From: Gerhard M. <Ger...@ru...> - 2012-10-30 10:48:56
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Dear proteomics community, attached there's the new version 3.36.0 of the psi-ms.obo file. It contains changes to some CV terms used in mzQuantML and a restructuring of the tree for the search engine input parameters, which has a little bit more structure now: - search engine input parameter (MS:1002093) - common search engine input parameter (MS:1002094) - ... (terms shared by more than one search engine) - search engine specific input parameter (MS:1001302) - Mascot input parameter - ... - Sequest input parameter - ... - ... - software input parameter (MS:1002103) - common software input parameter (MS:1002104) - ... (terms shared by more than one software) - software specific input parameter (MS:1002105) - Percolator input parameter - ... - Scaffold input parameter - ... Changed CV terms in version 3.36.0 of psi-ms.obo: ================================================= ************ The term 'Peptide raw area' is now obsolete. [Term] id: MS:1001130 name: peptide raw area def: "OBSOLETE Peptide raw area." [PSI:PI] comment: This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844). is_a: MS:1001805 ! quantification datatype is_obsolete: true ************ The term 'p-value (protein diff from 1 randomly)' is now obsolete. [Term] id: MS:1001136 name: p-value (protein diff from 1 randomly) def: "OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI] comment: This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855). is_a: MS:1001805 ! quantification datatype is_obsolete: true ************ Added String datatype to the term 'SRM transition ID'. [Term] id: MS:1001829 name: SRM transition ID def: "SRM transition ID." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001828 ! Feature attribute New CV terms in version 3.36.0 of psi-ms.obo: ============================================= [Term] id: MS:1002093 name: search engine input parameter def: "This branch contains search engine input parameters." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1002094 name: common search engine input parameter def: "This branch contains search engine input parameters that are shared by more than one search engine." [PSI:PI] is_a: MS:1002093 ! search engine input parameter [Term] id: MS:1002095 name: Mascot input parameter def: "Search engine input parameters specific to Mascot." [PSI:PI, source:http://www.matrixscience.com/help/search_field_help.html] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002096 name: Sequest input parameter def: "Search engine input parameters specific to Sequest." [PSI:PI, source:http://fields.scripps.edu/sequest/parameters.html] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002097 name: Phenyx input parameter def: "Search engine input parameters specific to Phenyx." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002098 name: ProteinExtractor input parameter def: "Search engine input parameters specific to ProteinExtractor." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002099 name: OMSSA input parameter def: "Search engine input parameters specific to OMSSA." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002100 name: ProteinScape input parameter def: "Search engine input parameters specific to ProteinScape." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002101 name: ProteomeDiscoverer input parameter def: "Search engine input parameters specific to ProteomeDiscoverer." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002103 name: software input parameter def: "This branch contains software input parameters." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1002104 name: common software input parameter def: "This branch contains software input parameters that are shared by more than one software." [PSI:PI] is_a: MS:1002103 ! software input parameter [Term] id: MS:1002105 name: software specific input parameter def: "This branch contains software input parameters that are shared by more than one software." [PSI:PI] is_a: MS:1002103 ! software input parameter [Term] id: MS:1002106 name: Scaffold input parameter def: "Search engine input parameters specific to Scaffold." [PSI:PI] is_a: MS:1002105 ! software specific input parameter [Term] id: MS:1002107 name: Percolator input parameter def: "Search engine input parameters specific to Percolator." [PSI:PI] is_a: MS:1002105 ! software specific input parameter 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 |