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From: <cod...@go...> - 2008-11-12 16:12:09
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Issue 30: Specifying the enzyme rules used in the search http://code.google.com/p/psi-pi/issues/detail?id=30 Comment #38 by eisenachM: TeleCon 12th Nov: We decided to use the has_a relationship, because its more formal. Martin: change has_a to has_regular_expression and delete the xrefs. -- 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...> - 2008-11-12 15:05:51
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Hi Pierre-Alain, Pierre-Alain Binz wrote: > Thanks David. > FYI, for mzML, we had generated a excel mapping spreadsheet (if you want > to see it...) Yes please. (I can't see it on psidev.info). > > The format is ok for me. About the notes: the descriptions of what > should be the content from a MIAPE point of view are in the MIAPE > document, in the Annex table. Oh yes... > > Note also that for mzML-MIAPE MS mapping, there were a few items not > covered by MIAPE, and also not covered by mzML. The latest have either > been annotated for a future version of mzML (similar to the quantitation > in AnalysisXML), or just left out and annotated as such (for instance > flow rates, detector sensitivity). Either they are independant or an > estimation that looks more like an interpretation. We there need to > decide whether those should be taken out of MIAPE or not. We will aim to add anything missing (apart from quantitation) before submission to the document process. > > I have commented two of the notes. If there are unclear items, just put > a note in and I can clarify Yes please! I can't remember what we intended from "Location of the files generated". The definition is: "The location of the data generated. If made available in a public repository, describe the URI (for instance an url, or the url of the repository and the information on how to retrieve the data). If not made available for public access, describe the contact person reference or source and the internal coordinates of the data." But _what_ data does this refer to? The peak list, the analysisXML document, intermediate files like Sequest .out files or any/all of these? If it's the analysisXML file, you presumably have it and you must know where you got it from ;) > > One more: for mzML, we have two (at least) levels of stringency for the > validators: basic semantic and MIAPE compliance. Therefore we can deal > with legacy being compliant woth the format, even if it does not comply > with MIAPE Sounds good, David > > > Cheers > Pierre-Alain > > David Creasy wrote: >> I've started on the MIAPE conformance doc: >> >> http://psidev.info/index.php?q=node/386 >> >> Can we discuss whether this is a suitable format on the call later. >> (Looks as though we may have a couple of things to add to the schema...) >> >> Thanks, >> David >> >> David Creasy wrote: >> >>> Hi everyone, >>> >>> There will be an AnalysisXML working group conference call on WEDNESDAY >>> (instead of Thursday) at: >>> http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 >>> >>> >>> Minutes from last meeting at: >>> http://psidev.info/index.php?q=node/384 >>> >>> >>> Agenda: (strangely identical to last week, although progress has been >>> made!) >>> 1. Review of minutes of last meeting >>> >>> 2. Status of mapping document and CV >>> >>> 3. Issue 30: Enzymes >>> http://code.google.com/p/psi-pi/issues/detail?id=30 >>> Almost complete now? >>> http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 >>> >>> 4. Other items on the issues list: >>> http://code.google.com/p/psi-pi/issues/list >>> >>> Dial in details: >>> >>> + Germany: 08001012079 >>> + Switzerland: 0800000860 >>> + UK: 08081095644 >>> + USA: 1-866-314-3683 >>> + Generic international: +44 2083222500 (UK number) >>> >>> access code: 297427 >>> >>> >> >> -- 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: Pierre-Alain B. <pie...@is...> - 2008-11-12 14:26:26
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Thanks David. FYI, for mzML, we had generated a excel mapping spreadsheet (if you want to see it...) The format is ok for me. About the notes: the descriptions of what should be the content from a MIAPE point of view are in the MIAPE document, in the Annex table. Note also that for mzML-MIAPE MS mapping, there were a few items not covered by MIAPE, and also not covered by mzML. The latest have either been annotated for a future version of mzML (similar to the quantitation in AnalysisXML), or just left out and annotated as such (for instance flow rates, detector sensitivity). Either they are independant or an estimation that looks more like an interpretation. We there need to decide whether those should be taken out of MIAPE or not. I have commented two of the notes. If there are unclear items, just put a note in and I can clarify One more: for mzML, we have two (at least) levels of stringency for the validators: basic semantic and MIAPE compliance. Therefore we can deal with legacy being compliant woth the format, even if it does not comply with MIAPE Cheers Pierre-Alain David Creasy wrote: > I've started on the MIAPE conformance doc: > > http://psidev.info/index.php?q=node/386 > > Can we discuss whether this is a suitable format on the call later. > (Looks as though we may have a couple of things to add to the schema...) > > Thanks, > David > > David Creasy wrote: > >> Hi everyone, >> >> There will be an AnalysisXML working group conference call on WEDNESDAY >> (instead of Thursday) at: >> http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 >> >> >> Minutes from last meeting at: >> http://psidev.info/index.php?q=node/384 >> >> >> Agenda: (strangely identical to last week, although progress has been >> made!) >> 1. Review of minutes of last meeting >> >> 2. Status of mapping document and CV >> >> 3. Issue 30: Enzymes >> http://code.google.com/p/psi-pi/issues/detail?id=30 >> Almost complete now? >> http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 >> >> 4. Other items on the issues list: >> http://code.google.com/p/psi-pi/issues/list >> >> 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...> - 2008-11-12 12:16:21
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I've started on the MIAPE conformance doc: http://psidev.info/index.php?q=node/386 Can we discuss whether this is a suitable format on the call later. (Looks as though we may have a couple of things to add to the schema...) Thanks, David David Creasy wrote: > Hi everyone, > > There will be an AnalysisXML working group conference call on WEDNESDAY > (instead of Thursday) at: > http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 > > > Minutes from last meeting at: > http://psidev.info/index.php?q=node/384 > > > Agenda: (strangely identical to last week, although progress has been > made!) > 1. Review of minutes of last meeting > > 2. Status of mapping document and CV > > 3. Issue 30: Enzymes > http://code.google.com/p/psi-pi/issues/detail?id=30 > Almost complete now? > http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 > > 4. Other items on the issues list: > http://code.google.com/p/psi-pi/issues/list > > Dial in details: > > + Germany: 08001012079 > + Switzerland: 0800000860 > + UK: 08081095644 > + USA: 1-866-314-3683 > + Generic international: +44 2083222500 (UK number) > > access code: 297427 > -- 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: David C. <dc...@ma...> - 2008-11-11 16:38:19
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Hi everyone, There will be an AnalysisXML working group conference call on WEDNESDAY (instead of Thursday) at: http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 Minutes from last meeting at: http://psidev.info/index.php?q=node/384 Agenda: (strangely identical to last week, although progress has been made!) 1. Review of minutes of last meeting 2. Status of mapping document and CV 3. Issue 30: Enzymes http://code.google.com/p/psi-pi/issues/detail?id=30 Almost complete now? http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 4. Other items on the issues list: http://code.google.com/p/psi-pi/issues/list Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 -- 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: Lennart M. <len...@gm...> - 2008-11-11 14:14:10
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Dear PSI PI Enthusiasts, Slight mixup here, wrong email list. Apologies! Cheers, lnnrt. Lennart Martens wrote: > Dear PSI MS enthusiasts, > > > Unfortunately, I am travelling today, and while I'll make sure the call > is started, I can not participate in the call. > > > Cheers, > > lnnrt. > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > |
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From: <cod...@go...> - 2008-11-11 12:59:36
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Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #17 by a.bertsch0815: Please find attached an output of the sematic validator for the example instance documents. Some errors might be due two missing CVTerms or missing mapping rules. Attachments: sematic_validation_output_examples.txt 22.7 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...> - 2008-11-11 12:55:41
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Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #16 by a.bertsch0815: http://psi-pi.googlecode.com/svn/trunk/cv/axml-mapping.html is a html-page which contains all mapping rules and the cv-terms which can be used. This may help to correct the example instance documents, validation errors of the examples will follow. -- 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...> - 2008-11-11 12:50:39
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Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #15 by a.bertsch0815: Unused cvParam locations (mapping cannot be defined, because we have no valid terms at the moment) /psi-pi:AnalysisXML/psi-pi:SequenceCollection/psi-pi:Peptide/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:SequenceCollection/psi-pi:Peptide/psi-pi:Modification/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:SequenceCollection/psi-pi:Peptide/psi-pi:SubstitutionModification/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:AnalysisCollection/psi-pi:SpectrumIdentification/psi-pi:_runtimeParams/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:AnalysisCollection/psi-pi:ProteinDetection/psi-pi:_analysisParams/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:AnalysisProtocolCollection/psi-pi:SpectrumIdentificationProtocol/psi-pi:ModificationParams/psi-pi:SearchModification/psi-pi:ModName /psi-pi:AnalysisXML/psi-pi:AnalysisProtocolCollection/psi-pi:SpectrumIdentificationProtocol/psi-pi:MassTable/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:AnalysisProtocolCollection/psi-pi:SpectrumIdentificationProtocol/psi-pi:MassTable/psi-pi:AmbiguousResidue/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:DataCollection/psi-pi:Inputs/psi-pi:SearchDatabase/pf:fileFormat/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:DataCollection/psi-pi:AnalysisData/psi-pi:SpectrumIdentificationList/psi-pi:SpectrumIdentificationResult/psi-pi:SpectrumIdentificationItem/psi-pi:PeptideEvidence/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:DataCollection/psi-pi:AnalysisData/psi-pi:SpectrumIdentificationList[3]/psi-pi:SpectrumIdentificationResult[4]/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:DataCollection/psi-pi:AnalysisData/psi-pi:SpectrumIdentificationList[5]/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:DataCollection/psi-pi:AnalysisData/psi-pi:ProteinDetectionList/pf:cvParam/@accession /psi-pi:AnalysisXML/psi-pi:DataCollection/psi-pi:AnalysisData/psi-pi:ProteinDetectionList/psi-pi:ProteinAmbiguityGroup/pf:cvParam/@accession -- 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: Lennart M. <len...@gm...> - 2008-11-11 12:49:41
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Dear PSI MS enthusiasts, Unfortunately, I am travelling today, and while I'll make sure the call is started, I can not participate in the call. Cheers, lnnrt. |
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From: Jones, A. <And...@li...> - 2008-11-10 15:02:21
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Hi all, As discussed on the call, I was going to make a change to the schema so that the value attribute on PropertyValue is mandatory. As it turns out, this attribute was already mandatory - so not sure how this issue arose now! Anyway, I've just updated the FuGE light schema with some slight changes to the documentation, Cheers Andy > -----Original Message----- > From: Phil Jones @ EBI [mailto:pj...@eb...] > Sent: 05 November 2008 17:50 > To: psi...@li... > Subject: [Psidev-pi-dev] Minutes of telecon, 5 November 2008 > > Hi, > > Please find the minutes here: > > http://psidev.info/index.php?q=node/384 > > Could attendees please take a look at these as some parts of the > discussion were difficult to follow - any corrections gratefully > received. > > best regards, > > Phil. > > -- > Phil Jones > Senior Software Engineer > InterPro Team > PANDA Group, EMBL-EBI > Wellcome Trust Genome Campus > Hinxton, Cambridge, CB10 1SD > UK. > > Work phone: +44 1223 494406 (NEW NUMBER) > Skype: philip-jones > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: David C. <dc...@ma...> - 2008-11-09 18:14:19
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Hi Andreas, Thanks. I've updated the Mascot examples, so if you could run them through the validator again, that would be great. I've removed: <AnalysisSampleCollection> from the examples because this information is not available for an automated export script. <SearchDatabase> <pf:fileFormat> We need CV for 'Fasta file' Cheers, David Andreas Bertsch wrote: > Hi all, > > I've updated the CV and the mapping file (thanks to Martins the CV is quite > well-structured). Please find attached output of the semantic validation using > the different CVs, the mapping file and the example instances. We have one > validating example (sequest), which are great news I think. Most of the errors > of the other files are due to not yet fully specified CV terms, so not really > critical. > > Cheers, > A. > > > > > -- 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: Phil J. @ E. <pj...@eb...> - 2008-11-07 14:32:12
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Hi Martin, I would be inclined to go for the separate term / relationship mechanism. I would not worry too much about OBO-edits failings as far as making this decision is concerned. I would also suggest that if you are going to define a new relationship type for this purpose, you could make it more specific, e.g. 'has_regular_expression' instead of just 'has_a'. When defining the relationship (which at the end of the day is just another term in the CV) you can also give it a definition so that the intent of the regular expressions is unambiguous and the OBO file is self documenting. Cheers, Phil. 2008/11/7 Martin Eisenacher <mar...@ru...>: > Hi Andreas, Angel, all, > > I tried two variants for encoding regular expressions > for the default enzymes into the OBO file: > 1) "xref" and 2) "has_a" relationship. > > See http://code.google.com/p/psi-pi/source/browse/trunk/cv/psi-pi.obo > > > Excerpt from obo file (for Trypsin): > > > [Term] > id: PI:00251 > name: Trypsin > xref_analog: regexp:(?<=[KR\])(?\!P) > is_a: PI:00045 ! cleavage agent name > relationship: has_a PI:00176 ! (?<=[KR])(?!P) > > For the 1st variant, the regular expression is only a string. > > For the 2nd variant, the regular expression is itself a > term (PI:00176) and child of a "regular expression" term. > > > Both methods have disadvantages: > In OBOEdit the xref gives a warning, because it contains non-URI characters. > > In OBOEdit the has_a relationship is not shown in the tree view, but only in > the Parent Plugin (see screenshot attached). > > @Angel, do you know a better method? > > @All: Which do we prefer? > > @Andreas, the obo file is yours now... > > > Bye > Martin > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > -- Phil Jones Senior Software Engineer InterPro Team PANDA Group, EMBL-EBI Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD UK. Work phone: +44 1223 494406 (NEW NUMBER) Skype: philip-jones |
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From: <cod...@go...> - 2008-11-07 14:21:21
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Issue 30: Specifying the enzyme rules used in the search http://code.google.com/p/psi-pi/issues/detail?id=30 Comment #37 by eisenachM: Two possible variants for encoding regular expressions for the default enzymes into the OBO file: 1) "xref" and 2) "has_a" relationship. [Term] id: PI:00251 name: Trypsin xref_analog: regexp:(?<=[KR\])(?\!P) is_a: PI:00045 ! cleavage agent name relationship: has_a PI:00176 ! (?<=[KR])(?!P) For the 1st variant, the regular expression is only a string. For the 2nd variant, the regular expression is itself a term (PI:00176) and child of a "regular expression" term. Both methods have disadvantages: In OBOEdit the xref gives a warning, because it contains non-URI characters. In OBOEdit the has_a relationship is not shown in the tree view, but only in the Parent Plugin (see screenshot attached). Which do we prefer? -- 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: Martin E. <mar...@ru...> - 2008-11-07 14:02:02
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Hi Andreas, Angel, all, I tried two variants for encoding regular expressions for the default enzymes into the OBO file: 1) "xref" and 2) "has_a" relationship. See http://code.google.com/p/psi-pi/source/browse/trunk/cv/psi-pi.obo Excerpt from obo file (for Trypsin): [Term] id: PI:00251 name: Trypsin xref_analog: regexp:(?<=[KR\])(?\!P) is_a: PI:00045 ! cleavage agent name relationship: has_a PI:00176 ! (?<=[KR])(?!P) For the 1st variant, the regular expression is only a string. For the 2nd variant, the regular expression is itself a term (PI:00176) and child of a "regular expression" term. Both methods have disadvantages: In OBOEdit the xref gives a warning, because it contains non-URI characters. In OBOEdit the has_a relationship is not shown in the tree view, but only in the Parent Plugin (see screenshot attached). @Angel, do you know a better method? @All: Which do we prefer? @Andreas, the obo file is yours now... Bye Martin |
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From: Martin E. <mar...@ru...> - 2008-11-05 17:56:48
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Hi! In the "psi-pi.obo" file http://code.google.com/p/psi-pi/source/browse/trunk/cv/psi-pi.obo there are some terms prefixed with "TODO" which need our/your attention: "TODO_add_others": These are search engine specific input parameters (beyond Enzyme, tolerance, modifications,...) like "mascot:RequireBoldRed". Please add further terms needed for your search engine as a comment to issue 42! "TODOpeak list generation details": This term is actually a branch of the ontology containing terms like "Clustering done" or "Deisotoping done". For me it looks like something for a PSI-MS CV and not PSI-PI and therefore like an artifact from the first round of collecting CV terms. Delete the whole branch? "TODOpeptide validation status": child term of "search result details". Is it necessary, does anyone remember its intention? Do we need child terms below it like "peptide manually validated"? There is already a branch for "peptide result information". If not deleted, it should at least be moved to there, agreement? "TODOscoring model": child term of "instrument details". We have already a branch "ions series considered in search" containing ion series terms for use as input parameters of a search. Is "scoring model" a summary of them or does it contain more? In the latter case, please provide some child terms. Please don't work on a local copy and commit, because of conflicts, add comments to the mailing list or CV term suggestions to issue 42. Thank you Martin |
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From: <cod...@go...> - 2008-11-05 17:54:41
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Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #14 by philip.j.r.jones: (Regarding comment 12 above). I have checked with Richard whether OLS uses an OBO file of NEWT / NCBI taxonomy for loading. Unfortunately this is not the case, so will need to look elsewhere for a solution. -- 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: Phil J. @ E. <pj...@eb...> - 2008-11-05 17:50:17
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Hi, Please find the minutes here: http://psidev.info/index.php?q=node/384 Could attendees please take a look at these as some parts of the discussion were difficult to follow - any corrections gratefully received. best regards, Phil. -- Phil Jones Senior Software Engineer InterPro Team PANDA Group, EMBL-EBI Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD UK. Work phone: +44 1223 494406 (NEW NUMBER) Skype: philip-jones |
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From: David C. <dc...@ma...> - 2008-11-05 17:25:16
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Hi All, As you may know, we've been using the list here: http://code.google.com/p/psi-pi/issues/list to keep track of issues while developing AnalysisXML. We decided to do this rather than using email because it gives a more permanent and traceable record of issues, and includes things that we have discussed in meetings and telephone conferences. However, when something is changed, those of us working on the issues don't always notice for a while. So, I've just changed the setting so a message is sent to the list when anything is changed. If you don't want to see these, I suggest that you filter out the messages using you email client. Apologies for the 'noise'... David cod...@go... wrote: > Issue 38: future extensions > http://code.google.com/p/psi-pi/issues/detail?id=38 > > Comment #4 by dcreasy: > Sequence tag generation and searching will be supported in version 2 > > > -- 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: <cod...@go...> - 2008-11-05 17:21:10
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Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #13 by a.bertsch0815: Here (attached) is a list of CV terms which are not mapped to the schema at the moment (along with their parents). Just write where to put specific CV terms (subtrees of the ontology) per Mail, and I'll fix the mapping file. Attachments: unused_cv_terms.txt 8.9 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...> - 2008-11-05 17:01:05
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Issue 38: future extensions http://code.google.com/p/psi-pi/issues/detail?id=38 Comment #4 by dcreasy: Sequence tag generation and searching will be supported in version 2 -- 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: Martin E. <mar...@ru...> - 2008-11-05 14:29:45
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Hi all! I made minor changes and medium-sized additions to the spec doc (with "Track Changes"). I hope, my svn commit does not conflict with someone's local copy (then tell me for merging). Bye Martin Von: Jones, Andy [mailto:And...@li...] Gesendet: Friday, October 17, 2008 12:34 PM An: psi...@li... Betreff: Re: [Psidev-pi-dev] Spec doc Hi Eric, This looks really good, thanks v much! Not wanting to give you more work... but there's a few minor things to fix if you get a chance, should be fairly simple I think: - Attributes - if required/optional is unspecified, currently "-" is shown. XSD default is optional - so replace "-" with "optional". - The attributes and documentation for FuGE elements is not being extracted e.g. Organization. If this is a big headache you could always generate a separate document for FuGElight and I'll manually compile them? - Documentation missing where elements have been referenced as sub-elements e.g. AnalysisSoftwareList --> AnalysisSoftware and all references to FuGE elements of this type say "?!?" Cheers Andy From: Eric Deutsch [mailto:ede...@sy...] Sent: 17 October 2008 07:43 To: psi...@li... Subject: Re: [Psidev-pi-dev] Spec doc Hi everyone, I updated the current draft of the on-line autogenerated schema docs to the latest svn. The result is at: http://www.peptideatlas.org/tmp/AnalysisXML_working.html It looks like the current mapping file is just a template without any term mappings themselves. Just as a test, I wrote into the axml-mapping.xml file the mapping information for SearchType and it seemed to pull it out of the CV nicely: http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType The autogeneration pulls examples out of one file. I randomly chose Mascot_MSMS_example.axml. Is there a better instance document to automatically pull examples out of? Regards, Eric _____ From: Jones, Andy [mailto:And...@li...] Sent: Monday, October 13, 2008 7:07 AM To: psi...@li... Subject: [Psidev-pi-dev] Spec doc Hi all, A new version of the spec document has been uploaded by SVN (in the specification_document directory), and previous versions have been put in a subfolder. I think the document is getting there... Main tasks still to do: - Finish section on use cases when we have finally agreed the list online and made all the example files. - Import some parts of the example files to demonstrate a few specific points - Import the autogenerated documentation Before we can submit, the main outstanding issues are: - CV - looking through the CV there is still a fair bit of work to do, there's quite a few terms with missing or incorrect documentation - Mapping file - Finish example files. Prior to the call on Thurs, can we have a think about how we plan to get the CV into shape and discuss it as a main agenda item... Also new schema uploaded with a few bits of improved documentation. Cheers Andy |
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From: David C. <dc...@ma...> - 2008-11-04 16:42:31
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Hi everyone, There will be an AnalysisXML working group conference call on WEDNESDAY (instead of Thursday) at: http://www.timeanddate.com/worldclock/fixedtime.html?day=5&month=11&year=2008&hour=16&min=0&sec=0&p1=136 Minutes from last meeting at: http://psidev.info/index.php?q=node/382 Agenda: 1. Review of minutes of last meeting 2. Status of mapping document and CV 3. Issue 30: Enzymes http://code.google.com/p/psi-pi/issues/detail?id=30 Any progress? 4. Other items on the issues list: http://code.google.com/p/psi-pi/issues/list Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 -- 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: Phil J. @ E. <pj...@eb...> - 2008-10-30 16:29:53
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Hi, Please find minutes of today's telephone conference here: http://psidev.info/index.php?q=node/382 best regards, Phil. 2008/10/30 Jones, Andy <And...@li...> > Quick reminder that we have a call later today. > > Cheers > > Andy > > > > *From:* Jones, Andy [mailto:And...@li...] > *Sent:* 28 October 2008 15:06 > *To:* psi...@li... > *Subject:* [Psidev-pi-dev] Call this week > > > > Hi all, > > > > We have planned a conference call this week on Thurs 30th at the usual > time: > http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=10&year=2008&hour=16&min=0&sec=0&p1=136 > > > > A couple of people are going to be away this week so we'll hold the call if > there is sufficient interest and if there's been any progress since last > week – so let me know! > > > > Proposed agenda: > > > > 1. Review minutes from last week > > 2. CV / mapping file > > 3. Any updated examples to review? > > 4. Review open issues: http://code.google.com/p/psi-pi/issues/list > > 5. Plan for submission to doc process > > 6. AOB > > > > 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 > > > > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's > challenge > Build the coolest Linux based applications with Moblin SDK & win great > prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > -- Phil Jones Senior Software Engineer InterPro Team PANDA Group, EMBL-EBI Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD UK. Work phone: +44 1223 494406 (NEW NUMBER) Skype: philip-jones |
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From: Jones, A. <And...@li...> - 2008-10-30 14:47:15
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Quick reminder that we have a call later today. Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 28 October 2008 15:06 To: psi...@li... Subject: [Psidev-pi-dev] Call this week Hi all, We have planned a conference call this week on Thurs 30th at the usual time: http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=10&year=2008&h our=16&min=0&sec=0&p1=136 A couple of people are going to be away this week so we’ll hold the call if there is sufficient interest and if there’s been any progress since last week – so let me know! Proposed agenda: 1. Review minutes from last week 2. CV / mapping file 3. Any updated examples to review? 4. Review open issues: http://code.google.com/p/psi-pi/issues/list 5. Plan for submission to doc process 6. AOB 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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