From: Don M. <dM...@ge...> - 2008-01-14 21:06:44
|
Hi again, Tim, With your proposal, there would be Term Accession Numbers in the IDF and SDRF -- but still not in the ADF (header). Is there a reason to omit term accession numbers in the ADF header, but to include them in the other two kinds of MAGE-TAB file? Regards, Don M. On Jan 14, 2008, at 10:40 AM, Don Maier wrote: > 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 > > |