<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri",sans-serif;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am making the following call (To localhost though not Ensembl)
<span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#505050;background:white">
<a href="%20http:/grch37.rest.ensembl.org%20/variant_recoder/human/13:g.32893310A%3eG?content-type=application/json&fields=hgvsg,id"> http://grch37.rest.ensembl.org /variant_recoder/human/13:g.32893310A>G?content-type=application/json&fields=hgvsg,id</a> to
a local ensemble setup. But I don’t get an ID back in the response. I loaded the ensembl_stable_ids_100 database but its was the one I found here
<a href="ftp://ftp.ensembl.org/pub/release-100/mysql/">ftp://ftp.ensembl.org/pub/release-100/mysql/</a>.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#505050;background:white"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif;color:#505050;background:white">Here is what I get back using my local Ensembl REST and Ensembl DB . If I change to your DB it gives the ID back. Any idea what I am going
wrong? Or how this should be configured differently? I am making my changes in the ensembl_rest.conf file<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:13.5pt;background:#FFFFFE"><span style="font-size:9.0pt;font-family:Consolas;color:black">[<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:13.5pt;background:#FFFFFE"><span style="font-size:9.0pt;font-family:Consolas;color:black"> {<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:13.5pt;background:#FFFFFE"><span style="font-size:9.0pt;font-family:Consolas;color:black"> </span><span style="font-size:9.0pt;font-family:Consolas;color:#A31515">"hgvsg"</span><span style="font-size:9.0pt;font-family:Consolas;color:black">: [<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:13.5pt;background:#FFFFFE"><span style="font-size:9.0pt;font-family:Consolas;color:black"> </span><span style="font-size:9.0pt;font-family:Consolas;color:#A31515">"NC_000013.10:g.32893310A>G"</span><span style="font-size:9.0pt;font-family:Consolas;color:black">,<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:13.5pt;background:#FFFFFE"><span style="font-size:9.0pt;font-family:Consolas;color:black"> </span><span style="font-size:9.0pt;font-family:Consolas;color:#A31515">"LRG_293:g.8694A>G"</span><span style="font-size:9.0pt;font-family:Consolas;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:13.5pt;background:#FFFFFE"><span style="font-size:9.0pt;font-family:Consolas;color:black"> ],<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:13.5pt;background:#FFFFFE"><span style="font-size:9.0pt;font-family:Consolas;color:black"> </span><span style="font-size:9.0pt;font-family:Consolas;color:#A31515">"input"</span><span style="font-size:9.0pt;font-family:Consolas;color:black">: </span><span style="font-size:9.0pt;font-family:Consolas;color:#0451A5">"13:g.32893310A>G"</span><span style="font-size:9.0pt;font-family:Consolas;color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:13.5pt;background:#FFFFFE"><span style="font-size:9.0pt;font-family:Consolas;color:black"> }<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:13.5pt;background:#FFFFFE"><span style="font-size:9.0pt;font-family:Consolas;color:black">]<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I do see that pointing to the ensemble DB gives this when starting up the REST server
<o:p></o:p></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from database 'homo_sapiens_core_100_37'<o:p></o:p></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_100_37'<o:p></o:p></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_100_37'<o:p></o:p></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_100_37'<o:p></o:p></p>
<p class="MsoNormal">homo_sapiens_variation_100_37 loaded<o:p></o:p></p>
<p class="MsoNormal">homo_sapiens_funcgen_100_37 loaded<o:p></o:p></p>
<p class="MsoNormal">ensembl_compara_100 loaded<o:p></o:p></p>
<p class="MsoNormal">No ancestral database found<o:p></o:p></p>
<p class="MsoNormal">ensembl_ontology_100 loaded<o:p></o:p></p>
<p class="MsoNormal">No taxonomy database found<o:p></o:p></p>
<p class="MsoNormal">No ensembl_metadata database found<o:p></o:p></p>
<p class="MsoNormal">No production database or adaptor found<o:p></o:p></p>
<p class="MsoNormal">ensembl_stable_ids_100 loaded<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">But it only finds the homo_sapiens_core DB when I point to my local DB (I definitely have the variation DB loaded )<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Will only load v100 databases<o:p></o:p></p>
<p class="MsoNormal">Species 'homo_sapiens' loaded from database 'homo_sapiens_core_100_37'<o:p></o:p></p>
<p class="MsoNormal">No variation databases found<o:p></o:p></p>
<p class="MsoNormal">No funcgen databases found<o:p></o:p></p>
<p class="MsoNormal">No Compara databases found<o:p></o:p></p>
<p class="MsoNormal">No ancestral database found<o:p></o:p></p>
<p class="MsoNormal">No ontology database found<o:p></o:p></p>
<p class="MsoNormal">No taxonomy database found<o:p></o:p></p>
<p class="MsoNormal">No ensembl_metadata database found<o:p></o:p></p>
<p class="MsoNormal">No production database or adaptor found<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="mso-line-height-alt:12.05pt;text-autospace:none"><b><span style="font-size:14.0pt;color:#004A97">Sage Hornung</span></b><span style="font-size:14.0pt;color:#004A97"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:7.0pt;line-height:12.05pt;text-autospace:none">
<i><span style="font-size:12.0pt;color:#004A97">Software Engineer </span></i><span style="font-size:12.0pt;color:#004A97"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.05pt;text-autospace:none"><b><span style="color:#424242">NeoGenomics Laboratories, Inc.</span></b><span style="color:#424242"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.05pt;text-autospace:none"><span style="color:#424242">2131 Faraday Avenue, Carlsbad, CA 92008<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.05pt;text-autospace:none"><b><span style="color:#424242">Phone:
</span></b><span style="color:#424242">760.516.5114<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.05pt;text-autospace:none"><b><span style="color:#424242">Cell:
</span></b><span style="color:#424242">760.755.3930<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.05pt;text-autospace:none"><a href="mailto:sage.hornung@neogenomics.com">sage.hornung@neogenomics.com</a><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><a href="http://neogenomics.com/"><span style="color:#004A97">neogenomics.com</span></a><span style="color:#004A97"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><a href="http://neogenomics.com/"><span style="color:#5B9BD5;text-decoration:none"><img border="0" width="120" height="50" style="width:1.25in;height:.5208in" id="Picture_x0020_1" src="cid:image001.png@01D6B1C0.AB03F9D0" alt="cid:image001.png@01D27B05.09A580E0"></span></a><span style="color:#5B9BD5"><o:p></o:p></span></p>
<p class="MsoNormal"><a href="https://www.linkedin.com/company/neogenomics-laboratories/"><span style="color:#5B9BD5;text-decoration:none"><img border="0" width="30" height="30" style="width:.3125in;height:.3125in" id="Picture_x0020_2" src="cid:image002.png@01D6B1C0.AB03F9D0" alt="cid:image002.png@01D2789A.338CAE00"></span></a><span style="color:#5B9BD5">
</span><a href="https://twitter.com/NeoGenomics"><span style="color:#5B9BD5;text-decoration:none"><img border="0" width="30" height="30" style="width:.3125in;height:.3125in" id="Picture_x0020_3" src="cid:image003.png@01D6B1C0.AB03F9D0" alt="cid:image003.png@01D2789A.338CAE00"></span></a><span style="color:#5B9BD5"> </span><a href="https://www.youtube.com/channel/UCBa0vLyn1ZO7tW-RyJOrxPA"><span style="color:#5B9BD5;text-decoration:none"><img border="0" width="30" height="30" style="width:.3125in;height:.3125in" id="Picture_x0020_4" src="cid:image004.png@01D6B1C0.AB03F9D0" alt="cid:image004.png@01D2789A.338CAE00"></span></a><span style="color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
This communication and its attachments contain confidential information and is intended only for the named addressee. If you are not the named addressee you should not disseminate, distribute or copy this communication. Please notify the sender immediately
if you have received this communication by mistake and delete or destroy this communication. Communications cannot be guaranteed to be secured or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain
viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this communication which arise as a result of transmission. If verification is required please request a hard-copy version. NeoGenomics Laboratories, 12701
Commonwealth Dr, Fort Myers, FL 33913, http://www.neogenomics.com (2020)
</body>
</html>