├── .bumpversion.cfg ├── .github ├── ISSUE_TEMPLATE │ ├── data_issue.md │ └── pypath_issue.md └── workflows │ └── sphinx-build.yml ├── .gitignore ├── .gitmodules ├── CONTRIBUTING.md ├── HISTORY.rst ├── LICENSE ├── README.rst ├── categorization_validation.yaml ├── curl_to_download_manager_migration.md ├── docs ├── Makefile └── source │ ├── _static │ ├── css │ │ └── pypathdocs.css │ └── img │ │ ├── omnipath-logo.svg │ │ ├── pypath-demo.webp │ │ └── saezlab-logo.svg │ ├── _templates │ ├── custom-class-template.rst │ └── custom-module-template.rst │ ├── conf.py │ ├── contents.rst │ ├── notebooks │ └── manual.ipynb │ ├── reference.rst │ ├── releasehistory.rst │ └── webservice.rst ├── input_module_maintenance ├── discover_input_modules.py ├── exploration │ ├── biological_tags_analysis.txt │ ├── categorization_instructions.md │ ├── fix_tags.py │ ├── module_groups.md │ ├── pypath_module_analysis_report.html │ ├── pypath_module_analysis_report.ipynb │ ├── result-1.yaml │ ├── result-10.yaml │ ├── result-2.yaml │ ├── result-3.yaml │ ├── result-4.yaml │ ├── result-5.yaml │ ├── result-6.yaml │ ├── result-7.yaml │ ├── result-8.yaml │ ├── result-9.yaml │ └── validate_categorization.py ├── module_test_status.md ├── modules.json ├── test_input_modules.py ├── todo.md └── workflow.md ├── poetry.lock ├── pypath ├── __init__.py ├── _metadata.py ├── biocypher │ ├── __init__.py │ └── adapter.py ├── bronze │ ├── __init__.py │ ├── loaders.py │ └── storage.py ├── core │ ├── __init__.py │ ├── annot.py │ ├── attrs.py │ ├── common.py │ ├── complex.py │ ├── entity.py │ ├── enz_sub.py │ ├── evidence.py │ ├── interaction.py │ ├── intercell.py │ ├── intercell_annot.py │ └── network.py ├── data │ ├── __init__.py │ ├── _data.py │ ├── bronze │ │ └── metadata.json │ ├── embl_colors │ ├── ensembl_biomart_query.xml │ ├── goose_ancestors.sql │ ├── goose_annotations.sql │ ├── goose_terms.sql │ ├── licenses │ │ ├── afl_v3.json │ │ ├── apache_2.0.json │ │ ├── artistic_2.0.json │ │ ├── biocarta.json │ │ ├── bsd.json │ │ ├── cc_by_2.5.json │ │ ├── cc_by_3.0.json │ │ ├── cc_by_4.0.json │ │ ├── cc_by_nc-nd_3.0.json │ │ ├── cc_by_nc-nd_4.0.json │ │ ├── cc_by_nc_2.0.json │ │ ├── cc_by_nc_3.0.json │ │ ├── cc_by_nc_4.0.json │ │ ├── cc_by_nc_sa_3.0.json │ │ ├── cc_by_nc_sa_4.0.json │ │ ├── cc_by_nd_3.0.json │ │ ├── cc_by_nd_4.0.json │ │ ├── cc_by_sa_2.5.json │ │ ├── cc_by_sa_3.0.json │ │ ├── cc_by_sa_4.0.json │ │ ├── cc_zero.json │ │ ├── cellcellinteractions.json │ │ ├── composite.json │ │ ├── cosmic.json │ │ ├── cytosig.json │ │ ├── dsl.json │ │ ├── elm.json │ │ ├── embl-ebi.json │ │ ├── eul.json │ │ ├── gnu_gpl_v2.json │ │ ├── gnu_gpl_v3.json │ │ ├── gnu_lgpl_v3.json │ │ ├── hgnc.json │ │ ├── hpo.json │ │ ├── hprd.json │ │ ├── i2d.json │ │ ├── informal.json │ │ ├── kegg.json │ │ ├── kinase-com.json │ │ ├── mirecords.json │ │ ├── mirtarbase.json │ │ ├── mit.json │ │ ├── mppi.json │ │ ├── nar.json │ │ ├── no_license.json │ │ ├── opentargets.json │ │ ├── pathwaycommons.json │ │ ├── pdb.json │ │ ├── phosphonetworks.json │ │ └── unspecified.json │ └── www │ │ ├── favicon.ico │ │ ├── http500.html │ │ └── index.html ├── examples │ └── new_input_system_demo.py ├── formats │ ├── obo.py │ ├── sdf.py │ ├── sqldump.py │ ├── sqlite.py │ └── xml.py ├── inputs │ ├── __init__.py │ ├── abs.py │ ├── acsn.py │ ├── adhesome.py │ ├── adrecs.py │ ├── almen2009.py │ ├── alzpathway.py │ ├── baccin2019.py │ ├── bindingdb │ │ ├── __init__.py │ │ ├── _interactions.py │ │ ├── _raw.py │ │ └── _records.py │ ├── biogps.py │ ├── biogrid.py │ ├── biogrid_new.py │ ├── biomart.py │ ├── biomodels.py │ ├── brenda │ │ └── _main.py │ ├── ca1.py │ ├── cancercellmap.py │ ├── cancerdrugsdb.py │ ├── cancersea.py │ ├── cell.py │ ├── cellcall.py │ ├── cellcellinteractions.py │ ├── cellchatdb.py │ ├── cellinker.py │ ├── cellphonedb.py │ ├── celltalkdb.py │ ├── celltypist.py │ ├── chembl │ │ ├── __init__.py │ │ ├── _activities.py │ │ ├── _assays.py │ │ ├── _common.py │ │ ├── _documents.py │ │ ├── _indications.py │ │ ├── _mechanisms.py │ │ ├── _molecules.py │ │ ├── _raw.py │ │ ├── _records.py │ │ ├── _sqlite.py │ │ └── _targets.py │ ├── clinvar.py │ ├── collectri.py │ ├── common.py │ ├── compath.py │ ├── compleat.py │ ├── complexportal.py │ ├── comppi.py │ ├── connectomedb.py │ ├── corum.py │ ├── cosmic.py │ ├── cpad.py │ ├── cpdb.py │ ├── credentials.py │ ├── csa.py │ ├── cspa.py │ ├── ctdbase.py │ ├── cytosig.py │ ├── dbptm.py │ ├── ddinter.py │ ├── deathdomain.py │ ├── depod.py │ ├── dgidb.py │ ├── dip.py │ ├── diseases.py │ ├── disgenet │ │ ├── __init__.py │ │ ├── _api │ │ │ ├── __init__.py │ │ │ ├── meta.py │ │ │ ├── schema.py │ │ │ └── simple.py │ │ ├── _auth.py │ │ ├── _client.py │ │ ├── _field.py │ │ ├── _proc.py │ │ ├── _records.py │ │ ├── _request.py │ │ ├── _schema.py │ │ └── _valid.py │ ├── domino.py │ ├── dorothea.py │ ├── drugbank.py │ ├── drugcentral.py │ ├── ebi.py │ ├── elm.py │ ├── embopress.py │ ├── embrace.py │ ├── encode.py │ ├── ensembl.py │ ├── eutils.py │ ├── exocarta.py │ ├── expasy.py │ ├── genecards.py │ ├── go.py │ ├── gpcrdb.py │ ├── graphviz.py │ ├── guide2pharma.py │ ├── guidetopharma │ │ ├── __init__.py │ │ ├── _constants.py │ │ ├── _interactions.py │ │ ├── _ligands.py │ │ ├── _raw.py │ │ ├── _records.py │ │ └── _targets.py │ ├── gutmgene.py │ ├── havugimana.py │ ├── hgnc.py │ ├── hint.py │ ├── hippie.py │ ├── hmdb │ │ ├── __init__.py │ │ ├── common.py │ │ ├── metabolites.py │ │ ├── proteins.py │ │ ├── schema │ │ │ ├── __init__.py │ │ │ ├── common.py │ │ │ ├── metabolites.py │ │ │ └── proteins.py │ │ ├── structures.py │ │ ├── visual.py │ │ └── xml.py │ ├── homologene.py │ ├── hpmr.py │ ├── hpo.py │ ├── hprd.py │ ├── htri.py │ ├── humancellmap.py │ ├── humap.py │ ├── humsavar.py │ ├── huri.py │ ├── i3d.py │ ├── icellnet.py │ ├── ielm.py │ ├── imweb.py │ ├── innatedb.py │ ├── input_module.py │ ├── instruct.py │ ├── intact.py │ ├── integrins.py │ ├── interpro.py │ ├── intogen.py │ ├── ipi.py │ ├── iptmnet.py │ ├── italk.py │ ├── kea.py │ ├── kegg.py │ ├── kegg_api.py │ ├── kinasedotcom.py │ ├── kirouac2010.py │ ├── lambert2018.py │ ├── laudanna.py │ ├── li2012.py │ ├── lincs.py │ ├── lipidmaps │ │ ├── __init__.py │ │ ├── _lipids.py │ │ ├── _raw.py │ │ └── _records.py │ ├── lmpid.py │ ├── lncdisease.py │ ├── lncrnadb.py │ ├── locate.py │ ├── lrdb.py │ ├── macrophage.py │ ├── main.py │ ├── matrisome.py │ ├── matrixdb.py │ ├── mcam.py │ ├── membranome.py │ ├── mimp.py │ ├── mir2disease.py │ ├── mirbase.py │ ├── mirdeathdb.py │ ├── mirecords.py │ ├── mirtarbase.py │ ├── mitab.py │ ├── mppi.py │ ├── mrclinksdb │ │ ├── __init__.py │ │ ├── _interactions.py │ │ └── _records.py │ ├── msigdb.py │ ├── ncrdeathdb.py │ ├── negatome.py │ ├── netbiol.py │ ├── netpath.py │ ├── new_stitch │ │ ├── __init__.py │ │ ├── _actions.py │ │ ├── _interactions.py │ │ ├── _links.py │ │ ├── _raw.py │ │ ├── _records.py │ │ └── actions_test.py │ ├── offsides.py │ ├── oma.py │ ├── ontology.py │ ├── opentargets.py │ ├── opm.py │ ├── oreganno.py │ ├── panglaodb.py │ ├── pathophenodb.py │ ├── pathwaycommons.py │ ├── pazar.py │ ├── pdb.py │ ├── pdzbase.py │ ├── pepcyber.py │ ├── pfam.py │ ├── pharos.py │ ├── phobius.py │ ├── phosphatome.py │ ├── phosphoelm.py │ ├── phosphonetworks.py │ ├── phosphopoint.py │ ├── phosphosite.py │ ├── pisa.py │ ├── pro.py │ ├── progeny.py │ ├── proteinatlas.py │ ├── proteins.py │ ├── protmapper.py │ ├── psimi.py │ ├── pubchem.py │ ├── pubmed.py │ ├── ramilowski2015.py │ ├── ramp │ │ ├── __init__.py │ │ ├── _common.py │ │ ├── _mapping.py │ │ ├── _rest.py │ │ ├── _sqldump.py │ │ └── _sqlite.py │ ├── rdata.py │ ├── reaction.py │ ├── reactome │ │ └── __init__.py │ ├── reactome_old.py │ ├── rhea │ │ └── __init__.py │ ├── scconnect.py │ ├── science.py │ ├── sider.py │ ├── signalink.py │ ├── signor.py │ ├── slc.py │ ├── spike.py │ ├── stitch.py │ ├── string.py │ ├── surfaceome.py │ ├── swisslipids │ │ ├── __init__.py │ │ ├── _raw.py │ │ ├── _records.py │ │ └── _tables.py │ ├── switches_elm.py │ ├── talklr.py │ ├── tcdb │ │ ├── __init__.py │ │ └── _substrates.py │ ├── tfcensus.py │ ├── threedcomplex.py │ ├── threedid.py │ ├── topdb.py │ ├── transmir.py │ ├── trip.py │ ├── trrust.py │ ├── twosides.py │ ├── unichem.py │ ├── uniprot.py │ ├── uniprot_db.py │ ├── uniprot_idmapping.py │ ├── wang.py │ ├── wojtowicz2020.py │ └── zhong2015.py ├── internals │ ├── __init__.py │ ├── annot_formats.py │ ├── input_formats.py │ ├── intera.py │ ├── license.py │ ├── maps.py │ ├── refs.py │ └── resource.py ├── legacy │ ├── __init__.py │ ├── db_categories.py │ └── main.py ├── omnipath │ ├── __init__.py │ ├── app.py │ ├── bel.py │ ├── cellphonedb.py │ ├── databases │ │ ├── __init__.py │ │ ├── build.py │ │ ├── builtins.json │ │ ├── classes.json │ │ └── define.py │ ├── export.py │ ├── legacy.py │ ├── param.py │ └── server │ │ ├── __init__.py │ │ ├── _html.py │ │ ├── build.py │ │ ├── generate_about_page.py │ │ ├── legacy.py │ │ └── run.py ├── reader │ ├── field.py │ └── network.py ├── resources │ ├── __init__.py │ ├── _network.py │ ├── controller.py │ ├── data │ │ ├── __init__.py │ │ ├── enz_sub_input_template.json │ │ └── resources.json │ ├── data_formats.py │ ├── descriptions.py │ ├── licenses.py │ ├── network.py │ ├── sources │ │ ├── README.md │ │ ├── biogrid.yaml │ │ ├── hgnc.yaml │ │ └── schema.yaml │ └── urls.py ├── share │ ├── __init__.py │ ├── cache.py │ ├── common.py │ ├── constants.py │ ├── curl.py │ ├── lookup │ │ ├── _manytomany.py │ │ ├── _onetomany.py │ │ └── _onetomany2.py │ ├── progress.py │ ├── session.py │ └── settings.py ├── utils │ ├── __init__.py │ ├── go.py │ ├── mapping.py │ ├── metabo │ │ ├── __init__.py │ │ └── struct │ │ │ └── visual.py │ ├── orthology.py │ ├── pdb.py │ ├── proteomicsdb.py │ ├── pyreact.py │ ├── reflists.py │ ├── residues.py │ ├── seq.py │ ├── taxonomy.py │ ├── unichem.py │ └── uniprot.py └── visual │ ├── __init__.py │ ├── drawing.py │ ├── igraph_drawing │ ├── __init__.py │ ├── edge.py │ └── vertex.py │ └── plot.py ├── pyproject.toml ├── scripts ├── 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