[Biojava-l] BioSQL

[Yasumasa Shigemoto]

Hi,

> Each BioSQL database contains multiple namespaces (called
> `biodatabases' in BioSQL terminology).  The SeqDumper example
> dumps all the sequences in a given biodatabase.
>
> If you've newly set up a PostgreSQL database, it won't contain any
> biodatabases.  You can easily load some sequences using the
> UploadFlat command:
>
>    java -Djdbc.drivers=... biosql.UploadFlat <url> <user> <passwd> mybiodatabase fasta some_sequence_file.fa
>
> This creates a new biodatabase and populates  it with sequences.
> You could then dump these out again using the SeqDumper command
> with "mybiodatabase" as the last argument.

I understood the 'biodatabases' and made it to execute the UploadFlat
and SeqDumper.

Thanks