Kent Shefchek
Oregon State University
15 Papers
33 Citations
Kent Shefchek is an academic researcher from Oregon State University. The author has contributed to research in topics: Biological Ontologies & Computer science. The author has an hindex of 7, co-authored 11 publications. Previous affiliations of Kent Shefchek include Oregon Health & Science University.
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Papers
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Christopher J. Mungall,Julie A. McMurry,Sebastian Köhler,James P. Balhoff,Charles D. Borromeo,Matthew H. Brush,Seth Carbon,Tom Conlin,Nathan Dunn,Mark Engelstad,Erin D. Foster,Jean-Philippe F. Gourdine,Julius O.B. Jacobsen,Daniel Keith,Bryan Laraway,Suzanna E. Lewis,Jeremy Nguyen-Xuan,Kent Shefchek,Nicole Vasilevsky,Zhou Yuan,Nicole L. Washington,Harry Hochheiser,Tudor Groza,Damian Smedley,Peter N. Robinson,Melissa A. Haendel +25 more
TL;DR: The Monarch Initiative as discussed by the authors integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search, and develops many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases.
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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 Shefchek,Benjamin M. Good,James P. Balhoff,Tommaso Fontana,Hannah Blau,Nicolas Matentzoglu,Nomi L. Harris,Monica Munoz-Torres,Monica Munoz-Torres,Melissa A. Haendel,Peter N. Robinson,Marcin P. Joachimiak,Christopher J. Mungall +18 more
- 08 Jan 2021
TL;DR: KG-COVID-19 is created, a flexible framework that ingests and integrates heterogeneous biomedical data to produce knowledge graphs (KGs) and can be applied to other problems in which siloed biomedical data must be quickly integrated for different research applications, including future pandemics.
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science
Deepak Unni,Sierra A. T. Moxon,Michael Bada,Matthew H. Brush,Richard Bruskiewich,Paul A. Clemons,Vlado Dančík,Michel Dumontier,Karamarie Fecho,Gustavo Glusman,Jenn J. Hadlock,Nomi L. Harris,Arpita Joshi,Timothy E. Putman,Guangrong Qin,Stephen A. Ramsey,Kent Shefchek,Harold R. Solbrig,Karthik Soman,Anne Thessen,Melissa A. Haendel,Chris Bizon,Christopher J. Mungall,the Biomedical Data Translator Consortium +23 more
TL;DR: The need for a standardized data model for KGs is highlighted, Biolink Model is described, its utility is demonstrated in various initiatives, and it is shown how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.
The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.
Tim E Putman,Kevin Schaper,Nicolas Matentzoglu,Vincent Rubinetti,Faisal Alquaddoomi,Corey Cox,J. Harry Caufield,Glass Elsarboukh,Sarah Gehrke,H. Hegde,J. Reese,Ian Braun,Richard M Bruskiewich,Luca Cappelletti,Seth Carbon,Anita Caron,L. Chan,Christopher G. Chute,Katherina G Cortes,Vinicius de Souza,Tommaso Fontana,Nomi L. Harris,Emily L Hartley,Eric Hurwitz,Julius O.B. Jacobsen,Madan Krishnamurthy,Bryan Laraway,James A McLaughlin,Julie A. McMurry,Sierra AT Moxon,K. R. Mullen,Shawn T O'Neil,Kent Shefchek,Ray Stefancsik,Sabrina Toro,Nicole Vasilevsky,Ramona L Walls,Patricia L. Whetzel,David Osumi-Sutherland,Damian Smedley,Peter N Robinson,Christopher J. Mungall,Melissa A. Haendel,Monica Munoz-Torres +43 more
TL;DR: The Monarch Initiative has migrated its system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features.
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SEPIO: A semantic model for the integration and analysis of scientific evidence
Matthew H. Brush,Kent Shefchek,Melissa Haendel +2 more
- 01 Jan 2016
TL;DR: The structure and principles behind the SEPIO model are described, and its applications in support of data integration, curation, knowledge discovery, and manual and computational evaluation of scientific claims are reviewed.