[ensembl-dev] Conversion of ENA xref ids into working URLs
Guy Cochrane EBI
cochrane at ebi.ac.uk
Sun Apr 24 12:14:35 BST 2016
> On 22 Apr 2016, at 12:19, Dmitry Kuznetsov <Dmitry.Kuznetsov at isb-sib.ch> wrote:
>
> Dan and Guy, thanks for your answers and suggestions.
>
> >You can resolve to ENA subsequences in HTML using http://www.ebi.ac.uk/ena/data/view/GG666297&range=18707-20086 <http://www.ebi.ac.uk/ena/data/view/GG666297&range=18707-20086>
> is there any way to rather end up at this [equivalent] URL: http://www.ebi.ac.uk/ena/data/view/ACGC01000047 <http://www.ebi.ac.uk/ena/data/view/ACGC01000047>
Not directly within this REST service. From the example, it looks as though you are trying to resolve to a contig record from a CONstructed entry assembled from multiple contigs. This information lies in the CO lines of the CON recort. I think the solution - but of course it’s heavier - is to retrieve the CON record, parse these CO lines and return to the rest retrieval service as above. Documentation on the CO lines is in section 3.4.14 of the European Nucleotide Archive annotated/assembled sequences User Manual at ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/doc/usrman.txt.
(Just to note if it is annotation that you are after - this may be relevant or not for your use. The original annotation can lie on the contig record or on the CON record.)
Guy.
> ?
>
> Thanks,
> Dmitry.
>
>
> From: dev-bounces at ensembl.org <mailto:dev-bounces at ensembl.org> [mailto:dev-bounces at ensembl.org <mailto:dev-bounces at ensembl.org>] On Behalf Of Guy Cochrane EBI
> Sent: Friday, April 22, 2016 12:37
> To: Ensembl developers list
> Cc: Nicole Silvester
> Subject: Re: [ensembl-dev] Conversion of ENA xref ids into working URLs
>
>
>> On 22 Apr 2016, at 10:27, Dan Staines <dstaines at ebi.ac.uk <mailto:dstaines at ebi.ac.uk>> wrote:
>>
>> Hi Dimitry,
>>
>>
>> KE159678.1:CDS:7103..8458
>>
>> GG666297.1:CDS:complement(18707..20086)
>>
>> These are provided as tracking IDs to indicate the piece of INSDC annotation from which the Ensembl object was loaded. INSDC do not have feature level identifiers, so on the advice of ENA these strings are constructed to provide at least some way to find the original piece of data from which the Ensembl object was constructed.
>>
>> These identifiers are of the form accession:feature_type:location e.g.
>> GG666297.1:CDS:complement(18707..20086)
>> which refers to this feature:
>> FT CDS complement(18707..20086)
>> FT /codon_start=1
>> FT /transl_table=11
>> FT /locus_tag="HMPREF0077_0851"
>> FT /product="ATPase/histidine kinase/DNA gyrase B/HSP90 domain
>> ...
>> FT /protein_id="EEI83065.1"
>> ...
>> from this expanded CON (i.e an entry composed of multiple sub-entries):
>> http://www.ebi.ac.uk/ena/data/view/GG666297&display=text&expanded=true <http://www.ebi.ac.uk/ena/data/view/GG666297&display=text&expanded=true>
>>
>> I'm not aware of any way to resolve these automatically in ENA - there is a REST service which can return entire entries in text or XML but it would return the whole record, not just the feature.
>
> You can resolve to ENA subsequences in HTML using http://www.ebi.ac.uk/ena/data/view/GG666297&range=18707-20086 <http://www.ebi.ac.uk/ena/data/view/GG666297&range=18707-20086>(see http://www.ebi.ac.uk/ena/browse/data-retrieval-rest#sequence_region_html <http://www.ebi.ac.uk/ena/browse/data-retrieval-rest#sequence_region_html>) Other formats available here. This doesn’t consider complement, rather it simply finds the sub-sequence and spanned features will be shown in complement if this is where they lie.
>
>>
>> If you're only interested in CDS features, you can also use the protein_id identifier (in this case EEI83065.1) which is an xref on the Ensembl transcript to link to ENA e.g.
>> http://www.ebi.ac.uk/ena/data/view/EEI83065.1 <http://www.ebi.ac.uk/ena/data/view/EEI83065.1>Indeed - protein IDs can be used for this. For non-coding features, an addressing system is used that combines accession version, feature type and locations. E.g. http://www.ebi.ac.uk/ena/data/view/Non-coding:KT289404.1:11505..11592:tRNA <http://www.ebi.ac.uk/ena/data/view/Non-coding:KT289404.1:11505..11592:tRNA>. Note that the ‘domain’ of data is also used here (’Non-coding’) and can be considered part of the ID for the feature. Thinking of it this way allows you to consider the generic pattern to be http://www.ebi.ac.uk/ena/data/view/<ENA_identifier> <http://www.ebi.ac.uk/ena/data/view/%3cENA_identifier%3e>.
>
> You could also see these non-coding features by coordinates only (http://www.ebi.ac.uk/ena/data/view/KT289404&range=11505-11592 <http://www.ebi.ac.uk/ena/data/view/KT289404&range=11505-11592>) as in the CDS example above.
>
>
> So - in all cases a little syntactic transformation to build these links, at least from your examples it seems that the information is there.
>
>
> Regarding linking to ENA, my best advice is for you to contact ENA directly at datasubs at ebi.ac.uk <mailto:datasubs at ebi.ac.uk>.
>
>
> Yes - broader documentation at http://www.ebi.ac.uk/ena/browse/data-retrieval-rest <http://www.ebi.ac.uk/ena/browse/data-retrieval-rest> and please do contact us at datasubs at ebi.ac.uk <mailto:datasubs at ebi.ac.uk>.
>
> Thanks,
>
> Guy.
>
>
>
>
>
> Sorry I can't be of more help.
>
> Dan.
>
> --
> Dan Staines, PhD
> Genomics Technology Infrastructure Coordinator
> EMBL-EBI, Wellcome Trust Genome Campus
> Cambridge CB10 1SD, UK
> Tel: +44-(0)1223-492507
>
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>
> ------------------------------------------------------------------------------------
> Guy Cochrane, PhD
> European Nucleotide Archive Team Leader.
>
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
>
> Tel: +44 1223 494444. Fax: +44 1223 494472
>
>
> datasubs at ebi.ac.uk <mailto:datasubs at ebi.ac.uk> (data submissions and general enquiries),
>
> http://www.ebi.ac.uk/ena <http://www.ebi.ac.uk/ena> (submissions, updates, services, info)
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------------------------------------------------------------------------------------
Guy Cochrane, PhD
European Nucleotide Archive Team Leader.
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 1223 494444. Fax: +44 1223 494472
datasubs at ebi.ac.uk (data submissions and general enquiries),
http://www.ebi.ac.uk/ena (submissions, updates, services, info)
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