Lexicon Tools

Documentation for these Lexicon Tools is managed via reStructuredText files and Sphinx <http://www.sphinx-doc.org/>. If you don't have Sphinx installed, you should check out a quick primer (First Steps with Sphinx <http://www.sphinx-doc.org/en/1.7/tutorial.html>) or install it as below:

  ## If you don't have Sphinx installed already
  pip install Sphinx

  ## Generate a locally viewable HTML version
  cd docs
  make html

The latest version of the documentation can be generated as locally viewable HTML: file:///path/to/git/repository/docs/_build/html/index.html

Leveraging SNOMED_CT concepts and relations

Running lex_gen with the provided sample problems file should create fairly small dictionary to inspect. Here you can see that we have set the --max-distance to zero, which will only return strings for the precise CUIs provide. (In contrast, the default -1 does an exhaustive search while 1 goes one relation away, etc.)

python3 lex_gen.py \
    --max-distance 0 \
    --source-type problems \
    --batch-name testBatch001 \
    --input-file in/tiny_problems.csv

wc out/*_problems_testBatch001.*
      50     312    2443 out/4waydict_problems_testBatch001.csv
      50     162    1399 out/binarydict_problems_testBatch001.csv
      57     181    2319 out/conceptMapper_problems_testBatch001.dict
      64     190    2307 out/kb_problems_testBatch001.ttl
       2     114     967 out/widedict_problems_testBatch001.csv
     223     959    9435 total
	 

Leveraging RxNorm concepts and relations

TODO: add tiny_allergens

python3 lex_gen.py \
    --max-distance 0 \
    --source-type allergens \
    --batch-name batchA \
    --input-file in/tiny_allergens.csv

UMLS Engines

Using the UMLS API

Follow instructions on the User Authentication <https://documentation.uts.nlm.nih.gov/rest/authentication.html>_ page about generating an authentication token. You'll need to set the value of UMLS_API_TOKEN to this value in ``umls_utils.py`.

Installing a Local UMLS Engine (Experimental)

After installing py-umls <https://github.com/chb/py-umls>_, follow the instructions provided to initialize local repositories for the different supported ontologies.

If you have checked out lexicon-tools as a git repository, then you'll need to install py-umls as a submodule:

git submodule add https://github.com/chb/py-umls umls

Otherwise, you should be able to down the py-umls source code just as you downloaded the lexicon-tools source code. Put the code in a directory named ``umls`.

Running Tests

Unit tests and code coverage can be verified using pytest and pytest-cov:

python -m pytest --cov-report html:cov_html --cov=./ tests

Branches to be merged into stable and develop should be verified using flake8 for code quality:

flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics

If the above command returns ``0`, then your code does not have any obvious errors.