ArticleJournal of biomedical semantics2016
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.
Article in Journal of biomedical semantics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 210 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.
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Who cites it
210 citing papers in PubMed.
- A high-throughput method to computationally develop candidate adverse outcome pathways in humans: a proof of concept with insecticides and Parkinson's Disease.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
- Multiscale harmonization, semantic integration, and immersive exploration of single-cell data in support of novel biological insights.bioRxiv : the preprint server for biology · 2026Article
- Single-cell splice isoform usage reveals distinct axes of cellular identity and senescence.bioRxiv : the preprint server for biology · 2026Article
- Reporting and representation of population descriptors in public RNA-seq databases.Cell genomics · 2026Article
- DNAviWEB: sequencing-free clinical screening of liquid biopsies.Nucleic acids research · 2026Article
- The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors.Cell genomics · 2026Article
- Exploring cell-type associations of rare disease phenotypes using non-diseased cell atlases.Briefings in bioinformatics · 2026Article
- Cross-dataset annotation harmonization for cell-type hierarchy construction.Bioinformatics (Oxford, England) · 2026Article
- CellExLink: End-to-end cell-type recognition and normalization in biomedical text.PLoS computational biology · 2026Article
- Cell type-specific contextualisation of the human phenome: towards the systematic treatment of all rare diseases.Genome medicine · 2026Article
- Article
- Hybrid crosses reveal a cell-type-specific landscape of mouse regulatory variation.bioRxiv : the preprint server for biology · 2026Article
- Transforming the cytokine literature into a resource for experimental analysis and discovery.bioRxiv : the preprint server for biology · 2026Article
- Evaluating completeness, coherence, and consistency of genome-scale function annotations.Briefings in bioinformatics · 2026Review
- A layered standards framework for integrating single-cell and spatial omics data into brain cell atlases.bioRxiv : the preprint server for biology · 2026Article
- scHilda: Hierarchical Integration of LLM with KG database for single cell type annotation.PLoS computational biology · 2026Article
- The Cell Ontology in the age of single-cell omics.Scientific data · 2026Article
- The Common Fund Data Ecosystem (CFDE).bioRxiv : the preprint server for biology · 2026Article
- Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains capture global and local expression variation.Cell genomics · 2026Article
- Cell Type Populations for 3D Anatomical Structures of the Human Reference Atlas.Scientific data · 2026Article
150 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
backgroundThe Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. CONSTRUCTION AND CONTENT: Recent work on the CL has focused on extending the representation of various cell types, and developing new modules in the CL itself, and in related ontologies in coordination with the CL. For example, the Kidney and Urinary Pathway Ontology was used as a template to populate the CL with additional cell types. In addition, subtypes of the class 'cell in vitro' have received improved definitions and labels to provide for modularity with the representation of cells in the Cell Line Ontology and Reagent Ontology. Recent changes in the ontology development methodology for CL include a switch from OBO to OWL for the primary encoding of the ontology, and an increasing reliance on logical definitions for improved reasoning. UTILITY AND DISCUSSION: The CL is now mandated as a metadata standard for large functional genomics and transcriptomics projects, and is used extensively for annotation, querying, and analyses of cell type specific data in sequencing consortia such as FANTOM5 and ENCODE, as well as for the NIAID ImmPort database and the Cell Image Library. The CL is also a vital component used in the modular construction of other biomedical ontologies-for example, the Gene Ontology and the cross-species anatomy ontology, Uberon, use CL to support the consistent representation of cell types across different levels of anatomical granularity, such as tissues and organs.
conclusionsThe ongoing improvements to the CL make it a valuable resource to both the OBO Foundry community and the wider scientific community, and we continue to experience increased interest in the CL both among developers and within the user community.
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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.