Semantic Web and Ontologies

TogoMCP: Natural Language Querying of Life-Science Knowledge Graphs via Schema-Guided LLMs and the Model Context Protocol

METRIN-KG: A knowledge graph integrating plant metabolites, traits, and biotic interactions

The paper introduces METRIN-KG, a knowledge graph integrating plant metabolites, traits, and biotic interactions to facilitate biodiversity data analysis.

Programmatic access to ICTV virus taxonomy through a public ontology API

The paper develops a public ontology API for programmatic access to ICTV virus taxonomy, enabling semantic and machine-actionable retrieval of taxonomic data across releases.

Enabling Semantic Queries Across Federated Bioinformatics Databases

The paper introduces a semantic model and federated approach to integrate heterogeneous biological databases, enabling joint queries across gene expression, orthology, and protein data sources.

Agronomic Linked Data (AgroLD): a Knowledge-based System to Enable Integrative Biology in Agronomy

The paper introduces AgroLD, a knowledge-based system integrating omics data from plant species to enable integrative biology research in agronomy.

Cross-linking BioThings APIs through JSON-LD to facilitate knowledge exploration

The paper implements JSON-LD on BioThings APIs to enhance interoperability through semantic annotations, enabling cross-linking and improved query capabilities.