[Biojava-l] Issue with SimpleNCBITaxon class

[Richard Holland]

I'm sorry but I don't understand your example. Could you provide a real example of correct values for each column from a sample taxon entry in NCBI, plus an example of what BioJava is doing wrong? (i.e. give a sample record to use as reference, then point out the correct value of parent_taxon_id, and point out what value BioJava is using instead).

thanks,
Richard

On 11 Apr 2010, at 20:16, Deepak Sheoran wrote:

> Hi,
> 
> Their is very fundamental issue in SimpleNCBITaxon class becuase of which it is producing wrong taxonomy hierarchy. I am explaing what I have found let me what you guys think of it, and me suggest how to fix it.
> 
> 1) Columns in taxon table are (taxon_id, ncbi_taxon_id, parent_taxon_id, nodeRank, geneticCode, mitoGeneticCode, leftValue, rightValue)
> 2) In the class SimpleNCBITaxon we are thinking "parent_taxon_id" to have parent ncbi_taxon_id for current ncbi_taxon_id value, but its not true. The value which "parent_taxon_id" have is "taxon_id" which have parent_ncbi_taxon_id of current ncbi_taxon_id.
> 
> <property name="NCBITaxID" column="ncbi_taxon_id" node="@NCBITaxId"/>
> <property name="nodeRank" column="node_rank"/>
> <property name="geneticCode" column="genetic_code"/>
> <property name="mitoGeneticCode" column="mito_genetic_code"/>
> <property name="leftValue" column="left_value"/>
> <property name="rightValue" column="right_value"/>
> <property name="parentNCBITaxID" column="parent_taxon_id"/>      ----- its not correct column parent_taxon_id stores the taxon_id which have parent_ncbi_taxon_id for current entry
> 
> Thanks
> Deepak Sheoran
> 
> 

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/