Cell Ontology
Names
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Cell Ontology
metasource: Fairsharing.org
version: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
CL
metasource: Fairsharing.org
version: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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Cell Ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
CL
metasource: Fairsharing.orgversion: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Names
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Cell Ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
CL
metasource: Fairsharing.orgversion: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
The Cell Ontology (CL) is a candidate OBO Foundry ontology for the representation of cell types. First described in 2005, the CL integrates cell types from the prokaryotic, fungal, and eukaryotic organisms. As a core component of the OBO Foundry, the CL merges information contained in species-specific anatomical ontologies as well as referencing other OBO Foundry ontologies such as the Protein Ontology (PR) for uniquely expressed biomarkers and the Gene Ontology (GO) for the biological processes a cell type participates in. The CL is under continuous revision to expand representation of cell types and to better integrate with other biomedical ontologies.
Description
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The Cell Ontology (CL) is a candidate OBO Foundry ontology for the representation of cell types. First described in 2005, the CL integrates cell types from the prokaryotic, fungal, and eukaryotic organisms. As a core component of the OBO Foundry, the CL merges information contained in species-specific anatomical ontologies as well as referencing other OBO Foundry ontologies such as the Protein Ontology (PR) for uniquely expressed biomarkers and the Gene Ontology (GO) for the biological processes a cell type participates in. The CL is under continuous revision to expand representation of cell types and to better integrate with other biomedical ontologies.
metasource: Fairsharing.orgversion: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Webpage:
https://github.com/obophenotype/cell-ontologyWebpage
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https://github.com/obophenotype/cell-ontology
metasource: Fairsharing.orgversion: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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Name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)Licence name
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Creative Commons Attribution 3.0 Unported (CC BY 3.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Licence URL
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https://creativecommons.org/licenses/by/3.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Logical development of the cell ontology
PMID: 21208450
metasource: Fairsharing.org
version: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability
PMID: 27377652
metasource: Fairsharing.org
version: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
Publications
More detailed information about this field from each metasource.
Logical development of the cell ontology
PMID: 21208450
metasource: Fairsharing.org
version: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability
PMID: 27377652
metasource: Fairsharing.org
version: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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Logical development of the cell ontology
PubMed citations: 78.
78 articles citing: Logical development of the cell ontology
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
A Literature-Derived Knowledge Graph Augments the Interpretation of Single Cell RNA-seq Datasets. PMID:34200671
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing. PMID:34088715
Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods. PMID:34031612
Reactome and the Gene Ontology: Digital convergence of data resources. PMID:33964129
VaximmutorDB: A Web-Based Vaccine Immune Factor Database and Its Application for Understanding Vaccine-Induced Immune Mechanisms. PMID:33777032
Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. PMID:33622235
Intake of Natural Compounds and Circulating microRNA Expression Levels: Their Relationship Investigated in Healthy Subjects With Different Dietary Habits. PMID:33519486
GenoSurf: metadata driven semantic search system for integrated genomic datasets. PMID:31820804
Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung. PMID:31651362
Reporting and connecting cell type names and gating definitions through ontologies. PMID:31272390
An ontology for representing hematologic malignancies: the cancer cell ontology. PMID:31272372
The cell line ontology-based representation, integration and analysis of cell lines used in China. PMID:31272367
The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. PMID:30930166
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories. PMID:30166985
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. PMID:30012108
Identification of errors in the IEDB using ontologies. PMID:29688357
Cell type discovery using single-cell transcriptomics: implications for ontological representation. PMID:29590361
ImmPort, toward repurposing of open access immunological assay data for translational and clinical research. PMID:29485622
Using OWL reasoning to support the generation of novel gene sets for enrichment analysis. PMID:29444698
Cell type discovery and representation in the era of high-content single cell phenotyping. PMID:29322913
Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature. PMID:29238346
SCPortalen: human and mouse single-cell centric database. PMID:29045713
An integrated expression atlas of miRNAs and their promoters in human and mouse. PMID:28829439
Dead simple OWL design patterns. PMID:28583177
Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions. PMID:28469412
An atlas of human long non-coding RNAs with accurate 5' ends. PMID:28241135
Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. PMID:28003147
Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources. PMID:27955641
The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. PMID:27627881
Modeling biochemical pathways in the gene ontology. PMID:27589964
First Proposal of Minimum Information About a Cellular Assay for Regenerative Medicine. PMID:27405781
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. PMID:27076900
The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database. PMID:27009807
Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types. PMID:26330083
A draft network of ligand-receptor-mediated multicellular signalling in human. PMID:26198319
Three-dimensional immersive virtual reality for studying cellular compartments in 3D models from EM preparations of neural tissues. PMID:26179415
Xenbase: Core features, data acquisition, and data processing. PMID:26150211
Development of an Ontology for Periodontitis. PMID:26140188
ImmuSort, a database on gene plasticity and electronic sorting for immune cells. PMID:25988315
TermGenie - a web-application for pattern-based ontology class generation. PMID:25937883
eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment. PMID:25815161
The GOA database: gene Ontology annotation updates for 2015. PMID:25378336
Semantic Web repositories for genomics data using the eXframe platform. PMID:25093072
Standardized description of scientific evidence using the Evidence Ontology (ECO). PMID:25052702
Representing kidney development using the gene ontology. PMID:24941002
A method for increasing expressivity of Gene Ontology annotations using a compositional approach. PMID:24885854
The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. PMID:24755304
A promoter-level mammalian expression atlas. PMID:24670764
Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS). PMID:24518066
The neurological disease ontology. PMID:24314207
CellFinder: a cell data repository. PMID:24304896
Protein Ontology: a controlled structured network of protein entities. PMID:24270789
HuPSON: the human physiology simulation ontology. PMID:24267822
Anatomical entity mention recognition at literature scale. PMID:24162468
Measuring the evolution of ontology complexity: the gene ontology case study. PMID:24146805
The Drosophila anatomy ontology. PMID:24139062
Functional tissue units and their primary tissue motifs in multi-scale physiology. PMID:24103658
Using ontologies to study cell transitions. PMID:24103098
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. PMID:24093723
The mouse pathology ontology, MPATH; structure and applications. PMID:24033988
Ontology based molecular signatures for immune cell types via gene expression analysis. PMID:24004649
CLASSIFYING PROCESSES: AN ESSAY IN APPLIED ONTOLOGY. PMID:23888086
CELDA -- an ontology for the comprehensive representation of cells in complex systems. PMID:23865855
FYPO: the fission yeast phenotype ontology. PMID:23658422
InterMOD: integrated data and tools for the unification of model organism research. PMID:23652793
Cell-type-specific predictive network yields novel insights into mouse embryonic stem cell self-renewal and cell fate. PMID:23468881
A unified anatomy ontology of the vertebrate skeletal system. PMID:23251424
The plant ontology as a tool for comparative plant anatomy and genomic analyses. PMID:23220694
Gene Ontology annotations and resources. PMID:23161678
Concept annotation in the CRAFT corpus. PMID:22776079
The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs. PMID:22347883
Uberon, an integrative multi-species anatomy ontology. PMID:22293552
The UniProt-GO Annotation database in 2011. PMID:22123736
The Gene Ontology: enhancements for 2011. PMID:22102568
CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses. PMID:22039163 -
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability
PubMed citations: 74.
74 articles citing: The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability
GOing Forward With the Cardiac Conduction System Using Gene Ontology. PMID:35309148
NETME: on-the-fly knowledge network construction from biomedical literature. PMID:35013714
DeepSVP: Integration of genotype and phenotype for structural variant prioritization using deep learning. PMID:34951628
Expression Atlas update: gene and protein expression in multiple species. PMID:34850121
DISCO: a database of Deeply Integrated human Single-Cell Omics data. PMID:34791375
Besca, a single-cell transcriptomics analysis toolkit to accelerate translational research. PMID:34761219
The Human Disease Ontology 2022 update. PMID:34755882
Experiment level curation of transcriptional regulatory interactions in neurodevelopment. PMID:34665801
scMRMA: single cell multiresolution marker-based annotation. PMID:34648021
Leveraging the Cell Ontology to classify unseen cell types. PMID:34548483
A compendium of uniformly processed human gene expression and splicing quantitative trait loci. PMID:34493866
Vision, challenges and opportunities for a Plant Cell Atlas. PMID:34491200
Annotated expression and activity data for murine recombinase alleles and transgenes: the CrePortal resource. PMID:34482425
Sfaira accelerates data and model reuse in single cell genomics. PMID:34433466
Comparison of the Results of Manual and Automated Processes of Cross-Mapping Between Nursing Terms: Quantitative Study. PMID:34345784
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
UniBind: maps of high-confidence direct TF-DNA interactions across nine species. PMID:34174819
Precision omics data integration and analysis with interoperable ontologies and their application for COVID-19 research. PMID:34159360
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses. PMID:34156446
Mapping the multiscale structure of biological systems. PMID:34139169
Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods. PMID:34031612
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. PMID:34015823
CTD Anatomy: analyzing chemical-induced phenotypes and exposures from an anatomical perspective, with implications for environmental health studies. PMID:33768211
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application. PMID:33677548
Knowledge Representation for Multi-Scale Physiology Route Modeling. PMID:33664662
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
HiDeF: identifying persistent structures in multiscale 'omics data. PMID:33413539
Common cell type nomenclature for the mammalian brain. PMID:33372656
The Gene Ontology resource: enriching a GOld mine. PMID:33290552
GTRD: an integrated view of transcription regulation. PMID:33231677
CSEA-DB: an omnibus for human complex trait and cell type associations. PMID:33211888
FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. PMID:33211864
Automatic Gene Function Prediction in the 2020's. PMID:33120976
Comparative Toxicogenomics Database (CTD): update 2021. PMID:33068428
CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean. PMID:32986829
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. PMID:32939051
COVID-19 Biomarkers in research: Extension of the OncoMX cancer biomarker data model to capture biomarker data from other diseases. PMID:32935101
Human Cell Atlas and cell-type authentication for regenerative medicine. PMID:32929224
Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management. PMID:32883995
Integrating Deep Supervised, Self-Supervised and Unsupervised Learning for Single-Cell RNA-seq Clustering and Annotation. PMID:32674393
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. PMID:32669714
Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST. PMID:32651388
Identifying persistent structures in multiscale 'omics data. PMID:32587977
ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses. PMID:32449934
GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest. PMID:32140729
The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. PMID:31796553
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:31701156
Comprehensive anatomic ontologies for lung development: A comparison of alveolar formation and maturation within mouse and human lung. PMID:31651362
SEAweb: the small RNA Expression Atlas web application. PMID:31598718
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. PMID:31548717
Supervised classification enables rapid annotation of cell atlases. PMID:31501545
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. PMID:31272389
Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies. PMID:31272374
An ontology for representing hematologic malignancies: the cancer cell ontology. PMID:31272372
A periodic table of cell types. PMID:31249003
scMatch: a single-cell gene expression profile annotation tool using reference datasets. PMID:31028376
CellSim: a novel software to calculate cell similarity and identify their co-regulation networks. PMID:30832570
Towards Building a Plant Cell Atlas. PMID:30777643
Human Disease Ontology 2018 update: classification, content and workflow expansion. PMID:30407550
The Immune Epitope Database (IEDB): 2018 update. PMID:30357391
iProX: an integrated proteome resource. PMID:30252093
Cell type discovery using single-cell transcriptomics: implications for ontological representation. PMID:29590361
Genomic and molecular control of cell type and cell type conversions. PMID:29348912
Comparison, alignment, and synchronization of cell line information between CLO and EFO. PMID:29322915
Cell ontology in an age of data-driven cell classification. PMID:29322914
Cell type discovery and representation in the era of high-content single cell phenotyping. PMID:29322913
Usage of cell nomenclature in biomedical literature. PMID:29322912
The Gene Ontology of eukaryotic cilia and flagella. PMID:29177046
Building bridges between cellular and molecular structural biology. PMID:28682240
Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions. PMID:28469412
Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. PMID:28003147
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. PMID:27899649
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:27899636
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annotation
metasource: Fairsharing.org
version: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
cell
metasource: Fairsharing.org
version: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
morphology
metasource: Fairsharing.org
version: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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More detailed information about this field from each metasource.
annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
cell
metasource: Fairsharing.orgversion: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
morphology
metasource: Fairsharing.orgversion: FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: Jan. 29, 2020, 7:42 p.m.; Last accessed: Jan 03 2022 7:12 p.m.
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