[Bioperl-l] linking of LL to SP

Stephen Wang stwang at ingenuity.com
Mon Mar 3 11:38:20 EST 2003


Hi all,

	I am relatively new to this and I would appreciate your help.

	I have a need to link our internal data source to LL and to SP. We already have a mapping file to LL. The problem I have is to link to SP. One approach is to use the common GenBank links in both LL and SP. For instance, our Brca1 human concept maps to LL ID of 672. LL ID of 672 has an ACCNUM of L78833., However, in SP, there are three entries linked to GenBank ID of L78833. There are P38398, P52198 and Q99536. P38398 is breast cancer type1 susceptibility protein and it is a correct mapping to our concept. However, P52198 is Rho-related GTP-binding protein RhoN (Rho7)(Rnd2) and Q99536 is Synaptic vesicle membrane protein VAT-1 homolog. Thus, using the GenBank reference alone would not always give us the correct mapping!

	I would really appreciate if anyone in the BioPerl community could give a hint on how to handle this. I am pretty sure many people have looked into this issue already.

	Thanks in advance.

-Stephen
 



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