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  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • metabolomics
  • 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)
  • While metabolomics can provide instantaneous information on the metabolites in a biological sample, metabolism is a dynamic process. (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)
  • 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)
  • 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)
  • Integrated knowledge founded on well-defined semantics provides a framework to enable computers to conceptually handle knowledge in a manner comparable to the handling of numerical data: it allows a computer to process expressed facts, look for patterns and make inferences, thereby extending human thinking about complex information. (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)
  • taxonomic
  • 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)
  • 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)
  • complexity
  • Systems biology recognizes the complexity of biological systems and has the broader goal of explaining and predicting this complex behavior. (wikipedia.org)
  • 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)
  • consistent
  • 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)
  • experiments
  • The EXPO (a generic ontology of scientific experiments) ontology formalizes domain-independent knowledge about the organization, execution and analysis of scientific experiments [ 7 ]. (royalsocietypublishing.org)
  • In systems biology, dynamic simulations with a model of a biological process serve as a means to validate the model's architecture and parameters, and to provide hypotheses for new experiments. (biomedcentral.com)
  • semantics
  • Furthermore, I will suggest solutions to these problems within the framework of Cybersemiotics, which combines Luhmann's autopoietic system theory with a Peircean biosemiotics, and with aspects of "embodied" cognitive semantics and ethology. (google.com)
  • Sequences
  • While it is easy to compare nucleic acid or polypeptide sequences from different bioinformatics resources, the biological knowledge contained in these resources is very difficult to compare as it is represented in a wide variety of lexical forms [ 13 - 15 ], and there are no tools that facilitate an easy comparison and integration of knowledge in this form. (biomedcentral.com)
  • NIFSTD
  • The initial entries in the NeuroLex were built from the NIFSTD ontologies which subsumed an earlier vocabulary BIRNLex. (wikipedia.org)
  • 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)
  • approach
  • Through querying and automated reasoning, it may provide new hypotheses to help steer a systems biology approach to biological network building. (biomedcentral.com)
  • The Cybersemiotic approach proposed in the present article integrates Luhmann's triple autopoietic theory of communication with pragmatic theories of levels and types of semiosis such as Intrasemiotics (between the psychic system and the biological self) and Thought-semiotics: the linguistic creation of a systematic and generative classification of the phenomenological, "silent" sign world. (google.com)
  • 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)
  • developmental
  • Bookchin interpreted the dialectical method's strength as its unity of "developmental causality" with ontology. (wikipedia.org)
  • Dialectic," he notes, "is simultaneously a way of reasoning and an account of the objective world, with a developmental ontology. (wikipedia.org)
  • biology
  • 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)
  • 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)
  • 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)
  • qualities
  • Therefore there was no obligation to unite the areas of nature, mind, language, human consciousness and society in an evolutionary framework and to explain the qualitative differences between these as levels of emerging qualities. (google.com)
  • metaphysics
  • The framework of Aristotelian physics-Aristotelian metaphysics-reflected the perspective of this principally biologist, who, amid living entities' undeniable purposiveness, formalized vitalism and teleology, an intrinsic morality in nature. (wikipedia.org)
  • annotation
  • It stemmed from a conversation between Mark D Wilkinson and Suzanna Lewis during a Gene Ontology developers meeting at the Carnegie Institute, Stanford, where the functionalities of the Genquire and Apollo genome annotation tools were being discussed and compared. (wikipedia.org)
  • medical
  • She has successfully secured funding from the European Union, the Defense Advanced Research Projects Agency (DARPA) in the US and UK funding agencies including the Engineering and Physical Sciences Research Council (EPSRC), Biotechnology and Biological Sciences Research Council (BBSRC), Economic and Social Research Council (ESRC), Medical Research Council (MRC), the Department of Health, The Open Middleware Infrastructure Institute and the Department of Trade and Industry. (wikipedia.org)
  • Data
  • Most of the interoperable behaviours seen in Moby are achieved through the Object (data-format) and Namespace (data-type) ontologies. (wikipedia.org)
  • The MOBY Object Ontology is an ontology consisting of IS-A, HAS-A, and HAS relationships between data formats. (wikipedia.org)
  • MOBY Central is aware of the Object, Namespace and Service ontologies, and thus can match consumers who have in-hand Moby data, with service providers who claim to consume that data-type (or some compatible ontological data-type) or to perform a particular operation on it. (wikipedia.org)
  • The BioMOBY Object Ontology controls the valid data structures in exactly the same way as an OWL ontology defines an RDF data instance. (wikipedia.org)
  • example
  • For example, Genbank has "gi" identifiers that are used to enumerate all of their sequence records - this is defined as "NCBI_gi" in the Namespace Ontology. (wikipedia.org)
  • structure
  • An XML serialization of this ontology is defined in the Moby API such that any given ontology node has a predictable XML structure. (wikipedia.org)
  • Thus, between these two ontologies, a service provider and/or a client program can receive a piece of Moby XML, and immediately know both its structure, and its "intent" (semantics). (wikipedia.org)
  • BioMOBY Web Services consume and generate BioMOBY XML, the structure of which is defined by the BioMOBY Object Ontology. (wikipedia.org)