Dear all, First and foremost, a Happy 2009 to everyone :)
I am a bioinformatics student from the National University of Singapore, working on a study on how to improve the current nomenclature standards for human SNPs. I hope to gather some useful feedback on the current problems bioinformaticians face regarding the current SNP nomenclature (What are the shortcomings of dbSNP rs numbers?). Currently, publications and articles cite dbSNP rs numbers (rs#) to refer to particular SNPs. To the best of my knowledge, I understand that rs# are volatile (i.e they could be merged or deleted during every quarter-yearly revision by NCBI). The missing or merged rs# could lead to confusion as we do not expect publications to be automatically updated with the latest dbSNP revision. Furthermore, from a database perspective, rs# are like indices for SNPs, and the idea of a volatile index creeps me out. Also, using rs numbers alone are not very intuitive in contrast with MGI's (e.g /Park2^rs6200232-G / The /Park2 /rs6200232 SNP allele with the G variant. http://www.informatics.jax.org/mgihome/nomen/gene.shtml ) With the reasons above (among other things), perhaps we may find a better SNP nomenclature than rs# for use in academia. I welcome any of your valuable feedback and suggestions! Yours Sincerely, Setoh Bioinformatics student (NUS) _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
