.copier-answers.yml
.gitignore
.readthedocs.yaml
CITATION.cff
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.dev.md
README.md
project_setup.md
pyproject.toml
sonar-project.properties
.github/workflows/build.yml
.github/workflows/cffconvert.yml
.github/workflows/documentation.yml
.github/workflows/publish.yml
.github/workflows/sonarcloud.yml
docs/Makefile
docs/abstract_analysis.ipynb
docs/conf.py
docs/index.rst
docs/make.bat
docs/usecase.ipynb
docs/_templates/.gitignore
src/aoptk/__init__.py
src/aoptk/chemical.py
src/aoptk/effect.py
src/aoptk/find_chemical.py
src/aoptk/regex_sentence_generator.py
src/aoptk/sentence.py
src/aoptk/sentence_generator.py
src/aoptk/spacy_processor.py
src/aoptk.egg-info/PKG-INFO
src/aoptk.egg-info/SOURCES.txt
src/aoptk.egg-info/dependency_links.txt
src/aoptk.egg-info/entry_points.txt
src/aoptk.egg-info/requires.txt
src/aoptk.egg-info/top_level.txt
src/aoptk/abbreviations/__init__.py
src/aoptk/abbreviations/abbreviation_translator.py
src/aoptk/abbreviations/abbreviation_translator_dictionary.py
src/aoptk/abbreviations/abbreviation_translator_dictionary_generator.py
src/aoptk/application/__init__.py
src/aoptk/application/chemical_identifier.py
src/aoptk/application/publication_tracker.py
src/aoptk/cleaning/__init__.py
src/aoptk/cleaning/html_tag_remover.py
src/aoptk/cleaning/text_cleaner.py
src/aoptk/literature/__init__.py
src/aoptk/literature/abbreviations.py
src/aoptk/literature/abstract.py
src/aoptk/literature/get_abstract.py
src/aoptk/literature/get_id.py
src/aoptk/literature/get_pdf.py
src/aoptk/literature/get_publication.py
src/aoptk/literature/id.py
src/aoptk/literature/pdf.py
src/aoptk/literature/pdf_parser.py
src/aoptk/literature/publication.py
src/aoptk/literature/publication_metadata.py
src/aoptk/literature/pymupdf_parser.py
src/aoptk/literature/utils.py
src/aoptk/literature/databases/__init__.py
src/aoptk/literature/databases/europepmc.py
src/aoptk/literature/databases/pubmed.py
src/aoptk/normalization/__init__.py
src/aoptk/normalization/mesh_terms.py
src/aoptk/normalization/normalize_chemical.py
src/aoptk/normalization/provide_mesh_term_dataframe_from_xml.py
src/aoptk/normalization/provide_normalization_dataframe.py
src/aoptk/normalization/pubchem_abbreviation_short.py
src/aoptk/normalization/pubchem_abbreviation_uppercase.py
src/aoptk/normalization/pubchem_api.py
src/aoptk/normalization/pubchem_local.py
src/aoptk/relationships/__init__.py
src/aoptk/relationships/find_relationship.py
src/aoptk/relationships/relationship.py
src/aoptk/relationships/zero_shot_classification.py
src/aoptk/relationships/zero_shot_classification_multiple.py
src/aoptk/relationships/zero_shot_classification_single.py
tests/__init__.py
tests/test_abbreviation_translator_dictionary.py
tests/test_abbreviation_translator_dictionary_generator.py
tests/test_chemical.py
tests/test_cleaning.py
tests/test_europepmc.py
tests/test_id.py
tests/test_mesh_terms.py
tests/test_pdf_parser.py
tests/test_provide_mesh_term_dataframe_from_xml.py
tests/test_pubchem_abbreviation_short.py
tests/test_pubchem_abbreviation_uppercase.py
tests/test_pubchem_api.py
tests/test_pubchem_local.py
tests/test_pubmed.py
tests/test_pubmed_mocked.py
tests/test_pymupdf_parser.py
tests/test_regex_sentence_generator.py
tests/test_spacy_processor.py
tests/test_spacy_processor_mocked.py
tests/test_utils.py
tests/test_zero_shot_classification_multiple.py
tests/test_zero_shot_classification_single.py
tests/test-data/test_mesh_term_database.xml
tests/test_pdfs/test_pdf.pdf