Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling

View ORCID ProfileAlexander Mazein, View ORCID ProfileAdrien Rougny, View ORCID ProfileJonathan R. Karr, View ORCID ProfileJulio Saez Rodriguez, View ORCID ProfileMarek Ostaszewski, View ORCID ProfileReinhard Schneider
doi: https://doi.org/10.1101/2020.12.08.416719
Alexander Mazein
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
2European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Alexander Mazein
  • For correspondence: alexander.mazein@uni.lu
Adrien Rougny
3Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo, Japan
4Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), AIST, Aomi, Tokyo, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Adrien Rougny
Jonathan R. Karr
5Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
6Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jonathan R. Karr
Julio Saez Rodriguez
7Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany
8Institute for Computational Biomedicine, Heidelberg University Hospital and Heidelberg University, Faculty of Medicine, Bioquant Heidelberg, Heidelberg 69120, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Julio Saez Rodriguez
Marek Ostaszewski
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Marek Ostaszewski
Reinhard Schneider
1Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Reinhard Schneider
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Detailed maps of the molecular basis of the disease are powerful tools for interpreting data and building predictive models. Modularity and composability are considered necessary network features for large-scale collaborative efforts to build comprehensive molecular descriptions of disease mechanisms. An effective way to create and manage large systems is to compose multiple subsystems. Composable network components could effectively harness the contributions of many individuals and enable teams to seamlessly assemble many individual components into comprehensive maps. We examine manually-built versions of the RAS-RAF-MEK-ERK cascade from the Atlas of Cancer Signalling Network, PANTHER and Reactome databases and review them in terms of their reusability and composability for assembling new disease models. We identify design principles for managing complex systems that could make it easier for investigators to share and reuse network components. We demonstrate the main challenges including incompatible levels of detail and ambiguous representation of complexes and highlight the need to address these challenges.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted December 08, 2020.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling
Alexander Mazein, Adrien Rougny, Jonathan R. Karr, Julio Saez Rodriguez, Marek Ostaszewski, Reinhard Schneider
bioRxiv 2020.12.08.416719; doi: https://doi.org/10.1101/2020.12.08.416719
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling
Alexander Mazein, Adrien Rougny, Jonathan R. Karr, Julio Saez Rodriguez, Marek Ostaszewski, Reinhard Schneider
bioRxiv 2020.12.08.416719; doi: https://doi.org/10.1101/2020.12.08.416719

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Systems Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4672)
  • Biochemistry (10338)
  • Bioengineering (7657)
  • Bioinformatics (26296)
  • Biophysics (13500)
  • Cancer Biology (10670)
  • Cell Biology (15412)
  • Clinical Trials (138)
  • Developmental Biology (8487)
  • Ecology (12805)
  • Epidemiology (2067)
  • Evolutionary Biology (16826)
  • Genetics (11382)
  • Genomics (15467)
  • Immunology (10599)
  • Microbiology (25166)
  • Molecular Biology (10203)
  • Neuroscience (54382)
  • Paleontology (399)
  • Pathology (1665)
  • Pharmacology and Toxicology (2889)
  • Physiology (4334)
  • Plant Biology (9235)
  • Scientific Communication and Education (1586)
  • Synthetic Biology (2554)
  • Systems Biology (6772)
  • Zoology (1461)