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Hi Genomeo,<br>
<br>
Indeed, we have an order of priority for sources.<br>
We check the first source and if there is a match, we keep it. Else,
we look at the next source.<br>
The order for all species is as follows:<br>
- official naming source where available (HGNC for human, MGI for
mouse, RGD for rat, etc)<br>
- RFAM<br>
- miRBase<br>
- Uniprot gene names<br>
- EntrezGene names<br>
- Havana names<br>
<br>
For ENSG00000243485, the other MIR symbols have been aligned because
these are short sequences and there is a lot of similarity.<br>
Hence, they match well enough to be added as external references.<br>
However, they all have a better match for another Ensembl gene.<br>
<a class="moz-txt-link-freetext" href="http://beta.rest.ensembl.org/lookup/symbol/homo_sapiens/MIR1302-2">http://beta.rest.ensembl.org/lookup/symbol/homo_sapiens/MIR1302-2</a><br>
<a class="moz-txt-link-freetext" href="http://beta.rest.ensembl.org/lookup/symbol/homo_sapiens/MIR1302-9">http://beta.rest.ensembl.org/lookup/symbol/homo_sapiens/MIR1302-9</a><br>
<a class="moz-txt-link-freetext" href="http://beta.rest.ensembl.org/lookup/symbol/homo_sapiens/MIR1302-11">http://beta.rest.ensembl.org/lookup/symbol/homo_sapiens/MIR1302-11</a><br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 26/03/2014 22:45, Genomeo Dev wrote:<br>
</div>
<blockquote
cite="mid:CAKry3c0BvVKaw-q8NF+5zmw_u9tdeke_DLdkuRhDX-WAEZ1cdQ@mail.gmail.com"
type="cite">
<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
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">
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 moz-do-not-send="true"
href="http://beta.rest.ensembl.org/lookup/id/ENSG00000261163"
target="_blank">http://beta.rest.ensembl.org/lookup/id/ENSG00000261163</a>)<br>
- RFAM (<a moz-do-not-send="true"
href="http://beta.rest.ensembl.org/lookup/id/ENSG00000252365"
target="_blank">http://beta.rest.ensembl.org/lookup/id/ENSG00000252365</a>)<br>
- miRBase (<a moz-do-not-send="true"
href="http://beta.rest.ensembl.org/lookup/id/ENSG00000265031"
target="_blank">http://beta.rest.ensembl.org/lookup/id/ENSG00000265031</a>)<br>
- Havana (<a moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
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 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>)<br>
>><br>
>><br>
</div>
</div>
>> 1. import httplib2, sys<br>
>> 2.<br>
>> 3. http = httplib2.Http(".cache")<br>
>> 4.<br>
>> 5. server = "<a moz-do-not-send="true"
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 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>):<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">>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">G.</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
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