From: Don M. <dM...@ge...> - 2008-01-14 18:41:08
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Hi Tim, Ok, Tim, I'll fold this into the compiled document, which I'll send out again just before next week's meeting. Thanks! Regards, Don M. On Jan 14, 2008, at 6:39 AM, Tim Rayner wrote: > Hi, > > Thanks for putting this together, Don. I only have one small > addition to suggest. When we discussed adding the "Term Accession > Number" column to SDRF we neglected the IDF, and a couple of groups > have asked me in the meantime whether we could rectify this. I'd > therefore suggest the addition of these (optional!) IDF tags, one > for each "* Term Source REF" tag: > > Experimental Design Term Accession Number > Experimental Factor Term Accession Number > Person Roles Term Accession Number > Quality Control Term Accession Number > Replicate Term Accession Number > Normalization Term Accession Number > Publication Status Term Accession Number > Protocol Term Accession Number > > I think we probably omitted these tags because we didn't see any > immediate need for them, but both the ISA-TAB and modENCODE > projects are keen to fully annotate with OBI terms with accessions. > > Cheers, > > Tim > > > On Thu, 20 Dec 2007, Don Maier wrote: > >> Hi all, >> >> To ease the chore of reading and comparing comments on MAGE-TAB v. >> 1.1, I've incorporated into my original feedback document all >> other published comments to date -- those of Michael, Junmin, >> Helen, and Alvis: >> >> >> >> Those people should check to make sure that I've transcribed their >> remarks correctly and completely. If anyone else sends out >> comments, I'll incorporate those in a final version of the >> document before we meet in January. >> >> Have a great holiday! >> >> Regards, >> Don M. >> >> >> On Dec 7, 2007, at 11:36 AM, Don Maier wrote: >> >>> Hi all, >>> Here is a set of problems and proposed solutions for MAGE-TAB >>> that we at Stanford would like to discuss at the MAGE-TAB >>> workshop in January: >>> >>> <MAGE-TAB Proposals.doc> >>> We would greatly appreciate your contribution of creative energy >>> to help with this! >>> Regards, >>> Don Maier >>> Sr. Software Designer/Research >>> Dept. of Biochemistry >>> Stanford University School of Medicine >>> On Nov 26, 2007, at 2:34 AM, Tim Rayner wrote: >>>> Hi, >>>> My apologies if you receive this email more than once. At the >>>> last couple >>>> of jamborees a set of requested changes to the MAGE-TAB >>>> specification >>>> emerged, and the least contentious of these changes have been >>>> incorporated >>>> into the ArrayExpress MAGE-TAB parser. We've also created a new >>>> draft >>>> MAGE-TAB v1.1 specification, and the document is now available for >>>> download here: >>>> http://www.ebi.ac.uk/systems-srv/mp/file-exchange/MAGE- >>>> TABv1.1.tar.gz >>>> Changes were made as discussed at the Stanford and Brisbane >>>> jamborees >>>> (2007): >>>> >>>> * Added "Experimental Design Term Source REF" to IDF. >>>> >>>> * Added "Term Accession Number" to SDRF. >>>> >>>> * Added "Assay Name" and "Technology Type" to SDRF. >>>> >>>> * Added notes indicating that lines starting with the # >>>> character are >>>> to be treated as ignorable comments. >>>> >>>> * Added free-text "Protocol REF" heading prefixes (e.g. "Growth >>>> Protocol REF"). >>>> Note that in each case a document compliant with the v1.0 >>>> specification >>>> remains compliant with this updated version. The following >>>> changes were >>>> made to clarify the specification where it seemed necessary: >>>> >>>> * Sections were added providing notes on all the IDF and SDRF >>>> fields >>>> and columns. >>>> >>>> * Table 7 (SDRF columns) was modified to remove the data file >>>> columns >>>> as attributes of Hybridization, Scan and Normalization name, in >>>> an attempt >>>> to disambiguate the grammar needed to parse SDRF column headings. >>>> >>>> * Added a note (section 3.3.7, point 8) regarding what to do >>>> with SDRF >>>> attribute columns when applied to empty node or edge column >>>> values (i.e., >>>> ignore the attributes in such cases). >>>> >>>> * Other minor clarifications were added to the text where >>>> necessary. >>>> Don Maier at Stanford has also proposed disambiguating the >>>> behaviour of >>>> Comment[] columns by restricting their use such that they always >>>> immediately follow the column to which they apply. This change >>>> has not yet >>>> been included as it is likely to break compatibility with older >>>> documents; >>>> I think that this proposal needs to be circulated more widely >>>> before >>>> inclusion. >>>> We would appreciate your feedback on this new draft specification. >>>> Best regards, >>>> Tim >>>> -- >>>> Tim Rayner, Ph.D. >>>> Scientific Database Curator >>>> Microarray Informatics Team >>>> European Bioinformatics Institute >>>> ------------------------------------------------------------------- >>>> ------ >>>> This SF.net email is sponsored by: Microsoft >>>> Defy all challenges. Microsoft(R) Visual Studio 2005. >>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>> _______________________________________________ >>>> Mged-mage mailing list >>>> Mge...@li... >>>> https://lists.sourceforge.net/lists/listinfo/mged-mage >>> -------------------------------------------------------------------- >>> ----- >>> SF.Net email is sponsored by: >>> Check out the new SourceForge.net Marketplace. >>> It's the best place to buy or sell services for >>> just about anything Open Source. >>> http://sourceforge.net/services/buy/ >>> index.php_______________________________________________ >>> Mged-MAGE2 mailing list >>> Mge...@li... >>> https://lists.sourceforge.net/lists/listinfo/mged-mage2 >> Don Maier Sr. Software Designer/Research Dept. of Biochemistry Stanford University School of Medicine |