Semantic Web and Ontologies

Ontology-driven software engineering using LLMs for knowledge graphs in engineering biology

The paper presents an ontology-driven approach using LLMs to create software libraries for knowledge graphs in engineering biology, demonstrating it with the SBOL3 Ontology and sbol-script library.

MCBO: Mammalian Cell Bioprocessing Ontology, A Hub-and-Spoke, IOF-Anchored Application Ontology

MCBO provides a standardized ontology for mammalian cell bioprocessing data to enable harmonization and querying of complex biomanufacturing datasets.

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.

Task Splitting and Prompt Engineering for Cypher Query Generation in Domain-Specific Knowledge Graphs

This paper introduces Prompt2Cypher, a method that uses task splitting and prompt engineering to improve Cypher query generation for domain-specific knowledge graphs, showing better accuracy in biological datasets.

A novel tool for standardizing clinical data in a realism-based common data model

The paper introduces a tool for standardizing clinical data using a realism-based common data model and semantic technologies.

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.

Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings

Vec2SPARQL integrates vector space representations with SPARQL queries to enable semantic similarity and classification within a single query for biomedical applications.

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.