5 papers
Why we need all the organisms: an exploration of the Monarch knowledge graph to aid mechanism discovery
Katherina Cortes, Daniel Korn, Sarah Gehrke +12
Research done using model organisms has been fundamental to the biological understanding of human genes, diseases and phenotypes. Model organisms provide tractable systems for expe…
Koza and Koza-Hub for born-interoperable knowledge graph generation using KGX
Daniel R Korn, Patrick Golden, Aaron Odell +10
Knowledge graph construction has become an essential domain for the future of biomedical research. But current approaches demand a high amount of redundant labor. These redundancie…
Improving Biomedical Knowledge Graph Quality: A Community Approach
Katherina G Cortes, Shilpa Sundar, Sarah Gehrke +13
Biomedical knowledge graphs (KGs) are widely used across research and translational settings, yet their design decisions and implementation are often opaque. Unlike ontologies that…
Chemical classification program synthesis using generative artificial intelligence
Christopher J. Mungall, Adnan Malik, Daniel R. Korn +4
Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molec…
A Dynamic Framework for Semantic Grouping of Common Data Elements (CDE) Using Embeddings and Clustering
Madan Krishnamurthy, Daniel Korn, Melissa A Haendel +2
This research aims to develop a dynamic and scalable framework to facilitate harmonization of Common Data Elements (CDEs) across heterogeneous biomedical datasets by addressing cha…