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Kent A. Shefchek

dblp:194/5175 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2023
0000-0001-6439-2224ORCID · verified

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 62% Computational science and engineering · 38%

Topics — the 3 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › network bioinformatics › biological network analysis
biological knowledge graph
0.712023
KG-Hub - building and exchanging biological knowledge graphs · Bioinform. 2023
Computational science and engineering
graph learning
0.212023
KG-Hub - building and exchanging biological knowledge graphs · Bioinform. 2023
Computational science and engineering › graph learning
link prediction
0.212023
KG-Hub - building and exchanging biological knowledge graphs · Bioinform. 2023

Methods — techniques the papers use, named apart from their topics

node embedding · 0.7graph machine learning · 0.7extract-transform-load · 0.7
YearPublicationVenuePosition
2023 KG-Hub - building and exchanging biological knowledge graphs
abstract
MOTIVATION: Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking. RESULTS: Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract-transform-load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial-environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate KGs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph ML, including node embeddings and training of models for link prediction and node classification. AVAILABILITY AND IMPLEMENTATION: https://kghub.org.
J. Harry Caufield, Tim E. Putman, Kevin Schaper, Deepak R. Unni, Harshad Hegde, Tiffany Callahan, Luca Cappelletti, Sierra A. T. Moxon, Vida Ravanmehr, Seth Carbon, Lauren E. Chan, Katherina G. Cortes, Kent A. Shefchek, Glass Elsarboukh, James P. Balhoff, Tommaso Fontana, Nicolas Matentzoglu, Richard M. Bruskiewich, Anne E. Thessen, Nomi L. Harris, Monica C. Munoz-Torres, Melissa A. Haendel, Peter N. Robinson, Marcin P. Joachimiak, Chris Mungall, Justin T. Reese
Bioinform.13