LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
docs/source/cli.rst
docs/source/conf.py
docs/source/index.rst
docs/source/installation.rst
docs/source/logo.png
docs/source/usage.rst
docs/source/api/semra.api.assemble_evidences.rst
docs/source/api/semra.api.assert_projection.rst
docs/source/api/semra.api.count_source_target.rst
docs/source/api/semra.api.deduplicate_evidence.rst
docs/source/api/semra.api.filter_many_to_many.rst
docs/source/api/semra.api.filter_mappings.rst
docs/source/api/semra.api.filter_minimum_confidence.rst
docs/source/api/semra.api.filter_prefixes.rst
docs/source/api/semra.api.filter_self_matches.rst
docs/source/api/semra.api.flip.rst
docs/source/api/semra.api.from_digraph.rst
docs/source/api/semra.api.get_index.rst
docs/source/api/semra.api.get_many_to_many.rst
docs/source/api/semra.api.get_priority_reference.rst
docs/source/api/semra.api.get_test_evidence.rst
docs/source/api/semra.api.get_test_reference.rst
docs/source/api/semra.api.infer_chains.rst
docs/source/api/semra.api.infer_dbxref_mutations.rst
docs/source/api/semra.api.infer_mutations.rst
docs/source/api/semra.api.infer_mutual_dbxref_mutations.rst
docs/source/api/semra.api.infer_reversible.rst
docs/source/api/semra.api.keep_object_prefixes.rst
docs/source/api/semra.api.keep_prefixes.rst
docs/source/api/semra.api.keep_subject_prefixes.rst
docs/source/api/semra.api.print_source_target_counts.rst
docs/source/api/semra.api.prioritize.rst
docs/source/api/semra.api.project.rst
docs/source/api/semra.api.project_dict.rst
docs/source/api/semra.api.str_source_target_counts.rst
docs/source/api/semra.api.summarize_prefixes.rst
docs/source/api/semra.api.tabulate_index.rst
docs/source/api/semra.api.to_digraph.rst
docs/source/api/semra.api.to_multidigraph.rst
docs/source/api/semra.api.unindex.rst
docs/source/api/semra.api.validate_mappings.rst
docs/source/api/semra.pipeline.Configuration.rst
docs/source/api/semra.pipeline.Input.rst
docs/source/api/semra.pipeline.Mutation.rst
docs/source/api/semra.pipeline.get_mappings_from_config.rst
docs/source/api/semra.pipeline.get_raw_mappings.rst
docs/source/api/semra.pipeline.process.rst
docs/source/api/semra.struct.Mapping.rst
docs/source/api/semra.struct.MappingSet.rst
docs/source/api/semra.struct.ReasonedEvidence.rst
docs/source/api/semra.struct.SimpleEvidence.rst
docs/source/api/semra.struct.line.rst
docs/source/api/semra.struct.triple_key.rst
src/semra/__init__.py
src/semra/__main__.py
src/semra/api.py
src/semra/cli.py
src/semra/client.py
src/semra/database.py
src/semra/gilda_utils.py
src/semra/io.py
src/semra/pipeline.py
src/semra/py.typed
src/semra/rules.py
src/semra/struct.py
src/semra/version.py
src/semra/wsgi.py
src/semra.egg-info/PKG-INFO
src/semra.egg-info/SOURCES.txt
src/semra.egg-info/dependency_links.txt
src/semra.egg-info/entry_points.txt
src/semra.egg-info/not-zip-safe
src/semra.egg-info/requires.txt
src/semra.egg-info/top_level.txt
src/semra/landscape/__init__.py
src/semra/landscape/__main__.py
src/semra/landscape/anatomy.py
src/semra/landscape/cells.py
src/semra/landscape/complexes.py
src/semra/landscape/diseases.py
src/semra/landscape/genes.py
src/semra/landscape/utils.py
src/semra/sources/__init__.py
src/semra/sources/biopragmatics.py
src/semra/sources/chembl.py
src/semra/sources/clo.py
src/semra/sources/famplex.py
src/semra/sources/gilda.py
src/semra/sources/intact.py
src/semra/sources/ncit.py
src/semra/sources/omim.py
src/semra/sources/pubchem.py
src/semra/sources/wikidata.py
src/semra/templates/base.html
src/semra/templates/concept.html
src/semra/templates/home.html
src/semra/templates/mapping.html
src/semra/templates/mapping_set.html
src/semra/templates/utils.html
tests/__init__.py
tests/test_api.py
tests/test_io.py
tests/test_pipeline.py