.gitignore
LICENSE.txt
MANIFEST.in
README.md
setup.py
.github/ISSUE_TEMPLATE/bug_report.md
.github/workflows/pythonpackage.yml
docs/sentences/Presentation.pptx
docs/sentences/Sentences.pdf
docs/sentences/Sentences_Annotation_Guidelines_20180409.pdf
docs/test_results/3.0b6.yml
python/biomedicus/__init__.py
python/biomedicus/__main__.py
python/biomedicus/biomedicus-all.jar
python/biomedicus/cli.py
python/biomedicus/config.py
python/biomedicus/defaultConfig.yml
python/biomedicus/tokenization.py
python/biomedicus/version.py
python/biomedicus.egg-info/PKG-INFO
python/biomedicus.egg-info/SOURCES.txt
python/biomedicus.egg-info/dependency_links.txt
python/biomedicus.egg-info/entry_points.txt
python/biomedicus.egg-info/requires.txt
python/biomedicus.egg-info/top_level.txt
python/biomedicus/core/__init__.py
python/biomedicus/core/dawg.py
python/biomedicus/dependencies/__init__.py
python/biomedicus/dependencies/conllu_reader.py
python/biomedicus/dependencies/split_conllu.py
python/biomedicus/dependencies/stanza_parser.py
python/biomedicus/dependencies/stanza_selective_parser.py
python/biomedicus/deployment/__init__.py
python/biomedicus/deployment/biomedicus_deploy_config.yml
python/biomedicus/deployment/deploy_biomedicus.py
python/biomedicus/examples/__init__.py
python/biomedicus/examples/add_pos_tags.py
python/biomedicus/examples/dependencies.py
python/biomedicus/examples/mipacq_csv_reader.py
python/biomedicus/examples/plaintext_biomedicus_pipeline.py
python/biomedicus/examples/rtf_biomedicus_pipeline.py
python/biomedicus/examples/sentences.py
python/biomedicus/negation/__init__.py
python/biomedicus/negation/deepen.py
python/biomedicus/negation/i2b2_va2010.py
python/biomedicus/negation/negex.py
python/biomedicus/negation/negex_triggers.py
python/biomedicus/negation/negex_triggers.txt
python/biomedicus/performance_testing/__init__.py
python/biomedicus/performance_testing/deploy.py
python/biomedicus/performance_testing/pipeline.py
python/biomedicus/performance_testing/wait.py
python/biomedicus/pipeline/__init__.py
python/biomedicus/pipeline/default_pipeline.py
python/biomedicus/sentences/__init__.py
python/biomedicus/sentences/bi_lstm.py
python/biomedicus/sentences/bi_lstm_pp.py
python/biomedicus/sentences/input.py
python/biomedicus/sentences/one_per_line_sentences.py
python/biomedicus/sentences/vocabulary.py
python/biomedicus/tagging/__init__.py
python/biomedicus/tagging/genia_xml_pipeline.py
python/biomedicus/tagging/ptb_evaluation_set.py
python/biomedicus/tagging/ptb_pipeline.py
python/biomedicus/utilities/__init__.py
python/biomedicus/utilities/embeddings.py
python/biomedicus/utilities/mimic.py
python/biomedicus/utilities/print_all_processors_metadata.py
python/biomedicus/utilities/pubmed.py
python/biomedicus/utilities/sample_mimic.py
python/biomedicus/utilities/train_eval_split.py
python/tests/conftest.py
python/tests/pytest.ini
python/tests/test_config.py
python/tests/acronyms/test_acronyms_performance.py
python/tests/concepts/test_concepts_performance.py
python/tests/core/__init__.py
python/tests/core/test_dawg.py
python/tests/dependencies/3.0b6.yml
python/tests/dependencies/test_dependencies.py
python/tests/deployment/test_deployment.py
python/tests/deployment/in/97_204.txt
python/tests/negation/test_negation_i2b2.py
python/tests/negation/test_negex_tagger.py
python/tests/normalization/97_95.pickle
python/tests/normalization/test_normalization.py
python/tests/sentences/test_sentences.py
python/tests/sentences/test_sentences_performance.py
python/tests/tnt_tagging/test_tnt_performance.py
tools/concepts/BannedTTYs.txt
tools/concepts/TUIsOfInterest.txt
tools/concepts/umls-level0.prop
tools/concepts/umls-snomed.prop