“…Since the first production release in 2008, NIF has grown significantly in content and functionality, particularly with respect to the ontologies and ontology-based services that drive the NIF system. …”
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“…BACKGROUND: Semantic similarity analysis facilitates automated semantic explanations of biological and clinical data annotated by biomedical ontologies. Gene ontology (GO) has become one of the most important biomedical ontologies with a set of controlled vocabularies, providing rich semantic annotations for genes and molecular phenotypes for diseases. …”
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“…BACKGROUND: Although policy providers have outlined minimal metadata guidelines and naming conventions, ontologies of today still display inter- and intra-ontology heterogeneities in class labelling schemes and metadata completeness. …”
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“…This phenomenon, called “length bias”, will influence subsequent analyses such as Gene Ontology enrichment analysis. In the presence of length bias, Gene Ontology categories that include longer genes are more likely to be identified as enriched. …”
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“…A recent study, however, challenged the ortholog conjecture on the basis of experimentally derived Gene Ontology (GO) annotations and microarray gene expression data in human and mouse. …”
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“…By analyzing the cellular functions of genetically imprinted genes as annotated in the Gene Ontology for human and mouse, we found that imprinted genes are often involved in developmental, transport and regulatory processes. …”
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“…At the time of writing the ontologies in dcGO include the Gene Ontology (GO); Enzyme Commission (EC) numbers; pathways from UniPathway; human phenotype ontology and phenotype ontologies from five model organisms, including plants; anatomy ontologies from three organisms; human disease ontology and drugs from DrugBank. …”
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“…ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. …”
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“…The ontology transforms the implicit relationships among syndromes into a machine-interpretable model. …”
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“…RESULTS: In this report, the detailed classification and definitions of vaccine components and vaccine administration processes are represented using OWL within the framework of the Vaccine Ontology (VO). Different use cases demonstrate how different vaccine formulations and routes of vaccine administration affect the protection efficacy, general immune responses, and adverse events following vaccination. …”
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“…METHODS: An obesity management ontology was developed in seven phases: (1) defining the scope of obesity management, (2) selecting a foundational ontology, (3) extracting the concepts, (4) assigning relationships between these concepts, (5) evaluating representative layers of ontology content, (6) representing the ontology formally with Protégé, and (7) developing a prototype application for obesity management. …”
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“…Firstly, semantic annotations will be given to the multimedia documents in the medical multimedia database. Secondly, the ontology that represented semantic information will be hidden in the head of the multimedia documents. …”
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“…By unifying ontology navigation activities with query widget generation, a user can perform fine-tuned full boolean queries based on the substructure of the ontology, with flexibility to enable or disable subsumption-based queries. …”
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“…BACKGROUND: In prior work, we presented the Ontology of Physics for Biology (OPB) as a computational ontology for use in the annotation and representations of biophysical knowledge encoded in repositories of physics-based biosimulation models. …”
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“…The principle is generalizable to other ontologies.…”
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“…PhylOnt is an extensible ontology with concepts describing tree types and tree building methodologies including estimation methods, models and programs. …”
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“…This paper presents the OntoTrader architecture, an Ontological Web Trading agent based on the OMG ODP trading standard. …”
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“…In this paper, we present the first fully functional release of this system and describe its architecture, which utilizes Web Ontology Language 2 (OWL 2) ontologies to formalize pharmacogenomic knowledge and to provide clinical decision support functionalities. …”
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“…The aim of this essay is to elaborate philosophical and ethical underpinnings of posthumous diagnosis of famous historical figures based on literary and artistic products, or commonly called retrospective diagnosis. It discusses ontological and epistemic challenges raised in the humanities and social sciences, and attempts to systematically reply to their criticisms from the viewpoint of clinical medicine, philosophy of medicine, particularly the ontology of disease and the epistemology of diagnosis, and medical ethics. …”
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“…In particular, there is no consensus how to include functions into a top-level ontology or whether to include them at all. METHODS: We first review current conceptions of functions in philosophy and formal ontology and evaluate them against a set of criteria. …”
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