[ensembl-dev] xref mapping

Genomeo Dev genomeodev at gmail.com
Tue Mar 25 18:55:04 GMT 2014 

Hi,

I was comparing the output from these lookupid and xref commands from
ensembl REST endpoint for ENSG00000243485:

wget -q --header='Content-type:application/json' '
http://beta.rest.ensembl.org/xrefs/id/ENSG00000243485?external_db=HGNC'  -O
-
ENSG00000243485 HGNC MIR1302-11 microRNA 1302-11 HGNC Symbol Generated via
refseq_manual DEPENDENT 38246 hsa-mir-1302-11 0
ENSG00000243485 HGNC MIR1302-10 microRNA 1302-10 HGNC Symbol Generated via
refseq_manual DEPENDENT 38233 hsa-mir-1302-10 0
ENSG00000243485 HGNC MIR1302-9 microRNA 1302-9 HGNC Symbol Generated via
refseq_manual DEPENDENT 38218 hsa-mir-1302-9 0
ENSG00000243485 HGNC MIR1302-2 microRNA 1302-2 HGNC Symbol Generated via
refseq_manual DEPENDENT 35294 hsa-mir-1302-2, MIRN1302-2 0

wget -q --header='Content-type:application/json' '
http://beta.rest.ensembl.org/lookup/id/ENSG00000243485?expand=1' -O -
ENSG00000243485 1 29554 31109 1 MIR1302-10 ensembl_havana
ensembl_havana_lincrna microRNA 1302-10 [Source:HGNC Symbol;Acc:38233]
lincRNA

What is the reason for the lookup command to show only one of the four
mapped HGNC  symbols?

Thanks,

G.


On 27 February 2014 11:20, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi,
>
> 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:
> (1)
> Using this rest API Endpoint python code (
> http://beta.rest.ensembl.org/documentation/info/xref_id)
>
>
>    1. import httplib2, sys
>    2.
>    3. http = httplib2.Http(".cache")
>    4.
>    5. server = "http://beta.rest.ensembl.org"
>    6. ext = "/xrefs/id/ENSG00000157764?"
>    7. resp, content = http.request(server+ext, method="GET", headers={
>    "Content-Type":"application/json"})
>    8.
>    9. if not resp.status == 200:
>    10. print "Invalid response: ", resp.status
>    11. sys.exit()
>    12. import json
>    13.
>    14. decoded = json.loads(content)
>    15. print repr(decoded)
>
>
> I get:
>
> {"display_id":"OTTHUMG00000000961","primary_id":"OTTHUMG00000000961","version":"2","description":null,"dbname":"OTTG","synonyms":[],"info_type":"NONE","info_text":"","db_display_name":"Havana
> gene"}
>
> {"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"}
>
> {"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"}
>
> {"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"}
>
> {"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"}
>
> {"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"}
>
>
> {"display_id":"ENSG00000223972","primary_id":"ENSG00000223972","version":"0","description":"","dbname":"ArrayExpress","synonyms":[],"info_type":"DIRECT","info_text":"","db_display_name":"ArrayExpress"}
>
> {"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"}
>
> {"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"}]
>
> (2)
>
> Using this perl API code (based on
> http://www.ensembl.org/info/docs/api/core/core_tutorial.html):
>
> # 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]);
>
>
> ...
>
>
> print "GENE ", $gene->stable_id(), "\n";
> print_DBEntries( $gene->get_all_DBEntries() );
>
> I get:
> XREF OTTHUMG00000000961 (OTTG)
> XREF ENSG00000223972 (ArrayExpress)
> XREF DDX11L1 (EntrezGene)
> XREF DDX11L5 (EntrezGene)
> XREF DDX11L1 (HGNC)
> XREF Hs.618434 (UniGene)
> XREF Hs.714157 (UniGene)
> XREF DDX11L1 (WikiGene)
> XREF DDX11L5 (WikiGene)
>
>
> Questions:
>
> 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)?
>
> 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?
>
> 3. The Rest code output format. Is tab separated text supported?
>
> 4. Is there a  file in the Ensembl ftp area which contains pre generated
> detailed cross ref mappings for all current Ensembl genes?
> --
>
> Thanks,
>
> G.
>



-- 
G.
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