[ensembl-dev] Biomart downloading inconsistencies

Wed Feb 4 14:51:23 GMT 2015

Denise,

Thank you for your reply.

My team is always downloading using the perl APIs and I did use them.
However, I still have the same problem even with those. The files I get
seem incomplete, in fact I got maximum 56330 genes through the perl APIs
and, through BIOMART the max I got was 34413. We are also downloading one
chromosome at a time when using the perl APIs.

I tried accessing the individual genes through BIOMART and, indeed, I can
see them on both servers. Also, when I perform a result count using the
same filters I do get the same numbers (60249 / 64814) but, as I
mentioned, I'm unable to download all of them. Is there a count for the
distinct transcripts as well?

So, do you have another suggestion as to how to download them and, is
there a way to confirm that the results I get are complete other than the
gene count?

Thank you again,
Venetia

On 2/3/15 3:59 PM, "Denise Carvalho-Silva" <denise at ebi.ac.uk> wrote:

>Hi Venetia,
>
>The useast is a mirror of the main site and should contain the same data
>as our www.ensembl.org in the UK.
>
>This is so much so that when I search for the genes from your list below,
>e.g. ENSG00000001084, ENSG00000090989 on useast.ensembl.org I do get
>results for them, so they are not missing on useast.
>
>http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000001
>084;r=6:53497341-53616970
>
>http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000090
>989;r=4:55853616-55905034
>
>http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000213
>347;r=5:177301461-177312757
>
>In addition to this, when I perform a query in BioMart (on both useast and
>main sites) using the filter you did, I do get the same number of entries
>as expected, i.e. 60249 / 64814 Genes (see the attached screenshots).
>
>BioMart is not the ideal tool for retrieval of genome wide data. So what I
>think it's happening here is that the results get truncated on the useast
>since the servers get overloaded there as it's working hours in the US
>(but almost bed time in the UK) and there is a time out on the website.
>
>You could perhaps try to perform this query in batches (for example for
>each chr at once).
>
>The best alternative for genome wide queries is to use our Perl APIs:
>
>http://www.ensembl.org/info/docs/api/core/index.html#api
>http://www.ensembl.org/info/docs/api/core/core_tutorial.html
>http://www.ensembl.org/info/docs/Doxygen/core-api/index.html
>
>Hope it makes sense.
>
>Kind regards,
>
>Denise
>Ensembl Outreach
>
>
>> Hello,
>>
>> I'm sending because I found a discrepancy between the
>> http://useast.ensembl.org/biomart/martview/ and
>> <http://www.ensembl.org/biomart/martservice>
>>
>>http://www.ensembl.org/biomart/<http://www.ensembl.org/biomart/martview>m
>>artview<http://www.ensembl.org/biomart/martview>
>> web services and would like to confirm that the data I have are
>>complete.
>>
>> I submitted the following search on both the UK and the US East servers:
>>
>> Dataset
>> Homo sapiens genes (GRCh38)
>> Filters
>> With protein(Genbank) ID(s): Excluded
>> Attributes
>> Ensembl Gene ID
>> Ensembl Transcript ID
>> Chromosome Name
>> Strand
>> Unspliced (Transcript)
>> Associated Gene Name
>>
>> But I got different results. The difference is quite big as they include
>> 67,482 and 78,820 sequences accordingly. As far as I checked the file
>>from
>> ensembl.org contained all entries that useast.ensembl.org had, including
>> some more.
>>
>> Here are some genes that weren't included in the useast.ensmbl.org but
>> were present in ensembl.org:
>> ENSG00000001084
>> ENSG00000090989
>> ENSG00000104723
>> ENSG00000108846
>> ENSG00000109158
>> ENSG00000109171
>> ENSG00000109180
>> ENSG00000109182
>> ENSG00000109184
>> ENSG00000109452
>> ENSG00000118564
>> ENSG00000118579
>> ENSG00000120708
>> ENSG00000123415
>> ENSG00000129187
>> ENSG00000133835
>> ENSG00000138678
>> ENSG00000145216
>> ENSG00000145868
>> ENSG00000151466
>> ENSG00000163138
>> ENSG00000170365
>> ENSG00000180104
>> ENSG00000196353
>> ENSG00000213347
>> ENSG00000234492
>> ENSG00000245526
>> ENSG00000250328
>> ENSG00000278610
>>
>> After noticing this I re-downloaded from useast.ensembl.org several
>>times.
>> Each time the file had a different size and none of the files had the
>>same
>> size as the ensembl.org one.
>>
>> I would like to know whether the data I downloaded from ensembl.org
>> include all results or if you suggest getting them again in a different
>> way.
>>
>> Thank you in advance,
>> Venetia
>>
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>

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