ArticleJournal of biomedical semantics2014
CLO: The cell line ontology.
Article in Journal of biomedical semantics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
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Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Tissue specificity of in vitro drug sensitivity.Journal of the American Medical Informatics Association : JAMIA · 2018Pooled it
- The Common Fund Data Ecosystem (CFDE).bioRxiv : the preprint server for biology · 2026Article
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- RNA-KG v2.0: an RNA-centered Knowledge Graph with Properties.NAR genomics and bioinformatics · 2026Article
- Integrating artificial intelligence and manual curation to enhance bioassay annotations in ChEMBL.Journal of cheminformatics · 2026Article
- Phosphoproteomic analysis of successive Jurkat CD19-CAR generations reveals TCRζ-driven signalling.Cellular signalling · 2026Article
- Pertpy: an end-to-end framework for perturbation analysis.Nature methods · 2026Article
- Application of large language models to the annotation of cell lines and mouse strains in genomics data.Database : the journal of biological databases and curation · 2026Article
- Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale.Nucleic acids research · 2026Article
- PaxDb v6.0: reprocessed, LLM-selected, curated protein abundance data across organisms.Nucleic acids research · 2026Article
- Assembly and reasoning over semantic mappings at scale for biomedical data integration.Bioinformatics (Oxford, England) · 2025Article
- A fourfold pathogen reference ontology suite.Journal of biomedical semantics · 2025Article
- A Fourfold Pathogen Reference Ontology Suite.ArXiv · 2025Article
- Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery.Genome medicine · 2025Article
- SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data.Nucleic acids research · 2025Article
- Annotation of biological samples data to standard ontologies with support from large language models.Computational and structural biotechnology journal · 2025Article
- Feasibility and barriers to rapid establishment of patient-derived primary osteosarcoma cell lines in clinical management.iScience · 2024Review
- Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation.Nucleic acids research · 2024Article
- An ontology-based knowledge graph for representing interactions involving RNA molecules.Scientific data · 2024Article
- Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.Database : the journal of biological databases and curation · 2024Article
30 more citing papers are in PubMed but not listed here.
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Authors and funding
25 authors.
Funding
Abstract
backgroundCell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions. CONSTRUCTION AND CONTENT: Collaboration among the CLO, CL, and OBI has established consensus definitions of cell line-specific terms such as 'cell line', 'cell line cell', 'cell line culturing', and 'mortal' vs. 'immortal cell line cell'. A cell line is a genetically stable cultured cell population that contains individual cell line cells. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The new hierarchical structure makes it easier to browse, query, and perform automated classification. We have recently added classes representing more than 2,000 cell line cells from the RIKEN BRC Cell Bank to CLO. Overall, the CLO now contains ~38,000 classes of specific cell line cells derived from over 200 in vivo cell types from various organisms. UTILITY AND DISCUSSION: The CLO has been applied to different biomedical research studies. Example case studies include annotation and analysis of EBI ArrayExpress data, bioassays, and host-vaccine/pathogen interaction. CLO's utility goes beyond a catalogue of cell line types. The alignment of the CLO with related ontologies combined with the use of ontological reasoners will support sophisticated inferencing to advance translational informatics development.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.