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Hi Genomeo,<br>
<br>
To find which attributes are available, the Ensembl Doxygen
documentation usually covers everything you need.<br>
Looking at
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Gene.html">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Gene.html</a><br>
will tell you that you can obtain the following from a gene:<br>
<br>
$gene->source()<br>
$gene->analysis->logic_name()<br>
$gene->description()<br>
$gene->external_name()<br>
$gene->biotype()<br>
$gene->seq_region_start()<br>
$gene->seq_region_end()<br>
$gene->seq_region_name()<br>
$gene->seq_region_strand()<br>
$gene->display_id()<br>
<br>
When using the API, you should always know what object_type you are
using, as it allows you to use the correct attributes.<br>
In this example, if you are using a Bio::EnsEMBL::Gene, object_type
is 'gene'<br>
<br>
For species and db_type as well, you need to know those beforehand
when using directly the perl API.<br>
They are the ones which will allow you to connect to the correct
database based on the data you are looking for.<br>
<br>
Regarding cross references to other organisms, do you have any
examples?<br>
Generally, we should be only mapping to other resources for the same
organism.<br>
For example, for pig, we will only assign cross references to
Uniprot pig proteins.<br>
<br>
The main exceptions I can think of are:<br>
- HGNC names<br>
Typically, if the coverage for a species is low (ie, not all 20 odd
thousand proteins have been submitted to Uniprot or RefSeq), we will
use HGNC names to fill in the gaps.<br>
Where no name can be found and there is a homolog in human, we use
the same name as in human.<br>
- Ensembl translations<br>
For some low coverage species, annotations was provided by
projecting human annotation via a whole genome alignment.<br>
For these models, we add an external reference to the human
translation which was used to build the model.<br>
<br>
<br>
Hope this helps,<br>
Magali<br>
<div><br>
</div>
<div class="moz-cite-prefix">On 27/02/2014 13:41, Genomeo Dev wrote:<br>
</div>
<blockquote
cite="mid:CAKry3c3QyokTn98SA=STYkNQGNNABtVJRq9oVusK4owpcASJyQ@mail.gmail.com"
type="cite">
<div dir="ltr">Thanks very much for the useful answer.
<div><br>
</div>
<div>I noticed that cross ref also maps to genes from organisms
other than that of the query gene ID. Any comment on that?<br>
<div><br>
</div>
<div>Related to the previous question, I use the following
Rest python code to do id lookup for particular Ensembl IDs:</div>
<div><br>
</div>
<div>
<div>pref= "/lookup/id/"</div>
<div>ext = "?"</div>
<div><br>
</div>
<div>for line in inputfile1:</div>
<div> geneid= line.rstrip('\n')</div>
<div><br>
</div>
<div> resp, content =
http.request(server+pref+geneid+ext, method="GET",
headers={"Content-Type":"application/json"})</div>
<div><br>
</div>
<div> if not resp.status == 200:</div>
<div> print "%s\t%s\t%s" % (geneid, "Invalid
response:", resp.status)</div>
<div> continue</div>
<div> #sys.exit()</div>
<div> print "%s\t%s" % (geneid,content)</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>And I get this output:</div>
<div><br>
</div>
<div>
<div>ENSG00000223972<span class="" style="white-space:pre">
</span>{"source":"ensembl_havana","object_type":"Gene","logic_name":"ensembl_havana_gene","species":"homo_sapiens","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box helicase 11 like 1 [Source:HGNC
Symbol;Acc:37102]","display_name":"DDX11L1","biotype":"pseudogene","end":14412,"seq_region_name":"1","db_type":"core","strand":1,"id":"ENSG00000223972","start":11869}</div>
</div>
<div><br>
</div>
<div>What would be the classes/attributes to use under the
Perl API to get that? i.e:</div>
<div><br>
</div>
<div>source</div>
<div>object_type</div>
<div>logic_name</div>
<div>species</div>
<div>description</div>
<div>display_name</div>
<div>biotype</div>
<div>end</div>
<div>seq_region_name<br>
</div>
<div>db_type</div>
<div>strand</div>
<div>id</div>
<div>start</div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>G.</div>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 27 February 2014 11:39, mag <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi Genomeo,<br>
<br>
The REST server only display the current/latest release.<br>
The release version can be found with this endpoint:<br>
<a moz-do-not-send="true"
href="http://beta.rest.ensembl.org/documentation/info/software"
target="_blank">http://beta.rest.ensembl.org/documentation/info/software</a><br>
<br>
To get more details with the Ensembl API, you only need to
update the print_DBEntries method to display all the
attributes you are looking for.<br>
Compared to the output from REST, we have the following:<br>
- display_id is $dbe->display_id()<br>
- primary_id is $dbe->primary_id()<br>
- version is $dbe->version()<br>
- description is $dbe->description()<br>
- dbname is $dbe->dbname()<br>
- synonyms is $dbe->get_all_synonyms()<br>
- info_type is $dbe->info_type()<br>
- info_text is $dbe->info_text()<br>
- db_display_name is $dbe->db_display_name()<br>
<br>
You can chose what format the REST will output.<br>
Details of all formats can be found in our user guide:<br>
<a moz-do-not-send="true"
href="http://beta.rest.ensembl.org/documentation/user_guide"
target="_blank">http://beta.rest.ensembl.org/documentation/user_guide</a><br>
For tab-delimited output, content_type=text/x-gff3 is
used, but it is only available for the /feature endpoint.<br>
<br>
There is no file in the Ensembl ftp dumps that contains
all the external references produced.<br>
<br>
<br>
Regards,<br>
Magali
<div>
<div class="h5"><br>
<br>
<div>On 27/02/2014 11:20, Genomeo Dev wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<div dir="ltr">
<div><font color="#000000" face="arial, helvetica,
sans-serif"><span
style="line-height:18px;white-space:pre-wrap">Hi,</span></font></div>
<div><font color="#000000" face="arial, helvetica,
sans-serif"><span
style="line-height:18px;white-space:pre-wrap"><br>
</span></font></div>
<div><span
style="line-height:18px;white-space:pre-wrap;font-family:arial,helvetica,sans-serif">I
am interested in getting wide cross references
to ensembl gene IDs. I found two programmatic
ways to do that which give consistent results
but different amount of details. Using
ENSG00000223972 as an example:</span><br>
</div>
<div><font color="#000000" face="arial, helvetica,
sans-serif"><span
style="line-height:18px;white-space:pre-wrap">(1)</span></font></div>
<div><font color="#000000" face="arial, helvetica,
sans-serif"><span
style="line-height:18px;white-space:pre-wrap">Using
this rest API Endpoint python code (<a
moz-do-not-send="true"
href="http://beta.rest.ensembl.org/documentation/info/xref_id"
target="_blank">http://beta.rest.ensembl.org/documentation/info/xref_id</a>)</span></font></div>
<div><br>
</div>
<ol>
<li
style="line-height:18px;list-style-type:decimal;color:rgb(190,190,197);padding-left:12px"><span
style="color:rgb(0,0,136)">import</span><span
style="color:rgb(0,0,0)"> httplib2</span><span
style="color:rgb(102,102,0)">,</span><span
style="color:rgb(0,0,0)"> sys</span></li>
<li
style="line-height:18px;list-style-type:decimal;background-color:rgb(238,238,238);color:rgb(190,190,197);padding-left:12px"><span
style="color:rgb(0,0,0)"> </span></li>
<li
style="line-height:18px;list-style-type:decimal;color:rgb(190,190,197);padding-left:12px"><span
style="color:rgb(0,0,0)">http </span><span
style="color:rgb(102,102,0)">=</span><span
style="color:rgb(0,0,0)"> httplib2</span><span
style="color:rgb(102,102,0)">.</span><span
style="color:rgb(102,0,102)">Http</span><span
style="color:rgb(102,102,0)">(</span><span
style="color:rgb(0,136,0)">".cache"</span><span
style="color:rgb(102,102,0)">)</span></li>
<li
style="line-height:18px;list-style-type:decimal;background-color:rgb(238,238,238);color:rgb(190,190,197);padding-left:12px"><span
style="color:rgb(0,0,0)"> </span></li>
<li
style="line-height:18px;color:rgb(190,190,197);list-style-type:decimal;padding-left:12px"><span
style="color:rgb(0,0,0)">server </span><span
style="color:rgb(102,102,0)">=</span><span
style="color:rgb(0,0,0)"> </span><span
style="color:rgb(0,136,0)">"<a
moz-do-not-send="true"
href="http://beta.rest.ensembl.org"
target="_blank">http://beta.rest.ensembl.org</a>"</span></li>
<li
style="line-height:18px;list-style-type:decimal;background-color:rgb(238,238,238);color:rgb(190,190,197);padding-left:12px"><span
style="color:rgb(0,0,0)">ext </span><span
style="color:rgb(102,102,0)">=</span><span
style="color:rgb(0,0,0)"> </span><span
style="color:rgb(0,136,0)">"/xrefs/id/ENSG00000157764?"</span></li>
<li
style="line-height:18px;list-style-type:decimal;color:rgb(190,190,197);padding-left:12px"><span
style="color:rgb(0,0,0)">resp</span><span
style="color:rgb(102,102,0)">,</span><span
style="color:rgb(0,0,0)"> content </span><span
style="color:rgb(102,102,0)">=</span><span
style="color:rgb(0,0,0)"> http</span><span
style="color:rgb(102,102,0)">.</span><span
style="color:rgb(0,0,0)">request</span><span
style="color:rgb(102,102,0)">(</span><span
style="color:rgb(0,0,0)">server</span><span
style="color:rgb(102,102,0)">+</span><span
style="color:rgb(0,0,0)">ext</span><span
style="color:rgb(102,102,0)">,</span><span
style="color:rgb(0,0,0)"> method</span><span
style="color:rgb(102,102,0)">=</span><span
style="color:rgb(0,136,0)">"GET"</span><span
style="color:rgb(102,102,0)">,</span><span
style="color:rgb(0,0,0)"> headers</span><span
style="color:rgb(102,102,0)">={</span><span
style="color:rgb(0,136,0)">"Content-Type"</span><span
style="color:rgb(102,102,0)">:</span><span
style="color:rgb(0,136,0)">"application/json"</span><span
style="color:rgb(102,102,0)">})</span></li>
<li
style="line-height:18px;list-style-type:decimal;background-color:rgb(238,238,238);color:rgb(190,190,197);padding-left:12px"><span
style="color:rgb(0,0,0)"> </span></li>
<li
style="line-height:18px;list-style-type:decimal;color:rgb(190,190,197);padding-left:12px"><span
style="color:rgb(0,0,136)">if</span><span
style="color:rgb(0,0,0)"> </span><span
style="color:rgb(0,0,136)">not</span><span
style="color:rgb(0,0,0)"> resp</span><span
style="color:rgb(102,102,0)">.</span><span
style="color:rgb(0,0,0)">status </span><span
style="color:rgb(102,102,0)">==</span><span
style="color:rgb(0,0,0)"> </span><span
style="color:rgb(0,102,102)">200</span><span
style="color:rgb(102,102,0)">:</span></li>
<li
style="line-height:18px;background-color:rgb(238,238,238);color:rgb(190,190,197);list-style-type:decimal;padding-left:12px"><span
style="color:rgb(0,0,0)"> </span><span
style="color:rgb(0,0,136)">print</span><span
style="color:rgb(0,0,0)"> </span><span
style="color:rgb(0,136,0)">"Invalid
response: "</span><span
style="color:rgb(102,102,0)">,</span><span
style="color:rgb(0,0,0)"> resp</span><span
style="color:rgb(102,102,0)">.</span><span
style="color:rgb(0,0,0)">status</span></li>
<li
style="line-height:18px;list-style-type:decimal;color:rgb(190,190,197);padding-left:12px"><span
style="color:rgb(0,0,0)"> sys</span><span
style="color:rgb(102,102,0)">.</span><span
style="color:rgb(0,0,136)">exit</span><span
style="color:rgb(102,102,0)">()</span></li>
<li
style="line-height:18px;list-style-type:decimal;background-color:rgb(238,238,238);color:rgb(190,190,197);padding-left:12px"><span
style="color:rgb(0,0,136)">import</span><span
style="color:rgb(0,0,0)"> json</span></li>
<li
style="line-height:18px;list-style-type:decimal;color:rgb(190,190,197);padding-left:12px"><span
style="color:rgb(0,0,0)"> </span></li>
<li
style="line-height:18px;list-style-type:decimal;background-color:rgb(238,238,238);color:rgb(190,190,197);padding-left:12px"><span
style="color:rgb(0,0,0)">decoded </span><span
style="color:rgb(102,102,0)">=</span><span
style="color:rgb(0,0,0)"> json</span><span
style="color:rgb(102,102,0)">.</span><span
style="color:rgb(0,0,0)">loads</span><span
style="color:rgb(102,102,0)">(</span><span
style="color:rgb(0,0,0)">content</span><span
style="color:rgb(102,102,0)">)</span></li>
<li
style="line-height:18px;color:rgb(190,190,197);list-style-type:decimal;padding-left:12px"><span
style="color:rgb(0,0,136)">print</span><span
style="color:rgb(0,0,0)"> repr</span><span
style="color:rgb(102,102,0)">(</span><span
style="color:rgb(0,0,0)">decoded</span><span
style="color:rgb(102,102,0)">)</span></li>
</ol>
<div><br>
</div>
<div>I get:</div>
<div><br>
</div>
<div>
<div>{"display_id":"OTTHUMG00000000961","primary_id":"OTTHUMG00000000961","version":"2","description":null,"dbname":"OTTG","synonyms":[],"info_type":"NONE","info_text":"","db_display_name":"Havana
gene"}</div>
<div><br>
</div>
<div>{"primary_id":"Hs.714157","dbname":"UniGene","ensembl_identity":98,"synonyms":[],"ensembl_start":6,"xref_start":1,"xref_end":1639,"db_display_name":"UniGene","display_id":"Hs.714157","ensembl_end":1657,"version":"0","score":8055,"cigar_line":"1200M1D299M12D140M","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box helicase 11 like
1","xref_identity":97,"evalue":null,"info_text":"","info_type":"SEQUENCE_MATCH"}</div>
<div><br>
</div>
<div>{"primary_id":"Hs.618434","dbname":"UniGene","ensembl_identity":58,"synonyms":[],"ensembl_start":669,"xref_start":1,"xref_end":974,"db_display_name":"UniGene","display_id":"Hs.618434","ensembl_end":1655,"version":"0","score":4757,"cigar_line":"537M1D299M12D138M","description":"Similar
to DEAD/H (Asp-Glu-Ala-Asp/His) box
polypeptide 11 isoform 1, mRNA (cDNA clone
IMAGE:6103207)","xref_identity":96,"evalue":null,"info_text":"","info_type":"SEQUENCE_MATCH"}</div>
<div><br>
</div>
<div>{"display_id":"DDX11L1","primary_id":"37102","version":"0","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box helicase 11 like
1","dbname":"HGNC","synonyms":[],"info_type":"DIRECT","info_text":"Generated
via ensembl_manual","db_display_name":"HGNC
Symbol"}</div>
<div><br>
</div>
<div>{"display_id":"DDX11L5","primary_id":"100287596","version":"0","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box helicase 11 like
5","dbname":"EntrezGene","synonyms":[],"info_type":"DEPENDENT","info_text":"","db_display_name":"EntrezGene"}</div>
<div><br>
</div>
<div>{"display_id":"DDX11L1","primary_id":"100287102","version":"0","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box helicase 11 like
1","dbname":"EntrezGene","synonyms":[],"info_type":"DEPENDENT","info_text":"","db_display_name":"EntrezGene"}</div>
<div><br>
</div>
<div>{"display_id":"ENSG00000223972","primary_id":"ENSG00000223972","version":"0","description":"","dbname":"ArrayExpress","synonyms":[],"info_type":"DIRECT","info_text":"","db_display_name":"ArrayExpress"}</div>
<div><br>
</div>
<div>{"display_id":"DDX11L5","primary_id":"100287596","version":"0","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box helicase 11 like
5","dbname":"WikiGene","synonyms":[],"info_type":"DEPENDENT","info_text":"","db_display_name":"WikiGene"}</div>
<div><br>
</div>
<div>{"display_id":"DDX11L1","primary_id":"100287102","version":"0","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box helicase 11 like
1","dbname":"WikiGene","synonyms":[],"info_type":"DEPENDENT","info_text":"","db_display_name":"WikiGene"}]</div>
<div><br>
</div>
</div>
<div>(2)</div>
<div><br>
</div>
<div>Using this perl API code (based on <a
moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/api/core/core_tutorial.html"
target="_blank">http://www.ensembl.org/info/docs/api/core/core_tutorial.html</a>):</div>
<div><br>
</div>
<div>
<pre style="margin-top:0px;margin-bottom:16px;border:1px solid rgb(204,204,204);background-color:rgb(240,240,240);padding:8px!important"><font color="#555555" face="courier new, monospace"><span style="line-height:16px"># Define a helper subroutine to print DBEntries
sub print_DBEntries
{
my $db_entries = shift;
foreach my $dbe ( @{$db_entries} ) {
printf "\tXREF %s (%s)\n", $dbe->display_id(), $dbe->dbname();
}
}
my $genes = $gene_adaptor->fetch_all_by_stable_id_list([@gene_list]);</span></font></pre>
<pre style="margin-top:0px;margin-bottom:16px;border:1px solid rgb(204,204,204);background-color:rgb(240,240,240);line-height:16px;color:rgb(85,85,85);padding:8px!important"><font face="courier new, monospace">
...</font></pre>
<pre style="margin-top:0px;margin-bottom:16px;border:1px solid rgb(204,204,204);background-color:rgb(240,240,240);line-height:16px;color:rgb(85,85,85);padding:8px!important"><font face="courier new, monospace">
print "GENE ", $gene->stable_id(), "\n";
print_DBEntries( $gene->get_all_DBEntries() );</font></pre>
</div>
<div>
<div><span style="white-space:pre-wrap">I get:</span></div>
<div><span style="white-space:pre-wrap"> </span></div>
<div>XREF OTTHUMG00000000961 (OTTG)</div>
<div>XREF ENSG00000223972 (ArrayExpress)</div>
<div>XREF DDX11L1 (EntrezGene)</div>
<div>XREF DDX11L5 (EntrezGene)</div>
<div>XREF DDX11L1 (HGNC)</div>
<div>XREF Hs.618434 (UniGene)</div>
<div>XREF Hs.714157 (UniGene)</div>
<div> XREF DDX11L1 (WikiGene)</div>
<div>XREF DDX11L5 (WikiGene)</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Questions:</div>
<div><br>
</div>
<div>1. am I correct in saying that the Rest code
uses the latest Ensembl release while the API
code uses the Ensembl release currently
installed as part of the VM (I am using release
74)?</div>
<div><br>
</div>
<div>2. Rest code gives more extensive details
(which I like) compared to the perl API code.
Could you suggest a simple way to use the API to
get the same details?</div>
<div><br>
</div>
<div>3. The Rest code output format. Is tab
separated text supported?<br>
</div>
<div><br>
</div>
<div>4. Is there a file in the Ensembl ftp area
which contains pre generated detailed cross ref
mappings for all current Ensembl genes?</div>
--
<div><br>
</div>
<div>Thanks,</div>
<div><br>
<div dir="ltr"> G.</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
<pre>_______________________________________________
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Ensembl Blog: <a moz-do-not-send="true" href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</div>
<br>
_______________________________________________<br>
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href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a
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target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">G.</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
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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>
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