[BiO BB] API for gene ontology retrieval?

Chris Mungall cjm at fruitfly.org
Thu Nov 16 18:51:10 EST 2006

On Nov 10, 2006, at 4:28 PM, Ahmed Moustafa wrote:

> Thank you all so much for your replies!!!
> I think Chri's approach, to download the database and deal with it,  
> is the way to go.
> Do you know whether the GO database holds beyond the models organisms?


> Or would I have to restrict the BLAST search to a model organism to  
> be able to retrieve the gene ontology later from the GO database  
> for the hit?

I don't think so. But not every hit in your blast would correspond to  
something annotated with GO; and even if it did you probably have to  
deal with ID mapping somewhere.

> BTW, is there a plan to make the GO database remotely accessible  
> (e.g. Ensembl core database)?

Do you mean permit mysql access remotely, or provide some kind of  
REST-based API?

When I looked into the former, there appeared to be a lack of good  
ways to throttle potential killer queries. For the latter we have  
nothing as yet, but should have something soon.

> Once again, thank you so much!
> Ahmed
> On 11/10/2006 12:22 AM, Chris Mungall wrote:
>> 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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