[ensembl-dev] MySQL query to retrieve protein annotation

mag mr6 at ebi.ac.uk
Fri Feb 24 13:47:14 GMT 2017


Hi Charles,

Could you please include a link to the display you are looking at?

The data you are retrieving from the MySQL database is displayed on the 
'Domains and Features' tab, for example
http://www.ensembl.org/Homo_sapiens/Transcript/Domains?db=core;g=ENSG00000167657;r=19:3959639-3961159;t=ENST00000594894
This displays a description like 'Protein kinase domain', which is the 
protein_feature.hit_description field from the SQL query.


Hope that helps,
mag

On 24/02/2017 13:39, Charles Joseph Murphy wrote:
> Thanks for your suggestion.
>
> Sorry to bother with another question, but I’ve spent a couple hours 
> trying to figure this out and wonder if either of you could help me 
> with something else. How might I go about getting the descriptions of 
> the protein annotations. For example, for PFAM domains I want what is 
> displayed on the Ensembl website. E.g. “Pkinase” instead of PF00069.
>
> Thanks!
>
>> On Feb 23, 2017, at 04:30, Michal Dabrowski 
>> <m.dabrowski at nencki.gov.pl <mailto:m.dabrowski at nencki.gov.pl>> wrote:
>>
>> How about removing the table "translation" in the FROM part of your 
>> query?
>> Or adding sth like " AND translation.translation_id='291089’ " to the 
>> WHERE part.
>> Now it seems you will get all the entries from the "translation" table.
>> m.
>>
>> Michal Dabrowski
>> Laboratory of Bioinformatics
>> Nencki Institute
>> Pasteur 3 Str
>> 02-093 Warsaw, Poland
>> phone: 48 22 58 92 575
>>
>>
>> On Feb 22, 2017, at 5:43 PM, Charles Joseph Murphy wrote:
>>
>>> Hi,
>>>
>>> I’ am trying to use the Ensembl public MySQL query to retrieve 
>>> protein annotation for all of a genome’s genes. While trying to 
>>> figure out the right MySQL queries to make, I’ am testing it out 
>>> with just one transcript’s translation (ENSMUST00000120187):
>>>
>>> mysql> use mus_musculus_core_75_38;
>>> mysql> SELECT protein_feature.hit_name, protein_feature.hit_start, 
>>> protein_feature.hit_end, protein_feature.seq_start, 
>>> protein_feature.seq_end, protein_feature.evalue, 
>>> protein_feature.perc_ident, protein_feature.hit_description, 
>>> protein_feature.translation_id FROM protein_feature, translation 
>>> WHERE protein_feature.translation_id = '291089’;
>>>
>>> But this returns around 1.4 million entries. What might be the best 
>>> way to get all the protein annotation for ENSMUST00000120187? I’ am 
>>> aware of BioMart and the Perl API, but would rather query via MySQL. 
>>> I’ am continuing to read into the InterProScan pipeline and Ensembl 
>>> documentation, but am not quite sure yet how to go about this.
>>>
>>> Thanks for any help!
>>> Charlie
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>
>
>
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