standards > terminology artifact > DOI:10.25504/FAIRsharing.j9y503


ready Cell Ontology

Abbreviation: CL


General Information
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.


This record replaces or incorporates the following deprecated resources:

Homepage https://github.com/obophenotype/cell-ontology

Countries that developed this resource European Union , United Kingdom , United States

Created in 2008

Taxonomic range




How to cite this record FAIRsharing.org: CL; Cell Ontology; DOI: https://doi.org/10.25504/FAIRsharing.j9y503; Last edited: June 27, 2019, 2:39 p.m.; Last accessed: Jul 20 2019 8:11 a.m.


This record is maintained by Alexander_Diehl

Record updated: June 24, 2019, 9:57 a.m. by The FAIRsharing Team.

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    No tools defined


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No XSD schemas defined


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Conditions of Use

Applies to: Data use




Publications

Logical development of the cell ontology.

Meehan TF,Masci AM,Abdulla A,Cowell LG,Blake JA,Mungall CJ,Diehl AD
BMC Bioinformatics 2011

View Paper (PubMed) View Publication

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Diehl AD,Meehan TF,Bradford YM,Brush MH,Dahdul WM,Dougall DS,He Y,Osumi-Sutherland D,Ruttenberg A,Sarntivijai S,Van Slyke CE,Vasilevsky NA,Haendel MA,Blake JA,Mungall CJ
J Biomed Semantics 2016

View Paper (PubMed) View Publication

CL Ontology Display

View in BioPortal.


Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.

View in OBO Foundry.




Implementing Databases (12)
Encyclopedia of DNA Elements at UCSC
Encyclopedia of DNA Elements (ENCODE) has created a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. UCSC coordinated data for the ENCODE Consortium from its inception in 2003 (Pilot phase) to the end of the first 5 year phase of whole-genome data production in 2012. All data produced by ENCODE investigators and the results of ENCODE analysis projects from this period are hosted in the UCSC Genome browser and database.

ModelDB
ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. ModelDB is tightly coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models.

Stem Cell Discovery Engine
Comparison system for cancer stem cell analysis

CellFinder
CellFinder maps validated gene and protein expression, phenotype and images related to cell types.The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development. CellFinder provides long-term data storage for validated and curated primary research data and provides additional expert-validation through relevant information extracted from text.

Rat Genome Database
The Rat Genome Database is the premier site for genetic, genomic, phenotype, and disease data generated from rat research. It provides easy access to corresponding human and mouse data for cross-species comparison and its comprehensive data and innovative software tools make it a valuable resource for researchers worldwide.

Xenopus laevis and tropicalis biology and genomics resource
Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. It includes gene expression patterns that incorporate image data from the literature, large scale screens and community submissions.

Immunology Database and Analysis Portal
The ImmPort system serves as a long-term, sustainable archive of immunology research data generated by investigators mainly funded through the NIAID/DAIT. The core component of the ImmPort system is an extensive data warehouse containing an integration of experimental data and clinical trial data. The analytical tools created and integrated as part of the ImmPort system are available to any researcher within ImmPort after registration and approval by DAIT. Additionally, the data provided mainly by NIAID/DAIT funded researchers in ImmPort will be available to all registered users after the appropriate embargo time. ImmPort, is the data submission portal where researchers upload, QC, and curate their data prior to sharing in OpenImmPort.

Library of Integrated Network-Based Cellular Signatures Data Portal
The LINCS Data Portal provides a unified interface for searching LINCS dataset packages and reagents. LINCS data are being made openly available as a community resource through a series of data releases, so as to enable scientists to address a broad range of basic research questions and to facilitate the identification of biological targets for new disease therapies. LINCS datasets consist of assay results from cultured and primary human cells treated with bioactive small molecules, ligands such as growth factors and cytokines, or genetic perturbations. Many different assays are used to monitor cell responses, including assays measuring transcript and protein expression; cell phenotype data are captured by biochemical and imaging readouts. Assays are typically carried out on multiple cell types, and at multiple timepoints; perturbagen activity is monitored at multiple doses.

Immune Epitope Database
The IEDB provides the scientific community with a central repository of freely accessible epitope data and epitope prediction and analysis resources. The IEDB is a publicly accessible, comprehensive immune epitope database containing peptidic linear and conformational epitopes and non peptidic epitopes such as lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody, T cell, MHC binding or MHC ligand elution experimental assays. Epitope data related to infectious diseases, allergy, autoimmunity and transplant tested in humans, non human primates, and any other species can be found in the IEDB.

OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.

Genome-wide Integrated Analysis of gene Networks in Tissues 2.0
GIANT2 (Genome-wide Integrated Analysis of gene Networks in Tissues) is an interactive web server that enables biomedical researchers to analyze their proteins and pathways of interest and generate hypotheses in the context of genome-scale functional maps of human tissues. With GIANT2, researchers can explore predicted tissue-specific functional roles of genes and reveal changes in those roles across tissues, all through interactive multi-network visualizations and analyses.

SCPortalen
SCPortalen is a single-cell database created to facilitate and enable researchers to access and explore published single-cell datasets. It integrates human and mouse single-cell transcriptomics datasets, single-cell metadata, cell images and sequence information.

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Grant Number(s)

  • DE-AC02-05CH11231 (U.S. Department of Energy)