[MOBY-l] Constructing MOBY objects

[Beatrice Schildknecht]

Hello Mark,

 > Perhaps you should send a message to the moby-l list describing (in 
words) the
 > objects that you need to consume/serve and we can have a public 
discussion on how to construct them.

Ok. I'll start by introducing myself. :-)   I have recently joined the 
Nottingham Arabidopsis Stock Centre (NASC) in the UK. We are part of the 
European PLANET consortium (which will be using BioMOBY). 
I'll describe our data. (If anything's unclear, please let me know.) We 
would firstly like, basically to construct an object containing 
Arabidopsis seed information using a Stock no. as input (and later by 
AGI/Locus code and EMBL Acc no., when our databases have been fully 
curated.) As MOBY objects are lightweight, perhaps only some of this 
information would be served. 

As each object has a unique stock number and may not have an EMBL Acc, I 
would like to register the namespace, Stock No. (or something 
similar...). At NASC, codes always start with N followed by the number. 
At ABRC/TAIR they use the same numbers but they prefix them with CS.  
(There are 2 exceptions to this. In both these cases the donor number 
has been used for the stock code. However, we have kept our own 
numbering system for these.)
This is open for discussion, (whether a separate NASC and ABRC code 
namespace, or integrate them somehow?).

Mutants have a:

--  Stock No.-- (Each stock has a unique code)

--  EMBL Acc -- (does not exist if donor has not submitted sequence or 
stock is an ecotype for example)
--  Locus /AGI-code--
--  Phenotype -- (Information on plant's phenotype
-- Allele symbol --
-- Donor last name -- (The name of the person who donated the line)
-- Donor number -- (Unique number given by donor for each stock donated)
-- Background -- (Name of line used to generate mutant)

In addition each ecotype has a:
-- Habitat --
--  Location --
-- Altitude --
-- Daily temp --
-- Long/latitude --

Mark, I have only described the phenomics (seed) data. Constructing 
objects containing our genomic and transcriptomic data should be easier 
after this discussion. :-)

Kind regards,
Beatrice