Re: [Mged-mage] Feedback on: Draft MAGE-TAB 1.1 specification - now including all comments

[Don M. <dM...@ge...>]

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
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>
> Don Maier
> Sr. Software Designer/Research
> Dept. of Biochemistry
> Stanford University School of Medicine
>
>