[ensembl-dev] Biomart downloading inconsistencies

Wed Feb 4 16:53:43 GMT 2015

Denise,

I need to make a correction on my previous email.

When I'm downloading from the perl APIs I use a subset of chromosomes so,
if I download from ensembl.org the gene counts I get are in agreement with
the gene counts from the BIOMART website.

To sum up I got:
Perl APIs + ensembl.org | all results
Perl APIs + useast.ensembl.org| partial results
BIOMART web app + ensembl.org| partial results
BIOMART web app + useast.ensembl.org| partial results

I'm quite confident that the results I got from Perl APIs + ensembl.org
are whole because I submitted several other queries and they all seem to
agree with the BIOMART web app counts. However, I would still like to know
whether there is a way to confirm that the transcript count is also
correct.

Thank you very much again,
Venetia

On 2/4/15 9:51 AM, "Venetia Pliatsika" <Venetia.Pliatsika at jefferson.edu>
wrote:

>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=ENSG0000000
>>1
>>084;r=6:53497341-53616970
>>
>>http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG0000009
>>0
>>989;r=4:55853616-55905034
>>
>>http://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG0000021
>>3
>>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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