[BiO BB] API for gene ontology retrieval?

[Chris Mungall]

You can download the GO MySQL database and access it using the go-db- 
perl API. This assumes you already have identifiers for your best  
hits, and those identifiers have annotations associated with them. At  
this time the API does no perform any kind of enrichment analysis; if  
you want to do this sort of thing have a look at some of the tools on  
the GO website.

There is no web service programmatic access for the database right  
now - you have to download it and access it that way. We'll hopefully  
have some kind of web service available soon, perhaps a SPARQL endpoint.

Details for the API can be found here:
http://www.godatabase.org/dev

On Nov 7, 2006, at 5:43 PM, Rob C wrote:

> If performance is not a consideration, you may try irobotsoft from  
> http://irobotsoft.com.
> It has a visual interface for programming web robots, and also has  
> an ActiveX interface
> for programmers.
>
> They have an example 'blastx.irb' for the blast search automation.
>
> Yours,
> rob
> On 11/7/06, Ahmed Moustafa <ahmed at pobox.com> wrote: Hi All,
> Is there some API or an automated method to retrieve the annotation
> (gene ontology?) of a set of sequences?
> I believe BLAST is necessary but after BLASTing the sequences, how  
> can I
> get the annotations (e.g. cellular component, pathway, biological
> function...) of (for example) the best hit for each sequence?
> Your help will be appreciated so much!
> Thanks in advance,
> Ahmed
>
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