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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>I am looking for a bit of clarification on retrieving Vega Identifiers for Genes, Transcripts and Translations through the API or directly through MySql (using the Xref, Object_Xref and external_db tables). <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>(I am using human Brca2 as an example, gene: <span style='font-size:10.0pt;font-family:Consolas;color:black'>ENSG00000139618, transcript: ENST00000380152, translation: ENSP00000369497, looking at Release 67 database here</span>)<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I can see that the database name I appear to need to use for a Gene’s Vega ID is OTTG and for a Transcript the database is OTTT<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>[however, there are ‘possible’? other databases available : Vega_gene, Vega_gene_like, Vega_transcript, Vega_mouse_transcript, Vega_transcript_like]<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>in the case of Translations, there are no xrefs for OTTP, but there are a couple of entries for the ‘Vega_translation’ - one of which appears to have the correct Vega ID: <span style='font-size:10.0pt;font-family:Consolas;color:black'>OTTHUMP00000018803, whilst the other – which is given the same ‘priority’ - appears to be an internal database id: 153814<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>Am I missing some obvious trick to pull these out<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>In the PerlAPI have gone down the route of using:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>@</span><span style='font-size:10.0pt;font-family:Consolas;color:#A000F0'>xrefs</span><span style='font-size:10.0pt;font-family:Consolas;color:black'> </span><span style='font-size:10.0pt;font-family:Consolas;color:#B22200'>= </span><span style='font-size:10.0pt;font-family:Consolas;color:black'>@</span><span style='font-size:10.0pt;font-family:Consolas;color:#A000F0'>{ $translation->get_all_object_xrefs('OTT%') }</span><span style='font-size:10.0pt;font-family:Consolas;color:#B22200'>;<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:#B22200'>and <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>@</span><span style='font-size:10.0pt;font-family:Consolas;color:#A000F0'>xrefs</span><span style='font-size:10.0pt;font-family:Consolas;color:black'> </span><span style='font-size:10.0pt;font-family:Consolas;color:#B22200'>= </span><span style='font-size:10.0pt;font-family:Consolas;color:black'>@</span><span style='font-size:10.0pt;font-family:Consolas;color:#A000F0'>{ $translation->get_all_object_xrefs('Vega%') }</span><span style='font-size:10.0pt;font-family:Consolas;color:#B22200'>;<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:#B22200'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>is there a better method?<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:Consolas;color:black'>I was hoping I would be consistently be able to use the database names ‘OTTG’, ‘OTTT’ and ‘OTTP’, but it looks like I also need ‘Vega%’ to be safe…<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB'>Trevor Paterson PhD<br></span></b><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB'><a href="mailto:trevor.paterson@roslin.ed.ac.uk"><span style='color:blue'>trevor.paterson@roslin.ed.ac.uk</span></a></span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:EN-GB'><o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB'>Bioinformatics <br>The Roslin Institute<br>Royal (Dick) School of Veterinary Studies<br>University of Edinburgh<br>Easter Bush<br>Midlothian<br>EH25 9RG<br>Scotland UK<br><br>phone +44 (0)131 651 9157<br><br><a href="http://bioinformatics.roslin.ed.ac.uk/"><span style='color:blue'>http://bioinformatics.roslin.ed.ac.uk/</span></a></span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";color:black;mso-fareast-language:EN-GB'><br></span><span style='font-size:10.0pt;font-family:"Times New Roman","serif";color:navy;mso-fareast-language:EN-GB'><br></span><span style='font-size:12.0pt;font-family:"Arial","sans-serif";color:green;mso-fareast-language:EN-GB'>Please consider the environment before printing this e-mail</span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:EN-GB'><o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><i><span style='font-size:10.0pt;font-family:"Times New Roman","serif";color:navy;mso-fareast-language:EN-GB'>The University of Edinburgh is a charitable body, registered in Scotland with registration number SC005336</span></i><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB'><br><b>Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender.</b></span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-language:EN-GB'> <o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>