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KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response

Justin T. Reese, Deepak Unni, Tiffany J. Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Kent A. Shefchek, Benjamin M. Good, James P. Balhoff, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu (+6 others)
2020 Patterns  
To address these challenges, we created KG-COVID-19, a flexible framework that ingests and integrates heterogeneous biomedical data to produce knowledge graphs (KGs), and applied it to create a KG for  ...  COVID-19 response.  ...  KG-COVID-19 is a framework for producing knowledge graphs that can be customized for downstream applications including machine learning tasks, hypothesis-based querying, and browsable user interface to  ... 
doi:10.1016/j.patter.2020.100155 pmid:33196056 pmcid:PMC7649624 fatcat:bkoqhgb7mjf7roajxw4ohxuvgu

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response [article]

Justin T Reese, Deepak R Unni, Tiffany J Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu, Nomi L Harris, Monica C Munoz-Torres, Peter N Robinson (+2 others)
2020 biorxiv/medrxiv  
To address these challenges, we created KG-COVID-19, a flexible framework that ingests and integrates biomedical data to produce knowledge graphs (KGs) for COVID-19 response.  ...  Integrated, up-to-date data about SARS-CoV-2 and coronavirus disease 2019 (COVID-19) is crucial for the ongoing response to the COVID-19 pandemic by the biomedical research community.  ...  KG-COVID-19 is a framework for producing knowledge graphs that can be customized for downstream applications including machine learning tasks, hypothesis-based querying, and browsable user interface to  ... 
doi:10.1101/2020.08.17.254839 pmid:32839776 pmcid:PMC7444288 fatcat:kiiqbvcigfcchm4v6ikoz5umju

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response

Justin T. Reese, Deepak R. Unni, Tiffany J. Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu, Nomi L. Harris, Monica C. Munoz-Torres, Peter N. Robinson (+3 others)
2020 Social Science Research Network  
as: Reese et al., KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response, Patterns (2020), https://doi.org/10.1016/j.patter.2020.100155  ...  Reese et al., KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response, Patterns (2020), https://doi.org/10.1016/j.patter.2020.100155 Please cite this article in press  ... 
doi:10.2139/ssrn.3681978 fatcat:pkm3aschdfajtg4v6mqzy47ofm

The National COVID Cohort Collaborative (N3C): Rationale, Design, Infrastructure, and Deployment

Melissa A Haendel, Chris Chute, N3C Consortium (See Attached Document)
2020 Zenodo  
data for COVID-19 analytics.  ...  Objective COVID-19 poses societal challenges that require expeditious data and knowledge sharing.  ...  ACKNOWLEDGEMENTS STATEMENT We acknowledge the Oregon Clinical and Translational Research Institute for their guidance and review of N3C plans and regulatory processes as they unfolded.  ... 
doi:10.5281/zenodo.3979622 fatcat:ocgmyerqtvfdhnw23r3jjy7r6i

The National COVID Cohort Collaborative (N3C): Rationale, Design, Infrastructure, and Deployment

Haendel Melissa, Chute Christopher, Gersing Kenneth
2020 JAMIA Journal of the American Medical Informatics Association  
data for COVID-19 analytics.  ...  Objective COVID-19 poses societal challenges that require expeditious data and knowledge sharing.  ...  and a variety of KGs covering a range of biological entities such as genes, biological processes, and diseases; the KG-COVID-19 98 knowledge graph also includes literature annotation.  ... 
doi:10.1093/jamia/ocaa196 pmid:32805036 pmcid:PMC7454687 fatcat:rgaafgl6k5hjvlbpphcdcdr6ie

A critical overview of computational approaches employed for COVID-19 drug discovery

Eugene N. Muratov, Rommie Amaro, Carolina H. Andrade, Nathan Brown, Sean Ekins, Denis Fourches, Olexandr Isayev, Dima Kozakov, José L. Medina-Franco, Kenneth M. Merz, Tudor I. Oprea, Vladimir Poroikov (+7 others)
2021 Chemical Society Reviews  
We cover diverse methodologies, computational approaches, and case studies illustrating the ongoing efforts to develop viable drug candidates for treatment of COVID-19.  ...  AWS has also generated a similar biological knowledge graph, called DRKG, to fight COVID-19.  ...  The use of knowledge graph approaches for COVID-19 drug repurposing Biomedical Knowledge Graphs (KG) aim to provide a high level overview of the association between diseases (symptoms, ontologies, etc.  ... 
doi:10.1039/d0cs01065k pmid:34212944 pmcid:PMC8371861 fatcat:n6dxyyjxifh6hoehd7myapjtwu

Learning deep translational patient representations: systematic integration of clinical records and biomedical knowledge [article]

Tiffany Callahan
2022
These experiments were used to develop a joint learning framework for inferring molecular characterizations of patients from clinical data.  ...  Finally, an algorithm that losslessly transforms complex knowledge graphs (KGs) into representations more suitable for inductive inference was developed and validated through the generation of expert-verified  ...  With respect to Availability and Usability, PheKnowLator and six other methods (i.e., the Clinical Knowledge Graph, Hetionet, KaBOB, kg-covid-19, KGTK, and Knowledge Graph Exchange) performed equally well  ... 
doi:10.25677/se22-we57 fatcat:sjoxgbfatvdvha7w6kgi2izape