I am glad you have posed the question about SNP metadata.  I would expect
Herve to provide more information later, but here are a few comments

1) an updated locations package is available
http://www.bioconductor.org/packages/2.4/data/annotation/html/SNPlocs.Hsapiens.dbSNP.20080617.html

2) in the SNPlocs* package(s) an inst/tools subdirectory includes the
parsing
and modeling tools for constructing the rda files -- i see a grep -v
relevant to
the Celera entries in there, and you would probably modify that

3) SNP metadata volume is a big concern for me.  I would like to know of
common use cases so that we can examine performance characteristics of
different solutions.
Some exploration of netCDF, SQLite and .rda has been conducted and for
GGtools
I decided derive an environment of tables of locations from SNPlocs* to
facilitate plotting on genomic coordinates and export to browser tracks.
ANother issue that
has not been resolved AFAIK is the mapping between affy SNP identifiers
propagated
by crlmm and the rs-numbers used by dbSNP.

until we know of a significant class of location use cases i do not see how
to make
decisions about additional tools or representations to be developed.  for
detailed
query resolution SQLite seems like a good technology, but my use case
involves
full chromosome or genome location vectors and .rda on a relatively powerful
machine seems adequate.

4) very detailed real-time queries on SNP metadata can be dealt with using
biomaRt

On Thu, Mar 5, 2009 at 8:13 AM, Paul Shannon <pshannon@systemsbiology.org>wrote:

> 'How to forge a BSgenome data package' answered my first question.
>
> Is there a comparable write up for building a SNPlocs data package?
>
> All I have found  is Herve's comments to Praveen on Feb 12 2009:
>
>  The information in SNPlocs.Hsapiens.dbSNP.20071016 was retrieved
>> from dbSNP, from this location to be precise:
>>
>>   ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ASN1_flat/
>>
>
> That flat file has snp information from other assemblies -- celera and
> HuRef, and that is some of the information I want.
> (See example below for one snp from ORM1 on chromosome 9.)
>
> If I want this level of detail, should I parse the original file myself?
> Are the parsing code and instructions for building a SNPlocs available?
>
> Thanks,
>
>  - Paul
>
>
>   rs1766074|human|9606|snp|genotype=NO|submitterlink=YES|updated 2004-10-04
> 13:51
>   ss2622917|SC_JCM|AL356796.4_74652|orient=+|ss_pick=YES
>   SNP|alleles='C/T'|het=?|se(het)=?
>   VAL|validated=NO|min_prob=?|max_prob=?|notwithdrawn
>
>
> CTG|assembly=Celera|chr=9|chr-pos=87735017|NW_924573.1|ctg-start=1222848|ctg-end=1222848|loctype=2|orient=-
>
> LOC|ORM1|locus_id=5004|fxn-class=coding-synonymous|allele=A|frame=3|residue=E|aa_position=149|mrna_acc=NM_000607.2|prot_acc=NP_000598.2
>
> LOC|ORM1|locus_id=5004|fxn-class=reference|allele=G|frame=3|residue=E|aa_position=149|mrna_acc=NM_000607.2|prot_acc=NP_000598.2
>
>
> CTG|assembly=HuRef|chr=9|chr-pos=86692957|NW_001839236.2|ctg-start=2686784|ctg-end=2686784|loctype=2|orient=+
>
> LOC|ORM1|locus_id=5004|fxn-class=coding-synonymous|allele=A|frame=3|residue=E|aa_position=141|mrna_acc=NM_000607.2|prot_acc=NP_000598.2
>
> LOC|ORM1|locus_id=5004|fxn-class=reference|allele=G|frame=3|residue=E|aa_position=141|mrna_acc=NM_000607.2|prot_acc=NP_000598.2
>
>
> CTG|assembly=reference|chr=9|chr-pos=116127163|NT_008470.18|ctg-start=24408547|ctg-end=24408547|loctype=2|orient=-
>
> LOC|ORM1|locus_id=5004|fxn-class=coding-synonymous|allele=A|frame=3|residue=E|aa_position=149|mrna_acc=NM_000607.2|prot_acc=NP_000598.2
>
> LOC|ORM1|locus_id=5004|fxn-class=reference|allele=G|frame=3|residue=E|aa_position=149|mrna_acc=NM_000607.2|prot_acc=NP_000598.2
>
>
>
>
> On Mar 4, 2009, at 5:12 AM, Paul Shannon wrote:
>
>  Has anyone created a BSgenome object from the Ventner (HuRef), Watson, or
>> other recently completed sequencing projects?  Or SNPlocs data packages for
>> these genomes?
>>
>> If not, can you offer any advice or cautions to me as I attempt to do so
>> myself?
>>
>> Thanks -
>>
>> - Paul Shannon
>>  Institute for Systems Biology
>>  Seattle
>>
>
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