ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases

NPJ Systems Biology and Applications
Daniel Domingo-FernándezMartin Hofmann-Apitius

Abstract

Although pathways are widely used for the analysis and representation of biological systems, their lack of clear boundaries, their dispersion across numerous databases, and the lack of interoperability impedes the evaluation of the coverage, agreements, and discrepancies between them. Here, we present ComPath, an ecosystem that supports curation of pathway mappings between databases and fosters the exploration of pathway knowledge through several novel visualizations. We have curated mappings between three of the major pathway databases and present a case study focusing on Parkinson's disease that illustrates how ComPath can generate new biological insights by identifying pathway modules, clusters, and cross-talks with these mappings. The ComPath source code and resources are available at https://github.com/ComPath and the web application can be accessed at https://compath.scai.fraunhofer.de/.

References

Mar 15, 2005·FEBS Letters·Michael P CaryChris Sander
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Jul 30, 2009·Molecular Systems Biology·Anna Bauer-MehrenFerran Sanz
Sep 11, 2010·Nature Biotechnology·Emek DemirGary D Bader
Nov 13, 2010·Nucleic Acids Research·Ethan G CeramiChris Sander
May 7, 2011·Bioinformatics·Arthur LiberzonJill P Mesirov
May 7, 2011·Nucleic Acids Research·Takuji YamadaPeer Bork
Oct 18, 2011·BMC Systems Biology·Miranda D StobbePerry D Moerland
Dec 27, 2011·Neurobiology of Disease·Aaron M GusdonCharleen T Chu
Mar 3, 2012·PLoS Computational Biology·Purvesh KhatriAtul J Butte
Jan 4, 2013·BMC Genomics·Mark S DodererYidong Chen
Dec 18, 2013·Bioinformatics·Andreas KrämerStuart Tugendreich
Feb 7, 2014·Journal of Biomedical Semantics·Victoria PetriHoward J Jacob
Jan 30, 2015·Database : the Journal of Biological Databases and Curation·Saikat Chowdhury, Ram Rup Sarkar
Jan 31, 2015·Cell·José BrásJohn Hardy
Feb 24, 2015·Molecular and Cellular Neurosciences·Rebecca M PerrettGeorge K Tofaris
Jul 3, 2015·Proceedings of the National Academy of Sciences of the United States of America·Tine HolemansPeter Vangheluwe
Oct 16, 2015·Nucleic Acids Research·Livia PerfettoGianni Cesareni
Oct 21, 2015·Nucleic Acids Research·Martina KutmonAlexander R Pico
Oct 23, 2015·BMC Bioinformatics·Michaela BayerlováTim Beißbarth
Jan 29, 2016·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Subramanian RajagopalanJulie K Andersen
Apr 16, 2016·Journal of Alzheimer's Disease : JAD·Anandhi IyappanMartin Hofmann-Apitius
Apr 22, 2016·Nucleic Acids Research·Jüri ReimandJaak Vilo
May 5, 2016·Nucleic Acids Research·Maxim V KuleshovAvi Ma'ayan
May 21, 2016·PLoS Computational Biology·Anwesha BohlerChris T Evelo
Aug 31, 2016·Nature Methods·Lina WadiJüri Reimand
Dec 3, 2016·Nucleic Acids Research·Minoru KanehisaKanae Morishima
Nov 15, 2017·Nucleic Acids Research·Denise N SlenterEgon L Willighagen
Nov 16, 2017·Nucleic Acids Research·David S WishartAugustin Scalbert
Nov 18, 2017·Nucleic Acids Research·Antonio FabregatPeter D'Eustachio
Jan 26, 2018·PloS One·Ivana IhnatovaEva Budinska
Mar 20, 2018·PLoS Computational Biology·Yered Pita-JuárezWinston Hide

❮ Previous
Next ❯

Citations

May 17, 2019·BMC Bioinformatics·Daniel Domingo-FernándezMartin Hofmann-Apitius
Dec 12, 2019·Frontiers in Genetics·Sarah MubeenDaniel Domingo-Fernández
May 22, 2020·Bioinformatics·Giuseppe AgapitoMario Cannataro
Nov 20, 2020·Nucleic Acids Research·Marvin MartensMartina Kutmon
Sep 28, 2021·NAR Genomics and Bioinformatics·Sarah MubeenDaniel Domingo-Fernández

❮ Previous
Next ❯

Software Mentioned

PDgset
Biological Pathway Exchange ( BioPAX
Clustergrammer
SIGNOR
Reactome
Flask
Bootstrap
js
PyPI
Cytoscape

Related Concepts

Related Feeds

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.