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From: andrewrobertjones <not...@gi...> - 2016-05-04 13:04:29
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Just opening a comment here to remind us we need to do this. In Ghent, we discussed making different CV terms for all of PSM, peptide, protein, protein group and mod localisation so that reading software could easily tell, say under SpectrumIdentificationItem, whether the score is for a PSM, peptide or mod localisation. Mod localisation will have to specific terms anyway, since the values have a special structure. Most important work therefore is separating PSM and peptide-level scores, so a reader can figure this out. I have assigned to @edeutsch since Eric offered to take a look in Ghent, but other helpers would be very welcome! --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/25 |
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From: andrewrobertjones <not...@gi...> - 2016-05-11 15:38:21
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ACTION: Gerhard going to make a brief report of the terms we have, and we will create new terms where needed separating PSMs and peptides --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/25#issuecomment-218498282 |
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From: Gerhard M. <not...@gi...> - 2016-05-19 14:44:40
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[CV-terms for PTM, PSM, peptide, protein and protein-group scores.docx](https://github.com/HUPO-PSI/mzIdentML/files/272801/CV-terms.for.PTM.PSM.peptide.protein.and.protein-group.scores.docx) --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/25#issuecomment-220346235 |
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From: Gerhard M. <not...@gi...> - 2016-05-25 14:41:34
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[CV-terms for PTM, PSM, peptide, protein and protein-group scores.docx](https://github.com/HUPO-PSI/mzIdentML/files/282210/CV-terms.for.PTM.PSM.peptide.protein.and.protein-group.scores.docx) --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/25#issuecomment-221597809 |
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From: andrewrobertjones <not...@gi...> - 2016-05-26 12:27:06
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Thanks @germa for this. I added some comments to the document, but there are still a few parts unclear to me. Perhaps we should discuss in detail on our next call --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/25#issuecomment-221856794 |
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From: andrewrobertjones <not...@gi...> - 2016-06-09 15:21:11
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Proposal from Eric: [PSI-MS_statisticEntries.xlsx](https://github.com/HUPO-PSI/mzIdentML/files/307250/PSI-MS_statisticEntries.xlsx) term component definitions: - attribute a general property of an entity (may be a statistic, or a more general property) - statistic a derived numerical metric generally related to confidence in a result - PTM localization related to the exact position of a mass modification (not necessarily a biological PTM) - PSM-level pertaining to one or more peptide-spectrum matches - peptide ion-level pertaining to one or more PSM with the same sequence, modifications, charge - modified peptide-level pertaining to one or more PSMs with the same sequence and modifications - peptide sequence-level pertaining to one or more distinct peptide sequences, irrespective of charge or modification - protein-level pertaining to one or more specific protein entries - protein group-level pertaining to one or more protein ambiguity groups ----------------------------------------- - analysis attribute - PTM localization attribute - PTM localization single result statistic - PTM localization PSM-level statistic - PTM localization distinct peptide-level statistic - PTM localization result list statistic - identification attribute - single identification result attribute - PSM-level identification attribute - PSM-level identification statistic - PSM-level identification confidence metric - PSM-level search engine specific statistic - cross-linking attribute - product ion attribute - peptide sequence-level identification attribute - peptide sequence-level identification statistic - protein-level identification attribute - protein-level identification statistic - protein group-level identification attribute - protein group-level identification statistic - result list attribute - PSM-level result list attribute - PSM-level result list statistic - distinct peptide-level result list attribute - distinct peptide-level result list statistic - protein-level result list attribute - protein-level result list statistic - protein group-level result list attribute - protein group-level result list statistic --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/25#issuecomment-224929441 |
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From: andrewrobertjones <not...@gi...> - 2016-06-09 15:46:45
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Reviewed current structure, looks good overall. Andy and Eric will continue to work on this and the mapping file --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/25#issuecomment-224937451 |
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From: andrewrobertjones <not...@gi...> - 2016-06-16 15:13:32
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I have checked in the Excel file into the CV branch on GitHub but this needs a bit more work. @edeutsch could you take another look next? --- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/HUPO-PSI/mzIdentML/issues/25#issuecomment-226516167 |
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