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