Release history§

This is a summary of the changelog.


  • First release of PyPath, for initial testing.


  • Lots of small improvements in almost every module

  • Networks can be read from local files, remote files, lists or provided by any function

  • Almost all redistributed data have been removed, every source downloaded from the original provider.


  • First version with partial Python 3 support.


  • pyreact module with BioPaxReader and PyReact classes

  • Process description databases, BioPax and PathwayCommons SIF conversion rules are supported

  • Format definitions for 6 process description databases included.


  • Many new classes in the plot module

  • All figures and tables in the manuscript can be generated automatically

  • This is supported by a new module, analysis, which implements a generic workflow in its Workflow class.


  • chembl, unichem, mysql and mysql_connect modules are Python3 compatible


  • Orthology translation of network

  • Homologene UniProt dict to translate between different organisms UniProt-to-UniProt

  • Orthology translation of PTMs

  • Better processing of PhosphoSite regulatory sites


  • TF-target, miRNA-mRNA and TF-miRNA interactions from many databases


  • New web server based on pandas data frames

  • New module export for generating data frames of interactions or enzyme-substrate interactions

  • New module websrvtab for exporting data frames for the web server

  • TF-target interactions from DoRothEA


  • New dataio methods for Gene Ontology


  • Many new docstrings


  • New module complex: a comprehensive database of complexes

  • New module annot: database of protein annotations (function, location)

  • New module intercell: special methods for data integration focusing on intercellular communication

  • New module bel: BEL integration

  • Module go and all the connected dataio methods have been rewritten offering a workaround for data access despite GO’s terrible web services and providing much more versatile query methods

  • Removed MySQL support (e.g. loading mapping tables from MySQL)

  • Modules mapping, reflists, complex, ptm, annot, go became services: these modules build databases and provide query methods, sometimes they even automatically delete data to free memory

  • New interaction category in data_formats: ligand_receptor

  • Improved logging and control over verbosity

  • Better control over paremeters by the settings module

  • Many methods in dataio have been improved or fixed, docs and code style largely improved

  • Started to add tests especially for methods in dataio


  • The network database is not dependent any more on python-igraph hence it has been removed from the mandatory dependencies

  • New API for the network, interactions, evidences, molecular entities


  • A complete reorganization of the module structure: submodules sorted into a few major groups: core, inputs, internals, omnipath, share, utils


  • A complete redesign of the intercellular communication database

  • License support


  • Reorganization of the inputs module: each resource has its own submodule


  • A large part of the input methods has been tested and updated


  • Reorganized repository tree: the contents of the former src directory have been moved to the root

  • Settings are stored in a YML file


  • Full support for multi-species molecular interaction networks (e.g. pathogene-host)

  • Better support for not protein only molecular interaction networks (metabolites, drug compounds, RNA)

  • Graph database (Neo4j) backend (biocypher)

  • Split into separate modules (core, inputs, utils, dlmanager, etc)