<div dir="ltr">Hi Magali,<div><br></div><div>Thanks for the response.</div><div><br></div><div>Is there a rule for how the display name is assigned for a given Ensembl gene ID? Something like use HGNC symbol if exists, otherwise Uniprot, otherwise PFAM, otherwise miRBASE otherwise Havana..</div>
<div><br></div><div>The other question is: In the case of the display name of <span style="font-size:13px;font-family:arial,sans-serif">ENSG00000243485 which is the HGNC symbol is </span><font face="arial, sans-serif">MIR1302-10, how was this one HGNC symbol chosen from the set of four mapped HGNC symbols retrievable with the xref command?</font></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px">G.</span></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On 25 March 2014 21:16, <span dir="ltr"><<a 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">
Hi Genomeo,<br>
<br>
The xref endpoint returns the whole list of external references associated<br>
to an ensembl object.<br>
This can be filtered for a given external source name, in this case HGNC.<br>
<br>
The lookup endpoint returns some information on the input object,<br>
including its location and display name, but excluding any external<br>
references.<br>
<br>
For this gene, the display name is an HGNC symbol.<br>
This is the case for most of our genes, but in can also be<br>
- Uniprot names (<a href="http://beta.rest.ensembl.org/lookup/id/ENSG00000261163" target="_blank">http://beta.rest.ensembl.org/lookup/id/ENSG00000261163</a>)<br>
- RFAM (<a href="http://beta.rest.ensembl.org/lookup/id/ENSG00000252365" target="_blank">http://beta.rest.ensembl.org/lookup/id/ENSG00000252365</a>)<br>
- miRBase (<a href="http://beta.rest.ensembl.org/lookup/id/ENSG00000265031" target="_blank">http://beta.rest.ensembl.org/lookup/id/ENSG00000265031</a>)<br>
- Havana (<a href="http://beta.rest.ensembl.org/lookup/id/ENSG00000228741" target="_blank">http://beta.rest.ensembl.org/lookup/id/ENSG00000228741</a>)<br>
<br>
<br>
Hope this helps,<br>
Magali<br>
<div><div class="h5"><br>
> Hi,<br>
><br>
> I was comparing the output from these lookupid and xref commands from<br>
> ensembl REST endpoint for ENSG00000243485:<br>
><br>
> wget -q --header='Content-type:application/json' '<br>
> <a href="http://beta.rest.ensembl.org/xrefs/id/ENSG00000243485?external_db=HGNC" target="_blank">http://beta.rest.ensembl.org/xrefs/id/ENSG00000243485?external_db=HGNC</a>'<br>
> -O<br>
> -<br>
> ENSG00000243485 HGNC MIR1302-11 microRNA 1302-11 HGNC Symbol Generated via<br>
> refseq_manual DEPENDENT 38246 hsa-mir-1302-11 0<br>
> ENSG00000243485 HGNC MIR1302-10 microRNA 1302-10 HGNC Symbol Generated via<br>
> refseq_manual DEPENDENT 38233 hsa-mir-1302-10 0<br>
> ENSG00000243485 HGNC MIR1302-9 microRNA 1302-9 HGNC Symbol Generated via<br>
> refseq_manual DEPENDENT 38218 hsa-mir-1302-9 0<br>
> ENSG00000243485 HGNC MIR1302-2 microRNA 1302-2 HGNC Symbol Generated via<br>
> refseq_manual DEPENDENT 35294 hsa-mir-1302-2, MIRN1302-2 0<br>
><br>
> wget -q --header='Content-type:application/json' '<br>
> <a href="http://beta.rest.ensembl.org/lookup/id/ENSG00000243485?expand=1" target="_blank">http://beta.rest.ensembl.org/lookup/id/ENSG00000243485?expand=1</a>' -O -<br>
> ENSG00000243485 1 29554 31109 1 MIR1302-10 ensembl_havana<br>
> ensembl_havana_lincrna microRNA 1302-10 [Source:HGNC Symbol;Acc:38233]<br>
> lincRNA<br>
><br>
> What is the reason for the lookup command to show only one of the four<br>
> mapped HGNC symbols?<br>
><br>
> Thanks,<br>
><br>
> G.<br>
><br>
><br>
> On 27 February 2014 11:20, Genomeo Dev <<a href="mailto:genomeodev@gmail.com">genomeodev@gmail.com</a>> wrote:<br>
><br>
>> Hi,<br>
>><br>
>> I am interested in getting wide cross references to ensembl gene IDs. I<br>
>> found two programmatic ways to do that which give consistent results but<br>
>> different amount of details. Using ENSG00000223972 as an example:<br>
>> (1)<br>
>> Using this rest API Endpoint python code (<br>
>> <a href="http://beta.rest.ensembl.org/documentation/info/xref_id" target="_blank">http://beta.rest.ensembl.org/documentation/info/xref_id</a>)<br>
>><br>
>><br>
</div></div>>> 1. import httplib2, sys<br>
>> 2.<br>
>> 3. http = httplib2.Http(".cache")<br>
>> 4.<br>
>> 5. server = "<a href="http://beta.rest.ensembl.org" target="_blank">http://beta.rest.ensembl.org</a>"<br>
>> 6. ext = "/xrefs/id/ENSG00000157764?"<br>
>> 7. resp, content = http.request(server+ext, method="GET", headers={<br>
>> "Content-Type":"application/json"})<br>
>> 8.<br>
>> 9. if not resp.status == 200:<br>
>> 10. print "Invalid response: ", resp.status<br>
>> 11. sys.exit()<br>
>> 12. import json<br>
>> 13.<br>
>> 14. decoded = json.loads(content)<br>
>> 15. print repr(decoded)<br>
<div class="HOEnZb"><div class="h5">>><br>
>><br>
>> I get:<br>
>><br>
>> {"display_id":"OTTHUMG00000000961","primary_id":"OTTHUMG00000000961","version":"2","description":null,"dbname":"OTTG","synonyms":[],"info_type":"NONE","info_text":"","db_display_name":"Havana<br>
>> gene"}<br>
>><br>
>> {"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<br>
>> (Asp-Glu-Ala-Asp/His) box helicase 11 like<br>
>> 1","xref_identity":97,"evalue":null,"info_text":"","info_type":"SEQUENCE_MATCH"}<br>
>><br>
>> {"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<br>
>> to DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 isoform 1, mRNA (cDNA<br>
>> clone<br>
>> IMAGE:6103207)","xref_identity":96,"evalue":null,"info_text":"","info_type":"SEQUENCE_MATCH"}<br>
>><br>
>> {"display_id":"DDX11L1","primary_id":"37102","version":"0","description":"DEAD/H<br>
>> (Asp-Glu-Ala-Asp/His) box helicase 11 like<br>
>> 1","dbname":"HGNC","synonyms":[],"info_type":"DIRECT","info_text":"Generated<br>
>> via ensembl_manual","db_display_name":"HGNC Symbol"}<br>
>><br>
>> {"display_id":"DDX11L5","primary_id":"100287596","version":"0","description":"DEAD/H<br>
>> (Asp-Glu-Ala-Asp/His) box helicase 11 like<br>
>> 5","dbname":"EntrezGene","synonyms":[],"info_type":"DEPENDENT","info_text":"","db_display_name":"EntrezGene"}<br>
>><br>
>> {"display_id":"DDX11L1","primary_id":"100287102","version":"0","description":"DEAD/H<br>
>> (Asp-Glu-Ala-Asp/His) box helicase 11 like<br>
>> 1","dbname":"EntrezGene","synonyms":[],"info_type":"DEPENDENT","info_text":"","db_display_name":"EntrezGene"}<br>
>><br>
>><br>
>> {"display_id":"ENSG00000223972","primary_id":"ENSG00000223972","version":"0","description":"","dbname":"ArrayExpress","synonyms":[],"info_type":"DIRECT","info_text":"","db_display_name":"ArrayExpress"}<br>
>><br>
>> {"display_id":"DDX11L5","primary_id":"100287596","version":"0","description":"DEAD/H<br>
>> (Asp-Glu-Ala-Asp/His) box helicase 11 like<br>
>> 5","dbname":"WikiGene","synonyms":[],"info_type":"DEPENDENT","info_text":"","db_display_name":"WikiGene"}<br>
>><br>
>> {"display_id":"DDX11L1","primary_id":"100287102","version":"0","description":"DEAD/H<br>
>> (Asp-Glu-Ala-Asp/His) box helicase 11 like<br>
>> 1","dbname":"WikiGene","synonyms":[],"info_type":"DEPENDENT","info_text":"","db_display_name":"WikiGene"}]<br>
>><br>
>> (2)<br>
>><br>
>> Using this perl API code (based on<br>
>> <a 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>):<br>
>><br>
>> # Define a helper subroutine to print DBEntries<br>
>> sub print_DBEntries<br>
>> {<br>
>> my $db_entries = shift;<br>
>><br>
>> foreach my $dbe ( @{$db_entries} ) {<br>
>> printf "\tXREF %s (%s)\n", $dbe->display_id(), $dbe->dbname();<br>
>> }<br>
>> }<br>
>><br>
>> my $genes = $gene_adaptor->fetch_all_by_stable_id_list([@gene_list]);<br>
>><br>
>><br>
>> ...<br>
>><br>
>><br>
>> print "GENE ", $gene->stable_id(), "\n";<br>
>> print_DBEntries( $gene->get_all_DBEntries() );<br>
>><br>
>> I get:<br>
>> XREF OTTHUMG00000000961 (OTTG)<br>
>> XREF ENSG00000223972 (ArrayExpress)<br>
>> XREF DDX11L1 (EntrezGene)<br>
>> XREF DDX11L5 (EntrezGene)<br>
>> XREF DDX11L1 (HGNC)<br>
>> XREF Hs.618434 (UniGene)<br>
>> XREF Hs.714157 (UniGene)<br>
>> XREF DDX11L1 (WikiGene)<br>
>> XREF DDX11L5 (WikiGene)<br>
>><br>
>><br>
>> Questions:<br>
>><br>
>> 1. am I correct in saying that the Rest code uses the latest Ensembl<br>
>> release while the API code uses the Ensembl release currently installed<br>
>> as<br>
>> part of the VM (I am using release 74)?<br>
>><br>
>> 2. Rest code gives more extensive details (which I like) compared to the<br>
>> perl API code. Could you suggest a simple way to use the API to get the<br>
>> same details?<br>
>><br>
>> 3. The Rest code output format. Is tab separated text supported?<br>
>><br>
>> 4. Is there a file in the Ensembl ftp area which contains pre generated<br>
>> detailed cross ref mappings for all current Ensembl genes?<br>
>> --<br>
>><br>
>> Thanks,<br>
>><br>
>> G.<br>
>><br>
><br>
><br>
><br>
> --<br>
> G.<br>
</div></div><div class="HOEnZb"><div class="h5">> _______________________________________________<br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">G.</div>
</div>