• organisms
  • Besides actively participating in the current discussions on evolutionary theory and genetics, Mosterín has also tackled issues like the definition of life itself or the ontology of biological organisms and species. (wikipedia.org)
  • constructed a lattice work of three ontologies (for anatomy and development of model organisms) on a novel framework ontology of generic organs. (wikipedia.org)
  • Gene Ontology Consortium The goal of the Gene Ontology (GO) consortium is to produce a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing. (wikipedia.org)
  • Complex systems biology (CSB) is a branch or subfield of mathematical and theoretical biology concerned with complexity of both structure and function in biological organisms, as well as the emergence and evolution of organisms and species, with emphasis being placed on the complex interactions of, and within, bionetworks, and on the fundamental relations and relational patterns that are essential to life. (wikipedia.org)
  • this is because the latter is restricted primarily to simplified models of biological organization and organisms, as well as to only a general consideration of philosophical or semantic questions related to complexity in biology. (wikipedia.org)
  • A complete definition of complexity for individual organisms, species, ecosystems, biological evolution and the biosphere has eluded researchers, and still is an ongoing issue. (wikipedia.org)
  • however, such approaches are not focused on, or do not include, the conceptual part of complexity related to organization and topological attributes or algebraic topology, such as network connectivity of genomes, interactomes and biological organisms that are very important. (wikipedia.org)
  • entities
  • This meta-model supports using shared biological ontologies to annotate biological entities in the models, allows semantic queries and automatic discoveries, enables easy model reuse and composition, and serves as a basis to embed external knowledge. (bl.uk)
  • There is, however, a gap in the current set of ontologies - one that describes the protein entities themselves and their relationships. (biomedcentral.com)
  • Bio-ontologies are artefacts used to represent, build, store, and share knowledge about a biological domain by capturing the domain entities and their interrelationships. (biomedcentral.com)
  • In computer science and information science, an ontology is a formal naming and definition of the types, properties, and interrelationships of the entities that really exist in a particular domain of discourse. (wikipedia.org)
  • What ontologies have in common in both computer science and philosophy is the representation of entities, ideas and events, along with their properties and relations, according to a system of categories. (wikipedia.org)
  • aims
  • Cell Cycle Ontology aims to extend the existing ontologies for cell cycle knowledge, to build a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects in OBO and OWL. (openwetware.org)
  • it aims to bring together biologists, bioinformaticians, and computer scientists who are developing and using standards and ontologies with an emphasis on describing high-throughput functional genomics experiments. (wikipedia.org)
  • Semantic Web
  • This thesis addresses the problem of collaboration among experimental biologists and modelers in the study of systems biology by using ontology and Semantic Web Services techniques. (bl.uk)
  • Ontology and Semantic Web Services potentially provide an infrastructure to meet this requirement. (bl.uk)
  • OBOF, RDF and OWL are among the most used ontology formats to capture terms and relationships in the Life Sciences, opening the potential to use the Semantic Web to support data integration and further exploitation of integrated resources via automated retrieval and reasoning procedures. (biomedcentral.com)
  • Moreover, it provides tools to translate OBO-formatted ontologies into Semantic Web formats such as RDF and OWL. (biomedcentral.com)
  • The fields of artificial intelligence, the Semantic Web, systems engineering, software engineering, biomedical informatics, library science, enterprise bookmarking, and information architecture all create ontologies to limit complexity and organize information. (wikipedia.org)
  • Neuroscience Informati
  • NeuroLex is supported by the Neuroscience Information Framework project. (wikipedia.org)
  • Neuroscience portal NeuroNames Neuroscience Information Framework Initial content for this article was adapted from the NeuroLex project which is licensed under a Creative Commons Attribution License. (wikipedia.org)
  • The Neuroscience Information Framework is a repository of global neuroscience web resources, including experimental, clinical, and translational neuroscience databases, knowledge bases, atlases, and genetic/genomic resources and provides many authoritative links throughout the neuroscience portal of Wikipedia. (wikipedia.org)
  • The Neuroscience Information Framework (NIF) is an initiative of the NIH Blueprint for Neuroscience Research, which was established in 2004 by the National Institutes of Health. (wikipedia.org)
  • data
  • We also develop means of transforming biological data sources and data analysis methods into Web Services. (bl.uk)
  • Biomedical ontologies are emerging as critical tools in genomic and proteomic research, where complex data in disparate resources need to be integrated. (biomedcentral.com)
  • We use ontologies to annotate, index and analyze Big Data in biomedicine for enabling data-driven decision making in medicine and health care. (stanford.edu)
  • Data driven medicine: The goal is to combine machine learning, text-mining, and prior knowledge in medical ontologies to discover hidden trends, build risk models, drive data driven decision making, and comparative effectiveness studies. (stanford.edu)
  • Semantic Mining - semantic interoperability and data mining in medicine ( ontologies ). (openwetware.org)
  • In order to capture and manage this diverse array of data, we have developed the Ontology-Based eXtensible conceptual model (OBX) to serve as a framework for clinical research data in the Immunology Database and Analysis Portal (ImmPort). (pubmedcentralcanada.ca)
  • www.immport.org ) as a web-based public resource to support not only the archiving of these valuable data sets, but also to support their integration with the biological knowledge contained in other public data repositories (e.g. (pubmedcentralcanada.ca)
  • The purpose of this study is to determine whether or not there exists nonrandom grouping of cis-regulatory elements within gene promoters that can be perceived independent of gene expression data and whether or not there is any correlation between this grouping and the biological function of the gene. (biomedcentral.com)
  • Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science. (bioontology.org)
  • The goals of this meeting are: To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and related fields. (bioontology.org)
  • The Investigation/Study/Assay (ISA), Nanopublications (NP), and Research Objects (RO) models are conceptual data modelling frameworks that can structure such information from scientific papers. (plos.org)
  • By structuring the information in the published paper using these data and scientific workflow modelling frameworks, it was possible to explicitly declare elements of experimental design, variables, and findings. (plos.org)
  • These limitations have led to the development of more general ontologies to provide a framework for recording not only experimental data with a limited set of associated metadata, but all essential information about biological experiments. (royalsocietypublishing.org)
  • The biosciences increasingly face the challenge of integrating a wide variety of available data, information and knowledge in order to gain an understanding of biological systems. (biomedcentral.com)
  • As a consequence, much of the available biological data remains disconnected or worse: becomes misconnected. (biomedcentral.com)
  • a variety of tools are available to exploit these ontologies, making them one of the cornerstones for biological data analysis. (biomedcentral.com)
  • We also show how these logical definitions can be used for data integration when combined with a unified multi-species anatomy ontology. (biomedcentral.com)
  • The GO [ 4 ] has been recognized as a key component in the integration of biological data, due in part to its wide use by disparate groups and its integration with other ontologies. (biomedcentral.com)
  • InterMine is used to create databases of biological data accessed by sophisticated web query tools. (wikipedia.org)
  • Support is provided for several common biological formats and there is a framework for adding other data. (wikipedia.org)
  • EMAGE (e-Mouse Atlas of Gene Expression) is an online biological database of gene expression data in the developing mouse (Mus musculus) embryo. (wikipedia.org)
  • The data held in EMAGE is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). (wikipedia.org)
  • Advantages of this approach include the general increased quality of the data returned in searches and with proper tagging, ontologies finding entries that may not explicitly state the search term but are still relevant. (wikipedia.org)
  • Another use of ontologies is within databases such as SwissProt, Ensembl and TrEMBL, which use this technology to search through the stores of human proteome-related data for tags related to the search term. (wikipedia.org)
  • the result was a data-warehouse like effect, with easy access to multiple databases through the use of ontologies. (wikipedia.org)
  • The data is captured using annotations that combine terms from an anatomy ontology, an accompanying taxonomic ontology, and quality terms from the PATO ontology of phenotype qualities. (wikipedia.org)
  • Ideally, such controlled vocabularies take the form of 'ontologies', which means that they are constructed in such a way as to support logical reasoning over the data annotated in their terms. (wikipedia.org)
  • Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery. (wikipedia.org)
  • The collection-specific identifier should be analysed within the framework of the data collection. (wikipedia.org)
  • Genes
  • Significance ranking of the class-determining transcription factor binding sites within these clusters show substantial overlap between the gene ontology terms of the transcriptions factors associated with the binding sites and the gene ontology terms of the regulated genes within each group. (biomedcentral.com)
  • principles
  • In the early 1990s, the widely cited Web page and paper "Toward Principles for the Design of Ontologies Used for Knowledge Sharing" by Tom Gruber is credited with a deliberate definition of ontology as a technical term in computer science. (wikipedia.org)
  • species
  • A number of different ontologies have been developed for describing phenotypes, and whilst this is a welcome improvement over free-text descriptions, one problem is that these ontologies are developed for use within a particular project or species, and are not mutually interoperable. (biomedcentral.com)
  • We demonstrate how our approach assists with the ontology development cycle, and we show how the addition of a multi-species anatomical ontology can enable queries across species. (biomedcentral.com)
  • For example, results from a search of 'heart' in this ontology would return the heart plans for each of the vertebrate species whose ontologies were included. (wikipedia.org)
  • The hierarchy of complexity levels of organization in the biosphere is also recognized in modern classifications of taxonomic ranks, such as: biological domain and biosphere, biological kingdom, Phylum, biological class, order, family, genus and species. (wikipedia.org)
  • defines
  • Often the terminology used in checklists is supplied by a relevant ontology that formally defines those terms. (royalsocietypublishing.org)
  • Some claim that all social sciences have explicit ontology issues because they do not have hard falsifiability criteria like most models in physical sciences, and that indeed the lack of such widely accepted hard falsification criteria is what defines a social or soft science. (wikipedia.org)
  • describe
  • A number of ontologies describe properties that can be attributed to proteins. (biomedcentral.com)
  • Filling this gap will support machine reasoning over the shared features of related proteins and will foster the interconnection between ontologies that describe protein attributes. (biomedcentral.com)
  • Will describe initial work on an ontology of cellular immune networks that is designed to capture the qualitative cytokine expression patterns and cellular phenotypes associated with specific immune activation networks (e.g. (bioontology.org)
  • One of the goals of OBO is to rationally partition the biological domain to minimize overlap between the ontologies, and to ensure logical coherence across ontologies, such that ontologies can be used in combination to describe complex biology. (biomedcentral.com)
  • metabolomics
  • While metabolomics can provide instantaneous information on the metabolites in a biological sample, metabolism is a dynamic process. (wikipedia.org)
  • SAS, PRS, and AGB received funding from the European Union Coordination of Standards in Metabolomics (COSMOS) FP7 E9RXDC00, the British Biotechnology and Biological Science Research Council BB/L024101/1, BB/I025840/1, and the University of Oxford e-Research Centre. (plos.org)
  • formally
  • We now have formally specified standards for representing and validating design patterns templates and software to generate ontology terms using these templates. (oregonstate.edu)
  • cellular
  • Partitional clustering of the transcription factor binding site composition within these promoter segments reveals a small number of gene groups that are selectively enriched for gene ontology terms consistent with distinct aspects of cellular function. (biomedcentral.com)
  • SBPAX import has been implemented by the cellular modeling framework Virtual Cell. (wikipedia.org)
  • biology
  • Modeling in systems biology is concerned with using experimental information and mathematical methods to build quantitative models across different biological scales. (bl.uk)
  • Systems biology recognizes the complexity of biological systems and has the broader goal of explaining and predicting this complex behavior. (wikipedia.org)
  • We demonstrate the utility of this framework by using it in a worked example from biology: demonstrating cycles of investigation formalization [ F ] and reuse [ R ] to generate new knowledge. (royalsocietypublishing.org)
  • An updated list of publications of theoretical biologist Robert Rosen Theory of Biological Anthropology (Documents No. 9 and 10 in English) Drawing the Line Between Theoretical and Basic Biology, a forum article by Isidro A. T. Savillo Synthesis and Analysis of a Biological System[permanent dead link], by Hiroyuki Kurata, 1999. (wikipedia.org)
  • organize
  • To make this search more effective, the NIF is constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g. stating that a neuron is a cell. (wikipedia.org)
  • development
  • Here we present the framework and initial development of the Protein O ntology (PRO) [ 5 ] that describes types of proteins and the relations between them. (biomedcentral.com)
  • Recent innovations have made design-pattern driven ontology development relatively straightforward. (oregonstate.edu)
  • We will run a hands on practical session on setting up ontology repositories for pattern-based development. (oregonstate.edu)
  • The development of the ontology was announced more officially in a message from Le Novère to Michael Hucka and Andrew Finney on October 19. (wikipedia.org)
  • complexity
  • The dialectical unfolding of evolution, both biological and cultural, leads to greater complexity and thus greater subjectivity. (wikipedia.org)
  • It is generally agreed that there is a hierarchy of complexity levels of organization that should be considered as distinct from that of the levels of reality in ontology. (wikipedia.org)
  • Approaches
  • Fluxomics describes the various approaches that seek to determine the rates of metabolic reactions within a biological entity. (wikipedia.org)
  • During the second half of the 20th century, philosophers extensively debated the possible methods or approaches to building ontologies without actually building any very elaborate ontologies themselves. (wikipedia.org)
  • consistency
  • Automated reasoning, performed on OWL-formatted ontologies via the so-called reasoners (such as HermiT [ 11 ]), allows bio-ontologists to perform various tasks such as classification (also known as subsumption), which enables the process of making explicit the relations that were hidden (i.e. implicitly captured), and in general provides help to ensure the consistency of an ontology. (biomedcentral.com)
  • Simulation tools can check the consistency of a rate law, convert reaction from one modelling framework to another (e.g., continuous to discrete), or distinguish between identical mathematical expressions based on different assumptions (e.g. (wikipedia.org)
  • terms
  • The resulting ONTO-ToolKit supports the analysis and handling of OBO-formatted ontologies via the Galaxy interface, and we demonstrated its functionality in different use cases that illustrate the flexibility to obtain sets of ontology terms that match specific search criteria. (biomedcentral.com)
  • The NIFSTD, or NIF Standard Ontology contains many of the terms, synonyms and abbreviations useful for neuroscience, as well as dynamic categories such as defined cell classes based on various properties like neuron by neurotransmitter or by circuit role or drugs of abuse according to the National Institutes on Drug Abuse. (wikipedia.org)
  • Computationally, semantic similarity can be estimated by defining a topological similarity, by using ontologies to define the distance between terms/concepts. (wikipedia.org)
  • databases
  • Users can seamlessly traverse references between biological databases and draw together annotations in an intuitive tabular interface. (springer.com)
  • The Framework is a dynamic inventory of neuroscience databases, annotated and integrated with a unified system of biomedical terminology (i.e. (wikipedia.org)