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Re: [Psidev-ms-dev] [Psidev-pi-dev] [Psidev-ms-vocab] Proteogenomics update in mzid 1.2
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From: Eric D. <ede...@sy...> - 2016-03-31 22:40:42
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Hi Andy, I fired up the schema generation script and refreshed everything based on what’s in github now. You can see the current result here: http://www.peptideatlas.org/PSI/schemas/mzIdentML/1.2/mzIdentML1.2.0.html The schema seems pretty fine, but the example files have some issues. Here are a few observations of things to fix: - Examples files still have older CV URLS like: <cv id="PSI-MS" uri=" http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.73.0" fullName="PSI-MS"/> <cv id="UO" uri="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" fullName="UNIT-ONTOLOGY"/> <cv id="PRIDE" uri="http://code.google.com/p/ebi-pride/source/browse/trunk/pride-core/schema/pride_cv.obo" fullName="PRIDE"/> I ran a few of the files through my validator and have the following things: PeptideShaker_mzid_1_2_example.mzid ERROR: cvParam software vendor has a value, but it should not! WARNING: MS:1000588 should be 'contact URL' instead of 'contact url' ERROR: cvParam Phospho has a value, but it should not! ERROR: cvParam Oxidation has a value, but it should not! ERROR: cvParam Glu->pyro-Glu has a value, but it should not! ERROR: cvParam Carbamidomethyl has a value, but it should not! combined_fdr_1.2.mzid WARNING: MS:1001400 should be 'OMSSA xml format' instead of 'OMSSA xml file' WARNING: MS:1001062 should be 'Mascot MGF format' instead of 'Mascot MGF file' ERROR: cvParam distinct peptide-level q-value should have units, but it does not! xiFDR-CrossLinkExample.mzid WARNING: MS:1002543 should be 'xiFDR' instead of 'XiFDR' ERROR: cvParam contact address should have a value, but it does not! ERROR: cvParam contact name should have a value, but it does not! ERROR: cvParam unknown modification should have a value, but it does not! This is not exhaustive, but just some results from a first foray into this. If someone is interested in fixing these things and checking them it, I can push further and report other problems. Regards, Eric *From:* Jones, Andy [mailto:And...@li...] *Sent:* Tuesday, March 29, 2016 8:10 AM *To:* psi...@li... *Cc:* psi...@li... *Subject:* Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 Hi all, Just confirming we will have a call to discuss mzid 1.2 this coming Thurs at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301 Agenda: 1. Discussion of encoding proteogenomics results in mzid 1.2 (review of docs sent previously) 2. General review of mzid 1.2 specifications (attached here) – please take a look in advance if you can. We will probably not have time for a full review on the call, but we will see how far we get 3. Any other business Juan – are you okay to start the call, and if so, can you circulate dial-in details? Thanks Andy *From:* Binz Pierre-Alain [mailto:Pie...@ch... <Pie...@ch...>] *Sent:* 22 March 2016 15:45 *To:* psi...@li... *Subject:* Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 Fine for me too Pierre-Alain *De :* Eric Deutsch [mailto:ede...@sy... <ede...@sy...>] *Envoyé :* mardi 22 mars 2016 14:53 *À :* psi...@li...; Mass spectrometry standard development; psi...@li... *Objet :* Re: [Psidev-pi-dev] [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 That works fine for me! *From:* Jones, Andy [mailto:And...@li...] *Sent:* Tuesday, March 22, 2016 2:49 AM *To:* Mass spectrometry standard development; psi...@li...; psi...@li... *Subject:* Re: [Psidev-ms-vocab] [Psidev-ms-dev] Proteogenomics update in mzid 1.2 Hi all, I think the 24th is out for various people as an Easter-related holiday in some countries. Eric is correct, that time zones will be changing. On the 31st, my preferred slot is actually 4pm British summer time: http://www.timeanddate.com/worldclock/fixedtime.html?msg=mzid+1.2+call&iso=20160331T16&p1=301 This would be 8am in Seattle; 5pm Germany; 5pm Norway; (and 4pm in the independent nation state of the EBI) Does this work for everyone? Best wishes Andy *From:* Eric Deutsch [mailto:ede...@sy... <ede...@sy...>] *Sent:* 22 March 2016 03:32 *To:* Mass spectrometry standard development < psi...@li...>; psi...@li...; psi...@li... *Cc:* Eric Deutsch <ede...@sy...> *Subject:* Re: [Psidev-ms-dev] Proteogenomics update in mzid 1.2 Thanks, Andy, I like this idea. The times are not good for me, however. Normally 4pm London time is 8am Seattle time, but for these few weeks, 4pm London time is 9am Seattle time and I have a standing meeting I cannot change. http://www.timeanddate.com/worldclock/fixedtime.html?iso=20160324T16&p1=1440 An hour earlier would be fine for the 24th. I hope I’m not getting confused between 4pm GMT and London local time? I think on the 24th 16:00 GMT = 4pm local London, but on the 31st, 16:00 GMT is 5pm London time? Thanks, Eric *From:* Jones, Andy [mailto:And...@li...] *Sent:* Monday, March 21, 2016 4:21 AM *To:* psi...@li...; psi...@li...; psi...@li... *Subject:* [Psidev-ms-dev] Proteogenomics update in mzid 1.2 Hi all, Over the coming weeks, I will be trying to get mzid 1.2 largely tied up for a final review in Ghent, before we submit the spec doc and associated manuscript. I have cross-posted this message (since PSI-PI has not been active lately), but probably will drop PSI-MS from the list in future. If you’re interested in mzid 1.2, please make sure to follow the PSI-PI list. One feature I would like to add into mzid 1.2 is better support for proteogenomics approaches. There are some parallel efforts to adapt genome formats BED and BAM for proteomics (and updates will be presented in Ghent I think). It would be nice if the info needed for proBed and proBAM was consistently expressed in mzid 1.2 files (mainly genome coordinates for peptides). Along with Juan et al., we have come up with a proposal for how this might be done in mzid 1.2. Please see attached. Feel free to annotate any comments on the document, or email back to the list any parts you feel need adapting or comments for discussion. It might be useful to have one or two conference calls on mzid 1.2 before Ghent. How would following dates suit: - This Thurs (24th March) at 4pm GMT - Next Thurs (31st March) at 4pm GMT Best wishes Andy |
