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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Guy, thanks a lot for the detailed and thoughtful answer!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Dmitry.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Guy Cochrane EBI<br><b>Sent:</b> Sunday, April 24, 2016 13:15<br><b>To:</b> Ensembl developers list<br><b>Cc:</b> Nicole Silvester<br><b>Subject:</b> Re: [ensembl-dev] Conversion of ENA xref ids into working URLs<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>On 22 Apr 2016, at 12:19, Dmitry Kuznetsov <<a href="mailto:Dmitry.Kuznetsov@isb-sib.ch">Dmitry.Kuznetsov@isb-sib.ch</a>> wrote:<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Dan and Guy, thanks for your answers and suggestions.</span><o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>>You can resolve to ENA subsequences in HTML using<span class=apple-converted-space> </span><a href="http://www.ebi.ac.uk/ena/data/view/GG666297&range=18707-20086"><span style='color:purple'>http://www.ebi.ac.uk/ena/data/view/GG666297&range=18707-20086</span></a><br><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>is there any way to rather end up at this [equivalent] URL:<span class=apple-converted-space> </span><a href="http://www.ebi.ac.uk/ena/data/view/ACGC01000047"><span style='color:purple'>http://www.ebi.ac.uk/ena/data/view/ACGC01000047</span></a></span><o:p></o:p></p></div></div></blockquote><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>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 <a href="ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/doc/usrman.txt">ftp://ftp.ebi.ac.uk/pub/databases/ena/sequence/release/doc/usrman.txt</a>.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>(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.)<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Guy.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><br><br><br><o:p></o:p></p><div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>?</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks,</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Dmitry.</span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> </span><o:p></o:p></p></div><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><div><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span class=apple-converted-space><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> </span></span><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'><a href="mailto:dev-bounces@ensembl.org"><span style='color:purple'>dev-bounces@ensembl.org</span></a><span class=apple-converted-space> </span>[<a href="mailto:dev-bounces@ensembl.org"><span style='color:purple'>mailto:dev-bounces@ensembl.org</span></a>]<span class=apple-converted-space> </span><b>On Behalf Of<span class=apple-converted-space> </span></b>Guy Cochrane EBI<br><b>Sent:</b><span class=apple-converted-space> </span>Friday, April 22, 2016 12:37<br><b>To:</b><span class=apple-converted-space> </span>Ensembl developers list<br><b>Cc:</b><span class=apple-converted-space> </span>Nicole Silvester<br><b>Subject:</b><span class=apple-converted-space> </span>Re: [ensembl-dev] Conversion of ENA xref ids into working URLs</span><o:p></o:p></p></div></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><p class=MsoNormal>On 22 Apr 2016, at 10:27, Dan Staines <<a href="mailto:dstaines@ebi.ac.uk"><span style='color:purple'>dstaines@ebi.ac.uk</span></a>> wrote:<o:p></o:p></p></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div><p class=MsoNormal>Hi Dimitry,<br><br><br><br><o:p></o:p></p></div><div><p class=MsoNormal>KE159678.1:CDS:7103..8458<br><br>GG666297.1:CDS:complement(18707..20086)<o:p></o:p></p></div><div><p class=MsoNormal><br>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.<br><br>These identifiers are of the form accession:feature_type:location e.g.<br>GG666297.1:CDS:complement(18707..20086)<br>which refers to this feature:<br>FT CDS complement(18707..20086)<br>FT /codon_start=1<br>FT /transl_table=11<br>FT /locus_tag="HMPREF0077_0851"<br>FT /product="ATPase/histidine kinase/DNA gyrase B/HSP90 domain<br>...<br>FT /protein_id="EEI83065.1"<br>...<br>from this expanded CON (i.e an entry composed of multiple sub-entries):<br><a href="http://www.ebi.ac.uk/ena/data/view/GG666297&display=text&expanded=true"><span style='color:purple'>http://www.ebi.ac.uk/ena/data/view/GG666297&display=text&expanded=true</span></a><br><br>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.<o:p></o:p></p></div></div></blockquote><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>You can resolve to ENA subsequences in HTML using<span class=apple-converted-space> </span><a href="http://www.ebi.ac.uk/ena/data/view/GG666297&range=18707-20086"><span style='color:purple'>http://www.ebi.ac.uk/ena/data/view/GG666297&range=18707-20086</span></a>(see <a href="http://www.ebi.ac.uk/ena/browse/data-retrieval-rest#sequence_region_html"><span style='color:purple'>http://www.ebi.ac.uk/ena/browse/data-retrieval-rest#sequence_region_html</span></a>) 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.<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal style='margin-bottom:12.0pt'><br>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.<br><a href="http://www.ebi.ac.uk/ena/data/view/EEI83065.1"><span style='color:purple'>http://www.ebi.ac.uk/ena/data/view/EEI83065.1</span></a><o:p></o:p></p></div></blockquote><div><div><p class=MsoNormal>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. <a href="http://www.ebi.ac.uk/ena/data/view/Non-coding:KT289404.1:11505..11592:tRNA"><span style='color:purple'>http://www.ebi.ac.uk/ena/data/view/Non-coding:KT289404.1:11505..11592:tRNA</span></a>. 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<span class=apple-converted-space> </span><a href="http://www.ebi.ac.uk/ena/data/view/%3cENA_identifier%3e"><span style='color:purple'>http://www.ebi.ac.uk/ena/data/view/<ENA_identifier></span></a>.<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>You could also see these non-coding features by coordinates only (<a href="http://www.ebi.ac.uk/ena/data/view/KT289404&range=11505-11592"><span style='color:purple'>http://www.ebi.ac.uk/ena/data/view/KT289404&range=11505-11592</span></a>) as in the CDS example above.<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>So - in all cases a little syntactic transformation to build these links, at least from your examples it seems that the information is there.<o:p></o:p></p></div></div><div><p class=MsoNormal><br><br><br><o:p></o:p></p></div><div><p class=MsoNormal style='margin-bottom:12.0pt'>Regarding linking to ENA, my best advice is for you to contact ENA directly at<span class=apple-converted-space> </span><a href="mailto:datasubs@ebi.ac.uk"><span style='color:purple'>datasubs@ebi.ac.uk</span></a>.<o:p></o:p></p></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>Yes - broader documentation at <a href="http://www.ebi.ac.uk/ena/browse/data-retrieval-rest"><span style='color:purple'>http://www.ebi.ac.uk/ena/browse/data-retrieval-rest</span></a><span class=apple-converted-space> </span>and please do contact us at<span class=apple-converted-space> </span><a href="mailto:datasubs@ebi.ac.uk"><span style='color:purple'>datasubs@ebi.ac.uk</span></a>.<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>Thanks,<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>Guy.<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><p class=MsoNormal><br><br><br><o:p></o:p></p></div><div><div><p class=MsoNormal>Sorry I can't be of more help.<br><br>Dan.<br><br>--<span class=apple-converted-space> </span><br>Dan Staines, PhD<br>Genomics Technology Infrastructure Coordinator<br>EMBL-EBI, Wellcome Trust Genome Campus<br>Cambridge CB10 1SD, UK<br>Tel: +44-(0)1223-492507<br><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org"><span style='color:purple'>Dev@ensembl.org</span></a><br>Posting guidelines and subscribe/unsubscribe info:<span class=apple-converted-space> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev"><span style='color:purple'>http://lists.ensembl.org/mailman/listinfo/dev</span></a><br>Ensembl Blog:<span class=apple-converted-space> </span><a href="http://www.ensembl.info/"><span style='color:purple'>http://www.ensembl.info/</span></a><o:p></o:p></p></div></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div><p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'> </span><o:p></o:p></p></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>------------------------------------------------------------------------------------</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>Guy Cochrane, PhD</span><o:p></o:p></p></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>European Nucleotide Archive Team Leader.</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>European Bioinformatics Institute (EMBL-EBI)</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>European Molecular Biology Laboratory</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>Wellcome Trust Genome Campus</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>Hinxton</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>Cambridge CB10 1SD</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>United Kingdom</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>Tel: +44 1223 494444. Fax: +44 1223 494472</span><o:p></o:p></p></div></div><div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'> </span><o:p></o:p></p></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'><br><a href="mailto:datasubs@ebi.ac.uk"><span style='color:purple'>datasubs@ebi.ac.uk</span></a> (data submissions and general enquiries), <br><br><a href="http://www.ebi.ac.uk/ena"><span style='color:purple'>http://www.ebi.ac.uk/ena</span></a> (submissions, updates, services, info)<br>------------------------------------------------------------------------------------</span><o:p></o:p></p></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'>_______________________________________________<br>Dev mailing list </span><a href="mailto:Dev@ensembl.org"><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:purple'>Dev@ensembl.org</span></a><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'><br>Posting guidelines and subscribe/unsubscribe info:<span class=apple-converted-space> </span></span><a href="http://lists.ensembl.org/mailman/listinfo/dev"><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:purple'>http://lists.ensembl.org/mailman/listinfo/dev</span></a><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif"'><br>Ensembl Blog:<span class=apple-converted-space> </span></span><a href="http://www.ensembl.info/"><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:purple'>http://www.ensembl.info/</span></a><o:p></o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>------------------------------------------------------------------------------------<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Guy Cochrane, PhD<o:p></o:p></span></p><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>European Nucleotide Archive Team Leader.<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>European Bioinformatics Institute (EMBL-EBI)<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>European Molecular Biology Laboratory<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Wellcome Trust Genome Campus<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Hinxton<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Cambridge CB10 1SD<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>United Kingdom<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'>Tel: +44 1223 494444. Fax: +44 1223 494472<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><p class=MsoNormal style='margin-bottom:12.0pt'><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";color:black'><br><a href="mailto:datasubs@ebi.ac.uk">datasubs@ebi.ac.uk</a> (data submissions and general enquiries), <br><br><a href="http://www.ebi.ac.uk/ena">http://www.ebi.ac.uk/ena</a> (submissions, updates, services, info)<br>------------------------------------------------------------------------------------<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p></div></body></html>