Jonathan C. Silverstein

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.

BiomarkerKB: An Integrated Knowledgebase Supporting Biomarker-Centric Exploration of Biomedical Data

BiomarkerKB integrates and standardizes biomarker data from multiple sources to enable structured exploration and discovery of biomarker-disease relationships.

The HuBMAP Framework for Advancing Data FAIRness

The paper describes the HuBMAP framework for creating FAIR data through standardized metadata reporting across diverse assays and institutions.

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.

SenNet Portal: Build, Optimization and Usage

The paper introduces the SenNet Portal, a resource for senescent cell data and tools, and discusses its usage and future developments.

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.

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage

This paper describes the construction and usage of the Human Reference Atlas (HRA) v2.0, which integrates multiscale data across 36 organs and provides tools for analysis and visualization.

Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data

Petagraph integrates biomolecular data into a unified knowledge graph using UMLS ontologies to enable efficient multi-omics analysis across multiple datasets.

Tissue Registration and Exploration User Interfaces in support of a Human Reference Atlas

The paper presents software tools and user interfaces for annotating and exploring tissue data in a human reference atlas, enabling data harmonization and public access.