An ontology for cell types

By J. Bard, Seung Yon Rhee, Michael Ashburner. Genome Biology, 2005

449 citations recorded by the source corpus.

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.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1ac7808108536fb08559c5fa383c23b0c4b414ea

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Citations in the corpus

Integrating phenotype ontologies across multiple species (2010, unknown): “The taxonomic partitioning of anatomical ontologies is largely at the gross anatomical level; cells and cellular components are represented in the OBO Cell ontology (CL) [10] and the GO cellular component ontology (GO-CC) and are applicable across multiple phyla.”
Concept annotation in the CRAFT corpus (2012, background): “…in each full-length article of the concepts from nine prominent ontologies and terminologies: the Cell Type Ontology (CL, representing cells) [18,19], the Chemical Entities of Biological Interest ontology (ChEBI, representing chemicals, chemical groups, atoms, subatomic particles, and…”
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability (2016, methodology): “The CL was originally developed using the OBO-Format and the OBO-Edit ontology editor [1, 44], without any automated quality control, release pipeline or automated procedures for building the ontology.”
Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation (2009, methodology): “Additionally we utilized the cell ontology for cell types (CL [26]), CHEBI for chemicals [27], the GO for sub-cellular components and biological processes, and PATO as the source of qualities presented by these varied entities.”
The Foundational Model of Anatomy Ontology (2008, background): “CL – employing multiple inheritance – classifies cells along the parallel axes of function, histology and lineage [6]; whereas”
Bio-ontologies: current trends and future directions (2006, methodology): “Ontologies of cell types (e.g. the OBO cell ontology [61]) and chemical entities (e.g. ChEBI—the Chemical Entities of Biological Interest) could be used as a reference and guide the development of the ontology of biological processes in the GO.”
Relations in biomedical ontologies (2005, methodology): “An example is provided by the simultaneous use in OBO's Cell Ontology of both derives_from and develops_from while no clear distinction is drawn between the two [11].”
ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression (2008, background): “It maps to several non-orthogonal ontologies, such as those for human anatomy, the Disease Ontology (17), the Cell Type Ontology (18) and the NCI Thesaurus (10).”
The Mammalian Phenotype Ontology: enabling robust annotation and comparative analysis (2009, background): “Ontologies are being developed in many domains of biology to facilitate information extraction from literature, aid in scientiﬁc discovery and experimental analysis, and to support database inter-operability [e.g., Gene ontology (GO), 9 Mouse Adult Anatomy (MA), 10 and Cell Line ontology (CL) 11 ).”
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources (2018, unknown): “A key feature of the HPO is its logical interoperability with basic research ontologies such as the Mammalian Phenotype Ontology (MP) (43), Uberon (44) and the Cell Ontology (45).”
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration (2007, methodology): “Membership in the Foundry initiative then flows from a commitment to incremental implementation of these principles as they evolve over time, with the Foundry coordinators (currently Ashburner, Lewis, Mungall and Smith) serving as analogs of journal editors, whereby the division of labor that result”
The Human Phenotype Ontology (2010, background): “Other biomedical ontologies of broad interest include the Mammalian Phenotype Ontology (20), the Foundational Model of Anatomy (FMA) ontology (21), the Sequence Ontology (22), the Cell-Type ontology (23), the Chemical Entities of Biological Interest (ChEBI) ontology (24), and the mouse pathology (MP”
Uberon, an integrative multi-species anatomy ontology (2012, methodology): “Similarly, GO and CL [15] classes such as ‘blood vessel development’, or ‘cerebellar granule cell’ are applicable across multiple species, and need to be defined in terms of generic anatomical classes rather than species-specific classes.”
Unsupervised biomedical named entity recognition: Experiments with clinical and biological texts (2013, methodology): “In order to verify the hypothesis that a more reliable seed term set is beneﬁcial, we replace UMLS with Cell Line Ontology[63] and Cell Ontology[64] targeting cell types and cell lines, and report performance on the two corresponding classes in GENIA.”
Gene Ontology Consortium: going forward (2014, background): “This formalization effort is still an ongoing task, which includes creating intra-ontology definitions (14), and using other domainspecific ontologies, such as PATO (10), ChEBI (8), PO (9), Uberon (7), Cell Ontology (CL) (15), Sequence Ontology (SO) (11), Ontology of Biological Attributes (OBA; (16)”