From: Tim R. <ra...@eb...> - 2008-01-14 14:39:50
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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 > |