AUTHORS.rst
CHANGELOG.rst
CONTRIBUTING.rst
LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
docs/Makefile
docs/source/PyBEL-square-100.png
docs/source/conf.py
docs/source/index.rst
docs/source/introduction/installation.rst
docs/source/introduction/overview.rst
docs/source/meta/postmortem.rst
docs/source/meta/references.rst
docs/source/meta/technology.rst
docs/source/reference/constants.rst
docs/source/reference/dsl.rst
docs/source/reference/io.rst
docs/source/reference/logging.rst
docs/source/reference/parser.rst
docs/source/reference/database/manager.rst
docs/source/reference/database/models.rst
docs/source/reference/mutations/collapse.rst
docs/source/reference/mutations/deletion.rst
docs/source/reference/mutations/expansion.rst
docs/source/reference/mutations/induction.rst
docs/source/reference/mutations/induction_expansion.rst
docs/source/reference/mutations/inference.rst
docs/source/reference/mutations/metadata.rst
docs/source/reference/mutations/mutations.rst
docs/source/reference/struct/datamodel.rst
docs/source/reference/struct/examples.rst
docs/source/reference/struct/filters.rst
docs/source/reference/struct/grouping.rst
docs/source/reference/struct/operators.rst
docs/source/reference/struct/pipeline.rst
docs/source/reference/struct/query.rst
docs/source/reference/struct/summary.rst
docs/source/topics/cli.rst
docs/source/topics/cookbook.rst
src/pybel/__init__.py
src/pybel/__main__.py
src/pybel/canonicalize.py
src/pybel/cli.py
src/pybel/config.py
src/pybel/constants.py
src/pybel/exceptions.py
src/pybel/grounding.py
src/pybel/language.py
src/pybel/tokens.py
src/pybel/typing.py
src/pybel/utils.py
src/pybel/version.py
src/pybel.egg-info/PKG-INFO
src/pybel.egg-info/SOURCES.txt
src/pybel.egg-info/dependency_links.txt
src/pybel.egg-info/entry_points.txt
src/pybel.egg-info/not-zip-safe
src/pybel.egg-info/requires.txt
src/pybel.egg-info/top_level.txt
src/pybel/dsl/__init__.py
src/pybel/dsl/constants.py
src/pybel/dsl/edges.py
src/pybel/dsl/exc.py
src/pybel/dsl/namespaces.py
src/pybel/dsl/node_classes.py
src/pybel/examples/__init__.py
src/pybel/examples/ampk_example.py
src/pybel/examples/braf_example.py
src/pybel/examples/egf_example.py
src/pybel/examples/homology_example.py
src/pybel/examples/sialic_acid_example.py
src/pybel/examples/statin_example.py
src/pybel/examples/tloc_example.py
src/pybel/examples/various_example.py
src/pybel/examples/vegf_example.py
src/pybel/io/__init__.py
src/pybel/io/api.py
src/pybel/io/aws.py
src/pybel/io/bel_commons_client.py
src/pybel/io/biodati_client.py
src/pybel/io/cx.py
src/pybel/io/emmaa.py
src/pybel/io/exc.py
src/pybel/io/extras.py
src/pybel/io/fraunhofer_orientdb.py
src/pybel/io/gpickle.py
src/pybel/io/graphdati.py
src/pybel/io/graphml.py
src/pybel/io/hipathia.py
src/pybel/io/indra.py
src/pybel/io/jgif.py
src/pybel/io/jinja_utils.py
src/pybel/io/line_utils.py
src/pybel/io/lines.py
src/pybel/io/neo4j.py
src/pybel/io/nodelink.py
src/pybel/io/pykeen.py
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src/pybel/io/spia.py
src/pybel/io/umbrella_nodelink.py
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src/pybel/io/hetionet/__init__.py
src/pybel/io/hetionet/__main__.py
src/pybel/io/hetionet/cli.py
src/pybel/io/hetionet/constants.py
src/pybel/io/hetionet/hetionet.py
src/pybel/io/jupyter/__init__.py
src/pybel/io/jupyter/constants.py
src/pybel/io/jupyter/inline.py
src/pybel/io/jupyter/visualization.py
src/pybel/io/jupyter/templates/graph_template.html
src/pybel/io/jupyter/templates/pybel_jupyter.js
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src/pybel/io/tsv/__init__.py
src/pybel/io/tsv/api.py
src/pybel/io/tsv/converters.py
src/pybel/manager/__init__.py
src/pybel/manager/base_manager.py
src/pybel/manager/cache_manager.py
src/pybel/manager/citation_utils.py
src/pybel/manager/database_io.py
src/pybel/manager/exc.py
src/pybel/manager/lookup_manager.py
src/pybel/manager/make_json_serializable.py
src/pybel/manager/models.py
src/pybel/manager/query_manager.py
src/pybel/manager/utils.py
src/pybel/parser/__init__.py
src/pybel/parser/baseparser.py
src/pybel/parser/constants.py
src/pybel/parser/exc.py
src/pybel/parser/parse_bel.py
src/pybel/parser/parse_concept.py
src/pybel/parser/parse_control.py
src/pybel/parser/parse_metadata.py
src/pybel/parser/utils.py
src/pybel/parser/modifiers/__init__.py
src/pybel/parser/modifiers/constants.py
src/pybel/parser/modifiers/fragment.py
src/pybel/parser/modifiers/fusion.py
src/pybel/parser/modifiers/gene_modification.py
src/pybel/parser/modifiers/gene_substitution.py
src/pybel/parser/modifiers/location.py
src/pybel/parser/modifiers/protein_modification.py
src/pybel/parser/modifiers/protein_substitution.py
src/pybel/parser/modifiers/truncation.py
src/pybel/parser/modifiers/variant.py
src/pybel/resources/__init__.py
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src/pybel/resources/update_resources.py
src/pybel/struct/__init__.py
src/pybel/struct/getters.py
src/pybel/struct/graph.py
src/pybel/struct/node_utils.py
src/pybel/struct/operations.py
src/pybel/struct/utils.py
src/pybel/struct/filters/__init__.py
src/pybel/struct/filters/edge_filters.py
src/pybel/struct/filters/edge_predicate_builders.py
src/pybel/struct/filters/edge_predicates.py
src/pybel/struct/filters/node_filters.py
src/pybel/struct/filters/node_predicate_builders.py
src/pybel/struct/filters/typing.py
src/pybel/struct/filters/utils.py
src/pybel/struct/filters/node_predicates/__init__.py
src/pybel/struct/filters/node_predicates/activities.py
src/pybel/struct/filters/node_predicates/misc.py
src/pybel/struct/filters/node_predicates/modifications.py
src/pybel/struct/filters/node_predicates/relations.py
src/pybel/struct/filters/node_predicates/types.py
src/pybel/struct/filters/node_predicates/utils.py
src/pybel/struct/grouping/__init__.py
src/pybel/struct/grouping/annotations.py
src/pybel/struct/grouping/provenance.py
src/pybel/struct/grouping/utils.py
src/pybel/struct/mutation/__init__.py
src/pybel/struct/mutation/induction_expansion.py
src/pybel/struct/mutation/metadata.py
src/pybel/struct/mutation/utils.py
src/pybel/struct/mutation/collapse/__init__.py
src/pybel/struct/mutation/collapse/collapse.py
src/pybel/struct/mutation/collapse/protein_rna_origins.py
src/pybel/struct/mutation/deletion/__init__.py
src/pybel/struct/mutation/deletion/deletion.py
src/pybel/struct/mutation/deletion/protein_rna_origins.py
src/pybel/struct/mutation/expansion/__init__.py
src/pybel/struct/mutation/expansion/neighborhood.py
src/pybel/struct/mutation/expansion/upstream.py
src/pybel/struct/mutation/induction/__init__.py
src/pybel/struct/mutation/induction/annotations.py
src/pybel/struct/mutation/induction/citation.py
src/pybel/struct/mutation/induction/neighborhood.py
src/pybel/struct/mutation/induction/paths.py
src/pybel/struct/mutation/induction/random_subgraph.py
src/pybel/struct/mutation/induction/upstream.py
src/pybel/struct/mutation/induction/utils.py
src/pybel/struct/mutation/inference/__init__.py
src/pybel/struct/mutation/inference/protein_rna_origins.py
src/pybel/struct/mutation/inference/transfer.py
src/pybel/struct/pipeline/__init__.py
src/pybel/struct/pipeline/decorators.py
src/pybel/struct/pipeline/exc.py
src/pybel/struct/pipeline/pipeline.py
src/pybel/struct/query/__init__.py
src/pybel/struct/query/constants.py
src/pybel/struct/query/exc.py
src/pybel/struct/query/query.py
src/pybel/struct/query/seeding.py
src/pybel/struct/query/selection.py
src/pybel/struct/summary/__init__.py
src/pybel/struct/summary/edge_summary.py
src/pybel/struct/summary/errors.py
src/pybel/struct/summary/node_summary.py
src/pybel/struct/summary/provenance.py
src/pybel/testing/__init__.py
src/pybel/testing/cases.py
src/pybel/testing/constants.py
src/pybel/testing/generate.py
src/pybel/testing/mock_manager.py
src/pybel/testing/mocks.py
src/pybel/testing/utils.py
src/pybel/testing/resources/bel/Cytotoxic T-cell Signaling-2.0-Hs.json
src/pybel/testing/resources/bel/isolated.bel
src/pybel/testing/resources/bel/misordered.bel
src/pybel/testing/resources/bel/obo.bel
src/pybel/testing/resources/bel/slushy.bel
src/pybel/testing/resources/bel/test_bel.bel
src/pybel/testing/resources/bel/thorough.bel
src/pybel/testing/resources/belanno/cell-line.belanno
src/pybel/testing/resources/belanno/confidence-1.0.0.belanno
src/pybel/testing/resources/belanno/mesh-diseases.belanno
src/pybel/testing/resources/belanno/species-taxonomy-id.belanno
src/pybel/testing/resources/belanno/test_an_1.belanno
src/pybel/testing/resources/belns/chebi-names.belns
src/pybel/testing/resources/belns/disease-ontology.belns
src/pybel/testing/resources/belns/go-names.belns
src/pybel/testing/resources/belns/hgnc-names.belns
src/pybel/testing/resources/belns/mesh-names.belns
src/pybel/testing/resources/belns/test_ns_1.belns
src/pybel/testing/resources/belns/test_ns_1_updated.belns
src/pybel/testing/resources/belns/test_ns_2.belns
src/pybel/testing/resources/belns/test_ns_empty.belns
tests/__init__.py
tests/constant_helper.py
tests/constants.py
tests/test_canonicalization.py
tests/test_cli.py
tests/test_dsl.py
tests/test_tokens.py
tests/test_utils.py
tests/test_io/__init__.py
tests/test_io/test_hetionet.py
tests/test_io/test_import.py
tests/test_io/test_jgif.py
tests/test_io/test_jupyter.py
tests/test_io/test_pynpa.py
tests/test_io/test_spia.py
tests/test_io/test_tsv.py
tests/test_io/test_umbrella_nodelink.py
tests/test_io/test_cx/__init__.py
tests/test_io/test_cx/cases.py
tests/test_io/test_cx/examples.py
tests/test_io/test_cx/test_import.py
tests/test_io/test_hipathia/__init__.py
tests/test_io/test_hipathia/hsa04370.att
tests/test_io/test_hipathia/hsa04370.sif
tests/test_io/test_hipathia/test_1.att
tests/test_io/test_hipathia/test_1.sif
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tests/test_io/test_hipathia/test_hipathia.py
tests/test_manager/__init__.py
tests/test_manager/test_citation_utils.py
tests/test_manager/test_connection.py
tests/test_manager/test_manager_definitions.py
tests/test_manager/test_manager_drop.py
tests/test_manager/test_manager_graph.py
tests/test_manager/test_manager_model.py
tests/test_manager/test_seeding.py
tests/test_parse/__init__.py
tests/test_parse/test_parse_bel.py
tests/test_parse/test_parse_bel_relations.py
tests/test_parse/test_parse_bel_variants.py
tests/test_parse/test_parse_control.py
tests/test_parse/test_parse_identifier.py
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tests/test_struct/__init__.py
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tests/test_struct/test_grouping.py
tests/test_struct/test_node_utils.py
tests/test_struct/test_struct_graph.py
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tests/test_struct/test_query/__init__.py
tests/test_struct/test_query/test_mocks.py
tests/test_struct/test_query/test_query.py
tests/test_struct/test_query/test_seeding.py
tests/test_struct/test_query/test_struct_pipeline.py
tests/test_struct/test_summary/__init__.py
tests/test_struct/test_summary/test_errors.py
tests/test_struct/test_summary/test_provenance.py
tests/test_struct/test_summary/test_struct_summary_edges.py
tests/test_struct/test_summary/test_summary_nodes.py
tests/test_struct/test_transformations/__init__.py
tests/test_struct/test_transformations/test_collapse.py
tests/test_struct/test_transformations/test_deletions.py
tests/test_struct/test_transformations/test_expansion.py
tests/test_struct/test_transformations/test_induction.py
tests/test_struct/test_transformations/test_metadata.py
tests/test_struct/test_transformations/test_random.py
tests/test_struct/test_transformations/test_transfer.py