• MGED Ontology
  • The Minimum Information about a Microarray Experiment (MIAME) was the original checklist [ 5 ], and the MGED Ontology provided definitions for the MIAME terms. (royalsocietypublishing.org)
  • In building the MGED ontology,it was recognized that it would be impractical to cover all the different types ofexperiments on all the different types of organisms by listing and defining all thetypes of organisms and their properties. (duhnnae.com)
  • The MGED ontology is a work in progress that needs additionalinstances and particularly needs constraints to be added. (duhnnae.com)
  • The applicationof an ontology of experimental conditions extends beyond microarray experimentsand, as the scope of MGED includes other aspects of functional genomics, so too willthe MGED ontology. (duhnnae.com)
  • 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)
  • 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)
  • Neuroscience Informati
  • 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)
  • 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)
  • data
  • We also develop means of transforming biological data sources and data analysis methods into Web Services. (bl.uk)
  • 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 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 more recent OBI (the Ontology for Biomedical Investigations) project ( http://obi-ontology.org ) aims to model the design of an investigation: the protocols, the instrumentation, and materials used in experiments and the data generated [ 8 ]. (royalsocietypublishing.org)
  • 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)
  • It is download Fundamentals of General, Organic, and Biological Chemistry 2006, they are, but then filter for Togetcomparative blues and demonstrating data are as they buy. (dataprintusa.com)
  • Ontologies provide domain knowledge to drive data integration and information retrieval. (swat4ls.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)
  • 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)
  • 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)
  • Systems Biology Pathway Exchange (SBPAX) is an extension for Level 3 and proposal for Level 4 to add quantitative data and systems biology terms (such as Systems Biology Ontology). (wikipedia.org)
  • The collection-specific identifier should be analysed within the framework of the data collection. (wikipedia.org)
  • 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)
  • 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)
  • 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)
  • Network-based approaches to disease have the potential to provide a framework for classifying disease, defining susceptibility, predicting disease outcome, and identifying tailored therapeutic strategiesBarabási et al. (slideshare.net)
  • organize
  • 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)
  • 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)
  • semantic
  • 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)
  • Computationally, semantic similarity can be estimated by defining a topological similarity, by using ontologies to define the distance between terms/concepts. (wikipedia.org)
  • Development
  • 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)
  • experimental
  • Modeling in systems biology is concerned with using experimental information and mathematical methods to build quantitative models across different biological scales. (bl.uk)
  • The ontology currentlycovers the experimental sample and design, and we have begun capturing aspects ofthe microarrays themselves as well. (duhnnae.com)
  • NIFSTD
  • 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)
  • The initial entries in the NeuroLex were built from the NIFSTD ontologies which subsumed an earlier vocabulary BIRNLex. (wikipedia.org)
  • databases
  • Users can seamlessly traverse references between biological databases and draw together annotations in an intuitive tabular interface. (springer.com)
  • The primary application of the ontology will beto develop forms for entering information into databases, and consequently allowingqueries, taking advantage of the structure provided by the ontology. (duhnnae.com)
  • The Framework is a dynamic inventory of neuroscience databases, annotated and integrated with a unified system of biomedical terminology (i.e. (wikipedia.org)
  • identifiers
  • 1. The ontology is open in the sense that it is available to be used by all under the following two constraints (1) its origin must be acknowledged and (2) it is not to be altered and subsequently redistributed under the original name or with the same identifiers. (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)
  • 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)
  • systems
  • In the 1980s, the AI community began to use the term ontology to refer to both a theory of a modeled world and a component of knowledge systems. (wikipedia.org)
  • Systems ecology focuses on interactions and transactions within and between biological and ecological systems, and is especially concerned with the way the functioning of ecosystems can be influenced by human interventions. (wikipedia.org)
  • Systems ecology seeks a holistic view of the interactions and transactions within and between biological and ecological systems. (wikipedia.org)
  • The project is headed by Maryann Martone, co-director of the National Center for Microscopy and Imaging Research (NCMIR), part of the multi-disciplinary Center for Research in Biological Systems (CRBS), headquartered at UC San Diego. (wikipedia.org)
  • project
  • Quine and Kripke in philosophy, Sowa and Guarino in computer science), and debates about whether a normative ontology is viable (e.g., debates about foundationalism in philosophy, and the Cyc project in AI). (wikipedia.org)
  • MSAG and JZ are supported by the European Union Workflow4ever project (EU Wf4Ever STREP, 270129), funded under European Union Framework Program 7 (EU-FP7 ICT-2009.4.1). (plos.org)
  • MR, MT, EH, and RK are supported by the European Union Workflow4ever project (EU Wf4Ever STREP, 270129) funded under European Union Framework Program 7 (EU-FP7 ICT-2009.4.1), the Innovative Medicines Initiative Joint Undertaking (IMI-JU) project Open PHACTS (grant agreement no. 115191), and the European Union RD-Connect (EU FP7/2007-2013, grant agreement no. 305,444). (plos.org)
  • defines
  • 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)