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[Psidev-ms-dev] PSI-MSS WG call minutes
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From: Eric D. <ede...@sy...> - 2008-11-12 07:58:41
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Hi everyone, here are the notes I took from the call. Let me know if I've missed anything. Present: Matt, Pierre-Alain, Marc, Fredrik, Wilfred, Eric - Schema changes: no one protested, so we should go ahead and make the changes? + Yes. Marc also has some other suggested changes. + Marc has sent around a TOPP-based mzML validator and it finds several problems with the mapping file + We should run all examples through the validator and address problems + Link to this from the web site - change location of <spectrum> cvParams - scan/acquisition issue. Multiple scans inside acquisition? We need examples of what we want + Marc suggests removing scan and putting everything in acquisition + Matt and Eric should make some examples of what we want to end up with - Update rev to mzML 1.0.1 and update all documentation and examples + Yes + Make sure schemaLocation exists and is valid. It isn't now - nativeID format: Resolved. Add to documentation + Fredrik volunteers to create the CV terms for the nativeIDs - Marc has raised a number of issues to discuss. He has volunteered to maintain an open issues list + Marc will be added to SF developers and tracker admin and will set up and maintain a tracker for us - dataProcessingRef + Add a defaultDataProcessingRef attr to spectrumList and chromatogramList + Move softwareRef to processingMethod + Sematic validator should enforce that mzArray and intensityArray may not have a dataprocessingRef. This should be handled at the spectrum level. Other binaryDataArrays may have it, though. - <scanWindow> questions from Marc? + <scanWindow> should be optional. Sometimes this information will be unavailable - Removing/fixing scanning method child terms in CV + Marc has some CV issues to change. He will email out for approval + Marc needs to add some types to some CV terms that aren't there yet + Marc has a nice display of the mapping rules via a link from the TOPP validator page + Marc will create a candidate for an expanded mapping file + Make sure that the mapping file has a proper version that is publicized - Export of CV to OLS - Validator (TOPP validator and EBI validator) + validator has found some problems like cvParam deisotoping value="false" + Did we have a discussion about this in the past? For deisotoping, if the term is present, then it means it was performed. But if the term is absent, we assume that it was not performed. But it could mean unknown. While deisotoping value="false" means we know for sure it wasn't done. How to resolve? - Other + Document better when acquisitionSettings term is supported to be. + acquisitionList is too generic and maybe should be targetList. We had originally had targetList, but backed off to make it more generic. But now there is confusion between acquisition (in scan) and acquisitionList. There is no way to reference acquisitionList from acquisition. Be we never intended it this way. This is a topic for future discussion. - Next call + Same time in two weeks Nov 25 at 8am PST _____ From: Eric Deutsch [mailto:ede...@sy...] Sent: Tuesday, November 11, 2008 12:02 AM To: 'Mass spectrometry standard development' Cc: 'Eric Deutsch'; 'Natalie Tasman' Subject: PSI-MSS WG call reminder Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PST (in 8 hr): http://www.timeanddate.com/worldclock/fixedtime.html?day=11 <http://www.timeanddate.com/worldclock/fixedtime.html?day=11&month=11&year=2 008&hour=16&min=0&sec=0&p1=136> &month=11&year=2008&hour=16&min=0&sec=0&p1=136 + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 Topics: - Schema changes: no one protested, so we should go ahead and make the changes? - change location of <spectrum> cvParams - scan/acquisition issue. Multiple scans inside acquisition? We need examples of what we want - Update rev to mzML 1.0.1 and update all documentation and examples - nativeID format: Resolved. Add to documentation - Marc has raised a number of issues to discuss. He has volunteered to maintain an open issues list - dataProcessingRef - <scanWindow> questions from Marc? - Removing/fixing scanning method child terms in CV - Export of CV to OLS - Validator (TOPP validator and EBI validator) - Next call |
