From: mayerg97 <ger...@ru...> - 2019-04-09 13:09:39
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Dear proteomics/metabolomics community, following are the new/changed terms for the version 4.1.25 of the psi-ms.obo file. It can be downloaded from https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo @Felipe: I left out PTMProphet:PTM Score (see Eric's last email): " PTM Prophet has quite a substantial number of metrics. At the PSM level, we have: normalized information content number of localized modifications At the site level, we have: modification localization probability O-score M-score " If you need such PTMProphet metrics, then please send me a list with proposal for their exact name and definitions. New CV terms in version 4.1.25 of psi-ms.obo: ============================================= [Term] id: MS:1003011 name: pFind def: "Sequence-tag-based search engine pFind." [PMID:30295672] is_a: MS:1001456 ! analysis software [Term] id: MS:1003012 name: KSDP score def: "Kernel mass spectral dot product scoring function." [PMID:15044235] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better [Term] id: MS:1003013 name: i3tms def: "i3-tms search engine and data-analysis software." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1003014 name: MSFragger def: "A database search-based peptide identification tool." [PMID:28394336] is_a: MS:1001456 ! analysis software [Term] id: MS:1003015 name: razor peptide def: "A peptide which is shared between protein groups and assigned to the protein group with the largest number of identified peptides." [PSI:PI] is_a: MS:1000860 ! peptide [Term] id: MS:1003016 name: ProteinProphet:peptide weight def: "Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins." [PSI:PI] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002490 ! peptide-level scoring is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1003017 name: ProteinProphet:peptide group weight def: "Fraction of peptide evidence attributable to a group of proteins." [PSI:PI] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1002490 ! peptide-level scoring is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1003018 name: Philosopher def: "General proteomics processing toolkit for shotgun proteomics." [https://philosopher.nesvilab.org/] is_a: MS:1001456 ! analysis software Changed CV terms in version 4.1.25 of psi-ms.obo: ================================================= ************ adde synonym 'InterProphet' [Term] id: MS:1002288 name: iProphet def: "A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format." [PMID:21876204] synonym: "InterProphet" EXACT [] is_a: MS:1002286 ! Trans-Proteomic Pipeline software Best Regards, Gerhard -- ---------------------------------------------------------------------- Dipl. Inform. med., Dipl. Wirtsch. Inf. GERHARD MAYER Scientific assistant 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... www.medizinisches-proteom-center.de |