Difference between revisions of "ModENCODE Analysis & metadata discussion"

From WormBaseWiki
Jump to navigationJump to search
Line 8: Line 8:
 
-- this is my suggestion pad --
 
-- this is my suggestion pad --
  
modEncode_<ID>_<PI>_<type>
+
modEncode_<ID>_<PI>_<type/Desc>
  
 
Where  
 
Where  
Line 16: Line 16:
 
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/Desc = The data/tissue/(something brief to define the data) type e.g. RACE, 454_seq, Chip_Chip L2_RNAseq etc. etc.
  
 
  Example
 
  Example
Line 34: Line 34:
 
  -------
 
  -------
 
   
 
   
  Waterston data.
+
  Waterston data Gary has been looking at.
  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  
 
  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
 
  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
 
  378 mid-L3_20dC_25hrs_post-L1 RNAseq unvetted Caenorhabditis elegans Waterston
 
  333 mid-L2_20dC_14hrs_post-L1 RNASeq unvetted Caenorhabditis elegans Waterston
 
  333 mid-L2_20dC_14hrs_post-L1 RNASeq unvetted Caenorhabditis elegans Waterston
 +
 +
modENCODE_333_Waterston_L2_RNAseq
 +
modENCODE_378_Waterston_L3_RNAseq
 +
modENCODE_438_Waterston_L4_RNAseq
 +
modENCODE_433_Waterston_Young_Adult_RNAseq
 +
 +
Grouped under modENCODE_Waterston
 +
 +
This would require a model change to allow Parent/Child_analysis connections.

Revision as of 05:38, 4 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/Desc>

Where

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

PI = PI surname responsible for projects

Type/Desc = The data/tissue/(something brief to define the data) type e.g. RACE, 454_seq, Chip_Chip L2_RNAseq 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 as there are some more complicated examples out there.

Example
-------

Waterston data Gary has been looking at.
----------------------------------------
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

modENCODE_333_Waterston_L2_RNAseq
modENCODE_378_Waterston_L3_RNAseq
modENCODE_438_Waterston_L4_RNAseq
modENCODE_433_Waterston_Young_Adult_RNAseq

Grouped under modENCODE_Waterston

This would require a model change to allow Parent/Child_analysis connections.