<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Dear Guillermo,<div><br></div><div><span style="line-height: 16.0029983520508px;">I am afraid we have renamed the "external_gene_id" attribute internal name to "external_gene_name" in release 76. Renaming the attribute in your script should resolve your problem.</span></div><div><span style="line-height: 16px;">We rarely rename attribute internal name but I am afraid we don't declare these at the moment since they don't impact the BioMart visual interface. If an important filter/attribute is remove from the interface or renamed on the interface then we always declare it.</span></div><div><span style="line-height: 16px;"><br></span></div><div><span style="line-height: 16px;">Apologies for any inconvenience cause,</span></div><div><span style="line-height: 16px;">Regards,</span></div><div><span style="line-height: 16px;">Thomas<br></span><div><div>On 24 Sep 2014, at 12:13, Guillermo Marco Puche <<a href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
<meta content="text/html; charset=windows-1252" http-equiv="Content-Type">
<div text="#000066" bgcolor="#FFFFFF">
Dear Thomas,<br>
<br>
I'm experiencing an error when querying to BioMart Ensembl 76
registry for both clean/cached.<br>
Using older Mart Registry to ensembl 75 registry archive works for
both clean/cached.<br>
<br>
my $action='clean';<br>
<blockquote>
<blockquote> my $initializer =
BioMart::Initializer->new('registryFile'=>$confFile,
'action'=>$action);<br>
my $registry = $initializer->getRegistry;<br>
<br>
my $query =
BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');<br>
<br>
$query->setDataset("hsapiens_gene_ensembl");<br>
if ( length($gene_name)==15 &&
substr($gene_name,0,4) eq "ENSG" ) {
$query->addFilter("ensembl_gene_id", @{$gene}); }<br>
else { $query->addFilter("hgnc_symbol", @{$gene}); }<br>
if ($query_type eq "gene_info"){<br>
#$query->addFilter("biotype",
["protein_coding"]);<br>
$query->addAttribute("ensembl_gene_id");<br>
$query->addAttribute("ensembl_transcript_id");<br>
$query->addAttribute("chromosome_name");<br>
<b>$query->addAttribute("external_gene_id");</b><br>
}<br>
</blockquote>
</blockquote>
Was this removed in Ensembl 76? Is there any documentation about
BioMart available queries per Ensembl release?<br>
<br>
Thank you and sorry for spam, I never had this issues when changing
Ensembl previously.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<br>
<div class="moz-cite-prefix">On 23/09/14 15:10, Guillermo Marco
Puche wrote:<br>
</div>
<blockquote cite="mid:5421714A.7050200@sistemasgenomicos.com" type="cite">
<meta content="text/html; charset=windows-1252" http-equiv="Content-Type">
Dear Thomas,<br>
<br>
Ok I didn't understand correctly, now I do.<br>
As you say biomart website registry is still showing ensembl 75.<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 23/09/14 14:01, Thomas Maurel
wrote:<br>
</div>
<blockquote cite="mid:F1A87ED1-E57D-4289-8CCD-2965E6FAAC28@ebi.ac.uk" type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Dear Guillermo,
<div><br>
</div>
<div>The <a moz-do-not-send="true" href="http://biomart.org/">biomart.org</a>
website seems to be very slow at the moment and I am afraid
the website is still displaying our release 75 marts on hg19
(GRCh37). According to the <a moz-do-not-send="true" href="http://biomart.org/">biomart.org</a> mart registry
page: <a moz-do-not-send="true" href="http://www.biomart.org/biomart/martservice?type=registry">http://www.biomart.org/biomart/martservice?type=registry</a>, port
'80' is still valid.</div>
<div>If you want to use hg38 (GRCh38), the best way would be to
point your mart XML config to the <a moz-do-not-send="true" href="http://ensembl.org/">ensembl.org</a> website in order
to access our release 76 mart databases on hg38 (GRCh38).</div>
<div>You can follow the previous instruction but just change the
mart registry URL page to get the mart release 76 registry
informations:</div>
<div><br>
</div>
<div>
<blockquote type="cite">
<div text="#000066" bgcolor="#FFFFFF">
<blockquote cite="mid:4B2EFDEF-33F9-4F59-8B37-30795F2DA7CA@ebi.ac.uk" type="cite">2) A BioMart perl script
<div>a) You first need to edit your configuration file
in "biomart-perl/conf/martURLLocation.xml" and paste
the content of the mart registry page for the </div>
</blockquote>
</div>
</blockquote>
<div text="#000066" bgcolor="#FFFFFF">
<div>Ensembl website on release 76 (hg38): <a moz-do-not-send="true" href="http://www.ensembl.org/biomart/martservice?type=registry">http://www.ensembl.org/biomart/martservice?type=registry</a></div>
</div>
<blockquote type="cite">
<div text="#000066" bgcolor="#FFFFFF">
<blockquote cite="mid:4B2EFDEF-33F9-4F59-8B37-30795F2DA7CA@ebi.ac.uk" type="cite">
<div>b) Then edit your script and make sure that "my
$confFile" variable is looking at
the martURLLocation.xml configuration file in
biomart-perl/conf</div>
<div>c) Finally, make sure to update the following line
in your script:</div>
<div><br>
</div>
<div>my $action='cached';</div>
<div>
<div><br>
</div>
<div>with:</div>
<div><br>
</div>
<div>my $action='clean';</div>
<div>
<div><br>
</div>
<div>The first run of your script on Ensembl 75
might be a bit slow as BioMart will cache some
data from the BioMart website.</div>
<div>Once you have run your script with the action
variable set to "clean", you can set the variable
to "cached" again.</div>
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
<div><br>
</div>
<div>I am afraid $action=clean is quite resource consuming but
you will only need to run your script with this setting when
you change the registry information.</div>
<div><br>
</div>
<div>Hope this helps,</div>
<div>Best regards,</div>
<div>Thomas</div>
<div>
<div>
<div>On 23 Sep 2014, at 12:43, Guillermo Marco Puche <<a moz-do-not-send="true" href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<meta content="text/html; charset=windows-1252" http-equiv="Content-Type">
<div text="#000066" bgcolor="#FFFFFF"> Dear Thomas,<br>
<br>
My BioMart perl script is using the following mart XML
config file:<br>
<br>
<pre><?xml version="1.0" encoding="UTF-8"?>
</pre>
<pre><!DOCTYPE MartRegistry>
</pre>
<pre><MartRegistry>
</pre>
<pre> <MartURLLocation
</pre>
<pre> name = "ensembl"
</pre>
<pre> displayName = "ensembl"
</pre>
<pre> host = "<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="http://www.biomart.org/">www.biomart.org</a>"
</pre>
<pre> port = "80"
</pre>
<pre> visible = "1"
</pre>
<pre> default = ""
</pre>
<pre> includeDatasets = "hsapiens_gene_ensembl"
</pre>
<pre> martUser = ""
</pre>
<pre> />
</pre>
<pre></MartRegistry>
</pre>
However, I'm getting BioMart queries from hg19 and not
hg38. Does the default port '80' still working on hg19?
how can I specify I would like to use hg38 biomart
service.<br>
<br>
On the other hand, it's always useful to know how to
query older Ensembl versions with Biomart. However using
$action=clean with conf file of ensembl 75 archive it's
leading me to massive amounts of RAM consumption in my
Perl script.<br>
<br>
Thanks.<br>
<br>
Best regards,<br>
Guillermo.<br>
<div class="moz-cite-prefix">On 19/09/14 15:48, Thomas
Maurel wrote:<br>
</div>
<blockquote cite="mid:4B2EFDEF-33F9-4F59-8B37-30795F2DA7CA@ebi.ac.uk" type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Dear Guillermo,
<div><br>
</div>
<div>If you are using:</div>
<div>1) the biomart-perl/scripts/webExample.pl script
and an xml file</div>
<div>You can change the path to the biomart website in
the following line:</div>
<blockquote style="margin: 0 0 0 40px; border: none;
padding: 0px;">
<div>my $path="<a moz-do-not-send="true" href="http://www.biomart.org/biomart/martservice?">http://www.biomart.org/biomart/martservice?</a>";</div>
</blockquote>
<div>With the path to our Ensembl release 75 archive:</div>
<blockquote style="margin: 0 0 0 40px; border: none;
padding: 0px;">
<div>my $path="<a moz-do-not-send="true" href="http://feb2014.archive.ensembl.org/biomart/martservice?">http://feb2014.archive.ensembl.org/biomart/martservice?</a>";</div>
</blockquote>
<div><br>
</div>
2) A BioMart perl script
<div>a) You first need to edit your configuration file
in "biomart-perl/conf/martURLLocation.xml" and paste
the content of the mart registry page for the
Ensembl release 75 archive website: <a moz-do-not-send="true" href="http://feb2014.archive.ensembl.org/biomart/martservice?type=registry">http://feb2014.archive.ensembl.org/biomart/martservice?type=registry</a></div>
<div>b) Then edit your script and make sure that "my
$confFile" variable is looking at
the martURLLocation.xml configuration file in
biomart-perl/conf</div>
<div>c) Finally, make sure to update the following
line in your script:</div>
<div><br>
</div>
<div>my $action='cached';</div>
<div>
<div><br>
</div>
<div>with:</div>
<div><br>
</div>
<div>my $action='clean';</div>
<div>
<div>
<div><br>
</div>
<div>The first run of your script on Ensembl 75
might be a bit slow as BioMart will cache some
data from the BioMart website.</div>
<div>Once you have run your script with the
action variable set to "clean", you can set
the variable to "cached" again.</div>
<div><br>
</div>
<div>Hope this helps,</div>
<div>Best regards,</div>
<div>Thomas</div>
<div>On 19 Sep 2014, at 13:28, Guillermo Marco
Puche <<a moz-do-not-send="true" href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<meta http-equiv="content-type" content="text/html; charset=windows-1252">
<div bgcolor="#FFFFFF" text="#000066"> Dear
developers,<br>
<br>
I would like to know how to specify BioMart
Perl code to query against older Ensembl
version (ie:75) and not latest (I believe
used by default).<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
</div>
_______________________________________________<br>
Dev mailing list <a moz-do-not-send="true" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe
info: <a moz-do-not-send="true" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a moz-do-not-send="true" href="http://www.ensembl.info/">http://www.ensembl.info/</a><br>
</blockquote>
</div>
<br>
<div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate;
font-family: Helvetica; font-style:
normal; font-variant: normal; font-weight:
normal; letter-spacing: normal;
line-height: normal; orphans: 2;
text-align: -webkit-auto; text-indent:
0px; text-transform: none; white-space:
normal; widows: 2; word-spacing: 0px;
border-spacing: 0px;
-webkit-text-decorations-in-effect: none;
-webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate;
font-family: Helvetica; font-style:
normal; font-variant: normal;
font-weight: normal; letter-spacing:
normal; line-height: normal; orphans:
2; text-indent: 0px; text-transform:
none; white-space: normal; widows: 2;
word-spacing: 0px; border-spacing:
0px;
-webkit-text-decorations-in-effect:
none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break:
after-white-space; "><span class="Apple-style-span" style="border-collapse: separate;
font-family: Helvetica;
font-style: normal; font-variant:
normal; font-weight: normal;
letter-spacing: normal;
line-height: normal; orphans: 2;
text-indent: 0px; text-transform:
none; white-space: normal; widows:
2; word-spacing: 0px;
border-spacing: 0px;
-webkit-text-decorations-in-effect:
none; -webkit-text-stroke-width:
0px;">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break:
after-white-space; ">
<div>--</div>
<div>Thomas Maurel<br>
Bioinformatician - Ensembl
Production Team<br>
European Bioinformatics
Institute (EMBL-EBI)<br>
European Molecular Biology
Laboratory<br>
Wellcome Trust Genome Campus<br>
Hinxton<br>
Cambridge CB10 1SD<br>
United Kingdom</div>
</div>
</span></div>
</span></div>
</span></div>
</span> </div>
<br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
</div>
_______________________________________________<br>
Dev mailing list <a moz-do-not-send="true" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a moz-do-not-send="true" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a moz-do-not-send="true" href="http://www.ensembl.info/">http://www.ensembl.info/</a><br>
</blockquote>
</div>
<br>
<div> <span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space; -webkit-line-break:
after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
-webkit-line-break: after-white-space; ">
<div>--</div>
<div>Thomas Maurel<br>
Bioinformatician - Ensembl Production Team<br>
European Bioinformatics Institute
(EMBL-EBI)<br>
European Molecular Biology Laboratory<br>
Wellcome Trust Genome Campus<br>
Hinxton<br>
Cambridge CB10 1SD<br>
United Kingdom</div>
</div>
</span></div>
</span></div>
</span></div>
</span> </div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
</div>
_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>--</div><div>Thomas Maurel<br>Bioinformatician - Ensembl Production Team<br>European Bioinformatics Institute (EMBL-EBI)<br>European Molecular Biology Laboratory<br>Wellcome Trust Genome Campus<br>Hinxton<br>Cambridge CB10 1SD<br>United Kingdom</div></div></span></div></span></div></span></div></span>
</div>
<br></div></body></html>