[BioRuby] Batch Entrez search

[Tomoaki NISHIYAMA]

Hi,

> Is there a way to batch search with BioRuby for a whole bunch of  
> Flybase
> IDs?


According to
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpgene&part=genefaq
the data for entrez gene are available in
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

If you need really a lot, perhaps its better to download that file  
(about 93 Mbytes).
(It contains data for other organisms, which is not necessary, but  
does not take forever)
The format seems simple enough that you can easily get the gene ID  
for a flybase ID.

#Format: tax_id GeneID Symbol LocusTag Synonyms dbXrefs chromosome  
map_location description type_of_gene  
Symbol_from_nomenclature_authority Full_name_from_nomenclatur
e_authority Nomenclature_status Other_designations Modification_date  
(tab is used as a separator, pound sign - start of a comment)

-- 
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan