Chemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsAnthropology, Education, Sociology and Social PhenomenaHumanitiesInformation ScienceHealth Care
Biological OntologiesVocabulary, ControlledInformation Storage and RetrievalGene OntologyTerminology as TopicComputational BiologySoftwareDatabases, GeneticAnatomyDatabase Management SystemsUser-Computer InterfaceNatural Language ProcessingSemanticsInternetMolecular Sequence AnnotationAlgorithmsGene Expression ProfilingMedicine, Chinese TraditionalDatabases, FactualSystems IntegrationIndividualized MedicineModels, BiologicalProgramming LanguagesOligonucleotide Array Sequence AnalysisKnowledge BasesGenomicsInternal MedicineDocumentationMedicine, TraditionalNuclear MedicineDatabases, ProteinData MiningMedicine, KampoArtificial IntelligenceMedicineClassificationCluster AnalysisProteinsUnified Medical Language SystemSystematized Nomenclature of MedicineInformation ScienceComputer GraphicsComputer SimulationMedical InformaticsTranscriptomeEvidence-Based MedicineGene Regulatory NetworksClinical MedicineBiologyPubMedExpressed Sequence TagsProtein Interaction MappingBiomedical ResearchHistory of MedicineDrugs, Chinese HerbalPattern Recognition, AutomatedKnowledgeRegenerative MedicineEmergency MedicineModels, TheoreticalBiological ProcessesAbstracting and Indexing as TopicReproducibility of ResultsComplementary TherapiesMedicine, AyurvedicSystems BiologyLogic
Infectious Disease OntologyBasic Formal ONational Center fDomain OntologiesControlled vocabulariesPathwaysGeneProcessesFoundryClinicalDataAbstractGenomic medicineClassifyConsortiumBarry SmithInformaticsEmory UniversityEnrichmentBiomedicalRepresentingComputational approachesApproachesImmuneResource DescriptiProteinAssistant ProfessorJohns HopkinsTaxonomiesTheoreticalTranslationalDevelopmentHttpsProvideResearchMeaningfulBiology and medicineKnowledgeSupportDefinesApplicationsMethodsStandardDisordersSystemsUniversityGenomicsWorkNetworkIdentifyPhilosophical
Infectious Disease Ontology3
  • The National Center for Biomedical Ontology (NCBO) in collaboration with the Protein Ontology (PRO) and the Infectious Disease Ontology (IDO) will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012. (bioontology.org)
  • Smith is one of the principal scientists of the NCBO, a Scientific Advisor to the Gene Ontology Consortium , and a Principal Investigator on the Protein Ontology and Infectious Disease Ontology projects. (buffalo.edu)
  • He has authored the Sleep Domain Ontology , the Core Data Elements model for Cardiothoracic Surgery ( SemanticDB , Cleveland Clinic), and collaborates with other researchers on the Ontology for General Medical Science and Infectious Disease Ontology projects. (buffalo.edu)
Basic Formal O1
  • A major contribution of PRO as a protein biology community informatics resource is that it provides a formal ontological structure with foundation in Basic Formal Ontology http://www.ifomis.org/bfo/ to describe types of protein complexes and gives these types unique, permanent identifiers http://www.obofoundry.org/id-policy.shtml . (biomedcentral.com)
National Center f1
  • This tutorial is one of a series of dissemination events sponsored by the National Center for Biomedical Ontology (NCBO). (buffalo.edu)
Domain Ontologies6
  • The Space Domain Ontologies. (philpapers.org)
  • The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. (philpapers.org)
  • This paper provides an overview of the Space Domain Ontologies and their development and use. (philpapers.org)
  • It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (philpapers.org)
  • also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. (philpapers.org)
  • The term semantic data mining denotes a data mining approach where domain ontologies are used as background knowledge. (poznan.pl)
Controlled vocabularies1
  • Projects should address health-related behavioral and social science problems not easily solved without improvement in semantic knowledge structures (e.g., controlled vocabularies, taxonomies, and ontologies). (nih.gov)
Pathways3
  • Specifically, the network uses hierarchical graph convolution that mimic the organization of a well-established gene ontology to track the convergence of genetic risk across biological pathways. (stanford.edu)
  • Additionally, bioinformatic analyses were conducted to discover target genes, signaling pathways and gene ontologies associated with the identified miRNAs. (biomedcentral.com)
  • This paper argues that some of the strong beliefs held by humans have deep biological roots in our evolutionary past, and the neuronal pathways and structures that support them can be found in other species. (bvsalud.org)
Gene8
  • The Gene Ontology contains a wealth of terms covering immune system processes for the annotation of proteins involved in the functioning of the immune system. (bioontology.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)
  • These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. (wikipedia.org)
  • This text annotation is carried out in collaboration with the MGI Gene Expression Database (GXD) using the EMAP mouse anatomy ontology. (wikipedia.org)
  • Liu Y, Zhang YZ, Imoto S . Microbial Gene Ontology informed deep neural network for microbe functionality discovery in human diseases. (google.com)
  • A miRNA-mRNA network was constructed, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed. (biomedcentral.com)
  • We calculated the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment scores of all fibrotic disease genes. (frontiersin.org)
  • ProComp leverages, and cross references, entries in existing protein-centric informatics resources, including the protein complexes that are represented in the Cellular Component branch of the Gene Ontology. (biomedcentral.com)
Processes4
  • Biomedical ontologies provide an organizational framework of the concepts involved in biological entities and processes in a system of hierarchical and associative relations that allows reasoning about biomedical knowledge. (nih.gov)
  • In Reactome we have integrated annotations of human TLR molecular functions with those of 6800 other human proteins involved in diverse biological processes to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. (bioontology.org)
  • The goal of the project "COMMITMENT - Modeling Comorbidity Processes by Integrative Machine Transfer Learning for Psychiatric Disorders" is to develop a computer-based systems medicine framework that enables clinically meaningful stratification of psychotic disorders and identification of biological processes. (fraunhofer.de)
  • Recently, miRNA-messenger RNA (mRNA) regulatory relationships have been confirmed during biological processes, including osteogenic differentiation. (frontiersin.org)
Foundry1
  • His pioneering work led to the formation of the OBO (Open Biomedical Ontologies) Foundry , a set of resources designed to support information-driven research in biology and biomedicine. (buffalo.edu)
Clinical12
  • He practices Internal Medicine for the reward of caring for patients and to inspire research, mining clinical data sources to inform recommendations for medical decision-making. (stanford.edu)
  • As Director of the Quantitative Sciences Unit (QSU), she manages a group of faculty and PhD and Master's level staff who collaborate with clinical and translational investigators throughout the School of Medicine. (stanford.edu)
  • Dr. Downing is a physician (Internal Medicine) and an expert in clinical decision support, electronic health records, clinician burnout, and applications of artificial intelligence in healthcare. (stanford.edu)
  • Dr. Downing joined BMIR in 2016 as a Clinical Assistant Professor of Medicine. (stanford.edu)
  • His research focuses on the intersection of machine learning, computational immunology, and translational medicine with the overarching goal of accelerating translation of immune response-based diagnostics and therapies to clinical practice across a broad spectrum of inflammatory diseases, including infections, autoimmune diseases, organ transplant, cancers, and vaccines. (stanford.edu)
  • We found that the majority of SPL drug labels are mapped to chemical ingredient concepts in both drug ontologies whereas a relatively small portion of SPL drug labels are mapped to clinical drug concepts. (biomedcentral.com)
  • The profiling outcomes produced by this study would provide useful insights on meaningful use of FDA SPL drug labels in clinical applications through standard drug ontologies such as NDF-RT and RxNorm. (biomedcentral.com)
  • Problems arise not least in translational medicine, where results of biological research need to be translated into a language which allows them to be used effectively in the clinical context. (buffalo.edu)
  • No prior knowledge of ontology is presupposed, but a background in clinical medicine or in informatics is required. (buffalo.edu)
  • We encourage submissions from scholars and students from all domains in the humanities, in the social, biological and medical sciences, including clinical practice, to discuss current developments - and alternatives to the existing research trends, models and practices- in the areas of brain, sex/gender and sexuality. (unil.ch)
  • The journal was launched to meet the need in the community for a platform to publish impactful and open science that advances basic and clinical research—using genetic, genomic, omic, and systems approaches—that has the potential to revolutionize the practice of medicine. (cdc.gov)
  • We have seen the journal evolve along with the changing landscape of health and disease, including the increasing use of genome-scale approaches in medical research and clinical practice, the generation and analysis of patient- and population-level data, and the clinical implementation of these approaches in precision medicine and public health. (cdc.gov)
Data25
  • 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 data held in EMAGE is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). (wikipedia.org)
  • First, I will showcase an end-to-end deep learning framework that fuses neuroimaging, genetic, and phenotypic data, while maintaining interpretability of the extracted biomarkers. (stanford.edu)
  • The approach is based on our initial experiences with implementing an integrated web of data for a selected use-case, i.e., the identification of plant species used in Chinese medicine that indicate potential antidepressant activities. (biomedcentral.com)
  • Based on these considerations, we explored current semantic resources and linked data technologies in order to identify their potential for improving the integration of findings from traditional medicines into modern pharmaceutical research. (biomedcentral.com)
  • In the implementation process, we employed a Semantic Web technology framework, in which we stored the data sets from NDF-RT and SPLs into a RDF triple store, and executed SPARQL queries to retrieve data from customized SPARQL endpoints. (biomedcentral.com)
  • Semantic Web Technology (SWT) [ 4 ] can be useful to provide a scalable framework for facilitating semantic data integration of heterogeneous resources and enabling semantic sharing through the standard query services. (biomedcentral.com)
  • Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. (biomedcentral.com)
  • Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. (biomedcentral.com)
  • These ontologies are increasingly being applied to annotate and classify biological data. (biomedcentral.com)
  • Additionally, the annotated biological data must be maintained and new annotations created. (biomedcentral.com)
  • Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. (philpapers.org)
  • To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. (philpapers.org)
  • The AETIONOMY concept foresees a primary role of the taxonomy in i) describing and organising the indication-specific data in the data cube, in ii) linking the data to disease models that are based on causal and correlative relationships and in iii) support of reasoning over the knowledge that is explicitly represented in related ontologies or knowledge-based disease models. (fraunhofer.de)
  • The Semantic Deep Learning approach can transform neural embeddings built from unstructured free-text data into reliable and reusable One Health knowledge using ontologies and content from BMJ Best Practice. (biomedcentral.com)
  • The Semantic Web embodies standards and tools for publishing and processing meta-data, with ontologies at its core. (biomedcentral.com)
  • Such approach is motivated by large amounts of data that are increasingly becoming openly available and described using real-life ontologies represented in Semantic Web languages, arguably most extensively in the domain of biology. (poznan.pl)
  • The availability of semantically annotated data poses requirements for new kinds of approaches for data mining that would be able to deal with the complexity, and expressivity of the semantic representation languages, leverage on availability of ontologies and explicit semantics of the described resources, and account for novel assumptions (e.g., open world) that underlie reasoning services exploiting ontologies. (poznan.pl)
  • The tutorial will address the above issues, focusing on the problems of how machine learning techniques can work directly on the richly structured Semantic Web data, exploit ontologies, and the Semantic Web technologies, what is the value added of machine learning methods exploiting ontologies, and what are the challenges for developers of semantic data mining methods. (poznan.pl)
  • Firstly, it will present a general framework for semantic data mining , following the work [NVTL09]. (poznan.pl)
  • Finally, it relies on a data mining ontology which distills extensive background knowledge concerning knowledge discovery itself . (poznan.pl)
  • Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. (biomedcentral.com)
  • Our Strategic Road Map defines strategies, standards, and policy frameworks to support responsible global use of genomic and related health data. (ga4gh.org)
  • Community members join together to develop technical standards, policy frameworks, and policy tools that overcome hurdles to international genomic data use. (ga4gh.org)
  • Help create new global standards and frameworks for responsible genomic data use. (ga4gh.org)
Abstract1
Genomic medicine2
Classify1
  • We also applied existing categorical annotations from the drug ontologies to classify SPL drug labels into corresponding classes. (biomedcentral.com)
Consortium1
  • The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. (biomedcentral.com)
Barry Smith1
  • Barry Smith is a prominent contributor to both theoretical and applied research in ontology. (buffalo.edu)
Informatics3
  • The research projects must include multi-disciplinary teams of subject matter experts in one or more BSSR fields, as well as ontology related informatics and computational approaches. (nih.gov)
  • He continued his work as a postdoc in radiology at Stanford and then established his lab in the department of medicine in biomedical informatics. (stanford.edu)
  • Dr. Khatri is a faculty member in Institute for Immunity, Transplantation and Infection (ITI) and Center for Biomedical Informatics Research (BMIR) in Department of Medicine at Stanford University. (stanford.edu)
Emory University1
  • It is being organized as part of a two -day Ontology for Newborn Screening Translational Research (ONSTR) Workshop organized under the auspices of the Department of Human Genetics, Division of Medical Genetics, Emory University and Children ' s Healthcare of Atlanta. (buffalo.edu)
Enrichment1
  • We will outline use of the ontology for immune assay integration and statistical enrichment analysis. (bioontology.org)
Biomedical3
  • This entry will review the philosophical literature (and some literature in allied fields, such as history of medicine) that scrutinizes the biomedical framework itself, in whole or in part. (stanford.edu)
  • Biomedical Ontologies. (nih.gov)
  • Although more than sixty terminological systems exist in the biomedical domain, few actually qualify as an ontology. (nih.gov)
Representing1
  • Logical and semantic access to related protein forms is critical for advancing bioinformatics approaches to representing, modeling, and reasoning about complex biological systems at the genomic and cellular level [ 1 ]. (biomedcentral.com)
Computational approaches1
  • The main purpose of a bioinformatics platform within SWEGENE should be to provide com- putational facilities and logistical support [databases & infrastructure] for scientists whose primary research in biology and medicine benefit from computational approaches. (lu.se)
Approaches1
  • The explicit representation of protein complexes in PRO--defining each member of the complex at the level of its isoform, variant, or modified form--provides the ability to represent complex biological knowledge as it is emerging in the experimental research community in structures that are both human readable and accessible to algorithmic approaches. (biomedcentral.com)
Immune3
  • 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)
  • An emerging scenario is uncovering immune response as a sophisticated biological process, which requires an intensive cross-talk between immunocytes, parenchymal and stromal cell types. (bioontology.org)
  • We will introduce the Liver Immunology Ontology (LIO), which has as primary goal the representation of the immune response induced in the context of the liver. (bioontology.org)
Resource Descripti1
  • They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. (philpapers.org)
Protein3
  • Day 2 will be focused on flow cytometry, including the question of the Cell and Protein Ontologies and of the role of surface protein expression in cell type classification. (bioontology.org)
  • Since his undergraduate degree in China, Jian Peng has pioneered the application of deep learning techniques to computational biology, including protein structure prediction, biological network analysis, and drug discovery, by developing highly innovative methods to successfully address non-trivial challenges. (iscb.org)
  • References to protein records in UniProtKB are made through entries in the ProForm sub-ontology within PRO (Figure 1 ). (biomedcentral.com)
Assistant Professor1
Johns Hopkins1
  • Steven L. Salzberg, Johns Hopkins University School of Medicine, is the winner of the Accomplishments by a Senior Scientist Award. (iscb.org)
Taxonomies1
  • With a standard set of taxonomies and ontologies for equipment, measurements and analysis, there is an opportunity to streamline the way companies manage test execution, samples and results so that they can predict stability issues early. (pharmamanufacturing.com)
Theoretical1
  • Biomedicine is the umbrella theoretical framework for most health science and health technology work done in academic and government settings. (stanford.edu)
Translational1
  • and to provide a hands-on illustration of ontology development and evaluation in the domain of translational research and newborn screening. (buffalo.edu)
Development6
  • We investigated the usefulness of openly available RDF/OWL tools and datasets to find evidence for pharmaceutical compounds from Chinese medicine that may treat depressive disorders or serve as lead compounds for the future pharmaceutical drug development. (biomedcentral.com)
  • Firstly, the development of traditional medicines such as Chinese medicine was mainly guided by symptomatological and introspective observations without the need for sophisticated experimental methods available only to modern medicine. (biomedcentral.com)
  • This Notice of Funding Opportunity (NOFO) invites applications to support research projects focused on the expansion of existing or development of new ontologies for behavioral or social science research (BSSR). (nih.gov)
  • Tools or resources must also account for socio-behavioral cultural context in vocabulary/ontology development. (nih.gov)
  • PAR-23-181 ) and the other funded projects in a Behavioral and Social Science Ontology Development U01 Research Network. (nih.gov)
  • All GA4GH standards, frameworks, and tools follow the Product Development and Approval Process before being officially adopted. (ga4gh.org)
Https1
  • Source code developed for this project is available at https://github.com/bio-ontology-research-group/phenomenet-vp , and analysis results at http://www.cbrc.kaust.edu.sa/onto/pvp/ . (plos.org)
Provide1
  • Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field. (bioontology.org)
Research6
  • EMAGE is a freely available web-based resource funded by the Medical Research Council (UK) and based at the MRC Human Genetics Unit in the Institute of Genetics and Molecular Medicine, Edinburgh, UK. (wikipedia.org)
  • This model integrates knowledge from research articles, reviews and various databases using Biological Expression Language (BEL). (fraunhofer.de)
  • TBI Knowledge map aims to build an integrated disease model based on Biological Expression Language (BEL) from a selected corpus of 500 research and review articles. (fraunhofer.de)
  • And this is where we believed that the novelty of our approach came in since our over-arching theme of the Book of Nature allowed us to re-contextualise and combine these research emphases into a larger inter-disciplinary framework for theologies of nature. (ed.ac.uk)
  • Research: I am interested in the philosophy of action, broadly conceived, as well as the philosophy of psychology/cognitive science and social ontology. (lu.se)
  • The idea was also to propose a framework where the SWEGENE platform users would get computerised support for their research projects. (lu.se)
Meaningful1
  • However, the lack of linkage to standard drug ontologies hinders their meaningful use. (biomedcentral.com)
Biology and medicine2
Knowledge3
  • The core ontology provides background knowledge about biological types and relations. (biomedcentral.com)
  • The information represented in the wiki should adhere to particular quality criteria, such as internal consistency (the wiki content does not contain contradictory information) and consistency with biological background knowledge (the wiki content should be factually accurate). (biomedcentral.com)
  • We have developed the BOWiki, a wiki system that uses a core ontology together with an automated reasoner to maintain a consistent knowledge base. (biomedcentral.com)
Support3
  • The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. (philpapers.org)
  • Tolk, A. "Extensible Modeling and Simulation Framework - Technical Support" $30,000. (odu.edu)
  • Tolk, A. "Extensible Modeling and Simulation Framework - Command and Control Support" $80,000. (odu.edu)
Defines1
Applications1
  • Both can be shared, but ontologies lend themselves to reuse, sometimes in widely differing applications from the ones for which they were originally designed. (nih.gov)
Methods1
  • He has also been a leader in building computational methods to make novel biological discoveries, in species ranging from viruses to bacteria to animals. (iscb.org)
Standard2
  • NDF-RT (National Drug File Reference Terminology) and NLM RxNorm as standard drug ontology were used to standardize and profile the product labels. (biomedcentral.com)
  • The second part of tutorial will cover the topic of learning from description logics (DL-learning) , motivated by the fact that the standard Web ontology language, OWL, is theoretically based on description logics. (poznan.pl)
Disorders1
  • Furthermore, in the field of regenerative medicine, recent studies have revealed their potential as a new treatment choice for systemic diseases such as diabetes, myocardial infarction and neurodegenerative disorders [ 7 ]. (biomedcentral.com)
Systems2
  • Interestingly, the most recent systems tend to be ontologies, developed either from the top down (e.g. (nih.gov)
  • Many published models of the biomimicry process include steps to identify, understand, and translate function of biological systems. (mdpi.com)
University1
Genomics1
  • Discover how a meeting of 50 leaders in genomics and medicine led to an alliance uniting more than 5,000 individuals and organisations to benefit human health. (ga4gh.org)
Work1
  • This entry will, as much as possible, avoid duplicating the work done in the thorough Philosophy of Medicine entry. (stanford.edu)
Network2
  • The architecture uses an ontology-driven approach to promote the integration of a network of sentinel hospitals or laboratories. (jmir.org)
  • Our investigation used a network medicine method to find possible T2DM-TB molecular mediators. (springeropen.com)
Identify1
  • It is possible to use traditional medicines to identify the source of pharmacological compounds that may otherwise be missed by modern rational drug design. (biomedcentral.com)
Philosophical2
  • It is a framework, a set of philosophical commitments, a global institution woven into Western culture and its power dynamics, and more. (stanford.edu)
  • The philosophical isolation friends of the g move biological for reasoning Recall, but be me this closing environment any time. (dependencylaw.com)