[BioRuby] Batch Entrez search

[John O. Woods]

Unfortunately, many Flybase IDs seem to be missing from BioMart, which leads
me to think they'd also be absent from Ensembl.

On Mon, Aug 24, 2009 at 12:36 AM, Marc Hoeppner
<marc.hoeppner at molbio.su.se>wrote:

> Hi,
>
> I suppose for FlyBase genes you could also use the ruby Ensembl API.
>
> Something like:
>
> require 'ensembl'
>
>
> Ensembl::Core::DBConnection('drosophila_melanogaster','55)
>
> IO.foreach('my_infile') do |flybase_id|
>
>   gene = Ensembl::Core::Gene.find_by_stable_id(flybase_id)
>     gene.all_xrefs.each do |xref|
>           puts xref
>     end
>
> end
>
> Well, you get the idea. The methods are well documented in the
> corresponding API, but when in doubt I can offer some help, too.
>
> P.S.: To make it real easy you could also use the BioMart on
> www.ensembl.org - unless you need this to be a script.
>
> Cheers,
>
> Marc
>
>> 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)
>>
>>
>
> --
>
> Marc P. Hoeppner
> PhD student
> Department of Molecular Biology and Functional Genomics
> Stockholm University, 10691 Stockholm, Sweden
>
> marc.hoeppner at molbio.su.se
> Tel: +46 (0)8 - 164195
>
>