Hi Hervé and Malcolm,
I have contacted the Ensembl genomes team who produce this database  
and have asked them to respond to you with an update.
Regards
Rhoda

On 13 Mar 2012, at 20:31, Hervé Pagès wrote:

> Hi Malcolm, Rhoda,
>
> Did you hear back from the Ensembl helpdesk about this issue?
>
> AFAICT the issue is still in Ensembl release 66 (released 10 days
> ago). For example, when querying directly the Ensembl Mart, I get
> the following for transcript FBtr0079414 (dmelanogaster):
>
>  Exon Rank in Transcript | Chromosome Name | Strand
>  1                       | 2L              | -1
>  2                       | 2L              | -1
>
>  Exon Chr Start (bp) | Exon Chr End (bp)
>  7218909             | 7220029
>  7218643             | 7218853
>
>  5' UTR Start | 5' UTR End | 3' UTR Start | 3' UTR End
>  7219112      | 7220029    |              |
>               |            | 7218643      | 7218853
>
>  CDS Start | CDS End | CDS Length
>  1         | 203     | 204
>  204       | 204     | 204
>
> Note that querying directly the Ensembl Mart thru the web interface
> allows me to choose database Ensembl Genes 66 but querying with the
> Bioconductor biomaRt package is still accessing Ensembl Genes 65,
> I wonder why, but this is a different story...
>
> So the "CDS Length" column (which, IIUC, is actually supposed to
> report the "Total CDS Length") is still incompatible with the
> exon/UTR starts and ends. If the exon/UTR starts and ends
> are correct then the total CDS length should be 203, not 204.
>
> But also, it could be that the exon/UTR starts and ends are
> incorrect.
>
> Finally note that there is no CDS region on exon 2 (the 3' UTR
> entirely spans exon 2) but the Ensembl Mart reports a CDS region
> of length 1 on this exon (CDS Start = CDS End = 204). This is
> probably why then the reported CDS Length is 204 (at least it's
> consistent with the highest "CDS End" value).
>
> Would be nice to see this dataset fixed.
>
> Thanks,
> H.
>
>
> On 02/15/2012 06:33 AM, Cook, Malcolm wrote:
>> Dear helpdesk@ensemblgenomes.org,
>>
>> I am following up on this issue which I understand Rhoda Kinsella  
>> at EBI to have forwarded to you.
>>
>> I originally identified and reported the issue, first to the  
>> bioconductor email list where Rhoda picked up on it and replied as  
>> below.
>>
>> I am trying to  ensure that there is a tracked issue with  
>> ensemblgenomes.org with my name on it – not that it has to be  
>> resolved with a fix, just I'd like to be assured I know as you  
>> resolve it.
>>
>> If there is anything further I can provide pertaining to describing  
>> or resolving the issue, please advise.
>>
>> Of course the issue may be in fact even further upstream – in  
>> flybase.  I've not tried to find the root cause myself.
>>
>> Thanks,
>>
>> Malcolm Cook
>>
>>
>> From: Rhoda Kinsella<rhoda@ebi.ac.uk<mailto:rhoda@ebi.ac.uk>>
>> Date: Wed, 8 Feb 2012 10:27:02 -0600
>> To: Malcolm Cook<mec@stowers.org<mailto:mec@stowers.org>>
>> Cc: Hervé Pagès<hpages@fhcrc.org<mailto:hpages@fhcrc.org>>, "bioconductor@r-project.org 
>> <mailto:bioconductor@r-project.org>"<bioconductor@r-project.org<mailto:bioconductor@r-project.org 
>> >>
>> Subject: Re: [Hinxton #251937] RE: [BioC]  
>> GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data  
>> anomaly: for some transcripts, the cds cumulative length inferred  
>> from the exon and UTR info doesn't match the "cds_length" attribute  
>> from BioMart
>>
>> Hi Malcolm and Hervé
>> This appears to be a data issue with the Drosophila core database  
>> which was then propagated into BioMart. I have forwarded the issue  
>> to the Ensembl Genomes project as they maintain this database and  
>> they will respond as soon as possible.
>> Regards
>> Rhoda
>>
>>
>> On 7 Feb 2012, at 21:35, Cook, Malcolm wrote:
>>
>> Herve, Thanks so much for digging into this.
>>
>> Rhonda, I had submitted a ticket as suggested to Ensembl helpdesk,  
>> and have included them as recipients to this message (after  
>> changing the subject to include the issue tracker number).
>>
>> Ensembl helpdesk, I expect that Herve's detailed report, below,  
>> provides an example of the reported data anomaly that will help  
>> resolve the underlying issue.
>>
>> Cheers,
>>
>> ~Malcolm
>>
>>
>> -----Original Message-----
>> From: Hervé Pagès [mailto:hpages@fhcrc.org]
>> Sent: Tuesday, February 07, 2012 2:37 PM
>> To: Rhoda Kinsella; bioconductor@r-project.org<mailto:bioconductor@r-project.org 
>> >
>> Cc: Cook, Malcolm
>> Subject: Re: [BioC] GenomicFeatures::makeTranscriptDbFromBiomart -
>> BioMart data anomaly: for some transcripts, the cds cumulative length
>> inferred from the exon and UTR info doesn't match the "cds_length"
>> attribute from BioMart
>>
>> Hi Rhoda, Malcolm, and others,
>>
>> So after taking a closer look at this, I can confirm that the  
>> reported
>> "cds_length" looks wrong for some Fly transcripts. Take for example
>> the FBtr0079414 transcript (minus strand):
>>
>> library(biomaRt)
>> mart1<- useMart(biomart="ensembl",
>> dataset="dmelanogaster_gene_ensembl")
>> attributes<- c("ensembl_transcript_id", "strand",
>> +                 "rank", "exon_chrom_start", "exon_chrom_end",
>> +                 "5_utr_start", "5_utr_end", "3_utr_start",  
>> "3_utr_end",
>> +                 "cds_length")
>> filters<- "ensembl_transcript_id"
>> values<- "FBtr0079414"
>> getBM(attributes=attributes, filters=filters, values=values,  
>> mart=mart1)
>>   ensembl_transcript_id strand rank exon_chrom_start exon_chrom_end
>> 5_utr_start
>> 1           FBtr0079414     -1    1          7218909        7220029
>> 7219112
>> 2           FBtr0079414     -1    2          7218643        7218853
>>      NA
>>   5_utr_end 3_utr_start 3_utr_end cds_length
>> 1   7220029          NA        NA        204
>> 2        NA     7218643   7218853        204
>>
>> 2 exons: The 3' UTR (located on exon 2) spans the entire exon so no
>> CDS on this exon. The start of the 5' UTR (located on exon 1) is 203
>> bases upstream of the exon start. But the reported cds_length is 204.
>> Something looks wrong.
>>
>> For other transcripts, e.g. FBtr0300689 (plus strand), things look  
>> OK:
>>
>> getBM(attributes=attributes, filters=filters, values=values,  
>> mart=mart1)
>>   ensembl_transcript_id strand rank exon_chrom_start exon_chrom_end
>> 5_utr_start
>> 1           FBtr0300689      1    1             7529           8116
>>    7529
>> 2           FBtr0300689      1    2             8193           9484
>>      NA
>>   5_utr_end 3_utr_start 3_utr_end cds_length
>> 1      7679          NA        NA        855
>> 2        NA        8611      9484        855
>>
>> 2 exons: The end of the 5' UTR (located on exon 1) is 437 bases
>> upstream of the exon end. The start of the 3' UTR (located on exon 2)
>> is 418 bases downstream of the exon start. So the CDS total length is
>> 437 + 418 = 855, as reported.
>>
>> @Malcolm and other makeTranscriptDbFromBiomart() users: I'm about to
>> commit a patch to this function so that this anomaly in the Ensembl
>> data causes a warning instead of an error. Also the warning will
>> display the first 6 affected transcripts. The patch will make it into
>> GenomicFeatures 1.6.8 (release) and 1.7.14 (devel), which will become
>> available via biocLite() in the next 24-36 hours.
>>
>> Cheers,
>> H.
>>
>>
>> On 02/06/2012 02:18 PM, Hervé Pagès wrote:
>> Hi Rhoda and others,
>>
>> I still need to check that this error issued by internal helper
>> .extractCdsRangesFromBiomartTable() about "the cds cumulative
>> length inferred from the exon and UTR not matching the cds_length
>> attribute from BioMart" is not a FALSE positive.
>>
>> I'm planning to patch the code in charge of this sanity check
>> so it issues a warning instead of an error and it displays
>> something more useful than just "for some transcripts etc...".
>> Would be nice to know at least for which transcript.
>>
>> I'll keep you informed, thanks!
>> H.
>>
>>
>> On 02/06/2012 12:53 AM, Rhoda Kinsella wrote:
>> Hi Malcolm and Marc,
>> Please submit an Ensembl helpdesk ticket about this issue along  
>> with a
>> detailed example to  
>> (helpdesk@ensembl.org<mailto:helpdesk@ensembl.org>) and we will  
>> look into it.
>> Kind regards
>> Rhoda
>>
>>
>> On 3 Feb 2012, at 20:32, Cook, Malcolm wrote:
>>
>> Hi Marc, and other `library(GenomicFeatures)` users working in fly,
>>
>> I just changed Subject to keep alive one of the issues I still have,
>> namely:
>>
>> I get the following error:
>>
>> library(GenomicFeatures)
>> txdb<-makeTranscriptDbFromBiomart(biomart="ensembl",
>> dataset="dmelanogaster_gene_ensembl", circ_seqs=NULL))
>> Download and preprocess the 'transcripts' data frame ... OK
>> Download and preprocess the 'chrominfo' data frame ... OK
>> Download and preprocess the 'splicings' data frame ... Error
>> in .extractCdsRangesFromBiomartTable(bm_table) :
>> BioMart data anomaly: for some transcripts, the cds cumulative
>> length inferred from the exon and UTR info doesn't match the
>> "cds_length" attribute from BioMart
>>
>>
>> Marc, you already observed that:
>>
>> the data for cds ranges and total cds length (both from biomaRt) no
>> longer agree with each other. In other words, the data from the
>> current
>> drosophila ranges in biomaRt seems to disagree with itself, and
>> so the
>> code is refusing to make a package out of this data as a result.
>> To get the 2nd issue fixed probably involves talking to ensembl
>> about
>> their CDS data for fly to see if we can resolve the discrepancy.
>> I would be happy to take this to them.
>>
>> I still wonder:
>>
>> Can you recommend a best way to get a more diagnostic trace from the
>> attempt at txdb creation so we can correctly report to ensembl team
>> the
>> errant transcript(s) ?
>>
>> I would be happy to take this up with Ensembl team, but, need
>> details which I don't know how to produce.
>>
>>
>> Finally, one the side, here is a tiny suggestion:
>>
>> * change the default for circ_seqs in makeTranscriptDbFromBiomart
>> to be NULL, instead of any organism (human) specific.
>>
>> Regards,
>>
>> --Malcolm
>>
>>
>> R version 2.14.0 (2011-10-31)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] GenomicFeatures_1.6.7 AnnotationDbi_1.16.11 Biobase_2.14.0
>> [4] GenomicRanges_1.6.6 IRanges_1.12.5
>>
>> loaded via a namespace (and not attached):
>> [1] BSgenome_1.22.0 Biostrings_2.22.0 DBI_0.2-5
>> RCurl_1.9-5
>> [5] RSQLite_0.11.1 XML_3.9-4 biomaRt_2.10.0
>> rtracklayer_1.14.4
>> [9] tools_2.14.0 zlibbioc_1.0.0
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org<mailto:Bioconductor@r-project.org>
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>> Rhoda Kinsella Ph.D.
>> Ensembl Production Project Leader,
>> European Bioinformatics Institute (EMBL-EBI),
>> Wellcome Trust Genome Campus,
>> Hinxton
>> Cambridge CB10 1SD,
>> UK.
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org<mailto:Bioconductor@r-project.org>
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages@fhcrc.org<mailto:hpages@fhcrc.org>
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>> Rhoda Kinsella Ph.D.
>> Ensembl Production Project Leader,
>> European Bioinformatics Institute (EMBL-EBI),
>> Wellcome Trust Genome Campus,
>> Hinxton
>> Cambridge CB10 1SD,
>> UK.
>>
>
>
> -- 
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.


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