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-------- Original Message --------
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<th valign="BASELINE" align="RIGHT" nowrap="nowrap">Subject: </th>
<td>Re: [ensembl-dev] Retrieving OMIM gene information</td>
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<th valign="BASELINE" align="RIGHT" nowrap="nowrap">Date: </th>
<td>Mon, 18 Apr 2011 14:54:51 +0100</td>
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<th valign="BASELINE" align="RIGHT" nowrap="nowrap">From: </th>
<td>Andrea Edwards <a class="moz-txt-link-rfc2396E" href="mailto:edwardsa@cs.man.ac.uk"><edwardsa@cs.man.ac.uk></a></td>
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<th valign="BASELINE" align="RIGHT" nowrap="nowrap">To: </th>
<td>Duarte Molha <a class="moz-txt-link-rfc2396E" href="mailto:duartemolha@gmail.com"><duartemolha@gmail.com></a></td>
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Hi<br>
<br>
Please find below some information i was given from ensembl
regarding this matter:<br>
<br>
<br>
<div><br>
</div>
<div>The data we import from OMIM are annotations of phenotypes
associated with dbSNP variations and as such, they are stored in
the variation_annotation table <br>
<br>
</div>
<div>There is some support in the API for working with these, you
may want to take a look at the VariationAnnotation and related
modules.</div>
<div><br>
</div>
<div>As you have noticed, there is also a variation set for
variations with OMIM phenotype annotations (this variation set is
a subset of the 'Phenotype-associated variations' set).<br>
</div>
<br>
<br>
<br>
2011/2/17 Andrea Edwards <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:edwardsa@cs.man.ac.uk">edwardsa@cs.man.ac.uk</a>></span><br>
hello<br>
<br>
I am trying to find whether the human SNPs (60,000) i have are
listed in OMIM. I believe most SNPs in ensembl have a primary source
of dbSNP. None of the human variations have a source id of 15 (OMIM)
There is a table variation_synonym to hold data about multiple
sources for a snp but I can't find any entries in this table which
have a source_id = 15 either. What am i doing wrong? There exists a
variation_set called OMIM which has 11509 SNPs and I investigated
some of these variations at random and I don't know how you have
linked them to the OMIM variation set<br>
<br>
I have seen there are methods get_all_synonyms and get
_all_synonym_sources on the perl api for a variation. I presume i
could call get_all_synonyms('OMIM') but I don't see how that can
work when no variation synonyms have a source of 15/OMIM<br>
<br>
Out of general curiosity, will the following 2 approaches give the
same results: getting the OMIM variation set and seeing whether each
of my 60,000 snps is in that or getting the OMIM variation_synonyms
for the 60,000 snps and seeing which return an actual result? I'm
presuming the second option will be far faster.<br>
<br>
thanks a lot<br>
<br>
On 18/04/11 09:33, Duarte Molha wrote:
<blockquote
cite="mid:BANLkTinzdo7voiMqLzoRjrLb-e1A=aOOOA@mail.gmail.com"
type="cite">
<p class="MsoNormal">Dear all</p>
<p class="MsoNormal">I am looking to retrieve the information of a
gene is on OMIM database using the API.</p>
<p class="MsoNormal">I’ve been looking though the api
documentation and have not found what I was looking for.</p>
<p class="MsoNormal">I apologise if it is really obvious.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Could you point me in the right direction?</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"><span style="font-size: 10pt; font-family:
"Arial","sans-serif";"> Duarte Molha</span></p>
<p class="MsoNormal"><font class="Apple-style-span" face="Arial,
sans-serif"><br>
</font></p>
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