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
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)