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

By A. Diehl, T. Meehan, Yvonne M. Bradford, Matthew H. Brush, W. Dahdul, D. Dougall, Yongqun Oliver He, David Osumi-Sutherland, A. Ruttenberg, Sirarat Sarntivijai and 5 more. Journal of Biomedical Semantics, 2016

322 citations recorded by the source corpus.

The 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. 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. 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. The 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.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3e0f55929cf8ce4e08c9a98c8a103ce58deb44dd

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Citations in the corpus

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities (2016, background): “org/obo/PR 000001809] requested by the Cell Ontology [CL] (17)), and to other members of the GO Consortium (for example, the hyperoxidized form of Tpxi1 [http://purl.”
The Gene Ontology of eukaryotic cilia and flagella (2017, methodology): “This is accomplished by referring to the Cell Ontology [47], which provides a broad coverage of ciliated cell classes, and using a compositional approach described by Huntley et al.”
Comparative Toxicogenomics Database (CTD): update 2021 (2020, background): “To promote interoperability, CTD Anatomy pages are enhanced with external synonyms, accession identifiers, and links to Uberon and Cell Ontology. which itself is a synonym for vorinostat), or other reasons.”
The Gene Ontology resource: enriching a GOld mine (2020, unknown): “GO makes extensive use of external ontologies, in particular Uberon (20), Cell Type Ontology (21), and ChEBI (13).”
iProX: an integrated proteome resource (2018, background): “NCBITAXON (NCBI organismal classification) for organismal taxonomy, DOID (Human Disease Ontology) (28) for human disease states, BTO (BRENDA tissue/enzyme source) (29) for tissues, CL (Cell Ontology) (30) for cell types, and PRIDE CV (PRIDE Controlled Vocabulary), PSI-MS CV (MS ontology) (6), MOD (P”
The Reactome Pathway Knowledgebase 2024 (2023, background): “A new entity type, cell, allows annotation of a cell type with terms from cell and tissue ontologies (Cell Ontology ( 18 ), and Uberon ( 19 ), respectively) and with associated proteins and RNAs as markers that identify and individuate the cell (Figure 2 A).”
The Immune Epitope Database (IEDB): 2018 update (2018, methodology): “We continue to expand our use of ontologies for more fields, and have recently incorporated the MRO, Uberon, cell type (13) and cell line ontologies (14).”
Human Disease Ontology 2018 update: classification, content and workflow expansion (2018, methodology): “ated with OBO Foundry ontologies), UBERON (anatomy) and the Cell Ontology (cell types) (41).”