<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 22 Apr 2016, at 10:27, Dan Staines <<a href="mailto:dstaines@ebi.ac.uk" class="">dstaines@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">Hi Dimitry,<br class=""><br class=""><blockquote type="cite" class="">KE159678.1:CDS:7103..8458<br class=""><br class="">GG666297.1:CDS:complement(18707..20086)<br class=""></blockquote><br class="">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 class=""><br class="">These identifiers are of the form accession:feature_type:location e.g.<br class="">GG666297.1:CDS:complement(18707..20086)<br class="">which refers to this feature:<br class="">FT CDS complement(18707..20086)<br class="">FT /codon_start=1<br class="">FT /transl_table=11<br class="">FT /locus_tag="HMPREF0077_0851"<br class="">FT /product="ATPase/histidine kinase/DNA gyrase B/HSP90 domain<br class="">...<br class="">FT /protein_id="EEI83065.1"<br class="">...<br class="">from this expanded CON (i.e an entry composed of multiple sub-entries):<br class=""><a href="http://www.ebi.ac.uk/ena/data/view/GG666297&display=text&expanded=true" class="">http://www.ebi.ac.uk/ena/data/view/GG666297&display=text&expanded=true</a><br class=""><br class="">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.<br class=""></div></blockquote><div><br class=""></div><div>You can resolve to ENA subsequences in HTML using <a href="http://www.ebi.ac.uk/ena/data/view/GG666297&range=18707-20086" class="">http://www.ebi.ac.uk/ena/data/view/GG666297&range=18707-20086</a> (see <a href="http://www.ebi.ac.uk/ena/browse/data-retrieval-rest#sequence_region_html" class="">http://www.ebi.ac.uk/ena/browse/data-retrieval-rest#sequence_region_html</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.</div><div><br class=""></div><blockquote type="cite" class=""><div class=""><br class="">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 class=""><a href="http://www.ebi.ac.uk/ena/data/view/EEI83065.1" class="">http://www.ebi.ac.uk/ena/data/view/EEI83065.1</a><br class=""><br class=""></div></blockquote><div>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" class="">http://www.ebi.ac.uk/ena/data/view/Non-coding:KT289404.1:11505..11592:tRNA</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 <a href="http://www.ebi.ac.uk/ena/data/view/<ENA_identifier>" class="">http://www.ebi.ac.uk/ena/data/view/<ENA_identifier></a>.</div><div><br class=""></div><div>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" class="">http://www.ebi.ac.uk/ena/data/view/KT289404&range=11505-11592</a>) as in the CDS example above.</div><div><br class=""></div><div><br class=""></div><div>So - in all cases a little syntactic transformation to build these links, at least from your examples it seems that the information is there.</div><br class=""><blockquote type="cite" class=""><div class="">Regarding linking to ENA, my best advice is for you to contact ENA directly at <a href="mailto:datasubs@ebi.ac.uk" class="">datasubs@ebi.ac.uk</a>.<br class=""><br class=""></div></blockquote><div><br class=""></div><div>Yes - broader documentation at <a href="http://www.ebi.ac.uk/ena/browse/data-retrieval-rest" class="">http://www.ebi.ac.uk/ena/browse/data-retrieval-rest</a> and please do contact us at <a href="mailto:datasubs@ebi.ac.uk" class="">datasubs@ebi.ac.uk</a>.</div><div><br class=""></div><div>Thanks,</div><div><br class=""></div><div>Guy.</div><div><br class=""></div><div><br class=""></div><div><br class=""></div><br class=""><blockquote type="cite" class=""><div class="">Sorry I can't be of more help.<br class=""><br class="">Dan.<br class=""><br class="">-- <br class="">Dan Staines, PhD<br class="">Genomics Technology Infrastructure Coordinator<br class="">EMBL-EBI, Wellcome Trust Genome Campus<br class="">Cambridge CB10 1SD, UK<br class="">Tel: +44-(0)1223-492507<br class=""><br class="">_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""><div apple-content-edited="true" class="">
<div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class="Apple-interchange-newline"><br class=""></div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">------------------------------------------------------------------------------------</div><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Guy Cochrane, PhD<br class=""><div class="">European Nucleotide Archive Team Leader.</div><div class=""><br class=""></div><div class="">European Bioinformatics Institute (EMBL-EBI)</div><div class="">European Molecular Biology Laboratory</div><div class="">Wellcome Trust Genome Campus</div><div class="">Hinxton</div><div class="">Cambridge CB10 1SD</div><div class="">United Kingdom</div><div class=""><br class=""></div><div class="">Tel: +44 1223 494444. Fax: +44 1223 494472</div><div class=""><br class=""></div><br class="Apple-interchange-newline"><a href="mailto:datasubs@ebi.ac.uk" class="">datasubs@ebi.ac.uk</a> (data submissions and general enquiries), <br class=""><br class="Apple-interchange-newline"><a href="http://www.ebi.ac.uk/ena" class="">http://www.ebi.ac.uk/ena</a> (submissions, updates, services, info)<br class="">------------------------------------------------------------------------------------<br class=""><br class=""></div>
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