[Biojava-dev] retrieving species (common name)

[Hubert Prielinger]

hi,
No, I'm not using BioSQL, it is an usual mySQL database and I have only 
the genbank accession id available. I want to get the taxonomy with the 
accession id, if that is possible.

regards
Hubert


Richard Holland wrote:
> I'm assuming your sequences and taxonomy data are stored in BioSQL. In
> which case, it's fairly straightforward to get this information out
> without having to drag all the features and annotations out as well, by
> using BioEntry instead of RichSequence to query the database. Code like
> this should work (hasn't been checked or anything, but it gives you an
> idea as to how things should go):
>
> 	// connect to BioSQL and establish a Hibernate Session
> 	Session sess = ...;
>
> 	// set up BioJavaX to use the session
> 	RichObjectFactory.connectToBioSQL(sess);
>
> 	// instantiate the class that gets BioEntries from BioSQL.
> 	// use BioSQLRichSequenceDB instead if you want features and
> 	// annotations included.
> 	BioEntryDB db = new BioSQLBioEntryDB(sess);
>
> 	// get BioEntry for accession (accession must be the
> 	// primary accession of the sequence, as found in the
> 	// 'name' column in the 'bioentry' table in the database).
> 	BioEntry be = db.getBioEntry("YPOL_IBDVS");
>
> 	// get BioEntry's taxon object
> 	NCBITaxon tax = be.getTaxon();
>
> 	// print the names. Each name belongs to a name class.
> 	for (Iterator i = tax.getNameClasses().iterator(); 
> 		i.hasNext(); 
> 	) {
> 		String nameClass = (String)i.next();
> 		for (Iterator k = tax.getNames(nameClass).iterator(); 
> 			k.hasNext(); 
> 		) {
> 			String name = (String)k.next();
> 			System.out.println(nameClass+" : "+name);
> 		}
> 	}
> 	
>
> If your sequences and taxonomy data are not stored in BioSQL, then the
> only way to do this is to parse the taxonomy data on startup, parse the
> sequences on startup into a simple in-memory system such as
> HashRichSequenceDB, then use the methods on the RichSequenceDB interface
> to obtain sequences by accession before continuing as per the example
> above.
>
> cheers,
> Richard
>
>
> On Fri, 2006-06-09 at 14:51 -0600, Hubert Prielinger wrote:
>   
>> hi,
>> sorry for replying that late,
>> I have XML blast outputs, which you can retrieve information like 
>> accession id, protein name, length of sequnence aso....
>> but there is no possibility to retrieve the taxonomy (especially the 
>> scientific name or common name)
>> I need the common and scientific name from each blast hit. I have found 
>> in biojava-live/src/org/biojava/bibliography/taxa  a few code examples 
>> that could suit my
>> task (e.g: simpleTaxon.java)
>>
>> eg: I have the accession id: YPOL_IBDVS
>> and I want to get the taxonomy of that protein, not neccessarily the 
>> entire taxonomy but mentioned above scientific and common name.
>> and I don't know exactly how to get the taxonomy, it seems that there is 
>> no directly way from the accession id, but over the taxon id, but I 
>> don't know how to get that either.....
>> it must be possible to map the accession id to the taxon id and then 
>> request with the taxon id the taxonomy, if I get it right.....
>>
>> thanks in advance
>> regards
>> Hubert
>>
>>
>> Richard Holland wrote:
>>     
>>> I'm not sure what you're asking for here. Could you explain in a little
>>> more detail? Maybe write some example program code that assumes BioJava
>>> works the way you'd like it to work in this situation, making up the
>>> names of classes/methods that you might call in BioJava but don't yet
>>> exist, then we can help you fill in the gaps. 
>>>
>>> cheers,
>>> Richard
>>>
>>> On Mon, 2006-06-05 at 16:49 -0600, Hubert Prielinger wrote:
>>>   
>>>       
>>>> hi,
>>>> Is it possible with biojava to retrieve the species not the entire 
>>>> taxonomy, only the common name if I only have the accession id or the 
>>>> name of the protein and if yes
>>>> how to start.....
>>>> In my case:
>>>> I would retrieve the accession id from my local database then assign as 
>>>> parameter to the program, retrieve common name and write the common name 
>>>> back into the database....
>>>> the thing I want to know is the retrieving possible with biojava?
>>>>
>>>> thanks for help
>>>>
>>>> Hubert
>>>> _______________________________________________
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>>>> biojava-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>>     
>>>>