Publications

Selected and recent publications. For the complete and continuously updated list, see David Osumi-Sutherland’s ORCID record.

2026

The Cell Ontology in the age of single-cell omics. Scientific Data. doi:10.1038/s41597-026-07173-8
A general strategy for generating expert-guided, simplified views of ontologies. Scientific Data. doi:10.1038/s41597-025-06383-w
A layered standards framework for integrating single-cell and spatial omics data into brain cell atlases. doi:10.64898/2026.04.30.722039
scFAIR Consortium: a decentralized hub for single-cell RNA-Seq data standardization and unification. doi:10.64898/2026.06.05.730084
Cell phenotypes in the biomedical literature: a systematic analysis and text mining corpus. doi:10.64898/2026.02.11.705457
VFB-MCP: Natural-Language Access to Drosophila Neuroscience Grounded by an Expert-Curated Ontology-Led Knowledgebase. doi:10.64898/2026.06.16.732577

Cross-species consensus atlas of the primate basal ganglia. doi:10.64898/2025.12.15.694496
OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem. Bioinformatics. doi:10.1093/bioinformatics/btaf279
The Unified Phenotype Ontology: a framework for cross-species integrative phenomics. Genetics. doi:10.1093/genetics/iyaf027
Mondo: Integrating Disease Terminology Across Communities. Genetics. doi:10.1093/genetics/iyaf215

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI). Journal of Biomedical Semantics. doi:10.1186/s13326-024-00320-3
The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species. Nucleic Acids Research. doi:10.1093/nar/gkad1082
Expression Atlas update: insights from sequencing data at both bulk and single cell level. Nucleic Acids Research. doi:10.1093/nar/gkad1021

A guide to the BRAIN Initiative Cell Census Network data ecosystem. PLoS Biology. doi:10.1371/journal.pbio.3002133
Brain Data Standards — A method for building data-driven cell-type ontologies. Scientific Data. doi:10.1038/s41597-022-01886-2
Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas. Scientific Data. doi:10.1038/s41597-023-01993-8
The Ontology of Biological Attributes (OBA) — computational traits for the life sciences. Mammalian Genome. doi:10.1007/s00335-023-09992-1
Virtual Fly Brain — An interactive atlas of the Drosophila nervous system. Frontiers in Physiology. doi:10.3389/fphys.2023.1076533

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database. doi:10.1093/database/baac087
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database. doi:10.1093/database/baac035
Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly. Science. doi:10.1126/science.abk2432

Cell type ontologies of the Human Cell Atlas. Nature Cell Biology. doi:10.1038/s41556-021-00787-7
Anatomical structures, cell types and biomarkers of the Human Reference Atlas. Nature Cell Biology. doi:10.1038/s41556-021-00788-6
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database. doi:10.1093/database/baab069

Cell type discovery using single-cell transcriptomics: implications for ontological representation. (2018) Human Molecular Genetics. doi:10.1093/hmg/ddy100
Cell ontology in an age of data-driven cell classification. (2017) BMC Bioinformatics. doi:10.1186/s12859-017-1980-6
Dead simple OWL design patterns. (2017) Journal of Biomedical Semantics. doi:10.1186/s13326-017-0126-0
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. (2016) Journal of Biomedical Semantics. doi:10.1186/s13326-016-0088-7