<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi<div class=""><br class=""></div><div class="">Can I ask what are your database connection details are? </div><div class=""><br class=""></div><div class="">Andy</div><div class=""><br class=""><div apple-content-edited="true" class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">------------<br class="">Andrew Yates - Ensembl Support Coordinator<br class="">European Molecular Biology Laboratory<br class="">European Bioinformatics Institute<br class="">Wellcome Trust Genome Campus<br class="">Hinxton, Cambridge<br class="">CB10 1SD, United Kingdom<br class="">Tel: +44-(0)1223-492538<br class="">Fax: +44-(0)1223-494468<br class="">Skype: andrewyatz<br class=""><a href="http://www.ensembl.org/" class="">http://www.ensembl.org/</a></div>
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<br class=""><div style=""><blockquote type="cite" class=""><div class="">On 30 Jan 2015, at 12:19, Duarte Molha <<a href="mailto:Duarte.Molha@ogt.com" class="">Duarte.Molha@ogt.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Dear Developers<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I am using the perl API to fetch details about a list of genes and am trying to understand why a gene symbol is failing to query against GRCH37.<o:p class=""></o:p></div><h1 style="margin-right: 0cm; margin-left: 0cm; font-size: 24pt; font-family: 'Times New Roman', serif; margin-bottom: 12pt; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; font-weight: normal;" class="">The gene SUGCT (ENSG00000175600) is on the database:<o:p class=""></o:p></span></h1><h1 style="margin-right: 0cm; margin-left: 0cm; font-size: 24pt; font-family: 'Times New Roman', serif; margin-bottom: 12pt; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; font-weight: normal;" class=""><a href="http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000175600;r=7:40174575-40900362" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000175600;r=7:40174575-40900362</a><o:p class=""></o:p></span></h1><h1 style="margin-right: 0cm; margin-left: 0cm; font-size: 24pt; font-family: 'Times New Roman', serif; margin-bottom: 12pt; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; font-weight: normal;" class="">The correct HGNC symbol is SUGCT, however, when querying for it<o:p class=""></o:p></span></h1><h1 style="margin-right: 0cm; margin-left: 0cm; font-size: 24pt; font-family: 'Times New Roman', serif; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; font-weight: normal;" class="">Using:<o:p class=""></o:p></span></h1><h1 style="margin-right: 0cm; margin-left: 0cm; font-size: 24pt; font-family: 'Times New Roman', serif; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; font-weight: normal;" class="">my @fetched_genes = @{$gene_adaptor->fetch_all_by_display_label (“SUGCT”)};<o:p class=""></o:p></span></h1><h1 style="margin-right: 0cm; margin-left: 0cm; font-size: 24pt; font-family: 'Times New Roman', serif; margin-bottom: 12pt; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; font-weight: normal;" class="">or<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></h1><h1 style="margin-right: 0cm; margin-left: 0cm; font-size: 24pt; font-family: 'Times New Roman', serif; margin-bottom: 12pt; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; font-weight: normal;" class="">my @fetched_genes = @{ $gene_adaptor->fetch_all_by_external_name(“SUGCT”) };<o:p class=""></o:p></span></h1><h1 style="margin-right: 0cm; margin-left: 0cm; font-size: 24pt; font-family: 'Times New Roman', serif; margin-bottom: 12pt; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; font-weight: normal;" class="">The query fails…This is because the HGNC symbol recorded for this gene on your database is “C7orf10”<o:p class=""></o:p></span></h1><h1 style="margin-right: 0cm; margin-left: 0cm; font-size: 24pt; font-family: 'Times New Roman', serif; margin-bottom: 12pt; background-color: white; background-position: initial initial; background-repeat: initial initial;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; font-weight: normal;" class="">This is not the current HGNC symbol for the gene and I am struggling to understand why, if your own display lists the correct symbol for the gene, why is the underlying database not updated accordingly.<o:p class=""></o:p></span></h1><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="">Best regards,<span class="Apple-converted-space"> </span></span><span lang="EN-US" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class=""> </span><span lang="EN-US" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt; font-family: Arial, sans-serif;" class="">Duarte Molha</span><span class=""><span lang="EN-US" class=""><o:p class=""></o:p></span></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; 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