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From: Jones, A. <And...@li...> - 2009-06-16 15:36:08
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Hi all, There will be an mzIdentML conference call tomorrow (17th June) at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?day=17&month=6&year=2009&hour=16&min=0&sec=0&p1=136 Agenda: 1. Review minutes from last time: http://www.psidev.info/index.php?q=node/423 2. Review issues list: http://code.google.com/p/psi-pi/issues/list 3. Discuss implementation issues and tool support 4. Plan for re-submission to process 5. AOB Please send me any other items, Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 cheers, Andy |
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From: <cod...@go...> - 2009-06-16 15:35:22
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Updates: Status: Fixed Comment #6 on issue 27 by andrewrobertjones: Tidy up the schema http://code.google.com/p/psi-pi/issues/detail?id=27 Schema has been altered to have a single root element and various other changes documented elsewhere - issue closed. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2009-06-12 17:05:38
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Comment #14 on issue 44 by dcreasy: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Regarding comment #13 - the Mascot examples now include taxonomy information for protein sequences -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: David C. <dc...@ma...> - 2009-06-12 11:48:13
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Hi, I've updated the Mascot examples under svn to include taxonomy information as described in http://code.google.com/p/psi-pi/issues/detail?id=44#c13 However, it doesn't validate because the obo file is wrong: id: MS:1001089 name: molecule taxonomy def: "The taxonomy of the resultant molecule from the search." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001085 ! protein result details also needs: is_a: MS:1001342 ! database sequence details There also seem to be two entries in the obo with: id: MS:1001477 ah - someone has just fixed that, thank you! (Validator will give an error with MS:1001478 until the obo is updated on the validator site). We are also getting validator errors with MS:1001364 at the moment. Cheers, David -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
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From: Jones, A. <And...@li...> - 2009-06-11 09:27:36
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Hi Juan-Antonio, The URL text is correct but it had embedded a link to the old minutes (page 419), this one is correct: http://www.psidev.info/index.php?q=node/423 I made a small change to the other topics part of the end about the journal submission. cheers Andy From: Juan Antonio Vizcaíno [mailto:ju...@eb...] Sent: 10 June 2009 18:06 To: Psi...@li... Subject: [Psidev-pi-dev] Minutes from Phone Conference (June 10) Hi all, Minutes from today's phone conference can be found here: http://www.psidev.info/index.php?q=node/423<http://www.psidev.info/index.php?q=node/419> Cheers, Juan Antonio Juan Antonio Vizcaíno, Ph.D. EMBL European Bioinformatics Institute Proteomics Services Team, PANDA Group Wellcome Trust Genome Campus Hinxton, Cambridge, UK CB10 1SD Tel: +44 (0) 1223 492 686 Fax: +44 (0) 1223 494 468 Skype: javizca |
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From: Juan A. V. <ju...@eb...> - 2009-06-10 17:06:37
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Hi all, Minutes from today's phone conference can be found here: http://www.psidev.info/index.php?q=node/423 Cheers, Juan Antonio Juan Antonio Vizcaíno, Ph.D. EMBL European Bioinformatics Institute Proteomics Services Team, PANDA Group Wellcome Trust Genome Campus Hinxton, Cambridge, UK CB10 1SD Tel: +44 (0) 1223 492 686 Fax: +44 (0) 1223 494 468 Skype: javizca |
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From: <cod...@go...> - 2009-06-10 15:23:43
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Comment #13 on issue 44 by andrewrobertjones: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Re-opening this issue: We don't currently have an example for MS:1001089 and MS:1001090 and they are not well defined. [Term] id: MS:1001089 name: protein taxonomy def: "The taxonomy of the resultant protein from the search." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1001085 ! protein result details [Term] id: MS:1001090 name: taxonomy nomenclature def: "The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT)." [PSI:PI] is_a: MS:1001089 ! protein taxonomy This seems a little unwieldy to me. How about just having different CV for each type of ID. For example <DBSequence id="x" length="449" SearchDatabase_ref="y" accession="z" > <seq>MGKEKFHINIVVIGHVDSGKSTTTGHLIY...</seq> <pf:cvParam accession="MS:1001088" name="protein description" cvRef="PSI-MS" value="Elongation factor..." /> <pf:cvParam accession="MS:xxxxxx1" name="taxonomy: NCBI TaxID" cvRef="PSI-MS" value="9606" /> <pf:cvParam accession="MS:xxxxxx2" name="taxonomy: common name" cvRef="PSI-MS" value="human" /> <pf:cvParam accession="MS:xxxxxx3" name="taxonomy: scientific name" cvRef="PSI-MS" value="Homo sapiens" /> <pf:cvParam accession="MS:xxxxxx4" name="taxonomy: Swiss-Prot ID" cvRef="PSI-MS" value="HUMAN" /> </DBSequence> -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: Jones, A. <And...@li...> - 2009-06-09 14:22:30
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Hi all, New schema committed: Several relatively major changes in the XSD design type used by mzIdentML_working.xsd and FuGElight_working.xsd. - Removed all global elements from mzIdentML schema except the root node - Removed abstract global elements and all substitution groups from FuGE, replaced with xsd:group Changes for instance docs: - no longer need pf: prefix on components re-used from FuGElight_working.xsd - Removed ReferenceableCollection from mzIdentML_working.xsd. This was no longer needed (and clashed with the intended use in FuGElight_working.xsd), bibliographic references if required can be put free standing at the end of the file. Most instance docs can probably be fixed by simply removing "pf:" throughout There will be a conference call tomorrow at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?day=10&month=6&year=2009&hour=16&min=0&sec=0&p1=136 Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 Agenda: 1. Review minutes from meeting on 28th May: http://www.psidev.info/index.php?q=node/419 2. Discuss changes made to the schema, some of this appears in the minutes from 3rd June: http://www.psidev.info/index.php?q=node/421 3. Review issues list: http://code.google.com/p/psi-pi/issues/list 4. AOB Please send me other agenda items, Cheers Andy |
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From: Juan A. V. <ju...@eb...> - 2009-06-04 08:14:33
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Hi all, Minutes from yesterday's brief phone conference can be found here: http://www.psidev.info/index.php?q=node/421 Cheers, Juan Antonio |
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From: Jones, A. <And...@li...> - 2009-06-03 09:38:31
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Hi all, Several people are away this week so there will only be a brief mzIdentML call this week to discuss one specific issue: altering the design pattern used in the XSDs, which Florian and others at the EBI have been looking at. The call will be this afternoon at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?day=3&month=6&year=2009&hour=16&min=0&sec=0&p1=136 Anyone is welcome to join, Cheers Andy Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 |
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From: David C. <dc...@ma...> - 2009-05-31 22:08:24
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Hi, > Updates to the example instance docs – problems identified > - We still need an example of substitution modification. http://code.google.com/p/psi-pi/issues/detail?id=44#c12 It's also in Mascot_MSMS_example.mzid: <SubstitutionModification location="7" originalResidue="X" replacementResidue="N"/> David Juan Antonio Vizcaíno wrote: > Hi all, > > Minutes from yesterday's phone conference can be found here: > > http://www.psidev.info/index.php?q=node/419 > > > Cheers, > > Juan Antonio > > > Juan Antonio Vizcaíno, Ph.D. > EMBL European Bioinformatics Institute > Proteomics Services Team, PANDA Group > Wellcome Trust Genome Campus > Hinxton, Cambridge, UK > CB10 1SD > Tel: +44 (0) 1223 492 686 > Fax: +44 (0) 1223 494 468 > Skype: javizca > > > > > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity professionals. Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp as they present alongside digital heavyweights like Barbarian > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
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From: Juan A. V. <ju...@eb...> - 2009-05-29 09:00:37
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Hi all, Minutes from yesterday's phone conference can be found here: http://www.psidev.info/index.php?q=node/419 Cheers, Juan Antonio Juan Antonio Vizcaíno, Ph.D. EMBL European Bioinformatics Institute Proteomics Services Team, PANDA Group Wellcome Trust Genome Campus Hinxton, Cambridge, UK CB10 1SD Tel: +44 (0) 1223 492 686 Fax: +44 (0) 1223 494 468 Skype: javizca |
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From: <cod...@go...> - 2009-05-28 15:56:19
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Updates: Labels: -Milestone-Release2.0 Milestone-Release1.0 Comment #5 on issue 27 by eisenachM: Tidy up the schema http://code.google.com/p/psi-pi/issues/detail?id=27 (No comment was entered for this change.) -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2009-05-28 15:52:24
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Updates: Status: Fixed Labels: Milestone-Release1.0 Comment #3 on issue 50 by eisenachM: Taxonomy for each protein (DBSequence) http://code.google.com/p/psi-pi/issues/detail?id=50 (No comment was entered for this change.) -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2009-05-28 15:48:16
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Comment #75 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 the term "MS:1001447 - prot:FDR threshold" as CVParam within <Threshold> should allow a value, because I want to specify 5 Percent. Or do we want to give here only the TYPE of threshold and the actual value within the ANALYSISPARAMS section? -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2009-05-28 15:44:14
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Comment #74 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 the term "MS:1001447 - prot:FDR threshold" as CVParam within <Threshold> should allow a value, because I want to specify 5 Percent. Or do we want to give here only the TYPE of threshold and the actual value within the protocol section? -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2009-05-28 15:36:14
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Comment #13 on issue 49 by eisenachM: Issues / schema updates prior to version 1 release http://code.google.com/p/psi-pi/issues/detail?id=49 comments 10,11,12: in TeleCon 28th May 2009 agreement to leave <Threshold> as mandatory, to have a "no threshold" CV term and to set passThreshold to true, if all reported peptides/proteins are accepted (because they've passed the "no threshold"). -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2009-05-28 15:32:05
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Updates: Status: WontFix Comment #12 on issue 31 by eisenachM: Specifying the Search Database(s) Unambiguously - MIRIAM? http://code.google.com/p/psi-pi/issues/detail?id=31 (No comment was entered for this change.) -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2009-05-28 15:28:02
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Comment #11 on issue 31 by eisenachM: Specifying the Search Database(s) Unambiguously - MIRIAM? http://code.google.com/p/psi-pi/issues/detail?id=31 In TeleCon May 20th agreement, NOT to use MIRIAM, because: Not suitable at the moment since MIRIAM cannot incorporate NCBI nr database or differentiate between TrEMBL and SwissProt for instance. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2009-05-28 15:24:07
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Comment #73 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 I remember the group having agreed to replace "DB composition forward+decoy" with "DB composition target+decoy" in a TeleCon or in Turku, but I cannot find it in minutes. The argument was, that we not only have decoy type "reverse", but others... -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2009-05-28 15:12:57
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Comment #72 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 need new CV terms for <Threshold>, at least "no threshold" -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2009-05-28 12:56:46
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Updates: Status: Started Comment #4 on issue 27 by andrewrobertjones: Tidy up the schema http://code.google.com/p/psi-pi/issues/detail?id=27 Re-opened this issue. Florian has made a proposal for a tidied up schema structure with only one root that we should consider. Attachments: mzIdentML_custom.xsd 73.0 KB PMF_example_temp.mzid 164 KB Mascot_MSMS_example_temp2.mzid 293 KB -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2009-05-28 11:28:29
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Comment #71 on issue 42 by margaretcreasy: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Terms required for: Mascot Parser, Mascot Distiller and Mascot Integra (Analysis Software) Percolator (Analysis software) and the following three scores: percolator:Q value percolator:score percolaror:PEP (Posterior error probability) is_a: MS:1001143 ! search engine specific score for peptides is_a: MS:1001153 ! search engine specific score -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: Jones, A. <And...@li...> - 2009-05-27 08:30:13
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Hi everyone, There will be an mzIdentML working group conference call tomorrow (28th May) 4:00pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?day=28&month=5&year=2009&hour=16&min=0&sec=0&p1=136 Agenda: - Review minutes from last call: http://www.psidev.info/index.php?q=node/417 - Discussion of items on issues list: http://code.google.com/p/psi-pi/issues/list - Outstanding issues with the CV: http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo - Updates to the example instance docs - problems identified - Plan for re-submission to document process Please send me any further items for the agenda. Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 cheers Andy |
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From: <cod...@go...> - 2009-05-27 08:15:02
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Comment #70 on issue 42 by jensiepen: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Terms needed for X!Tandem, Omssa and SpectraST software. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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