Oct 24, 2018

PathMe: Merging and exploring mechanistic pathway knowledge

BioRxiv : the Preprint Server for Biology
Daniel Domingo-FernándezMartin Hofmann-Apitius


Background The complexity of representing biological systems is compounded by an ever-expanding body of knowledge emerging from multi-omics experiments. A number of pathway databases have facilitated pathway-centric approaches that assist in the interpretation of molecular signatures yielded by these experiments. However, the lack of interoperability between pathway databases has hindered the ability to harmonize these resources and to exploit their consolidated knowledge. Such a unification of pathway knowledge is imperative in enhancing the comprehension and modeling of biological abstractions. Results Here, we present PathMe, a Python package that transforms pathway knowledge from three major pathway databases into a unified abstraction using Biological Expression Language as the pivotal, integrative schema. PathMe is complemented by a novel web application (freely available at <https://pathme.scai.fraunhofer.de/>) which allows users to comprehensively explore pathway crosstalks and compare areas of consensus and discrepancies. Conclusions This work has harmonized three major pathway databases and transformed them into a unified schema in order to gain a holistic picture of pathway knowledge. We demonstrate the utility of ...Continue Reading

  • References
  • Citations


  • We're still populating references for this paper, please check back later.
  • References
  • Citations


  • This paper may not have been cited yet.

Mentioned in this Paper

Biochemical Pathway
Abstract Thinking Ability
Signal Pathways
Gene Ontology
DNA Integration
Genetic Exchange

About this Paper

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Related Papers

Oliver RuebenackerMichael L Blinov
Molecular Systems Biology
Etienne CaronHiroaki Kitano
BioRxiv : the Preprint Server for Biology
Daniel Domingo-FernándezMartin Hofmann-Apitius
NPJ Systems Biology and Applications
Daniel Domingo-FernándezMartin Hofmann-Apitius
© 2020 Meta ULC. All rights reserved