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Ah, I see older Ensembl builds have NULL for all protein_feature.hit_description (in the case of PFAM at least). Such as homo_sapiens_core_75_37 and mus_musculus_core_75_38, where as builds like mus_musculus_core_84_38 to have non-NULL entries. What is the
reason?
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<div class="">On Feb 24, 2017, at 08:53, Charles Joseph Murphy <<a href="mailto:chm2059@med.cornell.edu" class="">chm2059@med.cornell.edu</a>> wrote:</div>
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Ah, I see! Got what I need then.
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<div class="">I did look at that before, but was looking at a protein that was NULL for for all of its protein_feature.hit_description—so I thought that must not be the column I wanted. Indeed, when I looked at another protein I see the relevant protein feature
descriptions.</div>
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<div class="">Thanks,</div>
<div class="">Charlie<br class="">
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<div class="">On Feb 24, 2017, at 08:47, mag <<a href="mailto:mr6@ebi.ac.uk" class="">mr6@ebi.ac.uk</a>> wrote:</div>
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<div bgcolor="#FFFFFF" text="#000000" class="">Hi Charles,<br class="">
<br class="">
Could you please include a link to the display you are looking at?<br class="">
<br class="">
The data you are retrieving from the MySQL database is displayed on the 'Domains and Features' tab, for example<br class="">
<a class="moz-txt-link-freetext" href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ensembl.org_Homo-5Fsapiens_Transcript_Domains-3Fdb-3Dcore-3Bg-3DENSG00000167657-3Br-3D19-3A3959639-2D3961159-3Bt-3DENST00000594894&d=DwMD-g&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=42JQQMixyqEk_50qjTplRgTZ_EGDJJsuQveAoAiYHF4&s=pqq2PH9CrrIMGHwMPH48uwxJ7PkIc0Z7zat21aZAxn0&e=">http://www.ensembl.org/Homo_sapiens/Transcript/Domains?db=core;g=ENSG00000167657;r=19:3959639-3961159;t=ENST00000594894</a><br class="">
This displays a description like 'Protein kinase domain', which is the protein_feature.hit_description field from the SQL query.<br class="">
<br class="">
<br class="">
Hope that helps,<br class="">
mag<br class="">
<br class="">
<div class="moz-cite-prefix">On 24/02/2017 13:39, Charles Joseph Murphy wrote:<br class="">
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<blockquote cite="mid:0B22C2A4-0D42-4340-B88C-B6894BAE1A24@med.cornell.edu" type="cite" class="">
Thanks for your suggestion.
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<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.
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<div class="">Thanks!<br class="">
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<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>
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<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>
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Michal Dabrowski<br class="">
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Laboratory of Bioinformatics</div>
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Nencki Institute</div>
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Pasteur 3 Str</div>
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02-093 Warsaw, Poland<br class="">
phone: 48 22 58 92 575</div>
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<div class="">On Feb 22, 2017, at 5:43 PM, Charles Joseph Murphy wrote:</div>
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<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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Ensembl Blog: <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ensembl.info_&d=DwICAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=O3yXKBF_L8Fov58BXORGXKqPP85pYddrOwCg4PV2BCY&m=sFzq4UGStyyyqxcYwKg1sYrx82JQgUeOKkdbO6WDTkk&s=JMBBIONVy389Y7sX5ni0e0yfHEyGM63l7RTeC83AAsI&e=" class="">
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