Retrieving large datasets from NCBI

Question

[Naresh]

Hi all, How to retrieve large datasets from NCBI for a particular species and then to connect NCBI database to our program so that we can get taxonomic ID of each species automatically without doing it manually.

for eg. Connect the NCBI database to Perl OR C#

Thanks Naresh

Answer 1

[pld]

If you plan on having very heavy access (very large queries, or many very small queries), I would just install a local copy of the NCBI taxonomy database.

Eutils asks that the query rate be no larger than 3 per second, so if you need to quickly bring up IDs for more than a few species, it probably wont work.

[Naresh]

How to install a local copy of the NCBI taxonomy database?

[Jean-Karim Heriche]

From their FTP site here.

Answer 2

[Jean-Karim Heriche]

It looks like what you're looking for is the eutils programs.

[Naresh]

Yes. exactly. I need to get taxonomic IDs of saccharomyces pombe. and need to connect to my C# program.,