Alpha 2.0
Login Register
» Articles » PMID: 15693950

An Ontology for Cell Types

Overview
Journal Genome Biol
Specialties Biology
Genetics
Date 2005 Feb 8
PMID 15693950
Citations 211
Authors
Jonathan Bard
Seung Y Rhee
Michael Ashburner
Affiliations
Soon will be listed here.
Abstract

We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. The ontology is freely available at http://obo.sourceforge.net/ and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA.

Citing Articles

Considerations for building and using integrated single-cell atlases.

Hrovatin K, Sikkema L, Shitov V, Heimberg G, Shulman M, Oliver A Nat Methods. 2024; 22(1):41-57.

PMID: 39672979 DOI: 10.1038/s41592-024-02532-y.

The Immunopeptidomics Ontology (ImPO).

Faria D, Eugenio P, Contreiras Silva M, Balbi L, Bedran G, Kallor A Database (Oxford). 2024; 2024.

PMID: 38857186 PMC: 11164101. DOI: 10.1093/database/baae014.

An open source knowledge graph ecosystem for the life sciences.

Callahan T, Tripodi I, Stefanski A, Cappelletti L, Taneja S, Wyrwa J Sci Data. 2024; 11(1):363.

PMID: 38605048 PMC: 11009265. DOI: 10.1038/s41597-024-03171-w.

scDOT: enhancing single-cell RNA-Seq data annotation and uncovering novel cell types through multi-reference integration.

Xiong Y, Zhang X Brief Bioinform. 2024; 25(2).

PMID: 38436563 PMC: 10939303. DOI: 10.1093/bib/bbae072.

Gene panel selection for targeted spatial transcriptomics.

Zhang Y, Petukhov V, Biederstedt E, Que R, Zhang K, Kharchenko P Genome Biol. 2024; 25(1):35.

PMID: 38273415 PMC: 10811939. DOI: 10.1186/s13059-024-03174-1.

References
1.
Drysdale R . Phenotypic data in FlyBase. Brief Bioinform. 2001; 2(1):68-80. DOI: 10.1093/bib/2.1.68. View
2.
Kiehart D, Franke J, Chee M, Montague R, Chen T, Roote J . Drosophila crinkled, mutations of which disrupt morphogenesis and cause lethality, encodes fly myosin VIIA. Genetics. 2004; 168(3):1337-52. PMC: 1448781. DOI: 10.1534/genetics.104.026369. View
3.
. Creating the gene ontology resource: design and implementation. Genome Res. 2001; 11(8):1425-33. PMC: 311077. DOI: 10.1101/gr.180801. View