J. Alan Simmons

ddkg.skill: A Compositional Agent Skill for Translating Biomedical and Bioinformatics Questions into Cypher for the Data Distillery Knowledge Graph

ddkg.skill translates biomedical questions into Cypher queries for the DDKG, improving accuracy through structured references and validation.

MOSAIC: Learning Graph Node Embeddings from Spectrally Isolated Dominant Subspaces of Accumulated Diffusion Operators

MOSAIC learns graph node embeddings by analyzing dominant spectral components of diffusion operators, outperforming existing methods in biomedical graph tasks.

BIFO: A Biological Information Flow Ontology for Directed Propagation in Heterogeneous Biomedical Knowledge Graphs

The paper introduces BIFO, an ontology that specifies biologically admissible directed transformations in biomedical knowledge graphs to enable meaningful signal propagation.

The Common Fund Data Ecosystem (CFDE)

The paper describes the Common Fund Data Ecosystem (CFDE), which integrates NIH Common Fund data resources to enable discovery, analysis, and collaboration across heterogeneous datasets.

The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data

The paper introduces a knowledge graph framework for integrating and querying biomedical data across domains, demonstrating its utility in eight use cases.