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Hello and Happy New Year<br>
<br>
I have some quick questions about the variation schema. <br>
<br>
1. Allele table<br>
<p class="MsoNormal">When considering population frequency data for
an allele, how do you know which source it is from.<br>
For example, imagine a SNP with alleles T/C that is described in
say, dbSNP and HGMD. The source id for the variation on the
variation table might be dbSNP and the variation would have a
variation_synonym entry for HGMD. Lets say both dbSNP and HGMD
have population frequency data for the variation which might look
something like this.<br>
</p>
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<td style="width: 88.55pt; border: 1pt solid windowtext;
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<p class="MsoNormal">Allele id</p>
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<p class="MsoNormal">Variation id</p>
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<p class="MsoNormal">Allele</p>
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<p class="MsoNormal">Frequency</p>
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<p class="MsoNormal">SampleID</p>
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<p class="MsoNormal">1</p>
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<p class="MsoNormal">1</p>
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<p class="MsoNormal">T</p>
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<p class="MsoNormal">1</p>
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<p class="MsoNormal">14</p>
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<p class="MsoNormal">2</p>
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<p class="MsoNormal">1</p>
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<p class="MsoNormal">C</p>
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<p class="MsoNormal">0</p>
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<p class="MsoNormal">14</p>
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<p class="MsoNormal">3</p>
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<p class="MsoNormal">1</p>
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<p class="MsoNormal">T</p>
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<p class="MsoNormal">0.5</p>
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<p class="MsoNormal">15</p>
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<p class="MsoNormal">4</p>
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<p class="MsoNormal">1</p>
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<p class="MsoNormal">C</p>
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<p class="MsoNormal">0.5</p>
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<p class="MsoNormal">15</p>
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<p class="MsoNormal"> </p>
In this case the dbSNP data is for population 14 and the HGMD is for
population 15 but how would you know from looking?<br>
A sample isn't linked to the source that 'created' it so you can't
tell from the sample.<br>
<br>
Also, what is the subsnp_id in the allele table?<br>
<br>
<br>
2. What is subsnp_handle table?<br>
<br>
3 Population genotype<br>
What is the subnp_id field (might be answered by the previous
question)?<br>
Am i correct in saying this table doesn't provide the source of the
data (might also be answered by a previous question)?<br>
<br>
4 Variation set<br>
What is the source of a variation set? I believe variation sets are
defined by ensembl so i presume the source is implicitly ensembl?<br>
<br>
<br>
I've made quite a detailed document about the variation schema which
i think might help other people like me learning the schema from
scratch. I'm more than happy to make it available if there is a
mechanism to do so.<br>
<br>
Thanks a lot<br>
<br>
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