Python scripts for processing USPTO inventor and patent data

The following collection of scripts performs pre- and post-processing on patent data as part of the patent inventor disambiguation process.

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Processing patents

There are two ways to get started:

• Run preprocess.sh. This will run the preprocessor on any files contained in the PATENTROOT directory (defaults to the root directory)

• run parse.py directly to customize which directories are processed and which regex is used to process the files. Run parse.py -h to see the relevant command-line options. Follow with clean.py then consolidate.py to obtain a full set of tables.

See "Configuring the Preprocessing Environment" below.

Contributing to the Patent Processor Project

Contributions are welcome, for source code development, testing (including validation and verification), uses cases, etc. We're targeting general PEP-compliance, so even an issue noting where we could do better is appreciated.

Contributing code

Pull requests are especially welcome. Here are a few pointers which will make everything easier:

• Small, tightly constrained commits.
• New files should be in their own commit, and committed before they are used in subsequent commits.
• Commits should tell a story in a logical sequence. It should be possible to understand the gist of the development just from reading the commits (hard, but worthwhile goal).
• The ideal commit:
  • Unit (or similar) test for a single functionality.
  • Implementation to pass the unit test.
  • Documentation (the "why") of the function/method in the appropriate location (platform dependent).
  • 0 or 1 use of the new functionality in production.
  • Further uses of functionality should go in future commits.
• Formatting updates, code cleanup and renaming should go into independent commits.
• Submit only code which is covered by working unit tests.
• Testing scripts, including unit tests, integration tests and functional tests go in the test directory.
• Code which does work goes in the lib directory.
• Code which provides a workflow (i.e., processing patents or building necessary infrastructure) goes in the top level directory. In the future, much of this code may be put into a bin directory.
• Test code should follow the pattern test/test_libfile.py. This pattern may change in the future, whence this documentation will change at that time.

You must rebase before issuing a pull request: git pull --rebase <upstream> master.

Coding style

Start with PEP8. A very large number of extremely intelligent software engineers working at the wealthiest corporations on the planet have more or less agreed on a standard set of conventions allowing J. Random Coder (that's you and I) to read and write Python like the Big Boys and Girls (PyLadies!). It highly unlikely we can improve on these guidelines.

That said, rules are rules and exists to broken once in a while. So, optimize for readability. Specifically:

• Use vowels, not secret shorthand 1337 cmptr cd fr nmng vrbls.
• Line length to 80 characters, no more.

Configuring the Preprocessing Environment

The python-based preprocessor is tested on Ubuntu 12.04 and MacOSX 10.6. Any flavor of unixen with the following installed should work:

• Python 2.7.3
• scipy package for Python
• sqlite3 --> Note: you need version 3.7.15.1 or higher
• More? Please file an issue if you find another dependency.

In order to properly configure the preprocessing environment, the end user must manually perform the following:

• Download the relevant XML files which need to be processed. These can be placed in any directory, but parse.py assumes the root directory /.

• Set the PATENTROOT environment variable (assuming a UNIX environment). This can be customized later using command line options, but for the purposes of running unit tests, it is necessary to actually export the environment variable, e.g.

  export PATENTROOT = /path/to/xml/files

• You do not need to have the .sqlite3 files already in the project root directory, as they will be automatically generated by parse.py.

Configuring for testing

Currently, testing requires having the environment configured as above, and having some of the processing results. That is, testing the "cleaning" phase requires having files from the parse phase.

This is sub-optimal for testing.

In the future, the small test xml file in the fixtures directory can be used to construct mock data such that testing the cleaning phase can proceed independently of any other phase.

Disambiguating inventor names

Inventor disambiguation is performed using order restricted Bayesian inference, implemented in c++ and hosted on github. The application compiles and runs on both Ubuntu Linux 12.04 and MacOS Snow Leopard (OSX 10.6). An external library for solving a quadratic program is required, which is free for academic use.

Postprocessing

After disambiguating, the resulting unique inventors are listed by number in an output file (e.g., final.txt). This output file then processed to tie the inventor number to the inventor name in the input database. The program which performs this linking is in the c++ disambiguation code. After the linking is done, verification proceeds.

Verification

Verifying the results of the disambiguation is performed using the benchmark.py script, which compares the linked results database with a (specially formatted) CSV file containing a list of inventor-patent instances which have been verified by direct communication with each inventor.

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