Literature DB >> 36093122

A biomedical open knowledge network harnesses the power of AI to understand deep human biology.

Sergio E Baranzini1,2, Katy Börner3, John Morris4, Charlotte A Nelson1, Karthik Soman1, Erica Schleimer1, Michael Keiser4,5, Mark Musen6, Roger Pearce7, Tahsin Reza7, Brett Smith8, Bruce W Herr3, Boris Oskotsky2, Angela Rizk-Jackson2, Katherine P Rankin1,2, Stephan J Sanders2,9, Riley Bove1,2, Peter W Rose10, Sharat Israni2, Sui Huang8.   

Abstract

Knowledge representation and reasoning (KR&R) has been successfully implemented in many fields to enable computers to solve complex problems with AI methods. However, its application to biomedicine has been lagging in part due to the daunting complexity of molecular and cellular pathways that govern human physiology and pathology. In this article we describe concrete uses of SPOKE, an open knowledge network that connects curated information from 37 specialized and human-curated databases into a single property graph, with 3 million nodes and 15 million edges to date. Applications discussed in this article include drug discovery, COVID-19 research and chronic disease diagnosis and management.

Entities:  

Keywords:  Knowledge graph; biomedical databases; drug development; electronic health record

Year:  2022        PMID: 36093122      PMCID: PMC9456356          DOI: 10.1002/aaai.12037

Source DB:  PubMed          Journal:  AI Mag        ISSN: 0738-4602            Impact factor:   2.524


  17 in total

1.  Node, Node-Link, and Node-Link-Group Diagrams: An Evaluation.

Authors:  Bahador Saket; Paolo Simonetto; Stephen Kobourov; Katy Börner
Journal:  IEEE Trans Vis Comput Graph       Date:  2014-12       Impact factor: 4.579

2.  The EBI SRS server--recent developments.

Authors:  Evgeni M Zdobnov; Rodrigo Lopez; Rolf Apweiler; Thure Etzold
Journal:  Bioinformatics       Date:  2002-02       Impact factor: 6.937

Review 3.  Development of novel pharmacotherapeutics for tobacco dependence: progress and future directions.

Authors:  Dympna Harmey; Patrick R Griffin; Paul J Kenny
Journal:  Nicotine Tob Res       Date:  2012-09-27       Impact factor: 4.244

4.  Systematic integration of biomedical knowledge prioritizes drugs for repurposing.

Authors:  Daniel Scott Himmelstein; Antoine Lizee; Christine Hessler; Leo Brueggeman; Sabrina L Chen; Dexter Hadley; Ari Green; Pouya Khankhanian; Sergio E Baranzini
Journal:  Elife       Date:  2017-09-22       Impact factor: 8.140

5.  A wellness study of 108 individuals using personal, dense, dynamic data clouds.

Authors:  Nathan D Price; Andrew T Magis; John C Earls; Gustavo Glusman; Roie Levy; Christopher Lausted; Daniel T McDonald; Ulrike Kusebauch; Christopher L Moss; Yong Zhou; Shizhen Qin; Robert L Moritz; Kristin Brogaard; Gilbert S Omenn; Jennifer C Lovejoy; Leroy Hood
Journal:  Nat Biotechnol       Date:  2017-07-17       Impact factor: 54.908

6.  Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings.

Authors:  Charlotte A Nelson; Atul J Butte; Sergio E Baranzini
Journal:  Nat Commun       Date:  2019-07-10       Impact factor: 14.919

7.  Embedding electronic health records onto a knowledge network recognizes prodromal features of multiple sclerosis and predicts diagnosis.

Authors:  Charlotte A Nelson; Riley Bove; Atul J Butte; Sergio E Baranzini
Journal:  J Am Med Inform Assoc       Date:  2022-01-29       Impact factor: 4.497

8.  Dexamethasone in Hospitalized Patients with Covid-19.

Authors:  Peter Horby; Wei Shen Lim; Jonathan R Emberson; Marion Mafham; Jennifer L Bell; Louise Linsell; Natalie Staplin; Christopher Brightling; Andrew Ustianowski; Einas Elmahi; Benjamin Prudon; Christopher Green; Timothy Felton; David Chadwick; Kanchan Rege; Christopher Fegan; Lucy C Chappell; Saul N Faust; Thomas Jaki; Katie Jeffery; Alan Montgomery; Kathryn Rowan; Edmund Juszczak; J Kenneth Baillie; Richard Haynes; Martin J Landray
Journal:  N Engl J Med       Date:  2020-07-17       Impact factor: 91.245

Review 9.  Artificial intelligence in COVID-19 drug repurposing.

Authors:  Yadi Zhou; Fei Wang; Jian Tang; Ruth Nussinov; Feixiong Cheng
Journal:  Lancet Digit Health       Date:  2020-09-18

10.  A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm.

Authors:  Michael R Garvin; Christiane Alvarez; J Izaak Miller; Erica T Prates; Angelica M Walker; B Kirtley Amos; Alan E Mast; Amy Justice; Bruce Aronow; Daniel Jacobson
Journal:  Elife       Date:  2020-07-07       Impact factor: 8.713

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