MySQL queries permission

[Flores, Mario (NIH/NLM/NCBI) [F]]

Hi

 

My name is Mario Flores and I am a postdoc at NCBI Computational Biology Branch at NIH.

 

Would you let me execute MySQL queries that may be excessive?

 

Please let me know if I should submit a request to a different department or format.

 

Thank you

 

[Brian Lee]

Dear Mario,

Thank you for using the UCSC Genome Browser and your question about accessing the MySQL server.

You can feel free to use the server, please see a note on http://genome.ucsc.edu/goldenPath/help/mysql.html that one of our conditions of use is to avoid excessive program-driven queries. Program-driven access is generally limited to a maximum of one hit every 15 seconds and no more than 5,000 hits per day.

You may find it more efficient to download the actual mysql tables by going to our downloads page (http://hgdownload.soe.ucsc.edu/downloads.html), finding the assembly you're interested in and clicking the "Annotation database" link. For example, here is a the link to the Human hg38 annotation tables: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/

Another option is to use Virtual Box to install a local version of the Genome Browser to operate what we call a Genome Browser in a Box (GBiB), where you can use a specific hgMirror tool to locally download the tables to your GBiB and then run MySQL queries or other operations on your local version of the Browser: 
http://genome.ucsc.edu/goldenpath/help/gbib.html
http://genome.ucsc.edu/goldenpath/help/gbib.html#GbibMirroring

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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