Cell Ontology
The Cell Ontology is an ontology that aims at capturing the diversity of cell types in animals.[1] It is part of the Open Biomedical and Biological Ontologies (OBO) Foundry. [2] The Cell Ontology identifiers and organizational structure are used to annotate data at the level of cell types, for example in single-cell RNA-seq studies.[3] It is one important resource in the construction of the Human Cell Atlas. [4]
The Cell Ontology was first described in an academic article in 2005. [5]
See also
- Gene ontology
- OBO Foundry
References
- ^ Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, et al. (July 2016). "The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability". Journal of Biomedical Semantics. 7 (1): 44. doi:10.1186/s13326-016-0088-7. PMC 4932724. PMID 27377652.
- ^ Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, et al. (November 2007). "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration". Nature Biotechnology. 25 (11): 1251–5. doi:10.1038/nbt1346. PMC 2814061. PMID 17989687.
- ^ Bernstein MN, Ma Z, Gleicher M, Dewey CN (January 2021). "CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology". iScience. 24 (1): 101913. Bibcode:2021iSci...24j1913B. bioRxiv 10.1101/634097. doi:10.1016/j.isci.2020.101913. PMC 7753962. PMID 33364592.
- ^ Osumi-Sutherland, David; Xu, Chuan; Keays, Maria C.; Kharchenko, Peter V.; Regev, Aviv; Lein, Ed S.; Teichmann, Sarah (2021-06-28). "Cell type ontologies of the Human Cell Atlas". Nature Cell Biology. 23 (11): 1129–1135. arXiv:2106.14443. doi:10.1038/s41556-021-00787-7. S2CID 235658396.
- ^ Bard, Jonathan; Rhee, Seung Y.; Ashburner, Michael (2005). "An ontology for cell types". Genome Biology. 6 (2): R21. doi:10.1186/gb-2005-6-2-r21. PMC 551541. PMID 15693950.
External links
- Cell Ontology GitHub page
- v
- t
- e
Bioinformatics
- Sequence databases: GenBank, European Nucleotide Archive, DNA Data Bank of Japan and China National GeneBank
- Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource
- Other databases: BioNumbers, Protein Data Bank, Ensembl, InterPro, KEGG, and Gene Ontology
- Specialised genomic databases: BOLD, Saccharomyces Genome Database, FlyBase, VectorBase, WormBase, Rat Genome Database, PHI-base, Arabidopsis Information Resource, GISAID and Zebrafish Information Network
- Server: ExPASy
- Rosalind (education platform)
- Broad Institute
- Computational Biology Department (CBD)
- Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI)
- Database Center for Life Science (DBCLS)
- DNA Data Bank of Japan (DDBJ)
- European Bioinformatics Institute (EMBL-EBI)
- European Molecular Biology Laboratory (EMBL)
- Flatiron Institute
- J. Craig Venter Institute (JCVI)
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)
- US National Center for Biotechnology Information (NCBI)
- Japanese Institute of Genetics
- Netherlands Bioinformatics Centre (NBIC)
- Philippine Genome Center (PGC)
- Scripps Research
- Swiss Institute of Bioinformatics (SIB)
- Wellcome Sanger Institute
- Whitehead Institute
- African Society for Bioinformatics and Computational Biology (ASBCB)
- Australia Bioinformatics Resource (EMBL-AR)
- European Molecular Biology network (EMBnet)
- International Nucleotide Sequence Database Collaboration (INSDC)
- International Society for Biocuration (ISB)
- International Society for Computational Biology (ISCB)
- Student Council (ISCB-SC)
- Institute of Genomics and Integrative Biology (CSIR-IGIB)
- Japanese Society for Bioinformatics (JSBi)
- Basel Computational Biology Conference ([BC2])
- European Conference on Computational Biology (ECCB)
- Intelligent Systems for Molecular Biology (ISMB)
- International Conference on Bioinformatics (InCoB)
- International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB)
- ISCB Africa ASBCB Conference on Bioinformatics
- Pacific Symposium on Biocomputing (PSB)
- Research in Computational Molecular Biology (RECOMB)
- CRAM format
- FASTA format
- FASTQ format
- NeXML format
- Nexus format
- Pileup format
- SAM format
- Stockholm format
- VCF format
- GFF format
- GTF format
Category
Commons
 | This biology article is a stub. You can help Wikipedia by expanding it. |
- v
- t
- e
