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Keywords {🔍}

cell, ontology, types, article, google, classes, scholar, data, ontologies, line, cells, gene, class, logical, clo, definitions, anatomy, development, representation, mungall, type, biology, content, biomedical, diehl, model, consortium, human, organism, biomed, database, obo, vivo, related, integration, bioinformatics, information, biological, speciesspecific, owl, improvements, community, developers, part, june, skeletal, system, cytometry, res, usa,

Topics {✒️}

/cmungall/nlx-pl] day-richter cerebrospinal-fluid-contacting neurons revealed entity/quality-based logical definitions neuroscience information framework templateless free-form additions high-dimensional flow cytometry high-level cell types virus-specific cell niches multi-ciliated epithelial cell species-specific anatomy ontology species-specific cell types generalizing human-specific classes cross-species anatomy ontology including species-specific proteins org/tr/owl2-primer large-scale data analyses species-specific anatomy ontologies nhgri grants hg002273-09z article download pdf ontology engineering framework �cross-product” class development �cell line cell cell line information obo foundry framework encompass vertebrate diversity make species-specific classes �t-helper 1 cell cell line ontology annual international conference class ‘epidermal cell �experimentally modified cell �experimentally modified cell cell line cells full access creative commons license revised cell ontology org/amigo/term/cl privacy choices/manage cookies cell type definitions human cell information �genetically modified cell specific intermediate classes vertebrate cell types zebrafish anatomy ontology fantom sample ontology mammalian cell types mammalian cell types human cell types additional cell types insect cell types

Schema {🗺️}

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         headline:The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability
         description: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.
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            Cell Line Cell
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      headline:The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability
      description: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.
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         Cell Line Cell
         Logical Definition
         Anatomy Ontology
         Neuroscience Information Framework
         Algorithms
         Computer Appl. in Life Sciences
         Data Mining and Knowledge Discovery
         Computational Biology/Bioinformatics
         Bioinformatics
         Combinatorial Libraries
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      name:European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
      name:ZFIN, the Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, USA
      name:Ontology Development Group, Library, Oregon Health and Science University, Portland, USA
      name:Department of Biology, University of South Dakota, Vermillion, USA
      name:National Evolutionary Synthesis Center, Durham, USA
      name:Southwestern Medical Center, University of Texas, Dallas, USA
      name:Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, USA
      name:European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
      name:Oral Diagnostics Sciences, University at Buffalo School of Dental Medicine, Buffalo, USA
      name:European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
      name:ZFIN, the Zebrafish Model Organism Database, 5291 University of Oregon, Eugene, USA
      name:Ontology Development Group, Library, Oregon Health and Science University, Portland, USA
      name:Ontology Development Group, Library, Oregon Health and Science University, Portland, USA
      name:The Jackson Laboratory, Bar Harbor, USA
      name:Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, USA

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