Hi. I am Belinda from PSU. The rs# may seem volatile in that in the standard downloads they may be merged or "deleted". But the records are kept and marked as merged or deleted. You can still find the record as well as the new rs# if it was merged.
Microattribution, headed by Miles Axton, is encouraging the use of the rs# or ss# in publications. (http://www.nature.com/ng/journal/v40/n1/full/ng0108-1.html and http://blogs.nature.com/ng/freeassociation/2007/11/towards_a_hermeneutics_of_quan.html) The short coming Myles found with the rs# is that it refers to the position not the allele or a specific submitter. Depending on the circumstances the ss# (submitted SNP) can be better. It credits the lab/individual who submitted the SNP and can have more allele specific information. The nomenclature for human variants has been worked on for some time, by the Human Genome Variation Society (HGVS) and Johan den Dunnen. (http://www.hgvs.org/mutnomen/) This is a more human readable nomenclature and is used by most LSDBs (Locus Specific Databases). Belinda > -------- Original Message -------- > Subject: [Genome] Suggestions for improvements on the current SNP > nomenclature > Date: Sun, 04 Jan 2009 15:09:57 +0800 > From: Situ Yi <[email protected]> > To: [email protected] > > 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 > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
