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Reactome enhanced pathway visualization

Konstantinos Sidiropoulos, Guilherme Viteri, Cristoffer Sevilla, Steve Jupe, Marissa Webber, Marija Orlic-Milacic, Bijay Jassal, Bruce May, Veronica Shamovsky, Corina Duenas, Karen Rothfels, Lisa Matthews (+8 others)
2017 Bioinformatics  
Here, we present new developments in the Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users' own research  ...  Motivation: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways.  ...  This top-down navigation of the Reactome pathways visualization begins with the Pathways Overview which provides a genome wide view of all the pathways in Reactome and their parentchild relationships.  ... 
doi:10.1093/bioinformatics/btx441 pmid:29077811 pmcid:PMC5860170 fatcat:ypdq4ibaandhnbs6ysoegcgab4

Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome

Marija Milacic, Robin Haw, Karen Rothfels, Guanming Wu, David Croft, Henning Hermjakob, Peter D'Eustachio, Lincoln Stein
2012 Cancers  
Reactome describes biological pathways as chemical reactions that closely mirror the actual physical interactions that occur in the cell.  ...  Using the Epidermal Growth Factor Receptor (EGFR) signaling pathway as an example, we show how Reactome annotates and presents the altered biological behavior of EGFR variants due to their altered kinase  ...  We have extended the Reactome data model and enhanced the web tools to permit the annotation and visualization of the altered biological behavior of protein variants.  ... 
doi:10.3390/cancers4041180 pmid:24213504 pmcid:PMC3712731 fatcat:yuq7zjs3z5edxngpwzncfa7jaq

A Comparison of the Pathway Tools Software with the Reactome Software [article]

Peter D. Karp
2020 arXiv   pre-print
This document compares SRI's Pathway Tools (PTools) software with the Reactome software.  ...  The comparison covers pathway bioinformatics capabilities, but does not cover other major facets of Pathway Tools that are completely absent from the Reactome software: Pathway Tools genome-informatics  ...  If the Reactome data were made available via PTools, the accessibility of those data would be greatly enhanced through legible pathway diagrams.  ... 
arXiv:2009.13690v1 fatcat:wwzmktiqdne7rlpttuvqonl2ve

Interleukins and their signaling pathways in the Reactome biological pathway database

Steve Jupe, Keith Ray, Corina Duenas Roca, Thawfeek Varusai, Veronica Shamovsky, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob
2018 Journal of Allergy and Clinical Immunology  
Objective-Reactome was established as a freely accessible knowledge base of human biological pathways.  ...  Background-There is a wealth of biological pathway information available in the scientific literature, but it is spread across many thousands of publications.  ...  In addition, analytic tools allow data set submission for the identification and visualization of pathway enrichment and representation of expression profiles as an overlay on Reactome pathways.  ... 
doi:10.1016/j.jaci.2017.12.992 pmid:29378288 pmcid:PMC5927619 fatcat:oy2ctphdqbehffj37pps24hsi4

The Reactome pathway knowledgebase

David Croft, Antonio Fabregat Mundo, Robin Haw, Marija Milacic, Joel Weiser, Guanming Wu, Michael Caudy, Phani Garapati, Marc Gillespie, Maulik R. Kamdar, Bijay Jassal, Steven Jupe (+11 others)
2013 Nucleic Acids Research  
Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions.  ...  The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness.  ...  ACKNOWLEDGEMENTS The authors are grateful to the many expert scientists who have collaborated with us as external authors and reviewers of Reactome content.  ... 
doi:10.1093/nar/gkt1102 pmid:24243840 pmcid:PMC3965010 fatcat:k6erba6xa5htfn3zzadwhk3cme

The Reactome Pathway Knowledgebase

Antonio Fabregat, Steven Jupe, Lisa Matthews, Konstantinos Sidiropoulos, Marc Gillespie, Phani Garapati, Robin Haw, Bijay Jassal, Florian Korninger, Bruce May, Marija Milacic, Corina Duenas Roca (+11 others)
2017 Nucleic Acids Research  
Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions.  ...  The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness.  ...  ACKNOWLEDGEMENTS The authors are grateful to the many expert scientists who have collaborated with us as external authors and reviewers of Reactome content.  ... 
doi:10.1093/nar/gkx1132 pmid:29145629 pmcid:PMC5753187 fatcat:2br73vnp4fbhbc3xlejyjmvyh4

Reactome Knowledgebase of Human Biological Pathways and Processes [chapter]

Peter D'Eustachio
2010 Msphere  
Toward this goal, Reactome has developed a beta version of an entity-level pathway visualization tool: through enhanced navigation features including improved zooming, scrolling and event highlighting,  ...  A new entitylevel pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets.  ... 
doi:10.1007/978-1-60761-977-2_4 pmid:21082427 fatcat:mrdugzz6zzal5e6guxopyt6dwe

Reactome knowledgebase of human biological pathways and processes

L. Matthews, G. Gopinath, M. Gillespie, M. Caudy, D. Croft, B. de Bono, P. Garapati, J. Hemish, H. Hermjakob, B. Jassal, A. Kanapin, S. Lewis (+8 others)
2009 Nucleic Acids Research  
Reactome (http://www.reactome.org) is an expertauthored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current  ...  Toward this goal, Reactome has developed a beta version of an entity-level pathway visualization tool: through enhanced navigation features including improved zooming, scrolling and event highlighting,  ...  A new entitylevel pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets.  ... 
doi:10.1093/nar/gkn863 pmid:18981052 pmcid:PMC2686536 fatcat:6oo2ou6qabaexb4zwngwpgp27y

Tools for visualization and analysis of molecular networks, pathways, and -omics data

Bianca Habermann, Jose Villaveces, Prasanna Koti
2015 Advances and Applications in Bioinformatics and Chemistry  
Biological pathways and networks are not only an appropriate approach to visualize molecular reactions. They have also become one leading method in -omics data analysis and visualization.  ...  Here, we review a set of pathway and network visualization and analysis methods and take a look at potential future developments in the field.  ...  Pathvisio is able to combine two datasets on the same pathway map. (C) The Reactome analysis toolbox was used to visualize -omics data on the Glycolysis pathway.  ... 
doi:10.2147/aabc.s63534 pmid:26082651 pmcid:PMC4461095 fatcat:vta2qzp3bbhohkb7hsm4hk6dxu

Reactome diagram viewer: data structures and strategies to boost performance

Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Pablo Marin-Garcia, Peipei Ping, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob, Janet Kelso
2017 Bioinformatics  
For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years.  ...  solution to pathway visualization.  ...  Aiming to address these challenges and enhance the overall user experience, a new version of the Pathway Diagram Viewer was implemented.  ... 
doi:10.1093/bioinformatics/btx752 pmid:29186351 pmcid:PMC6030826 fatcat:j4wrfd3v7fcwjb2ykhitis3apa

HINO: a BFO-aligned ontology representing human molecular interactions and pathways [article]

Yongqun He, Zoushuang Xiang
2013 arXiv   pre-print
Many database resources, such as Reactome, collect manually annotated reactions, interactions, and pathways from peer-reviewed publications.  ...  All human pathways and associated processes and interactors listed in Reactome and represented in BioPAX were first converted to ontology classes by aligning them under INO.  ...  The inclusion of OGG will likely further enhance the ontological representation of human interactions, pathways, and networks.  ... 
arXiv:1311.3355v1 fatcat:rhlzusljnvcu3habuax2p2govu

Gramene 2018: unifying comparative genomics and pathway resources for plant research

Marcela K Tello-Ruiz, Sushma Naithani, Joshua C Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J Geniza, Yinping Jiao, Young Koung Lee, Bo Wang (+27 others)
2017 Nucleic Acids Research  
Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks.  ...  All data in Gramene are accessible through both visual and programmatic interfaces.  ...  We also thank Peter van Buren from Cold Spring Harbor Laboratory for system administration support, and David Croft (EBI) and Robin Haw (OICR) for technical support of Plant Reactome development.  ... 
doi:10.1093/nar/gkx1111 pmid:29165610 pmcid:PMC5753211 fatcat:bxgarlrs6rab5lwpixua6gotgq

hiPathDB: a human-integrated pathway database with facile visualization

N. Yu, J. Seo, K. Rho, Y. Jang, J. Park, W. K. Kim, S. Lee
2011 Nucleic Acids Research  
PID, Reactome, BioCarta and KEGG.  ...  The layout algorithm is optimized for virtually automatic visualization of the pathways. hiPathDB is available at http://hiPathDB.kobic.re.kr.  ...  ACKNOWLEDGEMENT The authors gratefully acknowledge the dedicated effort of curation teams that are creating and sharing biological pathway information.  ... 
doi:10.1093/nar/gkr1127 pmid:22123737 pmcid:PMC3245021 fatcat:jgvmx22u3bebrn7sihq3v32lxq

Plant Reactome: a knowledgebase and resource for comparative pathway analysis

2019 Nucleic Acids Research  
Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project.  ...  It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model  ...  We acknowledge Robin Haw, Joel Weiser, Guanming Wu, and Lisa Matthews from the human Reactome project and the Ontario Institute for Cancer Research for providing access to the Reactome central curation  ... 
doi:10.1093/nar/gkz996 pmid:31680153 pmcid:PMC7145600 fatcat:ykzfjhf4hvgs7keopndswr5req

Automation of ReactomeFIViz via CyREST API

Fred Loney, Guanming Wu
2018 F1000Research  
ReactomeFIViz is a Cytoscape app, providing features for researchers to perform pathway-and network-based data analysis and visualization by leveraging manually curated Reactome pathways and highly reliable  ...  Pathway-and network-based approaches project seemingly unrelated genes onto the context of pathways and networks, enhancing the analysis power that cannot be achieved via gene-based approaches.  ...  To visualize mutated genes in the context of Reactome pathways, the notebook also generated two pathway diagrams, one for each cancer, and saved into the working directory as PDF files.  ... 
doi:10.12688/f1000research.14776.1 pmid:29946442 pmcid:PMC5998009 fatcat:l2y2r3trdzayxeyb75fcjcosve
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