Re: [Gusdev-gusdev] TIGR Data

[Angel P. <an...@pc...>]

Jinal Jhaveri wrote:

>Dear GUS Gurus,
>
>
>Has anyone tried to dump the tab delimited data available from tigr into gus? 
>We have annotation available from genbank, tigr and swissprot and would like 
>to store all of them in gus and then compare their overlaps and deltas. 
>Initially a workaround that came to my mind is to convert the tigr format to 
>gbk (using bioperl) and upload it using gbparser. But it seems like it is not 
>the ideal way to do this and there can be many inconsistencies in allocating 
>the genbank id . Can I directly parse the information from the tab-delimited 
>file and store it in the gus db w/o using any parser (or writing my own) 
>using perl/dbi. I ask this because, though I know that I can write such a 
>script, I am not too sure about what implications it can have on the perl and 
>java objects? 
>
The main reason not to do this is b/c folks usually forget about using
the PK sequences to insert rows into the DB, leading to oracle contraint
violations later on.

Another reason is that you circumvent the whole algorithmInvocation
mechanisms for data tracking. If you suddenly realize that you screwed
up someplace, deleting the data suddenly becomes much more complicated.

I'll leave it to someone else to comment on the best way to get the TIGR
data into the DB.
Angel

>Will they understand the data entered by me directly w/o using 
>any gus module? (or in the worst case by using submitRow)? Any other issues 
>that I am missing?
>
>
>thanks
>--Jinal
>
>
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