What Are The Public Sql Servers For Bioinformatics ?

Question

[Pierre Lindenbaum]

Do you know any public scientific SQL server ?

For example, I would cite:

• UCSC: http://genome.ucsc.edu/FAQ/FAQdownloads#download29
• ENSEMBL: http://uswest.ensembl.org/info/data/mysql.html
• GO: http://www.geneontology.org/GO.database.shtml#mirrors

(I'll give a +1 to each correct answer)

Answer 1

[Pierre Lindenbaum]

1000 Genomes: since June 16, 2011: http://www.1000genomes.org/public-ensembl-mysql-instance

mysql -h mysql-db.1000genomes.org -u anonymous -P 4272

Answer 2

[2184687-1231-83-]

Ensembl and EnsemblGenomes both have MySQL access to the main dbs and mart dbs:

mysql -hensembldb.ensembl.org -P5306 -uanonymous
mysql -hmysql.ebi.ac.uk -P4157 -uanonymous

MySQL DB (BioMart)

mysql -hensembldb.ensembl.org -P5316 -uanonymous

EnsemblGenomes

mysql -hmysql.ebi.ac.uk -P4157 -uanonymous

[Bert Overduin]

I am afraid that is not completely correct ....

Ensembl up to version 47:

mysql -hensembldb.ensembl.org -P3306 -uanonymous

Ensembl up from version 48 onwards:

mysql -hensembldb.ensembl.org -P5306 -uanonymous

Ensembl BioMart up to version 47:

mysql -hmartdb.ensembl.org -P3316 -uanonymous

Ensembl BioMart from version 48 onwards:

mysql -hmartdb.ensembl.org -P5316 -uanonymous

See also: http://www.ensembl.org/info/data/mysql.html

Answer 3

[Ian Simpson]

Flybase has direct access to its postgres chado database.

http://flybase.org/forums/viewtopic.php?f=14&t=114

hostname: flybase.org
port: 5432
username: flybase
password: no password
database name: flybase

e.g.

psql -h flybase.org -U flybase flybase

[Casey Bergman]

Very helpful sample queries for the FlyBase chado database can be found here:

http://gmod.org/wiki/FlyBase_Field_Mapping_Tables

Answer 4

[Neilfws]

PublicHouse - uses the BioWarehouse system; requires user registration.

Answer 5

[Ian Simpson]

This is quite an important one for people doing mouse work, though it is important to note that JAX offer Mart and Batch-Query functionality through the web site as well which may well suit many peoples needs.

• Direct SQL Access to MGI
• http://www.informatics.jax.org/software.shtml#sql

Note that this is a public 'free' service, but that you do need to contact user support to get your login and password. They are also happy to provide some custom SQL scripts to get you started.

Answer 6

[Reece]

http://unison-db.org/

Unison is a comprehensive set of protein sequences with lots of precomputed results of many types. Unison was designed primarily for rapid mining of complex combinations of protein features. There's a simple homology-based structure viewer that can map SNPs and arbitrary regions onto structures.

The Unison source and website were released under the Academic Free License, and the data are released under the Creative Commons. There's a public PostgreSQL service (Try 'psql -h unison-db.org -U PUBLIC -d unison'). Command line tools are available. Loading and computing are automated and incremental, and coordinated by a makefile.

See http://unison-db.org/tour/ and http://unison-db.org/doc/ for examples and connection information.

The site is currently hosted at Genentech, my former employer. Unison is used internally at Genentech, but not updated as often as I used to (but there's a page with versions of source databases).

-Reece

Answer 7

[Steve Moss]

Don't forget EnsEMBL's new US East MySQL mirror too:

mysql -h useastdb.ensembl.org -u anonymous -P 5306

See here http://www.ensembl.info/blog/2011/07/06/ensembl-now-has-a-second-public-mysql-server/

You can also run your own mirrors in the cloud http://www.ensembl.info/blog/2011/07/12/run-a-private-ensembl-mysql-in-the-cloud/ ;-)

Answer 8

[Sander Timmer]

Not really MySQL databases but next to proper SQL access there are quite a few datasources out there that are accessible through REST/SOAP. Many of these sources are listed on http://www.biocatalogue.org/.

Answer 9

[Pierre Lindenbaum]

(Update 2013-10-08)

The Nencki Genomics Database (NGD) extends the functionality of Ensembl funcgen.

The key enhancements over the Ensembl:

1. A user can add private data, analyze them alongside the public data, and manage access rights.
2. Inside the database, we provide efficient algorithms for computing intersections between the regulatory features, and for mapping them to the genes.

mysql -h database.nencki-genomics.org -u public

[always_learning]

If you wish then I can compile a single page document ( Essentially a copy paste) containing information on all these public sql server.