Author-sourced capture of pathway knowledge in computable form using Biofactoid
- University of Toronto, Canada
- Oregon Health and Science University, United States
- University of Massachusetts Boston, United States
- Technische Universität München, Germany
- Dana-Farber Cancer Institute, United States
- Harvard University, United States
Abstract
Making the knowledge contained in scientific papers machine-readable and formally computable would allow researchers to take full advantage of this information by enabling integration with other knowledge sources to support data analysis and interpretation. Here we describe Biofactoid, a web-based platform that allows scientists to specify networks of interactions between genes, their products, and chemical compounds, and then translates this information into a representation suitable for computational analysis, search and discovery. We also report the results of a pilot study to encourage the wide adoption of Biofactoid by the scientific community.
Data availability
All Biofactoid data are available under the Creative Commons CC0 public domain license. To download the data and code, please refer to the documentation on the Biofactoid GitHub repository (github.com/PathwayCommons/factoid). More information on software availability is available in Materials and methods.
Article and author information
Author details
Funding
National Human Genome Research Institute (U41 HG006623)
- Jeffrey V Wong
- Max Franz
- Metin Can Siper
- Dylan Fong
- Funda Durupinar
- Christian Dallago
- Augustin Luna
- John M Giorgi
- Igor Rodchenkov
- Özgün Babur
- Emek Demir
- Gary D Bader
- Chris Sander
National Human Genome Research Institute (U41 HG003751)
- Jeffrey V Wong
- Max Franz
- Metin Can Siper
- Dylan Fong
- Funda Durupinar
- Christian Dallago
- Augustin Luna
- John M Giorgi
- Igor Rodchenkov
- Özgün Babur
- Emek Demir
- Gary D Bader
- Chris Sander
National Human Genome Research Institute (R01 HG009979)
- Max Franz
- Gary D Bader
National Institute of General Medical Sciences (P41 GM103504)
- Jeffrey V Wong
- Max Franz
- Metin Can Siper
- Dylan Fong
- Funda Durupinar
- Christian Dallago
- Augustin Luna
- John M Giorgi
- Igor Rodchenkov
- Özgün Babur
- Emek Demir
- Gary D Bader
- Chris Sander
Defense Advanced Research Projects Agency (Big Mechanism,ARO W911NF-14-C-0119)
- Metin Can Siper
- Funda Durupinar
- Özgün Babur
- John A Bachman
- Benjamin Gyori
- Emek Demir
Defense Advanced Research Projects Agency (Communicating with Computers,ARO W911NF-15-1-054)
- Metin Can Siper
- Funda Durupinar
- Özgün Babur
- John A Bachman
- Benjamin Gyori
- Emek Demir
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Human subjects: Participants of user testing provided written consent to volunteer, have their testing sessions recorded and have quotes obtained in the session published.
Copyright
© 2021, Wong et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Author-sourced capture of pathway knowledge in computable form using Biofactoid
eLife 10:e68292.
https://doi.org/10.7554/eLife.68292
