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Hi Thomas,<br>
<br>
Only the display_xref of a gene has synonyms, so you could speed up
your script by limiting your query to those.<br>
<br>
This would replace the following lines:<br>
<br>
my @allsyn;<br>
my $dber = $gene->get_all_DBEntries($dbname);<br>
for my $db (@$dber) {<br>
my $synr = $db->get_all_synonyms();<br>
push(@allsyn, @$synr);<br>
}<br>
## Find unique synonyms (while maintaining order):<br>
my %seen;<br>
my @keep;<br>
for (0 .. $#allsyn) {<br>
unless ($seen{$allsyn[$_]}) {<br>
push(@keep, $_);<br>
$seen{$allsyn[$_]} = 1;<br>
}<br>
}<br>
print $of $geneid, "\t", join($sep, @allsyn[@keep]), "\n";<br>
<br>
with:<br>
my $db = $gene->display_xref;<br>
print $of $gene_id, "\t", join($sep,
@{$db->get_all_synonyms()});<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 25/05/2018 17:47, Thomas Danhorn
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:alpine.DEB.2.11.1805250957010.31788@Ntebonpgrevhz.ybpny">Hi
Beat,
<br>
<br>
I do this regularly and have attached my Perl script -- feel free
to adapt it for your purposes. It uses the Ensembl Perl API, so
you have to have the appropriate version installed. (I cloned the
git repo and get from there whichever version I need; if you run
into issues, feel free to ask me.) The script takes a list of
Ensembl gene IDs (with a header) and prints a table with the
orginal IDs and the synonyms. Be sure to specify the species with
the -s option, unless you want the default, 'Mouse'.
<br>
<br>
One thing to note is that sometime between releases 84 and 90, the
location of the synonyms in the databases switched from the
"EntrezGene" DB to elsewhere, so if you use a newer release with
the default parameters will likely find no synonyms -- use the
option `-b all' to search through each DB (or specify one that you
knnow has what you need). This takes a while (days for an entire
genome annotation), so if you have long lists, you may want to
split them up and parallelize the process.
<br>
<br>
Hope this helps,
<br>
<br>
Thomas
<br>
<br>
<br>
On Tue, 22 May 2018, Premanand Achuthan wrote:
<br>
<br>
<blockquote type="cite">Hi Beat Wolf,
<br>
<br>
The synonyms is not always empty. If the external source has
synonyms, then it should be available, for example look at HGNC
<br>
<br>
{"display_id": "BRCA2","primary_id": "HGNC:1101","version":
"0","description": "BRCA2, DNA repair associated","dbname":
"HGNC","synonyms":
["BRCC2","FACD","FAD","FAD1","FANCD","FANCD1","XRCC11"],"info_text":
"Generated via ensembl_manual","info_type":
"DIRECT","db_display_name": "HGNC Symbol"}
<br>
<br>
I am afraid that at the moment you can do it only gene by gene
via the REST endpoint or via the core API.
<br>
<br>
Thanks
<br>
Prem
<br>
<br>
<br>
On 22/05/2018 10:23, Wolf Beat wrote:
<br>
<blockquote type="cite">Thank you for the quick answer.
<br>
<br>
<br>
I did not know about this approach, but i have two issues with
it:
<br>
<br>
1) The synonyms attribute seems to be always empty, so
something seems wrong.
<br>
<br>
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.
<br>
<br>
<br>
Kind regards
<br>
<br>
<br>
Beat Wolf
<br>
<br>
________________________________
<br>
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>
<br>
Sent: Tuesday, May 22, 2018 11:20:09 AM
<br>
To: <a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a>
<br>
Subject: Re: [ensembl-dev] Gene Synonyms through REST or
Biomart
<br>
<br>
Hi Beat Wolf,
<br>
<br>
Please have a look at the /xrefs endpoint under "Cross
References" and
<br>
look for "synonyms" in the attribute list.
<br>
<br>
<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>
<br>
<br>
<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>
<br>
<br>
Hope it helps,
<br>
<br>
Best Regards
<br>
Prem
<br>
<br>
On 22/05/2018 10:09, Wolf Beat wrote:
<br>
<blockquote type="cite">Hello,
<br>
<br>
<br>
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?
<br>
<br>
<br>
Kind regards
<br>
<br>
<br>
Beat Wolf
<br>
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</blockquote>
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</blockquote>
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