[BioSQL-l] Can I just consider import HGI.101403 to biosequence table?

[Hilmar Lapp]

On Wednesday, December 17, 2003, at 07:15  AM, Jim Liu wrote:

> Dear All,
>
> I went to ftp://ftp.tigr.org/pub/data/tgi/Homo_sapiens/
> and downloaded HGI.release_13.zip.
> There are 4 data files:
>
> 479,047,691 HGI.101403
>   57,653,798 HGI.TC_EST.101403
>   12,629,591 HGI.TCs.101403
>   10,303,001 HGI.GO.101403
>
> I would like to import to MySQL database.
> I already applied BioSQL schema on MySQL.
> Can I just consider import HGI.101403 to biosequence table?

You'd also want to populate other tables. Generally I'd think you 
should be able to import those data into biosql; whether or not you can 
use the supplied tools to do it basically depends on whether there is a 
bioperl SeqIO parser for the format. So, check whether the 
SeqIO/tigr.pm XML parser is the one you need here; otherwise you could 
still write your own.

	-hilmar

> How about the other data files?
> How to find the detail definition of these data files?
>
> Thanks.
>
> Jim Liu
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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