[Mged-mage] Draft MAGE-TAB 1.1 specification (fwd)

[Tim R. <ra...@eb...>]

Hi,

So far we have not received any comments or suggestions regarding the 
proposed MAGE-TAB v1.1 specification document which I circulated on 
Monday. We would like to set Saturday Dec. 15 as a deadline for comments, 
after which time we will assume that the proposed changes are generally 
accepted.

Best regards,

Tim

-- 
Tim Rayner
ArrayExpress

---------- Forwarded message ----------
Date: Mon, 26 Nov 2007 10:34:40 +0000 (GMT)
From: Tim Rayner <ra...@eb...>
To: mge...@li..., mge...@li...
Subject: Draft MAGE-TAB 1.1 specification

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