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Hi Charles,<br>
<br>
Could you please include a link to the display you are looking at?<br>
<br>
The data you are retrieving from the MySQL database is displayed on
the 'Domains and Features' tab, for example<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Transcript/Domains?db=core;g=ENSG00000167657;r=19:3959639-3961159;t=ENST00000594894">http://www.ensembl.org/Homo_sapiens/Transcript/Domains?db=core;g=ENSG00000167657;r=19:3959639-3961159;t=ENST00000594894</a><br>
This displays a description like 'Protein kinase domain', which is
the protein_feature.hit_description field from the SQL query.<br>
<br>
<br>
Hope that helps,<br>
mag<br>
<br>
<div class="moz-cite-prefix">On 24/02/2017 13:39, Charles Joseph
Murphy wrote:<br>
</div>
<blockquote
cite="mid:0B22C2A4-0D42-4340-B88C-B6894BAE1A24@med.cornell.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Thanks for your suggestion.
<div class=""><br class="">
</div>
<div class="">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.
<div class=""><br class="">
</div>
<div class="">Thanks!<br class="">
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Feb 23, 2017, at 04:30, Michal
Dabrowski <<a moz-do-not-send="true"
href="mailto:m.dabrowski@nencki.gov.pl" class="">m.dabrowski@nencki.gov.pl</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space; "
class="">
<div class="">How about removing the table
"translation" in the FROM part of your query?</div>
<div class="">Or adding sth like " AND
translation.translation_id='291089’ " to the WHERE
part.</div>
<div class="">Now it seems you will get all the
entries from the "translation" table.</div>
<div class="">m.</div>
<br class="">
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white-space:
normal;
widows: 2;
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0px;
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none;
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style="word-wrap:
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<div class="">
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class="Apple-style-span" style="border-collapse: separate; font-family:
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0px;">
<div class="">
<div
style="word-wrap:
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after-white-space; " class="">
Michal
Dabrowski<br
class="">
</div>
<div
style="word-wrap:
break-word;
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space;
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after-white-space; " class="">
Laboratory of
Bioinformatics</div>
<div
style="word-wrap:
break-word;
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Nencki
Institute</div>
<div
style="word-wrap:
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Pasteur 3 Str</div>
<div
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02-093 Warsaw,
Poland<br
class="">
phone: 48 22
58 92 575</div>
</div>
</span></div>
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</div>
</div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></span><br
class="Apple-interchange-newline">
</div>
<br class="">
<div class="">
<div class="">On Feb 22, 2017, at 5:43 PM, Charles
Joseph Murphy wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite" class="">
<div class="">Hi,<br class="">
<br class="">
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):<br class="">
<br class="">
mysql> use mus_musculus_core_75_38;<br
class="">
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’;<br
class="">
<br class="">
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.<br class="">
<br class="">
Thanks for any help!<br class="">
Charlie<br class="">
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