[ensembl-dev] xref mapping
mag
mr6 at ebi.ac.uk
Thu Mar 27 09:31:56 GMT 2014
Hi Genomeo,
Indeed, we have an order of priority for sources.
We check the first source and if there is a match, we keep it. Else, we
look at the next source.
The order for all species is as follows:
- official naming source where available (HGNC for human, MGI for mouse,
RGD for rat, etc)
- RFAM
- miRBase
- Uniprot gene names
- EntrezGene names
- Havana names
For ENSG00000243485, the other MIR symbols have been aligned because
these are short sequences and there is a lot of similarity.
Hence, they match well enough to be added as external references.
However, they all have a better match for another Ensembl gene.
http://beta.rest.ensembl.org/lookup/symbol/homo_sapiens/MIR1302-2
http://beta.rest.ensembl.org/lookup/symbol/homo_sapiens/MIR1302-9
http://beta.rest.ensembl.org/lookup/symbol/homo_sapiens/MIR1302-11
Hope that helps,
Magali
On 26/03/2014 22:45, Genomeo Dev wrote:
> Hi Magali,
>
> Thanks for the response.
>
> 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..
>
> The other question is: In the case of the display name of
> ENSG00000243485 which is the HGNC symbol is MIR1302-10, how was this
> one HGNC symbol chosen from the set of four mapped HGNC
> symbols retrievable with the xref command?
>
> G.
>
>
> On 25 March 2014 21:16, <mr6 at ebi.ac.uk <mailto:mr6 at ebi.ac.uk>> wrote:
>
> Hi Genomeo,
>
> The xref endpoint returns the whole list of external references
> associated
> to an ensembl object.
> This can be filtered for a given external source name, in this
> case HGNC.
>
> The lookup endpoint returns some information on the input object,
> including its location and display name, but excluding any external
> references.
>
> For this gene, the display name is an HGNC symbol.
> This is the case for most of our genes, but in can also be
> - Uniprot names
> (http://beta.rest.ensembl.org/lookup/id/ENSG00000261163)
> - RFAM (http://beta.rest.ensembl.org/lookup/id/ENSG00000252365)
> - miRBase (http://beta.rest.ensembl.org/lookup/id/ENSG00000265031)
> - Havana (http://beta.rest.ensembl.org/lookup/id/ENSG00000228741)
>
>
> Hope this helps,
> Magali
>
> > 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
> <mailto: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.
> > _______________________________________________
> > Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
> > Posting guidelines and subscribe/unsubscribe info:
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> >
>
>
> _______________________________________________
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>
>
>
> --
> G.
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
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