├── .gitignore ├── .pylintrc ├── CHANGELOG.md ├── LICENSE ├── README.md ├── _config.yml ├── data └── enrich │ ├── populationids.txt │ └── studyids │ ├── 1q21o3.txt │ ├── COSMIC.txt │ ├── Gene_NCBI_Entrez.txt │ ├── Gene_names.txt │ ├── Metabolics_data.txt │ ├── Microarray_data.txt │ ├── UniProt.txt │ ├── molecules_ChEBI.txt │ └── molecules_KEGG.txt ├── doc ├── images │ ├── badge_pypi.svg │ └── badge_zenodo.2634376.svg └── md │ ├── README_analyses.md │ ├── README_cypher_cmd.md │ ├── README_download_hints.md │ ├── README_gdbdr.md │ ├── README_install_neo4j.md │ └── images │ ├── Neo4j_CommunityServer.png │ ├── anal00_analyze_data.png │ ├── anal01_load_study_ids.png │ ├── download.png │ ├── java_jdk_download.png │ ├── logo_reactome.png │ ├── neo4j_4o0o1_connection.png │ ├── neo4j_load_unsuccessful.png │ ├── neo4j_pwy_subpwy.png │ ├── neo4j_reactome_connect1.png │ ├── neo4j_reactome_connect2.png │ ├── neo4j_reactome_connect3_success.png │ ├── neo4j_reactome_connect4_dbs.png │ ├── python_neo4j_gdbdr.png │ ├── python_neo4j_gdbdr_url.png │ ├── reactome_analyze.png │ ├── results_files.png │ └── results_notfound.png ├── log └── reactome_data_schema.txt ├── makefile ├── notebooks └── tutorial │ ├── README.md │ ├── fig4a_2018_molecules_in_interleukin_signaling.ipynb │ ├── fig4b_2018_ccr5_pathways.ipynb │ ├── s1a_get_pathway.ipynb │ ├── s1b_get_protein.ipynb │ ├── s2a_get_protein_fields.ipynb │ ├── s2b_get_protein_fields_from_nodes.ipynb │ ├── s3a_get_participants_complexes.ipynb │ ├── s4a_pathway_subpathways.ipynb │ ├── s4b_pathway_superpathways.ipynb │ ├── s5a_pathway_reactions.ipynb │ ├── s6a_reaction_participants.ipynb │ ├── s6b_reaction_participants.ipynb │ └── s7a_pathway_molecules.ipynb ├── requirements.txt ├── setup.py └── src ├── bin ├── compare_reactome_version.py ├── prt_data_schema.py └── pwy_enrichment_reactome.py ├── bin_neo4j ├── tutorial │ ├── README.md │ ├── fig4a_2018_molecules_in_interleukin_signaling.py │ ├── fig4b_2018_ccr5_pathways.py │ ├── s1a_get_pathway.py │ ├── s1b_get_protein.py │ ├── s2a_get_protein_fields.py │ ├── s2b_get_protein_fields_from_nodes.py │ ├── s3a_get_participants_complexes.py │ ├── s4a_pathway_subpathways.py │ ├── s4b_pathway_superpathways.py │ ├── s5a_pathway_reactions.py │ ├── s6a_reaction_participants.py │ ├── s6b_reaction_participants.py │ └── s7a_pathway_molecules.py └── wrpy │ ├── disease.py │ ├── inferredfrom.py │ ├── pathway_molecules.py │ ├── reactome_version.py │ ├── referencedatabase.py │ └── species.py ├── reactomepy ├── __init__.py ├── code │ ├── __init__.py │ ├── cli │ │ ├── __init__.py │ │ └── bin_neo4j.py │ ├── describe_pathway.py │ ├── enrich │ │ ├── __init__.py │ │ └── enrich_pwy.py │ ├── ex │ │ ├── __init__.py │ │ └── uniprot_accession_list.py │ ├── neo4jnode.py │ ├── neo4jnodebasic.py │ ├── node │ │ ├── __init__.py │ │ ├── abstractmodifiedresidue.py │ │ ├── affiliation.py │ │ ├── blackboxevent.py │ │ ├── book.py │ │ ├── candidateset.py │ │ ├── catalystactivity.py │ │ ├── catalystactivityreference.py │ │ ├── chemicaldrug.py │ │ ├── compartment.py │ │ ├── complex.py │ │ ├── controlreference.py │ │ ├── crosslinkedresidue.py │ │ ├── databaseidentifier.py │ │ ├── databaseobject.py │ │ ├── dbinfo.py │ │ ├── definedset.py │ │ ├── depolymerisation.py │ │ ├── drug.py │ │ ├── entityfunctionalstatus.py │ │ ├── entityset.py │ │ ├── entitywithaccessionedsequence.py │ │ ├── event.py │ │ ├── externalontology.py │ │ ├── failedreaction.py │ │ ├── figure.py │ │ ├── format.py │ │ ├── fragmentdeletionmodification.py │ │ ├── fragmentinsertionmodification.py │ │ ├── fragmentmodification.py │ │ ├── fragmentreplacedmodification.py │ │ ├── functionalstatus.py │ │ ├── functionalstatustype.py │ │ ├── geneticallymodifiedresidue.py │ │ ├── genomeencodedentity.py │ │ ├── go_biologicalprocess.py │ │ ├── go_cellularcomponent.py │ │ ├── go_molecularfunction.py │ │ ├── go_term.py │ │ ├── groupmodifiedresidue.py │ │ ├── instanceedit.py │ │ ├── interchaincrosslinkedresidue.py │ │ ├── intrachaincrosslinkedresidue.py │ │ ├── literaturereference.py │ │ ├── modifiedresidue.py │ │ ├── negativegeneexpressionregulation.py │ │ ├── negativeregulation.py │ │ ├── otherentity.py │ │ ├── pathway.py │ │ ├── person.py │ │ ├── physicalentity.py │ │ ├── polymer.py │ │ ├── polymerisation.py │ │ ├── positivegeneexpressionregulation.py │ │ ├── positiveregulation.py │ │ ├── proteindrug.py │ │ ├── psimod.py │ │ ├── publication.py │ │ ├── reaction.py │ │ ├── reactionlikeevent.py │ │ ├── referencedatabase.py │ │ ├── referencednasequence.py │ │ ├── referenceentity.py │ │ ├── referencegeneproduct.py │ │ ├── referencegroup.py │ │ ├── referenceisoform.py │ │ ├── referencemolecule.py │ │ ├── referencesequence.py │ │ ├── referencetherapeutic.py │ │ ├── regulation.py │ │ ├── regulationreference.py │ │ ├── replacedresidue.py │ │ ├── requirement.py │ │ ├── schemaclass_factory.py │ │ ├── simpleentity.py │ │ ├── species.py │ │ ├── summation.py │ │ ├── taxon.py │ │ ├── toplevelpathway.py │ │ ├── translationalmodification.py │ │ ├── undirectedinteraction.py │ │ └── url.py │ ├── query │ │ ├── __init__.py │ │ ├── functions.py │ │ ├── get_nodes.py │ │ ├── node_tasks.py │ │ └── relationship_agg.py │ ├── relationships.py │ ├── rest │ │ ├── __init__.py │ │ ├── results_reader.py │ │ ├── service_analysis.py │ │ ├── service_content.py │ │ └── token_mgr.py │ ├── run │ │ └── __init__.py │ ├── schema │ │ ├── __init__.py │ │ ├── data_schema.py │ │ ├── hier.py │ │ ├── hier_init.py │ │ └── node.py │ ├── species.py │ ├── subdag │ │ ├── __init__.py │ │ ├── subdag.py │ │ └── subdag_init.py │ ├── taxid2genbankcommonname.py │ ├── utils.py │ └── wrpy │ │ ├── __init__.py │ │ ├── disease.py │ │ ├── inferredfrom.py │ │ ├── pathway_molecules.py │ │ ├── pathway_query.py │ │ ├── pathway_wrpy.py │ │ ├── referencedatabase.py │ │ ├── species.py │ │ └── utils.py ├── data │ ├── __init__.py │ ├── all │ │ ├── __init__.py │ │ ├── figures.py │ │ └── persons.py │ ├── disease_definitions.py │ ├── pwy │ │ ├── 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Contains Pathway information extracted from Reactome 2 | -------------------------------------------------------------------------------- /src/reactomepy/data/pwy/pwy2figs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dvklopfenstein/ReactomePy/HEAD/src/reactomepy/data/pwy/pwy2figs.py -------------------------------------------------------------------------------- /src/reactomepy/data/pwy/pwy2gos.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dvklopfenstein/ReactomePy/HEAD/src/reactomepy/data/pwy/pwy2gos.py -------------------------------------------------------------------------------- /src/reactomepy/data/pwy/pwy2summation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dvklopfenstein/ReactomePy/HEAD/src/reactomepy/data/pwy/pwy2summation.py 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