Brief installation instructions (Under Construction).  Please let me
know if there are problems, corrections, or updates -- Jeff
(jeffrey_chang@stanfordalumni.org).

Please obtain the latest version from the SVN repository.  From the
main project page, click on "Advanced" and then "Source Code
Repository" for instructions.

This is a Python/C package and has the following dependencies that can
be obtained under accepted Open Source licenses:
SWIG
mxTextTools
MySQLdb
Numeric Python
Biopython
libsvm

There are also some dependencies that may be harder to obtain:
Brill's tagger (RBT); can download online
Chris Manning's PnP Classifier; will need to obtain from Dr. Manning
     http://nlp.stanford.edu/~manning/

After you download and install the dependencies, modify the Makefile
in the directory and use it to compile the C code.

Create a database named "jchangdb".  Download data from:
http://bionlp.stanford.edu/~jchang/jchangdb.sql.gz
Uncompress the file then load it into the database.
mysql -u <username> -p jchangdb < jchangdb.sql

Configure the database password and some other stuff in
extracto/config.py.

After you make sure the directory is in Python's library path, check
to make sure things are working by typing:

abbreviation:~> python
Python 2.2.2 (#1, Apr 14 2003, 19:59:21) [GCC 2.96 20000731 (Red Hat
Linux 7.1 2.96-98)] on linux2 Type "help", "copyright", "credits" or
"license" for more information.
 >>> import extracto
 >>> from extracto import abbreviation
 >>> abbreviation.find("this is a test (at)") [('a test', 'at',
0.59675428975156986)]
 >>>

After the database is configured, you should be able to find gene
names:
 >>> genename.find("i'm looking for gene hdac1") [('looking',
0.052454372482526171), ('gene hdac1', 0.7867804275518312)]
 >>>