ArticleScientific data2023
Brain Data Standards - A method for building data-driven cell-type ontologies.
Article in Scientific data, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed.
- A Hierarchical Multimodal Knowledge Graph for Neural Cell-Type-Specific Regulation Integrating Single-Cell Transcriptomics and Literature Evidence.International journal of molecular sciences · 2026Article
- A layered standards framework for integrating single-cell and spatial omics data into brain cell atlases.bioRxiv : the preprint server for biology · 2026Article
- The Cell Ontology in the age of single-cell omics.Scientific data · 2026Article
- Cell Type Populations for 3D Anatomical Structures of the Human Reference Atlas.Scientific data · 2026Article
- Constructing and Using Cell Type Populations of the Human Reference Atlas.bioRxiv : the preprint server for biology · 2025Article
- Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph.Scientific data · 2025Article
- Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage.Nature methods · 2025Article
- Digital evolution: Novo Nordisk's shift to ontology-based data management.Journal of biomedical semantics · 2025Article
- Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph for Linked Open Data.bioRxiv : the preprint server for biology · 2025Article
- Navigating open-source waters: the pharmaceutical industry's role in bioontology development.Database : the journal of biological databases and curation · 2025Article
- A temporal cortex cell atlas highlights gene expression dynamics during human brain maturation.Nature genetics · 2024Article
- Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage.bioRxiv : the preprint server for biology · 2024Article
- Publication, funding, and experimental data in support of Human Reference Atlas construction and usage.Scientific data · 2024Article
- Cell type-specific gene expression dynamics during human brain maturation.bioRxiv : the preprint server for biology · 2024Article
- Article
- Concerted neuron-astrocyte gene expression declines in aging and schizophrenia.bioRxiv : the preprint server for biology · 2024Article
- Discovery of optimal cell type classification marker genes from single cell RNA sequencing data.BMC methods · 2024Article
- A guide to the BRAIN Initiative Cell Census Network data ecosystem.PLoS biology · 2023Article
- The past, present and future of neuroscience data sharing: a perspective on the state of practices and infrastructure for FAIR.Frontiers in neuroinformatics · 2023Review
Corrections and comments
- Erratum issued
Authors and funding
20 authors.
Funding
Abstract
Large-scale single-cell 'omics profiling is being used to define a complete catalogue of brain cell types, something that traditional methods struggle with due to the diversity and complexity of the brain. But this poses a problem: How do we organise such a catalogue - providing a standard way to refer to the cell types discovered, linking their classification and properties to supporting data? Cell ontologies provide a partial solution to these problems, but no existing ontology schemas support the definition of cell types by direct reference to supporting data, classification of cell types using classifications derived directly from data, or links from cell types to marker sets along with confidence scores. Here we describe a generally applicable schema that solves these problems and its application in a semi-automated pipeline to build a data-linked extension to the Cell Ontology representing cell types in the Primary Motor Cortex of humans, mice and marmosets. The methods and resulting ontology are designed to be scalable and applicable to similar whole-brain atlases currently in preparation.
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What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.