This directory contains a dump of the UCSC genome annotation database for
the Jul. 2007 assembly of the mouse genome (mm9, NCBI Build 37)
from the Mouse Genome Sequencing Consortium.
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Mouse Genome Sequencing Consortium,
and the National Center for Biotechnology Information (NCBI).
See also: http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=10090
Files included in this directory (updated nightly):
- *.sql files: the MySQL commands used to create the tables
- *.txt.gz files: the database tables in a tab-delimited format
compressed with gzip.
To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
If you plan to download a large file or multiple files from this
directory, we recommend you use ftp rather than downloading the files
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to
the directory goldenPath/mm9/database/. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP \
Or with wget, all files:
wget --timestamping \
With wget, a single file:
wget --timestamping \
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/
To uncompress the *.txt.gz files:
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.
To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql mm9 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql mm9 --local-infile=1 \
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
All the annotations in this directory are freely available for public use,
except for the Swiss-Prot/UniProt data in knownGene.txt, which has the
UniProt copyright (c) 2002 - 2004 UniProt consortium
For non-commercial use all databases and documents in the UniProt FTP
directory may be copied and redistributed freely, without advance
permission, provided that this copyright statement is reproduced with
For commercial use all databases and documents in the UniProt FTP
directory, except the files
may be copied and redistributed freely, without advance permission,
provided that this copyright statement is reproduced with each copy.
More information for commercial users can be found in:
From January 1, 2005, all databases and documents in the UniProt FTP
directory may be copied and redistributed freely by all entities,
without advance permission, provided that this copyright statement is
reproduced with each copy.
This file last updated: 2007-07-26 - 26 July 2007
Apache/2.2.15 (CentOS) Server at hgdownload-test.sdsc.edu Port 80