Author-sourced capture of pathway knowledge in computable form using Biofactoid

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 p...

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Bibliographic Details
Published in:eLife 2021-12, Vol.10
Main Authors: Wong, Jeffrey V, Franz, Max, Siper, Metin Can, Fong, Dylan, Durupinar, Funda, Dallago, Christian, Luna, Augustin, Giorgi, John, Rodchenkov, Igor, Babur, Özgün, Bachman, John A, Gyori, Benjamin M, Demir, Emek, Bader, Gary D, Sander, Chris
Format: Article
Language:English
Subjects:
Analysis
Chemicals
Computational and Systems Biology
Computational Biology - instrumentation
Computational Biology - methods
Computational linguistics
Computer applications
COVID-19
crowdsource
curation tool
Databases, Factual
Digital Object Identifier
E coli
Genes
Genetics and Genomics
Genomics
Genomics - instrumentation
Genomics - methods
Information management
Information sharing
Knowledge
knowledge base
Language processing
Natural language interfaces
Organisms
pathway analysis
Pilot Projects
Science Forum
Severe acute respiratory syndrome coronavirus 2
Software
User training
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Description
Summary: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.
ISSN:2050-084X
2050-084X
DOI:10.7554/eLife.68292