David Osumi-Sutherland

Iterative co-creation of harmonized human and non-human primate cellular and structural ontologies and 3D common coordinate frameworks for the basal ganglia

The paper describes the iterative creation of harmonized ontologies and 3D frameworks for the basal ganglia across human and non-human primates to enable cross-species comparisons of cellular and molecular data.

Organism-scale annotation with Pan-human Azimuth

Pan-human Azimuth maps diverse human cells into a unified hierarchical typology, enabling cross-tissue comparisons and spatial transcriptomic annotation.

VFB-MCP: Natural-Language Access to Drosophila Neuroscience Grounded by an Expert-Curated Ontology-Led Knowledgebase

Model Context Protocol tools over Virtual Fly Brain's graph let Claude answer 25/30 Drosophila neuroscience tasks precisely, vs 14/30 with web search, 2/30 bare.

scFAIR Consortium: a decentralized hub for single-cell RNA-Seq data standardization and unification

The scFAIR Consortium develops a unified metadata schema and portal to improve FAIRness of scRNA-seq data through standardized annotations and semantic search.

A layered standards framework for integrating single-cell and spatial omics data into brain cell atlases

This paper introduces a standards framework for integrating single-cell and spatial omics data into brain cell atlases, enabling interoperable and reusable knowledge-ready resources.

Cell phenotypes in the biomedical literature: a systematic analysis and text mining corpus

The paper creates a manually annotated corpus of cell phenotype mentions and shows its use in improving named entity recognition and entity linking models.

A general strategy for generating expert-guided, simplified views of ontologies

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

Cross-species consensus atlas of the primate basal ganglia

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

Differential neuronal vulnerability to C9orf72 repeat expansion driven by Xbp1 transcription signature

The paper identifies neuronal vulnerability to C9orf72 repeat expansion by analyzing transcriptional states in a Drosophila model, finding that Xbp1 expression correlates with resistance to toxicity.

Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework

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

The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics

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

The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences

This paper introduces OBA, a formalized ontology for biological attributes to facilitate data integration across phenotypic, genetic, and environmental data.

Specimen, Biological Structure, and Spatial Ontologies in Support of a Human Reference Atlas

This paper introduces the Common Coordinate Framework Ontology (CCFO) v2.0.1 to integrate specimen, biological structure, and spatial data for the Human Reference Atlas, enabling interoperability and programmatic access.

Brain Data Standards - A method for building data-driven cell-type ontologies

The paper introduces a data-driven method to extend cell ontologies for multi-modal single-cell omics data, focusing on the Primary Motor Cortex in humans, mice, and marmosets.

The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide

The paper provides a guide to the BRAIN Initiative Cell Census Network (BICCN) data ecosystem, its tools, and resources for analyzing brain cell types across species.

The Xenopus Phenotype Ontology: bridging model organism phenotype data to human health and development.

The paper introduces the Xenopus Phenotype Ontology (XPO) to standardize phenotype data from Xenopus experiments and link them to human health and development.

OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies

The paper describes how the OBO Foundry formalized its principles into operational rules and implemented automated checks to evaluate ontology compliance, improving interoperability and quality.

Big data and single cell transcriptomics: implications for ontological representation

The paper reviews how single cell RNA sequencing is identifying new human cell types and proposes a machine learning method to improve cell type definitions in the Cell Ontology.