Re: [Gusdev-gusdev] GBParser

[Steve F. <st...@pc...>]

jinal-

see below

jinal jhaveri wrote:

>Hi,
>
>I have some questions regarding the GBParser module 
>
>1) First required field  is --gbRel. As I understand this is genbank's db realease id. Now where do I get this number from? ( genbanks website????) Does anybody has idea about what is the release right now on web?
>  
>
yes, this is from the readme file .   it is stored in GUS in the 
created_rel_ver and updated_rel_ver attributes of the DoTS::NAEntry table:
http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=DoTS::NAEntry&path=DoTS::NAEntry

>2) --db_rel_id : As the documentation describes, this is external database id. Do I create this id on my own? Do I need to keep this entry in any other table? Does this id has one to one correspondence with the project I am working on (and the one I described in my .gus.properties file?)
>
gus is strict about its data.   we track pretty much everything.  so, 
for example, in order to put data in from an external database, or, to 
mention source ids of an external database, the external database must 
be known by gus.   the two tables that hold this are: 
SRes.ExternalDatabase and SRes.ExternalDatabaseRelease.  The former 
describes the DB, the latter the particular release of the DB, and it 
points back to the former.   The GBParser is asking you for a primary 
key in the ExternalDatabaseRelease table so that all the data you load 
will be associated with it.

in the case of GenBank, we at cbil only store one version of it, which 
we update periodically.  so, for it, we set the 'version' attribute to 
"continuous."   for other DBs, we store multiple copies.  in that case 
we use a real version number, and create a new ExternalDatabaseRelease 
row each time we load a new one in.

one of the known weaknesses of the current GUS install process is that 
we don't provide a bunch of standard databases as part of the data that 
we load to get you off the ground.   but, paul mooney has been handing 
out an xml file which you can load with the UpdateGusFromXML plugin.   
his mail is pj...@sa...

that file only works for databases that you will only maintain one 
release of.   if you want to load multiple versions of a db (eg, pfam), 
you will need to add new rows.

>3) --algoinvo=s: What is this? (I looked at the docs but they talk about some invocation id. Is this to change the algorithm to be invoked?)
>
>  
>
i see that michael answered this

>Any help will be really appreciated
>
>
>thanks
>--Jinal
>
>
>
>
>
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