Thank you Junjun. 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.
http://www.ncbi.nlm.nih.gov/protein/471128 (accession BAA05928) and http://www.ncbi.nlm.nih.gov/protein/11558488 (accession CAC17726) Thank you, Phillipe ________________________________ From: Junjun Zhang <[email protected]> To: pip pipster <[email protected]>; "[email protected]" <[email protected]> Cc: Rhoda Kinsella via RT <[email protected]> Sent: Monday, August 22, 2011 12:59 PM Subject: Re: [BioMart Users] Bug or User error with filtering? Hi Phillipe, I am forwarding your questions to the Ensembl Helpdesk. Ensembl team is the best to answer questions about data contents in Ensembl databases. Cheers, Junjun From: Elena Rivkin <[email protected]> Date: Mon, 22 Aug 2011 10:46:35 -0400 To: pip pipster <[email protected]>, Rhoda Kinsella <[email protected]>, "[email protected]" <[email protected]> Subject: Re: [BioMart Users] Bug or User error with filtering? Hi Phillipe, >Can you let me know, for these two transcripts, what are their Genbank protein >accessions. I cant find them. > > >Thank you. >Elena Rivkin, PhD >Outreach and Training Coordinator, Informatics and Bio-computing > >Ontario Institute for Cancer Research >MaRS Centre, South Tower >101 College Street, Suite 800 >Toronto, Ontario, Canada M5G 0A3 > > >Tel: 647-258-4316 >Toll-free: 1-866-678-6427 >www.oicr.on.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. > > >From: pip pipster <[email protected]> >Reply-To: pip pipster <[email protected]> >Date: Mon, 22 Aug 2011 10:32:43 -0400 >To: Rhoda Kinsella <[email protected]>, "[email protected]" <[email protected]> >Subject: Re: [BioMart Users] Bug or User error with filtering? > > > >After doing more investigation, something definitely isn't adding up. As it >turns out, filtering by 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? > > > >ENST00000169293 >http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=ENST00000169293 >http://www.ncbi.nlm.nih.gov/nuccore/D28593? > >http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000127241;r=3:186964149-187009745;t=ENST00000169293 > >ENST00000345514 >http://www.ncbi.nlm.nih.gov/gene?term=ENST00000345514 >http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000127152;r=14:99635624-99737822;t=ENST00000345514 > > > > >Filter used: >Manual (non-Perl) > Homo sapiens genes (GRCh37.p3) > Filters > with protein ID(s): Only > Attributes > Ensembl Gene ID > Ensembl Transcript ID > > >Same problem occurs using Perl filter as well > $query->addFilter("with_protein_id", ["Only"]); > > > >________________________________ >From: pip pipster <[email protected]> >To: Rhoda Kinsella <[email protected]> >Cc: "[email protected]" <[email protected]> >Sent: Monday, August 22, 2011 8:07 AM >Subject: Re: [BioMart Users] Bug or User error with filtering? > > >Rhoda, >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? > > >Thank you! >Phillipe > > > >________________________________ >From: Rhoda Kinsella <[email protected]> >To: pip pipster <[email protected]> >Cc: "[email protected]" <[email protected]> >Sent: Monday, August 22, 2011 5:04 AM >Subject: Re: [BioMart Users] Bug or User error with filtering? > > >Hi Phillipe >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. >Regards >Rhoda > > > > >On 21 Aug 2011, at 22:54, pip pipster wrote: > >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: >http://useast.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000127152;r=14:99635624-99737861;t=ENST00000345514 > . Any idea why this is being filtered? Could this be a bug in Biomart/Data >or User Error? >> >>Manual (non-Perl) >> Homo sapiens genes (GRCh37.p3) >> Filters >> with protein ID(s): Only >> Attributes >> Ensembl Gene ID >> Ensembl Transcript ID >> >> >>Same problem occurs using Perl filter as well >> $query->addFilter("with_protein_id", ["Only"]); >> >> >>Thank you, >>Phillipe >>_______________________________________________ >>Users mailing list >>[email protected] >>https://lists.biomart.org/mailman/listinfo/users >> > >Rhoda Kinsella Ph.D. >Ensembl Bioinformatician, >European Bioinformatics Institute (EMBL-EBI), >Wellcome Trust Genome Campus, >Hinxton >Cambridge CB10 1SD, >UK. > > > > >
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