ModENCODE Analysis & metadata discussion

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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 --

option 1) modEncode_<ID>_<PI>_<type/Desc>

Where

ID = modencode experiment ID (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.

or option 2) just use modENCODE_<column 1>_<column 2> to simplify design?

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

would give an analysis object named:

option 1) modENCODE_515_Piano_RACE
option 2) modENCODE_515_CEUP1

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_RNAseq

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