Forum:SQL-why do we need it in Bioinformatics ?
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6 months ago
iibrams07 ▴ 10

I would like to know if SQL and MySQL are important to know in Bioinformatics. Can you provide some context and an example in which you can underscore the importance of SQL in Bioinformatics ? In particular I will appreciate an answer which puts the context on genomics or omics in general.

Many thanks.

Programming Bioinformatics • 794 views
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Have you searched the forum for sql discussions? You don't need SQL 90% of the time but having some knowledge of the underlying operations will ease working with structured data. You don't need to know syntax/usage for WHERE and GROUP BY and HAVING keywords if you understand filtering and aggregation as concepts.

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My first comment would have been similar to Ram's & /or Pierre's.

I suppose one additional thing that I want to share from my journeys is:

  • Will YOU personally require lots of SQL for your own work? No, in particular if you try to avoid it, not knowing it won't slow you down.

  • But here's the thing. Could it happen that, for a job, position, project where OTHERS have done a lot of work, knowing SQL could be advantageous? I think yes.

I wouldn't make it my top priority until that time, necessarily (unless you just like SQL and want to use it - it's an incredible corpus of knowledge).

Good luck, let us know what happens!!!

VAL

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Thanks. In case one would like to have access to a genome browser such as Ensembl with SQL, is it at all possible? If one may do that, what one can do more than with the graphical interface alone?

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In case one would like to have access to a genome browser such as Ensembl with SQL, is it at all possible?

mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306 -D hg19

If one may do that, what one can do more than with the graphical interface alone?

what does that mean ?

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Thanks. You can retrieve information or data in general directly from the genome browser using click and drag options of the graphical user interface of the browser. I wanted to know what one can do more with SQL and MySQL than what one can do with only the click and drag. The best way to learn is by providing some example.

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In case one would like to have access to a genome browser such as Ensembl with SQL, is it at all possible?

Not sure what you exactly mean by that but you can create a local mirror of part of Ensembl browser. This uses mysql to hold the data. You can find the directions here: https://www.ensembl.org/info/docs/webcode/mirror/install/index.html?redirect=no

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Can you can provide an example (a bioinformatics task) in which you will show what you can do with MySQL and SQL once you created a local mirror ?

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