ModENCODE Analysis & metadata discussion
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.
-- this is my suggestion pad --
option 1) modEncode_<ID>_<PI>_<type/Desc>
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.
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.
Would be good to add Database connections to ?Condition or ?Analysis so that accessions can be added to the objects.