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: [email protected] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
