the mass shift (in Dalton)." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002939 name: TopMG:spectral cutoff type def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002940 name: TopMG:spectral cutoff value def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002941 name: TopMG:proteoform-level cutoff type def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002942 name: TopMG:proteoform-level cutoff value def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002943 name: TopMG:mod file def: "The text file containing the information of common PTMs." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002944 name: TopMG:thread number def: "Number of threads used in TopMG." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002945 name: TopMG:use TopFD feature def: "Proteoform identification using TopFD feature file." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002946 name: TopMG:proteoform graph gap size def: "Gap size in constructing proteoform graph." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002947 name: TopMG:variable PTM number def: "Maximum number of variable PTMs." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002948 name: TopMG:variable PTM number in proteoform graph gap def: "Maximum number of variable PTMs in a proteoform graph gap." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002949 name: TopMG:use ASF-DIAGONAL def: "Protein filtering using ASF-DIAGONAL method." [PMID:29327814] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002950 name: TopMG:spectral E-value def: "TopMG spectrum-level E-value." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better [Term] id: MS:1002951 name: TopMG:spectral FDR def: "TopMG spectrum-level FDR." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002351 ! PSM-level local FDR is_a: MS:1001143 ! PSM-level search engine specific statistic [Term] id: MS:1002952 name: TopMG:proteoform-level FDR def: "TopMG proteoform-level FDR." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002908 ! proteoform-level local FDR is_a: MS:1002901 ! search engine specific score for proteoforms [Term] id: MS:1002953 name: TopMG:spectral p-value def: "TopMG spectrum-level p-value." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002352 ! PSM-level p-value is_a: MS:1001143 ! PSM-level search engine specific statistic [Term] id: MS:1002954 name: collisional cross sectional area def: "Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1000861 ! chemical compound attribute relationship: has_units UO:0000324 ! square angstrom Changed CV terms in version 4.1.8 of psi-ms.obo: ================================================ No changed CV terms Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-05-29 09:26:11
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Dear proteomics community, following are new terms from the release candidate 4.1.8_rc1 of the psi-ms.obo file. It contains new terms for the TopPIC and TopMG software. New CV terms in version 4.1.8_rc1 of psi-ms.obo: ================================================ [Term] id: MS:1002899 name: msalign format def: "msalign file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002900 name: feature format def: "TopFD feature file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002901 name: TopPIC def: "TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization." [PMID:27423895, http://proteomics.informatics.iupui.edu/software/toppic/index.html] is_a: MS:1001456 ! analysis software [Term] id: MS:1002902 name: TopFD def: "Top-down mass spectral feature detection." [http://proteomics.informatics.iupui.edu/software/toppic/index.html] is_a: MS:1001456 ! analysis software [Term] id: MS:1002903 name: TopMG def: "A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra." [PMID:28453668, http://proteomics.informatics.iupui.edu/software/topmg/index.html] is_a: MS:1001456 ! analysis software [Term] id: MS:1002904 name: proteoform-level identification attribute def: "Proteoform level information." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002905 name: proteoform-level identification statistic def: "Identification confidence metric for a proteoform." [PSI:PI] is_a: MS:1002904 ! proteoform-level identification attribute [Term] id: MS:1002906 name: search engine specific score for proteoforms def: "Search engine specific proteoform scores." [PSI:PI] is_a: MS:1002905 ! proteoform-level identification statistic [Term] id: MS:1002907 name: proteoform-level global FDR def: "Estimation of the global false discovery rate of proteoforms." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002905 ! proteoform-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1002908 name: proteoform-level local FDR def: "Estimation of the local false discovery rate of proteoforms." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002905 ! proteoform-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1002909 name: proteoform-level statistical threshold def: "Estimated statistical threshold at proteoform-level." [PSI:PI] is_a: MS:1002573 ! spectrum identification statistical threshold [Term] id: MS:1002910 name: proteoform-level global FDR threshold def: "Threshold for the global false discovery rate of proteoforms." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002909 ! proteoform-level statistical threshold [Term] id: MS:1002911 name: proteoform-level local FDR threshold def: "Threshold for the local false discovery rate of proteoforms." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002909 ! proteoform-level statistical threshold [Term] id: MS:1002912 name: TopPIC input parameter def: "Search engine input parameters specific to TopPIC." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002913 name: TopPIC:fixed modification def: "Fixed modifications for TopPIC searching." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002914 name: TopPIC:N-term form def: "N-terminal forms of proteins allowed in TopPIC searching." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002915 name: TopPIC:error tolerance def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002916 name: TopPIC:max shift def: "Maximum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002917 name: TopPIC:min shift def: "Minimum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002918 name: TopPIC:shift num def: "Maximum number of unexpected modifications in a proteoform spectrum match." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002919 name: TopPIC:spectral cutoff type def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002920 name: TopPIC:spectral cutoff value def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002921 name: TopPIC:proteoform-level cutoff type def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002922 name: TopPIC:proteoform-level cutoff value def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002923 name: TopPIC:generating function def: "P-value and E-value estimation using generating function." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002924 name: TopPIC:combined spectrum number def: "Number of combined spectra." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002925 name: TopPIC:mod file def: "The text file containing the information of common PTMs." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002926 name: TopPIC:thread number def: "Number of threads used in TopPIC." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002927 name: TopPIC:use TopFD feature def: "Proteoform identification using TopFD feature file." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002928 name: TopPIC:spectral E-value def: "TopPIC spectrum-level E-value." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002353 ! PSM-level e-value relationship: has_order MS:1002109 ! lower score better [Term] id: MS:1002929 name: TopPIC:spectral FDR def: "TopPIC spectrum-level FDR." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002351 ! PSM-level local FDR [Term] id: MS:1002930 name: TopPIC:proteoform-level FDR def: "TopPIC proteoform-level FDR." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002908 ! proteoform-level local FDR is_a: MS:1002901 ! search engine specific score for proteoforms [Term] id: MS:1002931 name: TopPIC:spectral p-value def: "TopPIC spectrum-level p-value." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002352 ! PSM-level p-value [Term] id: MS:1002932 name: TopPIC:MIScore def: "Modification identification score." [PMID:27291504] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001968 ! PTM localization PSM-level statistic [Term] id: MS:1002933 name: TopPIC:MIScore threshold def: "TopPIC:MIScore threshold." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002555 ! PTM localization score threshold [Term] id: MS:1002934 name: TopMG input parameter def: "Search engine input parameters specific to TopMG." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002935 name: TopMG:fixed modification def: "Fixed modifications for TopMG searching." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002936 name: TopMG:N-term form def: "N-terminal forms of proteins allowed in TopMG searching." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002937 name: TopMG:error tolerance def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002938 name: TopMG:max shift def: "Maximum value of the mass shift (in Dalton)." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002939 name: TopMG:spectral cutoff type def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002940 name: TopMG:spectral cutoff value def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002941 name: TopMG:proteoform-level cutoff type def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002942 name: TopMG:proteoform-level cutoff value def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002943 name: TopMG:mod file def: "The text file containing the information of common PTMs." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002944 name: TopMG:thread number def: "Number of threads used in TopMG." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002945 name: TopMG:use TopFD feature def: "Proteoform identification using TopFD feature file." [PSI:PI] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002946 name: TopMG:proteoform graph gap size def: "Gap size in constructing proteoform graph." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002947 name: TopMG:variable PTM number def: "Maximum number of variable PTMs." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002948 name: TopMG:variable PTM number in proteoform graph gap def: "Maximum number of variable PTMs in a proteoform graph gap." [PSI:PI] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002949 name: TopMG:use ASF-DIAGONAL def: "Protein filtering using ASF-DIAGONAL method." [PMID:29327814] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002950 name: TopMG:spectral E-value def: "TopMG spectrum-level E-value." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better [Term] id: MS:1002951 name: TopMG:spectral FDR def: "TopMG spectrum-level FDR." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002351 ! PSM-level local FDR is_a: MS:1001143 ! PSM-level search engine specific statistic [Term] id: MS:1002952 name: TopMG:proteoform-level FDR def: "TopMG proteoform-level FDR." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002908 ! proteoform-level local FDR is_a: MS:1002901 ! search engine specific score for proteoforms [Term] id: MS:1002953 name: TopMG:spectral p-value def: "TopMG spectrum-level p-value." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002352 ! PSM-level p-value is_a: MS:1001143 ! PSM-level search engine specific statistic [Term] id: MS:1002954 name: collisional cross sectional area def: "Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1000861 ! chemical compound attribute relationship: has_units UO:0000324 ! square angstrom Changed CV terms in version 4.1.8_rc1 of psi-ms.obo: ==================================================== No changed CV terms Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-05-24 14:32:19
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Dear proteomics/metabolomics community, the new version 4.1.7 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains new and changed terms for mzTab-M annotation. New CV terms in version 4.1.7 of psi-ms.obo: ============================================ [Term] id: MS:1002894 name: InChIKey def: "Unique chemical structure identifier for chemical compounds." [PMID:273343401] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001405 ! spectrum identification result details [Term] id: MS:1002895 name: small molecule identification attribute def: "Compound identification information." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002896 name: compound identification confidence level def: "Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'." [PMID:29748461] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002895 ! small molecule identification attribute [Term] id: MS:1002897 name: isotopomer peak def: "Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'." [PSI:PI] xref: value-type:xsd:string "The allowed value-type for this CV term." is_a: MS:1000231 ! peak [Term] id: MS:1002898 name: Shimadzu Biotech QTOF nativeID format def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:PI] is_a: MS:1000767 ! native spectrum identifier format Changed CV terms in version 4.1.7 of psi-ms.obo: ================================================ ************ Changed definition and added publication reference [PMID:27824832] [Term] id: MS:1002599 name: splash key def: "Spectral Hash key, an unique identifier for spectra." [PMID:27824832] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001405 ! spectrum identification result details Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-05-18 12:51:05
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Dear proteomics/metabolomics community, following are new/changed terms from the release candidate 4.1.7_rc1 of the psi-ms.obo file. It contains new and changed terms for mzTab-M annotation. New CV terms in version 4.1.7_rc1 of psi-ms.obo: ================================================ [Term] id: MS:1002894 name: InChI key def: "Unique chemical structure identifier for chemical compounds." [PMID:273343401] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001405 ! spectrum identification result details [Term] id: MS:1002895 name: small molecule identification attribute def: "Compound identification information." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002896 name: compound identification confidence level def: "Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'." [PMID:29748461] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1002895 ! small molecule identification attribute [Term] id: MS:1002897 name: isotopomer peak def: "Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'." [PSI:PI] xref: value-type:xsd:string "The allowed value-type for this CV term." is_a: MS:1000231 ! peak Changed CV terms in version 4.1.7_rc1 of psi-ms.obo: ==================================================== ************ Changed definition and added publication reference [PMID:27824832] [Term] id: MS:1002599 name: splash key def: "Spectral Hash key, an unique identifier for spectra." [PMID:27824832] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001405 ! spectrum identification result details Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-05-15 09:03:50
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Dear proteomics/metabolomics community, the new version 4.1.6 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains new and modified CV terms for ion mobility. New CV terms in version 4.1.6 of psi-ms.obo: ============================================ [Term] id: MS:1002892 name: ion mobility attribute def: "An attribute describing ion mobility searches." [PSI:PI] is_a: MS:1000503 ! scan attribute is_a: MS:1002345 ! PSM-level attribute [Term] id: MS:1002893 name: ion mobility array def: "An array of ion mobility data." [PSI:PI] is_a: MS:1000513 ! binary data array Changed CV terms in version 4.1.6 of psi-ms.obo: ================================================ ************ New parent term (ion mobility attribute) [Term] id: MS:1001581 name: FAIMS compensation voltage def: "The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion." [PSI:MS] synonym: "FAIMS CV" EXACT [] is_a: MS:1002892 ! ion mobility attribute ************ New parent term (ion mobility attribute) [Term] id: MS:1002476 name: ion mobility drift time def: "Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute is_a: MS:1002892 ! ion mobility attribute relationship: has_units UO:0000028 ! millisecond ************ New parent term (ion mobility attribute) [Term] id: MS:1002815 name: inverse reduced ion mobility def: "Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute is_a: MS:1002892 ! ion mobility attribute relationship: has_units MS:1002814 ! "volt-second per square centimeter" ************ New parent term (ion mobility array) [Term] id: MS:1002477 name: mean drift time array def: "Array of drift times, averaged from a matrix of binned m/z and drift time values, corresponding to spectrum of individual peaks encoded with an m/z array." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second ************ Renamed 'mean ion mobility array' ************ --> 'mean inverse reduced ion mobility array' ************ and new parent term (ion mobility array) [Term] id: MS:1002816 name: mean inverse reduced ion mobility array def: "Array of drift times or inverse reduced ion mobilities, averaged from a matrix of binned m/z and ion mobility values, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second relationship: has_units MS:1002814 ! "volt-second per square centimeter" ************ Added a value to the following 3 CV-terms [Term] id: MS:1002889 name: Progenesis MetaScope score def: "The confidence score produced by Progenesis QI." [PSI:PI] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002888 ! small molecule confidence measure [Term] id: MS:1002890 name: fragmentation score def: "The fragmentation confidence score." [PSI:PI] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002888 ! small molecule confidence measure [Term] id: MS:1002891 name: isotopic fit score def: "The isotopic fit confidence score." [PSI:PI] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002888 ! small molecule confidence measure Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: Jones, A. <And...@li...> - 2018-05-15 08:40:13
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That’s great, thanks Da From: D....@li... [mailto:D....@li...] Sent: 12 May 2018 15:25 To: Qi, Da <dd...@li...>; Jones, Andy <jo...@li...>; 'psi...@li...' <psi...@li...> Subject: Re: [Psidev-pi-dev] mzTab broken links Hi Andy, The broken links are fixed. Please double check them. Thanks, Da On 11/05/2018 17:47, Qi, Da wrote: I can fix it. Da Huawei Mate9 -------- Original Message -------- Subject: [Psidev-pi-dev] mzTab broken links From: "Jones, Andy" To: "'psi...@li...'"<mailto:'psi...@li...'> CC: Just working on mzTab and spotted that since we re-factored GitHub most of the links here: http://www.psidev.info/mztab#mzTab_1_0 are broken. Anyone have a login to hand to fix? ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Psidev-pi-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: Da <D....@li...> - 2018-05-12 14:24:49
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Hi Andy, The broken links are fixed. Please double check them. Thanks, Da On 11/05/2018 17:47, Qi, Da wrote: > I can fix it. > > Da > > Huawei Mate9 > > -------- Original Message -------- > Subject: [Psidev-pi-dev] mzTab broken links > From: "Jones, Andy" > To: "'psi...@li...'" > CC: > > Just working on mzTab and spotted that since we re-factored GitHub > most of the links here: http://www.psidev.info/mztab#mzTab_1_0 are > broken. Anyone have a login to hand to fix? > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: Qi, D. <D....@li...> - 2018-05-11 16:47:56
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I can fix it. Da Huawei Mate9 -------- Original Message -------- Subject: [Psidev-pi-dev] mzTab broken links From: "Jones, Andy" To: "'psi...@li...'" CC: Just working on mzTab and spotted that since we re-factored GitHub most of the links here: http://www.psidev.info/mztab#mzTab_1_0 are broken. Anyone have a login to hand to fix? |
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From: Jones, A. <And...@li...> - 2018-05-11 11:47:21
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Just working on mzTab and spotted that since we re-factored GitHub most of the links here: http://www.psidev.info/mztab#mzTab_1_0 are broken. Anyone have a login to hand to fix? |
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From: mayerg97 <ger...@ru...> - 2018-05-07 14:06:07
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Dear proteomics/metabolomics community, following are the new terms from the release candidate 4.1.6_rc1 of the psi-ms.obo file. It contains new and modified CV terms for ion mobility. New CV terms in version 4.1.6_rc1 of psi-ms.obo: ================================================ [Term] id: MS:1002892 name: ion mobility attribute def: "An attribute describing ion mobility searches." [PSI:PI] is_a: MS:1000503 ! scan attribute is_a: MS:1002345 ! PSM-level attribute [Term] id: MS:1002893 name: ion mobility array def: "An array of ion mobility data." [PSI:PI] is_a: MS:1000513 ! binary data array Changed CV terms in version 4.1.6_rc1 of psi-ms.obo: ==================================================== ************ New parent term (ion mobility attribute) [Term] id: MS:1001581 name: FAIMS compensation voltage def: "The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion." [PSI:MS] synonym: "FAIMS CV" EXACT [] is_a: MS:1002892 ! ion mobility attribute ************ New parent term (ion mobility attribute) [Term] id: MS:1002476 name: ion mobility drift time def: "Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute is_a: MS:1002892 ! ion mobility attribute relationship: has_units UO:0000028 ! millisecond ************ New parent term (ion mobility attribute) [Term] id: MS:1002815 name: inverse reduced ion mobility def: "Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000455 ! ion selection attribute is_a: MS:1002892 ! ion mobility attribute relationship: has_units MS:1002814 ! "volt-second per square centimeter" ************ New parent term (ion mobility array) [Term] id: MS:1002477 name: mean drift time array def: "Array of drift times, averaged from a matrix of binned m/z and drift time values, corresponding to spectrum of individual peaks encoded with an m/z array." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second ************ Renamed 'mean ion mobility array' ************ --> 'mean inverse reduced ion mobility array' ************ and new parent term (ion mobility array) [Term] id: MS:1002816 name: mean inverse reduced ion mobility array def: "Array of drift times or inverse reduced ion mobilities, averaged from a matrix of binned m/z and ion mobility values, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second relationship: has_units MS:1002814 ! "volt-second per square centimeter" ************ Added a value to the following 3 CV-terms [Term] id: MS:1002889 name: Progenesis MetaScope score def: "The confidence score produced by Progenesis QI." [PSI:PI] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002888 ! small molecule confidence measure [Term] id: MS:1002890 name: fragmentation score def: "The fragmentation confidence score." [PSI:PI] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002888 ! small molecule confidence measure [Term] id: MS:1002891 name: isotopic fit score def: "The isotopic fit confidence score." [PSI:PI] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002888 ! small molecule confidence measure Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-05-02 11:33:56
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> Dear proteomics/metabolomics community, > > the new version 4.1.5 of the psi-ms.obo file can be downloaded from > https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo > > It contains new CV terms for usage in mzTab-M files. > > New CV terms in version 4.1.5 of psi-ms.obo: > ============================================ > [Term] > id: MS:1002878 > name: small molecule analysis software > def: "Software for the analysis of small molecules." [PSI:PI] > is_a: MS:1001456 ! analysis software > > [Term] > id: MS:1002879 > name: Progenesis QI > def: "Metabolomics analysis software for LC-MS data from Nonlinear > Dynamics." [PSI:PI] > is_a: MS:1002878 ! small molecule analysis software > > [Term] > id: MS:1002880 > name: Compound Discoverer > def: "Metabolomics analysis software from Thermo Fisher Scientific." > [PSI:PI] > is_a: MS:1002878 ! small molecule analysis software > > [Term] > id: MS:1002881 > name: MyCompoundID > def: "Metabolite identification tool MyCompoundID." [PSI:PI, > PMID:23373753] > is_a: MS:1002878 ! small molecule analysis software > > [Term] > id: MS:1002882 > name: study variable average function > def: "Function used to calculate the study variable quantification > value." [PSI:PI] > is_a: MS:1001184 ! search statistics > > [Term] > id: MS:1002883 > name: median > def: "Median function." [PSI:PI] > is_a: MS:1002882 ! study variable average function > > [Term] > id: MS:1002884 > name: study variable variation function > def: "Function used to calculate the study variable quantification > variation value." [PSI:PI] > is_a: MS:1001184 ! search statistics > > [Term] > id: MS:1002885 > name: standard error > def: "Standard error function." [PSI:PI] > is_a: MS:1002884 ! study variable variation function > > [Term] > id: MS:1002886 > name: small molecule quantification datatype > def: "The value reported in a small molecule quantification." [PSI:PI] > is_a: MS:1001805 ! quantification datatype > > [Term] > id: MS:1002887 > name: Progenesis QI normalised abundance > def: "The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI] > xref: value-type:xsd\:double "The allowed value-type for this CV term." > is_a: MS:1002886 ! small molecule quantification datatype > > [Term] > id: MS:1002888 > name: small molecule confidence measure > def: "The confidence score produced by a small molecule analysis > software." [PSI:PI] > is_a: MS:1002694 ! single identification result attribute > > [Term] > id: MS:1002889 > name: Progenesis MetaScope score > def: "The confidence score produced by Progenesis QI." [PSI:PI] > is_a: MS:1002888 ! small molecule confidence measure > > [Term] > id: MS:1002890 > name: fragmentation score > def: "The fragmentation confidence score." [PSI:PI] > is_a: MS:1002888 ! small molecule confidence measure > > [Term] > id: MS:1002891 > name: isotopic fit score > def: "The isotopic fit confidence score." [PSI:PI] > is_a: MS:1002888 ! small molecule confidence measure > > > Best Regards, > Gerhard > > -- > > *--------------------------------------------------------------------* > > *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* > > *PhD student* > > *Medizinisches Proteom-Center* > > *DEPARTMENT Medical Bioinformatics* > > *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum > > *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 > > *E-mail***ger...@ru... <mailto:ger...@ru...> > > www.medizinisches-proteom-center.de > <http://www.medizinisches-proteom-center.de/> > -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-04-30 11:42:20
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Dear proteomics/metabolomics community, the new version 4.1.5 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains new CV terms for usage in mzTab-M files. New CV terms in version 4.1.5 of psi-ms.obo: ============================================ [Term] id: MS:1002878 name: small molecule analysis software def: "Software for the analysis of small molecules." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002879 name: Progenesis QI def: "Metabolomics analysis software for LC-MS data from Nonlinear Dynamics." [PSI:PI] is_a: MS:1002878 ! small molecule analysis software [Term] id: MS:1002880 name: Compound Discoverer def: "Metabolomics analysis software from Thermo Fisher Scientific." [PSI:PI] is_a: MS:1002878 ! small molecule analysis software [Term] id: MS:1002881 name: MyCompoundID def: "Metabolite identification tool MyCompoundID." [PSI:PI, PMID:23373753] is_a: MS:1002878 ! small molecule analysis software [Term] id: MS:1002882 name: study variable average function def: "Function used to calculate the study variable quantification value." [PSI:PI] is_a: MS:1001184 ! search statistics [Term] id: MS:1002883 name: median def: "Median function." [PSI:PI] is_a: MS:1002882 ! study variable average function [Term] id: MS:1002884 name: study variable variation function def: "Function used to calculate the study variable quantification variation value." [PSI:PI] is_a: MS:1001184 ! search statistics [Term] id: MS:1002885 name: standard error def: "Standard error function." [PSI:PI] is_a: MS:1002884 ! study variable variation function [Term] id: MS:1002886 name: small molecule quantification datatype def: "The value reported in a small molecule quantification." [PSI:PI] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002887 name: Progenesis QI normalised abundance def: "The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002886 ! small molecule quantification datatype [Term] id: MS:1002888 name: small molecule confidence measure def: "The confidence score produced by a small molecule analysis software." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002889 name: Progenesis MetaScope score def: "The confidence score produced by Progenesis QI." [PSI:PI] is_a: MS:1002888 ! small molecule confidence measure [Term] id: MS:1002890 name: fragmentation score def: "The fragmentation confidence score." [PSI:PI] is_a: MS:1002888 ! small molecule confidence measure [Term] id: MS:1002891 name: isotopic fit score def: "The isotopic fit confidence score." [PSI:PI] is_a: MS:1002888 ! small molecule confidence measure Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-04-24 13:35:06
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Dear proteomics/metabolomics community, following are the new terms from the release candidate 4.1.5_rc1 of the psi-ms.obo file. It contains new CV terms for usage in mzTab-M files. New CV terms in version 4.1.5_rc1 of psi-ms.obo: ================================================ [Term] id: MS:1002878 name: small molecule analysis software def: "Software for the analysis of small molecules." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002879 name: Progenesis QI def: "Metabolomics analysis software for LC-MS data from Nonlinear Dynamics." [PSI:PI] is_a: MS:1002878 ! small molecule analysis software [Term] id: MS:1002880 name: Compound Discoverer def: "Metabolomics analysis software from Thermo Fisher Scientific." [PSI:PI] is_a: MS:1002878 ! small molecule analysis software [Term] id: MS:1002881 name: MyCompoundID def: "Metabolite identification tool MyCompoundID." [PSI:PI, PMID:26415007] is_a: MS:1002878 ! small molecule analysis software [Term] id: MS:1002882 name: study variable average function def: "Function used to calculate the study variable quantification value." [PSI:PI] is_a: MS:1001184 ! search statistics [Term] id: MS:1002883 name: median def: "Median function." [PSI:PI] is_a: MS:1002882 ! study variable average function [Term] id: MS:1002884 name: study variable variation function def: "Function used to calculate the study variable quantification variation value." [PSI:PI] is_a: MS:1001184 ! search statistics [Term] id: MS:1002885 name: standard error def: "Standard error function." [PSI:PI] is_a: MS:1002884 ! study variable variation function [Term] id: MS:1002886 name: small molecule quantification datatype def: "The value reported in a small molecule quantification." [PSI:PI] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002887 name: Progenesis QI normalised abundance def: "The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI] xref: value-type:xsd\:double "The allowed value-type for this CV term." is_a: MS:1002886 ! small molecule quantification datatype [Term] id: MS:1002888 name: small molecule confidence measure def: "The confidence score produced by a small molecule analysis software." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002889 name: Progenesis MetaScope score def: "The confidence score produced by Progenesis QI." [PSI:PI] is_a: MS:1002888 ! small molecule confidence measure [Term] id: MS:1002890 name: fragmentation score def: "The fragmentation confidence score." [PSI:PI] is_a: MS:1002888 ! small molecule confidence measure [Term] id: MS:1002891 name: isotopic fit score def: "The isotopic fit confidence score." [PSI:PI] is_a: MS:1002888 ! small molecule confidence measure Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: Mayer, G. <may...@ru...> - 2018-04-17 17:32:31
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see message from Sandra -------- Weitergeleitete Nachricht -------- Betreff: [Psi-sc] Bus timetable for attendees Datum: Tue, 17 Apr 2018 12:25:01 +0100 Von: Sandra Orchard <or...@eb...> An: ps...@eb..., ps...@eb..., psi...@eb... Hi As I suspect Andy is traveling and has the attendee mailing list, I've pasted the bus timetable to get you up to EMBL in the mornings on the event webpage http://www.psidev.info/content/hupo-psi-meeting-2018 Please spread the word to anyone you see in Heidelberg who is not on any of these mailing lists, and also please can someone forward to the mass spec list. German buses leave promptly so don't be late. If you are making your own way up the hill, please head for the Large Operon. It costs about E15 in a taxi. Sandra -- Sandra Orchard Protein Function Content Team Leader European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom phone: 01223 494675 fax: 01223 494468 email: or...@eb... _______________________________________________ Psi-sc mailing list Ps...@eb... https://listserver.ebi.ac.uk/mailman/listinfo/psi-sc |
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From: mayerg97 <ger...@ru...> - 2018-04-16 12:55:40
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Dear proteomics community, the new version 4.1.4 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains four new terms for Thermo Scientific instruments. New CV terms in version 4.1.4 of psi-ms.obo: ============================================ [Term] id: MS:1002874 name: TSQ Altis def: "Thermo Scientific TSQ Altis Triple Quadrupole MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002875 name: TSQ Quantis def: "Thermo Scientific TSQ Quantis Triple Quadrupole MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002876 name: TSQ 9000 def: "Thermo Scientific TSQ 9000 Triple Quadrupole MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002877 name: Q Exactive HF-X def: "Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-04-09 08:39:48
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Dear proteomics community, following are the changes for the release candidate 4.1.4_rc1 of the psi-ms.obo file. There are four new terms for Thermo Scientific instruments. New CV terms in version 4.1.4_rc1 of psi-ms.obo: ================================================ [Term] id: MS:1002874 name: TSQ Altis def: "Thermo Scientific TSQ Altis Triple Quadrupole MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002875 name: TSQ Quantis def: "Thermo Scientific TSQ Quantis Triple Quadrupole MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002876 name: TSQ 9000 def: "Thermo Scientific TSQ 9000 Triple Quadrupole MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002877 name: Q Exactive HF-X def: "Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-04-06 08:11:39
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Dear proteomics community, the new version 4.1.3 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains two new terms for the Panorama repository. New CV terms in version 4.1.3 of psi-ms.obo: ============================================ [Term] id: MS:1002872 name: Panorama Public dataset identifier def: "Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier [Term] id: MS:1002873 name: Panorama Public dataset URI def: "URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] xref: value-type:xsd\:anyURI "The allowed value-type for this CV term." is_a: MS:1000878 ! external reference identifier Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-03-28 09:55:34
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Dear proteomics community, the new version 4.1.2 of the psi-ms.obo file can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo It contains three new terms for Bioconductor software packages. New CV terms in version 4.1.2 of psi-ms.obo: ============================================ [Term] id: MS:1002869 name: mzR def: "Bioconductor package mzR for reading and writing mass spectrometry data files." [PSI:PI] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002870 name: MSnbase def: "Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data." [PMID:22113085] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002871 name: CAMERA def: "Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments." [PMID:22111785] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: mayerg97 <ger...@ru...> - 2018-03-22 09:44:22
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Dear proteomics community, following are the changes for the release candidate 4.1.2_rc1 of the psi-ms.obo file. There are three new terms for Bioconductor software packages. New CV terms in version 4.1.2_rc1 of psi-ms.obo: ================================================ [Term] id: MS:1002869 name: mzR def: "Bioconductor package mzR for reading and writing mass spectrometry data files." [PSI:PI] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002870 name: MSnbase def: "Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data." [PMID:22113085] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002871 name: CAMERA def: "Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments." [PMID:22111785] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software Changed CV terms in version 4.1.2_rc1 of psi-ms.obo: ==================================================== ************ No changed terms Best Regards, Gerhard -- *--------------------------------------------------------------------* *Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER* *PhD student* *Medizinisches Proteom-Center* *DEPARTMENT Medical Bioinformatics* *Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum *Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554 *E-mail***ger...@ru... <mailto:ger...@ru...> www.medizinisches-proteom-center.de <http://www.medizinisches-proteom-center.de/> |
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From: Hannes R. <han...@gm...> - 2018-03-16 19:09:31
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Dear list I have a question regarding the drift time array: [Term] id: MS:1002816 name: mean ion mobility array def: "Array of drift times or inverse reduced ion mobilities, averaged from a matrix of binned m/z and ion mobility values, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000513 ! binary data array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second relationship: has_units MS:1002814 ! "volt-second per square centimeter" it seems to me that the formulation is somewhat unclear, what does "averaged from a maxtrix of binned m/z and ion mobility values" mean here. It seems strange that we have this term but no term for the general case where we simply want to display ion mobility data. I therefore suggest to change the existing term or add a new term [Term] id: MS:xxx name: ion mobility array def: "Array of drift times or inverse reduced ion mobilities corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000513 ! binary data array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second relationship: has_units MS:1002814 ! "volt-second per square centimeter" I think this would allow us to reprenst 3 dimensional data with one array of m/z, one of intensity and one of ion mobility, right? Or maybe I misunderstood the point of MS:1002816 Best Hannes |
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From: Jones, A. <And...@li...> - 2018-03-14 11:11:30
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Dear colleagues, I am sending a reminder about the upcoming PSI meeting next month, details below. We hope to see lots of you there! Best wishes Andy http://www.psidev.info/content/hupo-psi-meeting-2018 ********************* We are pleased to announce that the PSI 2018 Spring meeting is open for registration (http://www.psidev.info/content/hupo-psi-meeting-2018). PSI2018 will take place April 18-20th 2018 at EMBL, Heidelberg in Germany. The meeting is free of charge for participants (including lunches, refreshments and a workshop dinner). The main topics for discussion will working on the new spectral library data format, the Universal spectrum ID, PEFF (extended fasta format) and PROXI (web services API). There will be a track focussing on metabolomics (mzTab format), further work on quality control (qcML) and developments in the molecular interactions group including implementations of MI XML 3.0, CausalTab format, and identification of novel interactions in interactomes. The PSI always welcomes new participants with an interest in getting involved in proteomics data standards. Please feel free to register and come along to see what we are doing, or forward this message on to other colleagues who may be interested. |
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