Converter of COVID-19 CellDesigner diagrams “raw SIF” files obtained using CaSQ and MINERVA to HiPathia “SIF” and “ATT” file format.

The present directory contains the code and files necessary to convert Simple Interaction Files (SIF), generated with CaSQ python package, from curated COVID-19 related CellDesigner diagrams to HiPathia’s SIF and ATT (attribute) files. The ATT files are generated using Minerva, as a proxy between CaSQ and CellDesigner, to retrieve details of each node. These SIF and ATT files are needed by the HiPathia mechanistic modelling metagraphinfo database in order to run the algorithm over the diagrams. After running the conversor, each diagram will count with a “diagram.sif” and a “diagram.att” file,moreover a “names.pathways.txt” file listing the names of the diagrams converted will be also generated.

The directory is structured into 2 folders and 2 scripts.

Scripts

** - functions_retrieve_sif_att_hipathia_from_CellDesigner.R**:

The present script contains the functions needed for converting raw SIF files from CellDesigner to HiPathia SIF and ATT files. The script is autodescriptive and counts with 5 functions for the retrieval, preprocessing and formatting of the raw SIF files. The functions enable to handle API querys, retrieve detailed information of each node from a CellDesigner diagram and format the information into HiPathia’s SIF and ATT files. Each function is fully describe in the script. DO NOT EDIT (only edit for coding purposes).

** - example_sif_Hipathia.R**

The present script contains the example code to run over the existing diagrams on the https://git-r3lab.uni.lu/covid/models/-/tree/master/ repository, please in order to run the code correctly clone the repository on a local directory and recode the “base_dir” variable to that directory. The script will read the Simple Interaction Files (SIF) from the CellDesigner diagrams located in /models-master/Executable Modules/SBML_qual_build/sif in the repository, generate HiPathia formatted SIF and ATT files for each diagram and a “names.pathways.txt” file listing the names of the diagrams converted. The files are by default stored in the test folder, this parameter can be change in the outputfolder parameter of the hipathia.att.sif function.

CAUTION: Please when running the script make sure you recode the variable “base_dir” to the local directory where the repo models-master was cloned.

Resources folder

Contains the “exceptions.txt” file, which contains for the nodes we desire to avoid, nodes that are not allowed in the metagraphinfo database such as viral gene nodes.

Test folder

Empty folder that will store the results of running the “example_sif_Hipathia.R”

figure

figure