From: Gerald F. <gvf...@lb...> - 2008-04-09 23:46:54
|
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 |
From: Joe W. <jw...@ji...> - 2008-04-10 16:47:00
|
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 > > >------------------------------------------------------------------------- >This SF.net email is sponsored by the 2008 JavaOne(SM) Conference >Don't miss this year's exciting event. There's still time to save $100. >Use priority code J8TL2D2. >http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone >_______________________________________________ >Mged-mage mailing list >Mge...@li... >https://lists.sourceforge.net/lists/listinfo/mged-mage > > |