[ensembl-dev] GO (Joseph Steinberger)

Wed Jan 29 09:04:12 GMT 2020

Please see attached screenshots.

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".

Am I making a mistake?
If not, how do I find the correspondences between contigs and chromosomes?

Best,
Yossi

please see the last column of each of the two screenshots below, for genes and dna associated seq_region_ids, respectively  -

[cid:a9bc14d5-c5c4-48c0-8020-4c45a34ee7ae]

[cid:d6dda68f-1ef7-484f-b83a-7274e34efb63]

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Today's Topics:

   1. G.O. (Joseph Steinberger)
   2. Re: G.O. (Emily Perry)

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Message: 1
Date: Mon, 27 Jan 2020 14:20:08 +0000
From: Joseph Steinberger <joseph.steinberger at weizmann.ac.il>
To: "dev at ensembl.org" <dev at ensembl.org>
Subject: [ensembl-dev] G.O.
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        <DB8P191MB06674E3269802C63DF217875B50B0 at DB8P191MB0667.EURP191.PROD.OUTLOOK.COM>

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Hello All,

What query will get me all the genes of a given GO annotation from a given species from the Ensembl MySQL database?

Sincerely,
Joseph Steinberger

PhD student, laboratory of Naama Barkai, Weizmann Institute
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Message: 2
Date: Mon, 27 Jan 2020 17:46:23 +0000
From: Emily Perry <emily at ebi.ac.uk>
To: Ensembl developers list <dev at ensembl.org>
Subject: Re: [ensembl-dev] G.O.
Message-ID: <9385A72F-8DA8-4A6A-B0C7-B9D21CF9B692 at ebi.ac.uk>
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Hi Joseph

The GO terms are stored in the xref table. They are linked to the transcripts via the object_xref table. The schema is here:
http://www.ensembl.org/info/docs/api/core/core_schema.html <http://www.ensembl.org/info/docs/api/core/core_schema.html>

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.

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.

All the best

Emily

> On 27 Jan 2020, at 14:20, Joseph Steinberger <joseph.steinberger at weizmann.ac.il> wrote:
>
> Hello All,
>
> What query will get me all the genes of a given GO annotation from a given species from the Ensembl MySQL database?
>
> Sincerely,
> Joseph Steinberger
>
> PhD student, laboratory of Naama Barkai, Weizmann Institute
> _______________________________________________
> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org>
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org <https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org>
> Ensembl Blog: http://www.ensembl.info/ <http://www.ensembl.info/>
--
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader
(she/her)

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Genome Campus
Hinxton
Cambridge
CB10 1SD
UK

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