Difference between revisions of "ModENCODE Analysis & metadata discussion"

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(New page: Please edit/add to this page regarding the storage of meta data and the nomenclature we should adopt for ?Analysis/?Condition objects in the AceDB database. == ?Analysis Naming == -- ...)
 
Line 7: Line 7:
  
 
-- this is my suggestion pad --
 
-- this is my suggestion pad --
 +
 
modEncode_<ID>_<PI>_<type>
 
modEncode_<ID>_<PI>_<type>
  
Line 12: Line 13:
  
 
ID = modencode experiment ID (1st Column in download table)
 
ID = modencode experiment ID (1st Column in download table)
 +
 
PI = PI surname responsible for projects
 
PI = PI surname responsible for projects
 +
 
Type = The data type e.g. RACE, 454_seq, Chip_Chip etc. etc.
 
Type = The data type e.g. RACE, 454_seq, Chip_Chip etc. etc.
  
Example
+
Example
-------
+
-------
515  CEUP1  vetted and released  Caenorhabditis elegans Piano
+
515  CEUP1  vetted and released  Caenorhabditis elegans Piano
 
+
would give an analysis object named:
+
would give an analysis object named:
modENCODE_515_Piano_RACE
+
 +
modENCODE_515_Piano_RACE
  
  
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We could then group all the experiments together under some parent ?Analysis
 
We could then group all the experiments together under some parent ?Analysis
  
Example
+
Example
-------
+
-------
Waterston data.
+
 +
Waterston data.
 +
485  Waterston_Reinke_JKL4-NDT  unvetted  Caenorhabditis elegans Waterston
 +
484 Waterston_Reinke_L1-NDT unvetted Caenorhabditis elegans Waterston
 +
481 Waterston_Reinke_GON unvetted Caenorhabditis elegans Waterston
 +
479 Waterston_Reinke_N2LE unvetted Caenorhabditis elegans Waterston
 +
478 Waterston_Reinke_MALE unvetted Caenorhabditis elegans Waterston
 +
476 Waterston_Reinke_N2EE unvetted Caenorhabditis elegans Waterston
 +
475 Waterston_Reinke_YA unvetted Caenorhabditis elegans Waterston
 +
474 Waterston_Reinke_L3 unvetted Caenorhabditis elegans Waterston
 +
473 Waterston_Reinke_L4 unvetted Caenorhabditis elegans Waterston
 +
472 Waterston_Reinke_L2 unvetted Caenorhabditis elegans Waterston
 +
448 Waterston-CelegansIntronsS3-2008-12 -02 vetted and released Caenorhabditis elegans Waterston
 +
447 Waterston-CelegansIntronsS2-2008-12 -02 vetted and released Caenorhabditis elegans Waterston
 +
446 Waterston-CelegansIntronsS1-2008-12 -02 vetted and released Caenorhabditis elegans Waterston
 +
445 Waterston-CelegansIntronsS4-2008-12 -02 vetted and released Caenorhabditis elegans Waterston
 +
438 mid-L4_20dC_36hrs_post-L1 RNAseq.2 unvetted Caenorhabditis elegans Waterston
 +
433 Young_Adult_25dC_46hrs_post-L1 RNAs eq unvetted Caenorhabditis elegans Waterston
 +
378 mid-L3_20dC_25hrs_post-L1 RNAseq unvetted Caenorhabditis elegans Waterston
 +
333 mid-L2_20dC_14hrs_post-L1 RNASeq unvetted Caenorhabditis elegans Waterston

Revision as of 08:32, 3 June 2009

Please edit/add to this page regarding the storage of meta data and the nomenclature we should adopt for ?Analysis/?Condition objects in the AceDB database.


?Analysis Naming

-- this is my suggestion pad --

modEncode_<ID>_<PI>_<type>

Where

ID = modencode experiment ID (1st Column in download table)

PI = PI surname responsible for projects

Type = The data type e.g. RACE, 454_seq, Chip_Chip etc. etc.

Example
-------
515  	 CEUP1   	 vetted and released  	Caenorhabditis elegans Piano

would give an analysis object named:

modENCODE_515_Piano_RACE


It would be good to decide on a nomenclature as there are lots of modENCODE projects that we are going to extract data from, and the ?Analysis class might get a bit confusing.

We could then group all the experiments together under some parent ?Analysis

Example
-------

Waterston data.
485  	Waterston_Reinke_JKL4-NDT   	 unvetted  	Caenorhabditis elegans Waterston
484 	Waterston_Reinke_L1-NDT 	unvetted 	Caenorhabditis elegans Waterston
481 	Waterston_Reinke_GON 	unvetted 	Caenorhabditis elegans Waterston
479 	Waterston_Reinke_N2LE 	unvetted 	Caenorhabditis elegans Waterston 
478 	Waterston_Reinke_MALE 	unvetted 	Caenorhabditis elegans Waterston 
476 	Waterston_Reinke_N2EE 	unvetted 	Caenorhabditis elegans Waterston
475 	Waterston_Reinke_YA 	unvetted 	Caenorhabditis elegans Waterston
474 	Waterston_Reinke_L3 	unvetted 	Caenorhabditis elegans Waterston
473 	Waterston_Reinke_L4 	unvetted 	Caenorhabditis elegans Waterston
472 	Waterston_Reinke_L2 	unvetted 	Caenorhabditis elegans Waterston
448 	Waterston-CelegansIntronsS3-2008-12 -02 	vetted and released 	Caenorhabditis elegans Waterston 	
447 	Waterston-CelegansIntronsS2-2008-12 -02 	vetted and released 	Caenorhabditis elegans Waterston 	
446 	Waterston-CelegansIntronsS1-2008-12 -02 	vetted and released 	Caenorhabditis elegans Waterston 	
445 	Waterston-CelegansIntronsS4-2008-12 -02 	vetted and released 	Caenorhabditis elegans Waterston 	
438 	mid-L4_20dC_36hrs_post-L1 RNAseq.2 	unvetted 	Caenorhabditis elegans Waterston 
433 	Young_Adult_25dC_46hrs_post-L1 RNAs eq 	unvetted 	Caenorhabditis elegans Waterston
378 	mid-L3_20dC_25hrs_post-L1 RNAseq 	unvetted 	Caenorhabditis elegans Waterston
333 	mid-L2_20dC_14hrs_post-L1 RNASeq 	unvetted 	Caenorhabditis elegans Waterston