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<p>Hi Beat Wolf,</p>
<p>The synonyms is not always empty. If the external source has
synonyms, then it should be available, for example look at HGNC <br>
</p>
<p><span class="b" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; font-weight: bold; color: rgb(68, 68, 68); font-family: monospace; font-size: 13px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-style: initial; text-decoration-color: initial;">{</span><span class="ell" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(68, 68, 68); font-family: monospace; font-size: 13px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-style: initial; text-decoration-color: initial;"></span><span class="blockInner" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 24px; border-left: 1px dotted rgb(187, 187, 187); margin-left: 2px; color: rgb(68, 68, 68); font-family: monospace; font-size: 13px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-style: initial; text-decoration-color: initial;"><span class="kvov objProp" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;">"<span class="k" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(0, 0, 0);">display_id</span>": <span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">BRCA2</span>"</span>,</span><span class="kvov objProp" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;">"<span class="k" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(0, 0, 0);">primary_id</span>": <span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">HGNC:1101</span>"</span>,</span><span class="kvov objProp" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;">"<span class="k" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(0, 0, 0);">version</span>": <span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">0</span>"</span>,</span><span class="kvov objProp" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;">"<span class="k" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(0, 0, 0);">description</span>": <span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">BRCA2, DNA repair associated</span>"</span>,</span><span class="kvov objProp" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;">"<span class="k" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(0, 0, 0);">dbname</span>": <span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">HGNC</span>"</span>,</span><span class="kvov objProp" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;"><span class="e" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; width: 20px; height: 18px; position: absolute; left: -2px; top: 1px; z-index: 5; background-image: url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAgAAAAICAYAAADED76LAAAAGXRFWHRTb2Z0d2FyZQBBZG9iZSBJbWFnZVJlYWR5ccllPAAAAD1JREFUeNpiYGBgOADE%2F3Hgw0DM4IRHgSsDFOzFInmMAQnY49ONzZRjDFiADT7dMLALiE8y4AGW6LoBAgwAuIkf%2F%2FB7O9sAAAAASUVORK5CYII%3D"); background-repeat: no-repeat; background-position: center center; display: block; opacity: 0.15;"></span>"<span class="k" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(0, 0, 0);">synonyms</span>": <span class="b" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; font-weight: bold;">[</span><span class="ell" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;"></span><span class="blockInner" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 24px; border-left: 1px dotted rgb(187, 187, 187); margin-left: 2px;"><span class="kvov arrElem" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;"><span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">BRCC2</span>"</span>,</span><span class="kvov arrElem" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;"><span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">FACD</span>"</span>,</span><span class="kvov arrElem" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;"><span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">FAD</span>"</span>,</span><span class="kvov arrElem" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;"><span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">FAD1</span>"</span>,</span><span class="kvov arrElem" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;"><span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">FANCD</span>"</span>,</span><span class="kvov arrElem" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;"><span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">FANCD1</span>"</span>,</span><span class="kvov arrElem" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;"><span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">XRCC11</span>"</span></span></span><span class="b" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; font-weight: bold;">]</span>,</span><span class="kvov objProp" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;">"<span class="k" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(0, 0, 0);">info_text</span>": <span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">Generated via ensembl_manual</span>"</span>,</span><span class="kvov objProp" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;">"<span class="k" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(0, 0, 0);">info_type</span>": <span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">DIRECT</span>"</span>,</span><span class="kvov objProp" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; display: block; padding-left: 20px; margin-left: -20px; position: relative;">"<span class="k" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(0, 0, 0);">db_display_name</span>": <span class="s" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; color: rgb(11, 117, 0); word-wrap: break-word;">"<span style="-webkit-font-smoothing: antialiased; white-space: pre-wrap;">HGNC Symbol</span>"</span></span></span><span class="b" style="white-space: pre-wrap; color: rgb(68, 68, 68); font-family: monospace; font-size: 13px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-style: initial; text-decoration-color: initial;">}</span></p>
<p><span class="b" style="white-space: pre-wrap; color: rgb(68, 68, 68); font-family: monospace; font-size: 13px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-style: initial; text-decoration-color: initial;">I am afraid that at the moment you can do it only gene by gene via the REST endpoint or via the core API.</span></p>
<span class="b" style="white-space: pre-wrap; color: rgb(68, 68, 68); font-family: monospace; font-size: 13px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-style: initial; text-decoration-color: initial;">Thanks</span><br>
<span class="b" style="white-space: pre-wrap; color: rgb(68, 68, 68); font-family: monospace; font-size: 13px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-style: initial; text-decoration-color: initial;">Prem
</span>
<p><span class="b" style="-webkit-font-smoothing: antialiased; white-space: pre-wrap; font-weight: bold; color: rgb(68, 68, 68); font-family: monospace; font-size: 13px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-style: initial; text-decoration-color: initial;">
</span></p>
<br>
<div class="moz-cite-prefix">On 22/05/2018 10:23, Wolf Beat wrote:<br>
</div>
<blockquote type="cite"
cite="mid:f5f8e64a5b20466f96cbec124ae98436@hefr.ch">
<pre wrap="">Thank you for the quick answer.
I did not know about this approach, but i have two issues with it:
1) The synonyms attribute seems to be always empty, so something seems wrong.
2) Sadly i need all synonyms for all genes for a specific species. Downloading it through that endpoint would be too slow. Thats why i initially looked at biomart, because all i need is a list of Ensembl gene id + all synonyms.
Kind regards
Beat Wolf
________________________________
From: Dev <a class="moz-txt-link-rfc2396E" href="mailto:dev-bounces@ensembl.org"><dev-bounces@ensembl.org></a> on behalf of Premanand Achuthan <a class="moz-txt-link-rfc2396E" href="mailto:prem@ebi.ac.uk"><prem@ebi.ac.uk></a>
Sent: Tuesday, May 22, 2018 11:20:09 AM
To: <a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a>
Subject: Re: [ensembl-dev] Gene Synonyms through REST or Biomart
Hi Beat Wolf,
Please have a look at the /xrefs endpoint under "Cross References" and
look for "synonyms" in the attribute list.
<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/xrefs/name/human/BRCA2?content-type=application/json">http://rest.ensembl.org/xrefs/name/human/BRCA2?content-type=application/json</a>
<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/xrefs/id/ENSG00000157764?content-type=application/json">http://rest.ensembl.org/xrefs/id/ENSG00000157764?content-type=application/json</a>
Hope it helps,
Best Regards
Prem
On 22/05/2018 10:09, Wolf Beat wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hello,
I'm looking for a complete list of all synonyms of a gene or a set of genes. I can not find a way to get this information through biomart or the REST interface. Is there a way to do it?
Kind regards
Beat Wolf
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</blockquote>
<pre wrap="">
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