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MRIO: the Magnetic Resonance Imaging Acquisition and Analysis Ontology
Magnetic resonance imaging of the brain is a useful tool in both the clinic and research settings, aiding in the diagnosis and treatments of neurological disease and expanding our knowledge of the brain. Howev...
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Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project
An important need exists to better understand and stratify kidney disease according to its underlying pathophysiology in order to develop more precise and effective therapeutic agents. National collaborative e...
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Open AccessCells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies
Cell cultures and cell lines are widely used in life science experiments. In conjunction with the 2018 International Conference on Biomedical Ontology (ICBO-2018), the 2nd International Workshop on Cells in Ex...
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Open AccessAn ontology for representing hematologic malignancies: the cancer cell ontology
Within the cancer domain, ontologies play an important role in the integration and annotation of data in order to support numerous biomedical tools and applications. This work seeks to leverage existing standa...
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Open AccessReporting and connecting cell type names and gating definitions through ontologies
Human immunology studies often rely on the isolation and quantification of cell populations from an input sample based on flow cytometry and related techniques. Such techniques classify cells into populations ...
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Open AccessOSCI: standardized stem cell ontology representation and use cases for stem cell investigation
Stem cells and stem cell lines are widely used in biomedical research. The Cell Ontology (CL) and Cell Line Ontology (CLO) are two community-based OBO Foundry ontologies in the domains of in vivo cells and in ...
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Open AccessCells in experimental life sciences - challenges and solution to the rapid evolution of knowledge
Cell cultures used in biomedical experiments come in the form of both sample biopsy primary cells, and maintainable immortalised cell lineages. The rise of bioinformatics and high-throughput technologies has l...
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Open AccessThe Cell Ontology 2016: enhanced content, modularization, and ontology interoperability
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 ex...
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Open AccessRepresenting vision and blindness
There have been relatively few attempts to represent vision or blindness ontologically. This is unsurprising as the related phenomena of sight and blindness are difficult to represent ontologically for a varie...
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Open AccessGateways to the FANTOM5 promoter level mammalian expression atlas
The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and deve...
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Open AccessCLO: The cell line ontology
Cell 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 year...
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Open AccessThe neurological disease ontology
We are develo** the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representati...
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Open AccessOntology based molecular signatures for immune cell types via gene expression analysis
New technologies are focusing on characterizing cell types to better understand their heterogeneity. With large volumes of cellular data being generated, innovative methods are needed to structure the resultin...
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Open AccessHow the gene ontology evolves
Maintaining a bio-ontology in the long term requires improving and updating its contents so that it adequately captures what is known about biological phenomena. This paper illustrates how these processes are ...
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Open AccessLogical Development of the Cell Ontology
The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making th...
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Open AccessAn improved ontological representation of dendritic cells as a paradigm for all cell types
Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological o...
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Open AccessMuscle Research and Gene Ontology: New standards for improved data integration
The Gene Ontology Project provides structured controlled vocabularies for molecular biology that can be used for the functional annotation of genes and gene products. In a collaboration between the Gene Ontolo...
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Impaired immune responses and altered peptide repertoire in tapasin-deficient mice
Tapasin is a component of the major histocompatibility complex (MHC) class I antigen-loading complex. Here we show that mice with a disrupted tapasin gene display reduced MHC class I expression. Cytotoxic T ce...
