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Pathway Commons: 2019 Update

Igor Rodchenkov, View ORCID ProfileOzgun Babur, Augustin Luna, Bulent Arman Aksoy, View ORCID ProfileJeffrey V. Wong, Dylan Fong, Max Franz, Metin Can Siper, Manfred Cheung, Michael Wrana, Harsh Mistry, Logan Mosier, Jonah Dlin, Qizhi Wen, Caitlin O’Callaghan, Wanxin Li, Geoffrey Elder, Peter T. Smith, View ORCID ProfileChristian Dallago, Ethan Cerami, Benjamin Gross, Ugur Dogrusoz, Emek Demir, View ORCID ProfileGary D. Bader, Chris Sander
doi: https://doi.org/10.1101/788521
Igor Rodchenkov
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Ozgun Babur
2Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
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  • ORCID record for Ozgun Babur
Augustin Luna
3cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
4Department of Cell Biology, Harvard Medical School, Boston, MA, 02215, USA
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Bulent Arman Aksoy
5Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
6Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA
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Jeffrey V. Wong
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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  • ORCID record for Jeffrey V. Wong
Dylan Fong
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Max Franz
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Metin Can Siper
2Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
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Manfred Cheung
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Michael Wrana
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Harsh Mistry
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Logan Mosier
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Jonah Dlin
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Qizhi Wen
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Caitlin O’Callaghan
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Wanxin Li
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Geoffrey Elder
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Peter T. Smith
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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Christian Dallago
4Department of Cell Biology, Harvard Medical School, Boston, MA, 02215, USA
7Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA
8Department of Informatics, Technische Universität München, 85748 Garching, Germany
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  • ORCID record for Christian Dallago
Ethan Cerami
9Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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Benjamin Gross
10Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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Ugur Dogrusoz
11Department of Computer Engineering, Bilkent University, Ankara, 06800, Turkey
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Emek Demir
2Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
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  • For correspondence: chris@sanderlab.org gary.bader@utoronto.ca demire@ohsu.edu
Gary D. Bader
1The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
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  • For correspondence: chris@sanderlab.org gary.bader@utoronto.ca demire@ohsu.edu
Chris Sander
3cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
4Department of Cell Biology, Harvard Medical School, Boston, MA, 02215, USA
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  • For correspondence: chris@sanderlab.org gary.bader@utoronto.ca demire@ohsu.edu
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ABSTRACT

Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g., metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (1) tools to search this comprehensive resource, (2) a download site offering integrated bulk sets of pathway data (e.g., tables of interactions and gene sets), (3) reusable software libraries for working with pathway information in several programming languages (Java, R, Python, and Javascript), and (4) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4,794 detailed human biochemical processes (i.e., pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.

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.
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Posted October 01, 2019.
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Pathway Commons: 2019 Update
Igor Rodchenkov, Ozgun Babur, Augustin Luna, Bulent Arman Aksoy, Jeffrey V. Wong, Dylan Fong, Max Franz, Metin Can Siper, Manfred Cheung, Michael Wrana, Harsh Mistry, Logan Mosier, Jonah Dlin, Qizhi Wen, Caitlin O’Callaghan, Wanxin Li, Geoffrey Elder, Peter T. Smith, Christian Dallago, Ethan Cerami, Benjamin Gross, Ugur Dogrusoz, Emek Demir, Gary D. Bader, Chris Sander
bioRxiv 788521; doi: https://doi.org/10.1101/788521
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Pathway Commons: 2019 Update
Igor Rodchenkov, Ozgun Babur, Augustin Luna, Bulent Arman Aksoy, Jeffrey V. Wong, Dylan Fong, Max Franz, Metin Can Siper, Manfred Cheung, Michael Wrana, Harsh Mistry, Logan Mosier, Jonah Dlin, Qizhi Wen, Caitlin O’Callaghan, Wanxin Li, Geoffrey Elder, Peter T. Smith, Christian Dallago, Ethan Cerami, Benjamin Gross, Ugur Dogrusoz, Emek Demir, Gary D. Bader, Chris Sander
bioRxiv 788521; doi: https://doi.org/10.1101/788521

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