[Biojava-l] accessing data in servers(ex. NCBI) from our java programmes

mark.schreiber at novartis.com mark.schreiber at novartis.com
Wed May 11 05:40:06 EDT 2005

Welcome to Biojava!

to get data from NCBI I reccomend using their eutils 

to read sequence text files (or the sequence text returned by NCBI) have a 
look at the tutorials about SeqIO on 

to interact with a SQL database I would reccomend getting a very recent 
version of biojava from CVS and a very recent version of BioSQL 
(http://obda.open-bio.org/) from the open-bio cvs server 
(http://cvs.open-bio.org/) the have a look at the BioSQL tutorials at the 
bottom of the Biojava in Anger page 

Keep posted for updates on the biojava / biosql interface. This is an area 
of active development.

Best of luck.

- Mark

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670

phone +65 6722 2973
fax  +65 6722 2910

Simon Moses <ks_moses at yahoo.com>
Sent by: biojava-l-bounces at portal.open-bio.org
05/11/2005 05:22 PM

        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] accessing data in servers(ex. NCBI) from our java   programmes

dear sir,
i am new to biojava. 
i want to access data from NCBI(or other Databanks) with my programme. is 
there any possibility to send a 'select query' and get data? 
how to know the format in which the data is stored? like textfile, oracle 
database, mysql etc..
if data is stored in any RDBMS what is the connection string?
if data is in textfiles how to know the path and file names? are the paths 
are fixed?
my intention is to send an sql query, get data, process it and display in 
my programme after checking few conditions.
i have seen an application which runs in client machine and accesses these 
for example, if we give our DNA in that programme and select the server 
and database, programme will search in NCBI server and give DNA sequences 
which are nealy equal.
thanks in advance
--Simon Moses

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