mged-mage

[Mged-mage] question about Characteristics and Terms in MAGE-TAB

[Gerald F. <gvf...@lb...>]

Hi,

I have a simple question and apologies if this is in the MAGE-TAB 1.1 doc..
Please consider the column header: Characteristics[CellLine].
If I assume that the value in the subsequent Term Source REF column 
defines the term source of the value in the previous Characteristics row,
where should I state  that "CellLine" comes from the MO, for example?
I suppose a cellline database should also contain the term  "CellLine". 
Is that implied or am I a sandwich short of a picnic?

TIA,
-g

Re: [Mged-mage] question about Characteristics and Terms in MAGE-TAB

[Joe W. <jw...@ji...>]

Hi Gerald,

I think you can still have your picnic--but you may have to guess the 
source of your mustard. 

The 'Term Source REF' column describes the source of the term used in 
each row  in the Characteristics column.  In the absense of the Term 
Source REF column, the ontology is assumed to be the MO, and the data 
values are either drawn from MO or are user defined.  If Term Source REF 
is used, it is applied to the rows and not the column heading, so your 
cell line database would be the term source.  The bracketted term  is 
the category of the annotation supplied in the BMC column, and is 
assumed to be drawn from the MO.  There is no good way to specify the 
source of the category at the present time. 

There is another way to do this without Term Source REF: use a [Comment] 
column. In the column specify the data source for the BMC cell lines.  
Since Term Source REF is not provided, the Characteristic[cellLine] will 
be assumed to be a MO term, and the individual data values will be user 
defined.  The Comment column is treated as an NVT--a local property--and 
is not guarentteed to be processed by the MAGE-TAB parser.  So this 
method has this drawback. 

An alternate syntax has been discussed in past sessions, but I cannot 
find my notes on this; does anyone else have notes describing a syntax 
similar to this: Characteristic [term: term source] ? 

Cheers,
Joe

Gerald Fontenay wrote:

>Hi,
>
>I have a simple question and apologies if this is in the MAGE-TAB 1.1 doc..
>Please consider the column header: Characteristics[CellLine].
>If I assume that the value in the subsequent Term Source REF column 
>defines the term source of the value in the previous Characteristics row,
>where should I state  that "CellLine" comes from the MO, for example?
>I suppose a cellline database should also contain the term  "CellLine". 
>Is that implied or am I a sandwich short of a picnic?
>
>TIA,
>-g
>
>
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