<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Sending this thread to the Ensembl mailing list now as it appears it may be Ensembl data related. Any ideas why the ENSEMBL transcripts aren't mapped correctly to the GenBank Protein Accessions? </span></div><div><br><span></span></div><div><span>Thank you for the help.</span></div><div><br><span></span></div><div><span>Best regards,</span></div><div><span>Phillipe<br></span></div><div><br></div><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"><font face="Arial" size="2">----- Forwarded Message -----<br><b><span style="font-weight:bold;">From:</span></b> Elena Rivkin <Elena.Rivkin@oicr.on.ca><br><b><span style="font-weight: bold;">To:</span></b> pip pipster
<pipsterpip@yahoo.com><br><b><span style="font-weight: bold;">Cc:</span></b> Junjun Zhang <Junjun.Zhang@oicr.on.ca><br><b><span style="font-weight: bold;">Sent:</span></b> Tuesday, August 23, 2011 1:11 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [BioMart Users] Bug or User error with filtering?<br></font><br><div id="yiv1619547202"><div><div><div style="font-family:Calibri, sans-serif;"><span class="yiv1619547202Apple-style-span" style="font-size:12px;font-family:Verdana;">Hi Phillipe,</span></div><div style="font-family:Calibri, sans-serif;"><span class="yiv1619547202Apple-style-span" style="font-size:12px;"><span style="font-family:Verdana;">From the data you provided, as you said, it looks like these </span><span class="yiv1619547202Apple-style-span" style="font-family:Verdana;">Emsembl transcripts (ENST00000169293) (and many others in similar categories) are not mapped to the GenBank Protein Accessions, and
therefore are not retrieved via quries to BioMart. </span></span></div><div style="font-family:Calibri, sans-serif;"><span class="yiv1619547202Apple-style-span" style="font-size:12px;font-family:Verdana;"><br></span></div><div><font class="yiv1619547202Apple-style-span" style="font-size:12px;" face="times new roman,new york,times,serif"><span style="font-family:Verdana;">Unfortunately, I don't know why that is. I recommned forwarding your question to Ensembl helpdesk, and they might be able to assist you in this matter. </span></font></div><div><font class="yiv1619547202Apple-style-span" style="font-size:12px;" face="times new roman,new york,times,serif"><span style="font-family:Verdana;"><br></span></font></div><div><font class="yiv1619547202Apple-style-span" style="font-size:12px;" face="times new roman,new york,times,serif"><span style="font-family:Verdana;">Thank you. </span></font></div><div style="font-family:Calibri,
sans-serif;font-size:14px;"><br></div><div style="font-family:Calibri, sans-serif;font-size:14px;"><div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><b><font color="#39793b" face="Verdana" size="1"><span style="font-size:9pt;font-family:Verdana;color:rgb(57, 121, 59);font-weight:bold;" lang="EN-CA">Elena Rivkin, PhD</span></font></b><b><font color="black" face="Verdana" size="1"><span style="font-size:9pt;font-family:Verdana;color:black;font-weight:bold;" lang="EN-CA"><br></span></font></b><font color="black" face="Verdana" size="1"><span style="font-size:8pt;font-family:Verdana;color:black;" lang="EN-CA">Outreach and Training Coordinator, Informatics and Bio-computing<br></span></font><font color="black" size="1"><span style="font-size:6pt;color:black;" lang="EN-CA"><br></span></font><b><font color="#39793b" face="Verdana" size="1"><span
style="font-size:9pt;font-family:Verdana;color:rgb(57, 121, 59);font-weight:bold;" lang="EN-CA">Ontario Institute for Cancer Research</span></font></b><font color="black" size="1"><span style="font-size:9pt;color:black;" lang="EN-CA"><br></span></font><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">MaRS Centre, South Tower</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">101 College Street, Suite 800</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font
class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">Toronto, Ontario, Canada M5G 0A3</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;"><br></span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">Tel: 647-258-4316</span></font></div><div class="yiv1619547202MsoNormal"
style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">Toll-free: 1-866-678-6427</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font color="black" face="Verdana" size="1"><span style="font-size:8pt;font-family:Verdana;color:black;" lang="EN-CA">www.oicr.on.ca</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font color="black" face="Verdana" size="1"><span style="font-size:8pt;font-family:Verdana;color:black;" lang="EN-CA"><br></span></font></div><div class="yiv1619547202MsoNormal"
style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font color="black" face="Arial" size="1"><span style="font-size:8pt;font-family:Arial;color:black;" lang="EN-CA">This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font face="Times New Roman" size="3"><span style="font-size:12pt;">
</span></font></div></div></div></div></div><div style="font-family:Calibri, sans-serif;font-size:14px;"><br></div><span id="yiv1619547202OLK_SRC_BODY_SECTION" style="font-size:14px;font-family:Calibri, sans-serif;"><div style="font-family:Calibri;font-size:11pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt;"><span style="font-weight:bold;">From: </span> pip pipster <<a rel="nofollow" ymailto="mailto:pipsterpip@yahoo.com" target="_blank" href="mailto:pipsterpip@yahoo.com">pipsterpip@yahoo.com</a>><br><span style="font-weight:bold;">Reply-To: </span> pip pipster <<a rel="nofollow" ymailto="mailto:pipsterpip@yahoo.com" target="_blank" href="mailto:pipsterpip@yahoo.com">pipsterpip@yahoo.com</a>><br><span style="font-weight:bold;">Date: </span> Tue, 23 Aug 2011 11:50:00 -0400<br><span
style="font-weight:bold;">To: </span> Microsoft Office User <<a rel="nofollow" ymailto="mailto:Elena.Rivkin@oicr.on.ca" target="_blank" href="mailto:Elena.Rivkin@oicr.on.ca">Elena.Rivkin@oicr.on.ca</a>>, Junjun Zhang <<a rel="nofollow" ymailto="mailto:Junjun.Zhang@oicr.on.ca" target="_blank" href="mailto:Junjun.Zhang@oicr.on.ca">Junjun.Zhang@oicr.on.ca</a>>, "<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>" <<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>><br><span style="font-weight:bold;">Cc: </span> Rhoda Kinsella via RT <<a rel="nofollow" ymailto="mailto:helpdesk@ensembl.org" target="_blank" href="mailto:helpdesk@ensembl.org">helpdesk@ensembl.org</a>><br><span style="font-weight:bold;">Subject: </span> Re: [BioMart Users] Bug or User error with
filtering?<br></div><div><br></div><div><div><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt;"><div style="font-family:times, serif;font-size:12pt;"><span>Elena,</span></div><div style="font-family:times, serif;font-size:12pt;"><span>You should be able to follow this up the chain in getting accession numbers.</span></div><div style="font-family:times, serif;font-size:12pt;"><span><br></span></div><div style="font-family:times, serif;font-size:12pt;"><span>a. From Transcript</span></div><div><span><a rel="nofollow" target="_blank" href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=ENST00000169293">http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=ENST00000169293</a><br></span></div><div><span><br></span></div><div><span>b. To Gene (link to this Gene URL is located on Transcript link
above)</span></div><div><span><a rel="nofollow" target="_blank" href="http://www.ncbi.nlm.nih.gov/nuccore/D28593.1">http://www.ncbi.nlm.nih.gov/nuccore/D28593.1</a><br></span></div><div><span><br></span></div><div><span>c. To Protein (link to this Protein URL is located on Gene link above)</span></div><div><span><a rel="nofollow" target="_blank" href="http://www.ncbi.nlm.nih.gov/protein/471128">http://www.ncbi.nlm.nih.gov/protein/471128</a><br></span></div><div><span><br></span></div><div><span>From this stand-point, I am led to believe that the Transcript maps to a </span><span class="yiv1619547202Apple-style-span" style="font-size:16px;">Genbank protein accession and should not be filtered out with the </span><span class="yiv1619547202Apple-style-span" style="font-size:16px;">$query->addFilter("with_protein_id", ["Only"]) filter. But in either case I would like to understand why it's being filtered out since I have to trust
the data I get back and deal with it accordingly.</span></div><div><span class="yiv1619547202Apple-style-span" style="font-size:16px;"><br></span></div><div><span class="yiv1619547202Apple-style-span" style="font-size:16px;">Likewise, the following URL also appears to chain the Gene to the proper transcripts.</span></div><div><a rel="nofollow" target="_blank" href="http://www.ebi.ac.uk/ena/data/view/D28593">http://www.ebi.ac.uk/ena/data/view/D28593</a><br></div><div><br></div><div>It appears that for some reason the data in Emsembl is not mapping transcript ENST00000169293 (and many others in similar categories) to the proper Protein Accession. But that's just my theory and would love to understand it better. Thoughts?</div><div><br></div><div>Best regards,</div><div>Phillipe</div><div><br></div><div><span class="yiv1619547202Apple-style-span" style="font-size:16px;"><br></span></div><div><span class="yiv1619547202Apple-style-span"
style="font-size:16px;"><br></span></div><div><span><br></span></div><div style="font-family:times, serif;font-size:12pt;"><br></div><div style="font-size:12pt;font-family:times, serif;"><div style="font-size:12pt;font-family:times, serif;"><font face="Arial" size="2"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> Elena Rivkin <<a rel="nofollow" ymailto="mailto:Elena.Rivkin@oicr.on.ca" target="_blank" href="mailto:Elena.Rivkin@oicr.on.ca">Elena.Rivkin@oicr.on.ca</a>><br><b><span style="font-weight:bold;">To:</span></b> pip pipster <<a rel="nofollow" ymailto="mailto:pipsterpip@yahoo.com" target="_blank" href="mailto:pipsterpip@yahoo.com">pipsterpip@yahoo.com</a>>; Junjun Zhang <<a rel="nofollow" ymailto="mailto:Junjun.Zhang@oicr.on.ca" target="_blank" href="mailto:Junjun.Zhang@oicr.on.ca">Junjun.Zhang@oicr.on.ca</a>>; "<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank"
href="mailto:users@biomart.org">users@biomart.org</a>" <<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>><br><b><span style="font-weight:bold;">Cc:</span></b> Rhoda Kinsella via RT <<a rel="nofollow" ymailto="mailto:helpdesk@ensembl.org" target="_blank" href="mailto:helpdesk@ensembl.org">helpdesk@ensembl.org</a>><br><b><span style="font-weight:bold;">Sent:</span></b> Monday, August 22, 2011 2:04 PM<br><b><span style="font-weight:bold;">Subject:</span></b> Re: [BioMart Users] Bug or User error with filtering?<br></font><br><div id="yiv1619547202"><div><div><div style="color:rgb(0, 0, 0);font-family:Calibri, sans-serif;"><span class="yiv1619547202Apple-style-span" style="font-size:12px;font-family:Verdana;">Hi Philliple, </span></div><div style="color:rgb(0, 0, 0);font-family:Calibri, sans-serif;"><span class="yiv1619547202Apple-style-span"
style="font-size:12px;font-family:Verdana;">When entering Protein GeneBank ID: BAA05928, and retrieving Ensembl gene id and transcript id, I get the following:</span></div><div style="font-family:Calibri, sans-serif;"><span class="yiv1619547202Apple-style-span" style="font-size:12px;"><span class="yiv1619547202Apple-style-span" style="border-collapse:collapse;line-height:18px;font-family:HelveticaNeue, Helvetica, Arial, sans-serif;"><a rel="nofollow" target="_blank" href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000127241" style="text-decoration:none;"><span style="font-family:Verdana;">ENSG00000127241</span></a><span style="font-family:Verdana;"> </span></span><span class="yiv1619547202Apple-style-span" style="border-collapse:collapse;line-height:18px;font-family:Verdana;"><a rel="nofollow" target="_blank" href="http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=ENST00000337774"
style="text-decoration:underline;">ENST00000337774</a></span></span></div><div style="color:rgb(0, 0, 0);font-family:Calibri, sans-serif;"><span class="yiv1619547202Apple-style-span" style="font-size:12px;font-family:Verdana;"><br></span></div><div style="color:rgb(0, 0, 0);font-family:Calibri, sans-serif;"><span class="yiv1619547202Apple-style-span" style="font-size:12px;"><span class="yiv1619547202Apple-style-span" style="font-family:Verdana;">When entering Protein GeneBank ID: </span><span class="yiv1619547202Apple-style-span" style="font-family:Verdana;">CAC17726</span><span class="yiv1619547202Apple-style-span" style="font-family:Verdana;">, and retrieving Ensembl gene id and transcript id, I get the following:</span></span></div><div style="color:rgb(0, 0, 0);font-family:Calibri, sans-serif;"><span class="yiv1619547202Apple-style-span" style="font-size:12px;font-family:Verdana;">ENSG000000127152, ENST000000357195</span></div><div
style="color:rgb(0, 0, 0);font-family:Calibri, sans-serif;"><span class="yiv1619547202Apple-style-span" style="font-size:12px;font-family:Verdana;"><br></span></div><div style="color:rgb(0, 0, 0);font-family:Calibri, sans-serif;"><span class="yiv1619547202Apple-style-span" style="font-size:12px;font-family:Verdana;">It appears that in the Ensembl mart that you are querying, these GeneBank Ids coorespond to a different transcripts (although to the same gene ID).</span></div><div style="color:rgb(0, 0, 0);font-family:Calibri, sans-serif;"><span class="yiv1619547202Apple-style-span" style="font-size:12px;font-family:Verdana;">Regards, </span></div><div style="color:rgb(0, 0, 0);font-size:14px;font-family:Calibri, sans-serif;"><div><div class="yiv1619547202MsoNormal" style="
margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><b><font color="#39793b" face="Verdana" size="1"><span style="font-size:9pt;color:rgb(57, 121, 59);font-weight:bold;font-family:Verdana;" lang="EN-CA">Elena Rivkin, PhD</span></font></b><b><font color="black" face="Verdana" size="1"><span style="font-size:9pt;color:black;font-weight:bold;font-family:Verdana;" lang="EN-CA"><br></span></font></b><font color="black" face="Verdana" size="1"><span style="font-size:8pt;color:black;font-family:Verdana;" lang="EN-CA">Outreach and Training Coordinator, Informatics and Bio-computing<br></span></font><font color="black" size="1"><span style="font-size:6pt;color:black;" lang="EN-CA"><br></span></font><b><font color="#39793b" face="Verdana" size="1"><span style="font-size:9pt;color:rgb(57, 121, 59);font-weight:bold;font-family:Verdana;" lang="EN-CA">Ontario Institute for
Cancer Research</span></font></b><font color="black" size="1"><span style="font-size:9pt;color:black;" lang="EN-CA"><br></span></font><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">MaRS Centre, South Tower</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">101 College Street, Suite 800</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">Toronto,
Ontario, Canada M5G 0A3</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;"><br></span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">Tel: 647-258-4316</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span
class="yiv1619547202Apple-style-span" style="font-size:11px;">Toll-free: 1-866-678-6427</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font color="black" face="Verdana" size="1"><span style="font-size:8pt;color:black;font-family:Verdana;" lang="EN-CA">www.oicr.on.ca</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font color="black" face="Verdana" size="1"><span style="font-size:8pt;color:black;font-family:Verdana;" lang="EN-CA"><br></span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font color="black" face="Arial" size="1"><span
style="font-size:8pt;color:black;font-family:Arial;" lang="EN-CA">This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font face="Times New Roman" size="3"><span style="font-size:12pt;"> </span></font></div></div></div></div></div><div style="color:rgb(0, 0, 0);font-size:14px;font-family:Calibri, sans-serif;"><br></div><span id="yiv1619547202OLK_SRC_BODY_SECTION"
style="color:rgb(0, 0, 0);font-size:14px;font-family:Calibri, sans-serif;"><div style="font-size:11pt;text-align:left;color:black;border-bottom-width:medium;border-bottom-style:none;border-bottom-color:initial;border-left-width:medium;border-left-style:none;border-left-color:initial;padding-bottom:0in;padding-left:0in;padding-right:0in;border-top-color:rgb(181, 196, 223);border-top-width:1pt;border-top-style:solid;border-right-width:medium;border-right-style:none;border-right-color:initial;padding-top:3pt;font-family:Calibri;"><span style="font-weight:bold;">From: </span> pip pipster <<a rel="nofollow" ymailto="mailto:pipsterpip@yahoo.com" target="_blank" href="mailto:pipsterpip@yahoo.com">pipsterpip@yahoo.com</a>><br><span style="font-weight:bold;">Reply-To: </span> pip pipster <<a rel="nofollow" ymailto="mailto:pipsterpip@yahoo.com" target="_blank" href="mailto:pipsterpip@yahoo.com">pipsterpip@yahoo.com</a>><br><span
style="font-weight:bold;">Date: </span> Mon, 22 Aug 2011 13:51:56 -0400<br><span style="font-weight:bold;">To: </span> Junjun Zhang <<a rel="nofollow" ymailto="mailto:Junjun.Zhang@oicr.on.ca" target="_blank" href="mailto:Junjun.Zhang@oicr.on.ca">Junjun.Zhang@oicr.on.ca</a>>, "<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>" <<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>><br><span style="font-weight:bold;">Cc: </span> Rhoda Kinsella via RT <<a rel="nofollow" ymailto="mailto:helpdesk@ensembl.org" target="_blank" href="mailto:helpdesk@ensembl.org">helpdesk@ensembl.org</a>><br><span style="font-weight:bold;">Subject: </span> Re: [BioMart Users] Bug or User error
with filtering?<br></div><div><br></div><div><div><div style="color:rgb(0, 0, 0);background-color:rgb(255, 255, 255);font-size:12pt;font-family:times, serif;"><div><span>Thank you Junjun.</span></div><div><br><span></span></div><div><span>Elena, to answer your question, I believe the ncbi links in the below thread include a link to the protein where you can get the protein accession number. For example, for the 2 transcripts below you will find links to the following proteins. You will also see that the transcripts are correctly showing up on the URL's as being protein coding.</span></div><div><span><br></span></div><div><span><a rel="nofollow" target="_blank" href="http://www.ncbi.nlm.nih.gov/protein/471128">http://www.ncbi.nlm.nih.gov/protein/471128</a> (accession BAA05928)</span></div><div><span> and</span></div><div><span><a rel="nofollow" target="_blank"
href="http://www.ncbi.nlm.nih.gov/protein/11558488">http://www.ncbi.nlm.nih.gov/protein/11558488</a> (accession CAC17726)</span></div><div><br></div><div>Thank you,</div><div>Phillipe<br></div><div><br></div><div style="font-size:12pt;font-family:times, serif;"><div style="font-size:12pt;font-family:times, serif;"><font face="Arial" size="2"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> Junjun Zhang <<a rel="nofollow" ymailto="mailto:Junjun.Zhang@oicr.on.ca" target="_blank" href="mailto:Junjun.Zhang@oicr.on.ca">Junjun.Zhang@oicr.on.ca</a>><br><b><span style="font-weight:bold;">To:</span></b> pip pipster <<a rel="nofollow" ymailto="mailto:pipsterpip@yahoo.com" target="_blank" href="mailto:pipsterpip@yahoo.com">pipsterpip@yahoo.com</a>>; "<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>" <<a rel="nofollow" ymailto="mailto:users@biomart.org"
target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>><br><b><span style="font-weight:bold;">Cc:</span></b> Rhoda Kinsella via RT <<a rel="nofollow" ymailto="mailto:helpdesk@ensembl.org" target="_blank" href="mailto:helpdesk@ensembl.org">helpdesk@ensembl.org</a>><br><b><span style="font-weight:bold;">Sent:</span></b> Monday, August 22, 2011 12:59 PM<br><b><span style="font-weight:bold;">Subject:</span></b> Re: [BioMart Users] Bug or User error with filtering?<br></font><br><div id="yiv1619547202"><div><div><div>Hi Phillipe,</div></div></div><div><br></div><div>I am forwarding your questions to the Ensembl Helpdesk. Ensembl team is the best to answer questions about data contents in Ensembl
databases.</div><div><br></div><div>Cheers,</div><div>Junjun</div><div><br></div><div><br></div><span id="yiv1619547202OLK_SRC_BODY_SECTION"><div style="font-size:11pt;text-align:left;color:black;border-bottom-width:medium;border-bottom-style:none;border-bottom-color:initial;border-left-width:medium;border-left-style:none;border-left-color:initial;padding-bottom:0in;padding-left:0in;padding-right:0in;border-top-color:rgb(181, 196, 223);border-top-width:1pt;border-top-style:solid;border-right-width:medium;border-right-style:none;border-right-color:initial;padding-top:3pt;font-family:Calibri;"><span style="font-weight:bold;">From: </span> Elena Rivkin <<a rel="nofollow" ymailto="mailto:Elena.Rivkin@oicr.on.ca" target="_blank" href="mailto:Elena.Rivkin@oicr.on.ca">Elena.Rivkin@oicr.on.ca</a>><br><span style="font-weight:bold;">Date: </span> Mon, 22 Aug 2011 10:46:35 -0400<br><span style="font-weight:bold;">To:
</span> pip pipster <<a rel="nofollow" ymailto="mailto:pipsterpip@yahoo.com" target="_blank" href="mailto:pipsterpip@yahoo.com">pipsterpip@yahoo.com</a>>, Rhoda Kinsella <<a rel="nofollow" ymailto="mailto:rhoda@ebi.ac.uk" target="_blank" href="mailto:rhoda@ebi.ac.uk">rhoda@ebi.ac.uk</a>>, "<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>" <<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>><br><span style="font-weight:bold;">Subject: </span> Re: [BioMart Users] Bug or User error with filtering?<br></div><div><br></div><blockquote id="yiv1619547202MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT:#b5c4df 5 solid;PADDING:0 0 0 5;MARGIN:0 0 0 5;"><div><div style="word-wrap:break-word;color:rgb(0, 0, 0);font-size:14px;font-family:Calibri, sans-serif;"><div><div><div>Hi
Phillipe, </div><div>Can you let me know, for these two transcripts, what are their Genbank protein accessions. I cant find them. </div><div><br></div><div>Thank you. </div><div><div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><b><font color="#39793b" face="Verdana" size="1"><span style="font-size:9pt;color:rgb(57, 121, 59);font-weight:bold;font-family:Verdana;" lang="EN-CA">Elena Rivkin, PhD</span></font></b><b><font color="black" face="Verdana" size="1"><span style="font-size:9pt;color:black;font-weight:bold;font-family:Verdana;" lang="EN-CA"><br></span></font></b><font color="black" face="Verdana" size="1"><span style="font-size:8pt;color:black;font-family:Verdana;" lang="EN-CA">Outreach and Training Coordinator, Informatics and Bio-computing<br></span></font><font color="black" size="1"><span
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Research</span></font></b><font color="black" size="1"><span style="font-size:9pt;color:black;" lang="EN-CA"><br></span></font><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">MaRS Centre, South Tower</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">101 College Street, Suite 800</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">Toronto, Ontario,
Canada
M5G 0A3</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;"><br></span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span" style="font-size:11px;">Tel: 647-258-4316</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font class="yiv1619547202Apple-style-span" face="Verdana" size="3"><span class="yiv1619547202Apple-style-span"
style="font-size:11px;">Toll-free: 1-866-678-6427</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font color="black" face="Verdana" size="1"><span style="font-size:8pt;color:black;font-family:Verdana;" lang="EN-CA">www.oicr.on.ca</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font color="black" face="Verdana" size="1"><span style="font-size:8pt;color:black;font-family:Verdana;" lang="EN-CA"><br></span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font color="black" face="Arial" size="1"><span style="font-size:8pt;color:black;font-family:Arial;" lang="EN-CA">This
message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.</span></font></div><div class="yiv1619547202MsoNormal" style="margin-top:0in;margin-right:0in;margin-bottom:0.0001pt;margin-left:0in;font-size:12pt;font-family:'Times New Roman';"><font face="Times New Roman" size="3"><span style="font-size:12pt;"> </span></font></div></div></div></div></div><div><br></div><span id="yiv1619547202OLK_SRC_BODY_SECTION"><div
style="font-size:11pt;text-align:left;color:black;border-bottom-width:medium;border-bottom-style:none;border-bottom-color:initial;border-left-width:medium;border-left-style:none;border-left-color:initial;padding-bottom:0in;padding-left:0in;padding-right:0in;border-top-color:rgb(181, 196, 223);border-top-width:1pt;border-top-style:solid;border-right-width:medium;border-right-style:none;border-right-color:initial;padding-top:3pt;font-family:Calibri;"><span style="font-weight:bold;">From: </span> pip pipster <<a rel="nofollow" ymailto="mailto:pipsterpip@yahoo.com" target="_blank" href="mailto:pipsterpip@yahoo.com">pipsterpip@yahoo.com</a>><br><span style="font-weight:bold;">Reply-To: </span> pip pipster <<a rel="nofollow" ymailto="mailto:pipsterpip@yahoo.com" target="_blank" href="mailto:pipsterpip@yahoo.com">pipsterpip@yahoo.com</a>><br><span style="font-weight:bold;">Date: </span> Mon, 22 Aug 2011 10:32:43 -0400<br><span
style="font-weight:bold;">To: </span> Rhoda Kinsella <<a rel="nofollow" ymailto="mailto:rhoda@ebi.ac.uk" target="_blank" href="mailto:rhoda@ebi.ac.uk">rhoda@ebi.ac.uk</a>>, "<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>" <<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>><br><span style="font-weight:bold;">Subject: </span> Re: [BioMart Users] Bug or User error with filtering?<br></div><div><br></div><div><div><div style="color:rgb(0, 0, 0);background-color:rgb(255, 255, 255);font-size:12pt;font-family:times, serif;"><div><span>After doing more investigation, something definitely isn't adding up. As it turns out, filtering by </span>Genbank protein accession is what we want and we need the ability to exclude. The 2 transcripts below are examples (they show up as protein coding
Genbank as well as Ensembl) but there are thousands more like this. The filter below
is taking them out despite them having a Genbank protein accession. What may be causing this?<br></div><div><span><br></span></div><div><span><span style="font-weight:bold;">ENST00000169293</span><br><a rel="nofollow" target="_blank" href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=ENST00000169293">http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=ENST00000169293</a></span></div><div><span><a rel="nofollow" target="_blank" href="http://www.ncbi.nlm.nih.gov/nuccore/D28593">http://www.ncbi.nlm.nih.gov/nuccore/D28593</a>?<br></span></div><div><span><a rel="nofollow" target="_blank" href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000127241;r=3:186964149-187009745;t=ENST00000169293">http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000127241;r=3:186964149-187009745;t=ENST00000169293</a><br><br><span style="font-weight:bold;">ENST00000345514</span><br><a
rel="nofollow" target="_blank" href="http://www.ncbi.nlm.nih.gov/gene?term=ENST00000345514">http://www.ncbi.nlm.nih.gov/gene?term=ENST00000345514</a><br><a rel="nofollow" target="_blank" href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000127152;r=14:99635624-99737822;t=ENST00000345514">http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000127152;r=14:99635624-99737822;t=ENST00000345514</a></span></div><div><br><span></span></div><div><br><span></span></div><div><span>Filter used:</span></div><div>Manual (non-Perl)<br><span class="yiv1619547202tab"> </span>Homo sapiens genes (GRCh37.p3)<br> <span class="yiv1619547202tab"> </span><span style="font-weight:bold;">Filters</span><br> <span class="yiv1619547202tab"> </span><span class="yiv1619547202tab"> </span>with protein ID(s): Only<br> <span class="yiv1619547202tab"> </span><span
style="font-weight:bold;">Attributes</span><br> <span class="yiv1619547202tab"> </span><span class="yiv1619547202tab">
</span>Ensembl Gene ID<br> <span class="yiv1619547202tab"> </span><span class="yiv1619547202tab"> </span>Ensembl Transcript ID</div><div><br></div><div>Same problem occurs using Perl filter as well<br> $query->addFilter("with_protein_id", ["Only"]);</div><div><br></div><div style="font-size:12pt;font-family:times, serif;"><div style="font-size:12pt;font-family:times, serif;"><font face="Arial" size="2"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> pip pipster <<a rel="nofollow" ymailto="mailto:pipsterpip@yahoo.com" target="_blank" href="mailto:pipsterpip@yahoo.com">pipsterpip@yahoo.com</a>><br><b><span style="font-weight:bold;">To:</span></b> Rhoda Kinsella <<a rel="nofollow" ymailto="mailto:rhoda@ebi.ac.uk" target="_blank" href="mailto:rhoda@ebi.ac.uk">rhoda@ebi.ac.uk</a>><br><b><span style="font-weight:bold;">Cc:</span></b> "<a rel="nofollow"
ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>" <<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>><br><b><span style="font-weight:bold;">Sent:</span></b> Monday, August 22, 2011 8:07 AM<br><b><span style="font-weight:bold;">Subject:</span></b> Re: [BioMart Users] Bug or User error with filtering?<br></font><br><div id="yiv1619547202"><div style="color:rgb(0, 0, 0);background-color:rgb(255, 255, 255);font-size:12pt;font-family:times, serif;"><div><span>Rhoda,</span></div><div><span>Thank you for the feedback, very helpful. The Gene Type filter, 'protein_coding' will
likely work, however it doesn't allow me to do an 'exclude' type filter (i.e. give me everything except for the non protein-coding genes). Do you know if you can still do an exclude using the method you described?</span></div><div><br><span></span></div><div><span>Thank
you!</span></div><div><span>Phillipe</span></div><div><br></div><div style="font-size:12pt;font-family:times, serif;"><div style="font-size:12pt;font-family:times, serif;"><font face="Arial" size="2"><hr size="1"><b><span style="font-weight:bold;">From:</span></b> Rhoda Kinsella <<a rel="nofollow" ymailto="mailto:rhoda@ebi.ac.uk" target="_blank" href="mailto:rhoda@ebi.ac.uk">rhoda@ebi.ac.uk</a>><br><b><span style="font-weight:bold;">To:</span></b> pip pipster
<<a rel="nofollow" ymailto="mailto:pipsterpip@yahoo.com" target="_blank" href="mailto:pipsterpip@yahoo.com">pipsterpip@yahoo.com</a>><br><b><span style="font-weight:bold;">Cc:</span></b> "<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>" <<a rel="nofollow" ymailto="mailto:users@biomart.org" target="_blank" href="mailto:users@biomart.org">users@biomart.org</a>><br><b><span style="font-weight:bold;">Sent:</span></b> Monday, August 22, 2011 5:04 AM<br><b><span style="font-weight:bold;">Subject:</span></b> Re: [BioMart Users] Bug or User error with filtering?<br></font><br><div id="yiv1619547202">Hi Phillipe<div>You are filtering using the protein ID (Genbank protein accession) and as this Ensembl protein ID does not have a corresponding Genbank protein accession, you will not get this ENSP. Please filter using the Gene type filter and select protein_coding. That way you
will get the ENSP data you require.</div><div>Regards</div><div>Rhoda</div><div><br></div><div><br><div><div>On 21 Aug 2011, at 22:54, pip pipster wrote:</div><br class="yiv1619547202Apple-interchange-newline"><blockquote type="cite"><div><div style="color:rgb(0, 0, 0);background-color:rgb(255, 255, 255);font-size:12pt;font-family:times, serif;"><div>We are seeing strange things occur with the protein ID filter. For example, transcript ENST00000345514 is being filtered out by the following search below. However, you can see that it indeed has a Preotin ID shown here: <a rel="nofollow" target="_blank" href="http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000127152;r=14:99635624-99737861;t=ENST00000345514">http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000127152;r=14:99635624-99737861;t=ENST00000345514</a> . Any idea why this is being
filtered? Could this be a bug in
Biomart/Data or User Error?<br><br>Manual (non-Perl)<br><span class="yiv1619547202tab"> </span>Homo sapiens genes (GRCh37.p3)<br> <span class="yiv1619547202tab"> </span><span style="font-weight:bold;">Filters</span><br> <span class="yiv1619547202tab"> </span><span class="yiv1619547202tab"> </span>with protein ID(s): Only<br> <span class="yiv1619547202tab"> </span><span style="font-weight:bold;">Attributes</span><br> <span class="yiv1619547202tab"> </span><span class="yiv1619547202tab"> </span>Ensembl Gene ID<br> <span class="yiv1619547202tab"> </span><span class="yiv1619547202tab"> </span>Ensembl Transcript ID</div><div><br></div><div>Same problem occurs using Perl filter as well<br> $query->addFilter("with_protein_id", ["Only"]);</div><div><br></div><div>Thank
you,</div><div>Phillipe<br></div></div></div>_______________________________________________<br>Users mailing list<br><a rel="nofollow" ymailto="mailto:Users@biomart.org" target="_blank" href="mailto:Users@biomart.org">Users@biomart.org</a><br><a rel="nofollow" target="_blank" href="https://lists.biomart.org/mailman/listinfo/users">https://lists.biomart.org/mailman/listinfo/users</a><br></blockquote></div><br><div> <span class="yiv1619547202Apple-style-span" style="border-collapse:separate;color:rgb(0, 0, 0);font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;orphans:2;text-indent:0px;text-transform:none;white-space:normal;widows:2;word-spacing:0px;font-family:Helvetica;"><div style="word-wrap:break-word;"><span class="yiv1619547202Apple-style-span" style="border-collapse:separate;color:rgb(0, 0,
0);font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;orphans:2;text-indent:0px;text-transform:none;white-space:normal;widows:2;word-spacing:0px;font-family:Helvetica;"><div style="word-wrap:break-word;"><div>Rhoda Kinsella Ph.D.</div><div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;font:normal normal normal 12px/normal Helvetica;">Ensembl Bioinformatician,</div></div><div>European Bioinformatics
Institute (EMBL-EBI),<br>Wellcome Trust Genome Campus, </div><div>Hinxton<br>Cambridge CB10 1SD,</div><div>UK.</div></div></span></div></span> </div><br></div></div><br><br></div></div></div></div><br><br></div></div></div></div></div></span></div></div></blockquote></span>
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