James Alastair McLaughlin

This paper describes an AI semantics workflow using LLM agents to integrate multimodal biomedical data through ontologies and knowledge graphs.

The paper presents tools to validate and simplify ontology term hierarchies for better usability in biomedical research.

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.

The paper describes the International Mouse Phenotyping Consortium's data portal, its expansion to over 100 million data points, and improvements to its web interface and data access tools.

PhEval provides a standardized framework to benchmark phenotype-driven variant and gene prioritisation algorithms using real-world patient data and controlled test corpora.

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.

The paper introduces uPheno, a framework for cross-species phenomics integration by harmonizing phenotype data across species and ontologies.

The GWAS Catalog now holds 625,113 curated SNP-trait associations from 6,921 publications plus >85K summary statistics datasets, with a new GWAS-SSF submission standard and GRCh38 harmonisation.

The paper demonstrates how the SBOL standard can represent multicellular biological systems, enabling better sharing of complex designs across multiple cells.

The paper introduces SBOL-OWL, an ontology that enables machine-readable semantic representation of synthetic genetic circuits, enhancing computational tools' ability to understand and validate designs.