Hello<br><br><div class="gmail_quote">On 10 January 2011 18:26, Andrea Edwards <span dir="ltr"><<a href="mailto:edwardsa@cs.man.ac.uk">edwardsa@cs.man.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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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>
<p class="MsoNormal"> </p>
<table style="border-collapse:collapse;border:medium none" border="1" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td style="width:88.55pt;border:1pt solid windowtext;padding:0cm 5.4pt" valign="top" width="118">
<p class="MsoNormal">Allele id</p>
</td>
<td style="width:92.9pt;border-width:1pt 1pt 1pt medium;border-style:solid solid solid none;border-color:windowtext windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="124">
<p class="MsoNormal">Variation id</p>
</td>
<td style="width:82.85pt;border-width:1pt 1pt 1pt medium;border-style:solid solid solid none;border-color:windowtext windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="110">
<p class="MsoNormal">Allele</p>
</td>
<td style="width:80.9pt;border-width:1pt 1pt 1pt medium;border-style:solid solid solid none;border-color:windowtext windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="108">
<p class="MsoNormal">Frequency</p>
</td>
<td style="width:80.9pt;border-width:1pt 1pt 1pt medium;border-style:solid solid solid none;border-color:windowtext windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="108">
<p class="MsoNormal">SampleID</p>
</td>
</tr>
<tr>
<td style="width:88.55pt;border-width:medium 1pt 1pt;border-style:none solid solid;border-color:-moz-use-text-color windowtext windowtext;padding:0cm 5.4pt" valign="top" width="118">
<p class="MsoNormal">1</p>
</td>
<td style="width:92.9pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="124">
<p class="MsoNormal">1</p>
</td>
<td style="width:82.85pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="110">
<p class="MsoNormal">T</p>
</td>
<td style="width:80.9pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="108">
<p class="MsoNormal">1</p>
</td>
<td style="width:80.9pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="108">
<p class="MsoNormal">14</p>
</td>
</tr>
<tr>
<td style="width:88.55pt;border-width:medium 1pt 1pt;border-style:none solid solid;border-color:-moz-use-text-color windowtext windowtext;padding:0cm 5.4pt" valign="top" width="118">
<p class="MsoNormal">2</p>
</td>
<td style="width:92.9pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="124">
<p class="MsoNormal">1</p>
</td>
<td style="width:82.85pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="110">
<p class="MsoNormal">C</p>
</td>
<td style="width:80.9pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="108">
<p class="MsoNormal">0</p>
</td>
<td style="width:80.9pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="108">
<p class="MsoNormal">14</p>
</td>
</tr>
<tr>
<td style="width:88.55pt;border-width:medium 1pt 1pt;border-style:none solid solid;border-color:-moz-use-text-color windowtext windowtext;padding:0cm 5.4pt" valign="top" width="118">
<p class="MsoNormal">3</p>
</td>
<td style="width:92.9pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="124">
<p class="MsoNormal">1</p>
</td>
<td style="width:82.85pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="110">
<p class="MsoNormal">T</p>
</td>
<td style="width:80.9pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="108">
<p class="MsoNormal">0.5</p>
</td>
<td style="width:80.9pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="108">
<p class="MsoNormal">15</p>
</td>
</tr>
<tr>
<td style="width:88.55pt;border-width:medium 1pt 1pt;border-style:none solid solid;border-color:-moz-use-text-color windowtext windowtext;padding:0cm 5.4pt" valign="top" width="118">
<p class="MsoNormal">4</p>
</td>
<td style="width:92.9pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="124">
<p class="MsoNormal">1</p>
</td>
<td style="width:82.85pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="110">
<p class="MsoNormal">C</p>
</td>
<td style="width:80.9pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="108">
<p class="MsoNormal">0.5</p>
</td>
<td style="width:80.9pt;border-width:medium 1pt 1pt medium;border-style:none solid solid none;border-color:-moz-use-text-color windowtext windowtext -moz-use-text-color;padding:0cm 5.4pt" valign="top" width="108">
<p class="MsoNormal">15</p>
</td>
</tr>
</tbody>
</table>
<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></div></blockquote><div><br></div><div>Correct, samples do not have a source. This is not usually a problem, since the vast majority of our frequency data comes from dbSNP. The only exceptions to this in human are the COSMIC data, the samples for which are only associated with variations with source COSMIC.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff">
<br>
Also, what is the subsnp_id in the allele table?<br>
<br></div></blockquote><div><br></div><div>This represents a submission of data on a variant to dbSNP. When people submit data to dbSNP, each variant they submit is assigned a subsnp_id (ssID). Since several groups or individuals may submit the same variant to dbSNP, each of the ssIDs corresponding to the same variant is merged together to form one rsID. ssIDs are normally shown as e.g ss12345, but we only store the numerical part of the identifier.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff">
<br>
2. What is subsnp_handle table?<br></div></blockquote><div><br></div><div>Each submitter as described above is assigned a handle, or name, by dbSNP. For example, when Ensembl submits data to dbSNP, it gets assigned the handle of ENSEMBL. This table keeps track of which ssIDs were submitted by which submitters, thus allowing our users to distinguish between what they may consider to be different standards of data.</div>
<div> </div><div>For a working example, take a look at this page:</div><div><br></div><div><a href="http://www.ensembl.org/Homo_sapiens/Variation/Population?r=9:22125003-22126003;v=rs1333049;vdb=variation;vf=18123086">http://www.ensembl.org/Homo_sapiens/Variation/Population?r=9:22125003-22126003;v=rs1333049;vdb=variation;vf=18123086</a></div>
<div><br></div><div>From here you can click through to the dbSNP website from both the subsnp ID and the submitter handle to see more information.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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<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></div></blockquote><div><br></div><div>Same as above.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff">
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></div></blockquote><div><br></div><div>All variation sets are loaded by Ensembl, so yes you can consider the source to be Ensembl.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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<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></div></blockquote><div><br></div><div>If you email it to us we can see if we can integrate your document into our current documentation on the website.</div><div><br></div><div>Cheers</div><div>
<br></div><div>Will</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div text="#000000" bgcolor="#ffffff">
<br>
Thanks a lot<br>
<br>
</div>
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<br></blockquote></div><br>