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Please see attached screenshots.</div>
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I find that while fungi_ascomycota1_collection_core_45_98_1 associates genes with the seq_region_id corresponding to the "contig", the dna genomic sequences are associated with the seq_region_id corresponding to the "chromosomes".</div>
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Am I making a mistake? <br>
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If not, how do I find the correspondences between contigs and chromosomes?</div>
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Best,</div>
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Yossi<br>
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<div class="PlainText"><b>please see the last column of each of the two screenshots below, for genes and dna associated seq_region_ids, respectively -</b>
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________________________________________<br>
From: Dev <dev-bounces@ensembl.org> on behalf of dev-request@ensembl.org <dev-request@ensembl.org><br>
Sent: Tuesday, 28 January 2020 14:00<br>
To: dev@ensembl.org<br>
Subject: Dev Digest, Vol 11, Issue 9<br>
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Today's Topics:<br>
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1. G.O. (Joseph Steinberger)<br>
2. Re: G.O. (Emily Perry)<br>
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Message: 1<br>
Date: Mon, 27 Jan 2020 14:20:08 +0000<br>
From: Joseph Steinberger <joseph.steinberger@weizmann.ac.il><br>
To: "dev@ensembl.org" <dev@ensembl.org><br>
Subject: [ensembl-dev] G.O.<br>
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Hello All,<br>
<br>
What query will get me all the genes of a given GO annotation from a given species from the Ensembl MySQL database?<br>
<br>
Sincerely,<br>
Joseph Steinberger<br>
<br>
PhD student, laboratory of Naama Barkai, Weizmann Institute<br>
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Message: 2<br>
Date: Mon, 27 Jan 2020 17:46:23 +0000<br>
From: Emily Perry <emily@ebi.ac.uk><br>
To: Ensembl developers list <dev@ensembl.org><br>
Subject: Re: [ensembl-dev] G.O.<br>
Message-ID: <9385A72F-8DA8-4A6A-B0C7-B9D21CF9B692@ebi.ac.uk><br>
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Hi Joseph<br>
<br>
The GO terms are stored in the xref table. They are linked to the transcripts via the object_xref table. The schema is here:<br>
<a href="http://www.ensembl.org/info/docs/api/core/core_schema.html">http://www.ensembl.org/info/docs/api/core/core_schema.html</a> <<a href="http://www.ensembl.org/info/docs/api/core/core_schema.html">http://www.ensembl.org/info/docs/api/core/core_schema.html</a>><br>
<br>
It is not our job to write your MySQL queries for you, but we can point you to the appropriate tables if it is not obvious. I agree that in the case of GO terms, it is not obvious which tables contain this information, but it is up to you to craft a suitable
query.<br>
<br>
Just like many of the other tasks you have asked about, MySQL is not a great way to do this. Any MySQL query you do will not be ontology aware - only the most specific GO terms will be linked to the transcripts in the tables. This means that a query for all
associations for a GO term with daughter terms will not return associations with the daughter terms, which would be an incomplete dataset. BioMart and our APIs are written to be ontology aware, which means that a similar query with those would return the associations
with the daughter terms too ? we recommend using one of those for a query like this.<br>
<br>
All the best<br>
<br>
Emily<br>
<br>
> On 27 Jan 2020, at 14:20, Joseph Steinberger <joseph.steinberger@weizmann.ac.il> wrote:<br>
><br>
> Hello All,<br>
><br>
> What query will get me all the genes of a given GO annotation from a given species from the Ensembl MySQL database?<br>
><br>
> Sincerely,<br>
> Joseph Steinberger<br>
><br>
> PhD student, laboratory of Naama Barkai, Weizmann Institute<br>
> _______________________________________________<br>
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--<br>
Dr Emily Perry (Pritchard)<br>
Ensembl Outreach Project Leader<br>
(she/her)<br>
<br>
European Bioinformatics Institute (EMBL-EBI)<br>
European Molecular Biology Laboratory<br>
Wellcome Genome Campus<br>
Hinxton<br>
Cambridge<br>
CB10 1SD<br>
UK<br>
<br>
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