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Generation of prior knowledge network for OCEAN

This repository contains a set of functions to generate organism-specific prior knowledge networks (PKNs) for the ocean R package. It is structured as follows:

  • data: it contains the starting data needed to generate PKNs for every organism. These data come from this repository, a platform of genome-scale metabolic models (GEMs) for different organisms. For more details about how these GEMs were generated, see Wang et al., 2021. In this repository, GEMs for human (Homo sapiens), mouse (Mus musculus) and rat (Ratus norvegicus) are available, but the rest can be easily downloaded from their corresponding repositories. In addition, information to determine cofactors from KEGG is also already downloaded and stored as an RDS file.
  • notebooks: Rmd with a descriptive analysis of the mouse PKN.
  • output: final PKNs in form of RDS files.
  • reports: HTML and plots (png) generated after rendering Rmds in notebooks.
  • src: there are two R files:
    • final_functions_PKN_OCEAN.R: contains the set of functions in charge of generating the PKNs.
    • generation_networks_OCEAN.R: script which loads final_functions_PKN_OCEAN.R functions and write the final output as RDS files in output.

These functions will be available through the OmnipathR R package in the future.

References

  • Wang H, Robinson JL, Kocabas P, Gustafsson J, Anton M, Cholley PE, et al. Genome-scale metabolic network reconstruction of model animals as a platform for translational research. Proceedings of the National Academy of Sciences. 2021 Jul 27;118(30):e2102344118.