Results for 'Open Biomedical Ontologies (OBO) Foundry'

21 found
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  1. Survey-Based Naming Conventions for Use in OBO Foundry Ontology Development.Schober Daniel, Barry Smith, Lewis Suzanna, E. Kusnierczyk, Waclaw Lomax, Jane Mungall, Chris Taylor, F. Chris, Rocca-Serra Philippe & Sansone Susanna-Assunta - 2009 - BMC Bioinformatics 10 (1):125.
    A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex (...)
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  2.  25
    OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies.Rebecca C. Jackson, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D. Diehl, Damion Dooley, William Duncan, Nomi L. Harris, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert, Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall & Bjoern Peters - 2021 - Bioarchiv.
    Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge (...)
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  3. Constructing a Lattice of Infectious Disease Ontologies From a Staphylococcus Aureus Isolate Repository.Albert Goldfain, Lindsay G. Cowell & Barry Smith - 2012 - In Proceeedings of the Third International Conference on Biomedical Ontology (CEUR 897).
    A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy (...)
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  4. Ontology Based Annotation of Contextualized Vital Signs.Goldfain Albert, Xu Min, Bona Jonathan & Barry Smith - 2013 - In Proceedings of the Fourth International Conference on Biomedical Ontology (ICBO). Montreal: pp. 28-33.
    Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. (...)
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  5. The Protein Ontology: A Structured Representation of Protein Forms and Complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results (...)
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  6.  79
    A Unified Framework for Biomedical Terminologies and Ontologies.Werner Ceusters & Barry Smith - 2010 - Studies in Health Technology and Informatics 160:1050-1054.
    The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by (...)
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  7. Saliva Ontology: An Ontology-Based Framework for a Salivaomics Knowledge Base.Jiye Ai, Barry Smith & David Wong - 2010 - BMC Bioinformatics 11 (1):302.
    The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations (...)
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  8.  14
    The Industrial Ontologies Foundry (IOF) Perspectives.Mohamed Karray, Neil Otte, Rahul Rai, Farhad Ameri, Boonserm Kulvatunyou, Barry Smith, Dimitris Kiritsis, Chris Will, Rebecca Arista & Others - 2021 - Proceedings: Industrial Ontology Foundry (IOF) Achieving Data Interoperability Workshop, International Conference on Interoperability for Enterprise Systems and Applications, Tarbes, France, March 17-24, 2020.
    In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set of (...)
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  9. Dispositions and the Infectious Disease Ontology.Albert Goldfain, Barry Smith & Lindsay Cowell - 2010 - In Formal Ontology in Information Systems: Proceedings of the Sixth International Conference (FOIS). IOS Press. pp. 400-413.
    This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of (...)
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  10. TGF-Beta Signaling Proteins and the Protein Ontology.Arighi Cecilia, Liu Hongfang, Natale Darren, Barker Winona, Drabkin Harold, Blake Judith, Barry Smith & Wu Cathy - 2009 - BMC Bioinformatics 10 (Suppl 5):S3.
    The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. (...)
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  11. A Plant Disease Extension of the Infectious Disease Ontology.Ramona Walls, Barry Smith, Elser Justin, Goldfain Albert & W. Stevenson Dennis - 2012 - In Proceedings of the Third International Conference on Biomedical Ontology (CEUR 897). pp. 1-5.
    Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...)
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  12. Ontologies of Cellular Networks.Arp Robert & Barry Smith - 2008 - Science Signalling 1 (50):1--3.
    A comparison of six alternative definitions of the term 'cellular pathway' against the background of ontological realism.
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  13. Ontological Realism: A Methodology for Coordinated Evolution of Scientific Ontologies.Barry Smith & Werner Ceusters - 2010 - Applied Ontology 5 (3):139-188.
    Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes (...)
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  14. Semantics in Support of Biodiversity: An Introduction to the Biological Collections Ontology and Related Ontologies.Ramona L. Walls, John Deck, Robert Guralnik, Steve Baskauf, Reed Beaman, Stanley Blum, Shawn Bowers, Pier Luigi Buttigieg, Neil Davies, Dag Endresen, Maria Alejandra Gandolfo, Robert Hanner, Alyssa Janning, Barry Smith & Others - 2014 - PLoS ONE 9 (3):1-13.
    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in (...)
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  15. Coordinating Coronavirus Research: The COVID-19 Infectious Disease Ontology.John Beverley, Shane Babcock, Gustavo Carvalho, Lindsay Cowell, Sebastian Duesing, Regina Hurley & Barry Smith - 2020 - Open Science Foundation Preprints.
    Rapidly, accurately and easily interpreting generated data is of fundamental concern. Ontologies – structured controlled vocabularies – support interoperability and prevent the development of data silos which undermine interoperability. The Open Biological and Biomedical Ontologies (OBO) Foundry serves to ensure ontologies remain interoperable through adherence by its members to core ontology design principles. For example, the Infectious Disease Ontology (IDO) Core includes terminological content common to investigations of all infectious diseases. Ontologies covering more (...)
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  16.  78
    Dealing with Elements of Medical Encounters: An Approach Based on Ontological Realism.Farinelli Fernanda, Almeida Mauricio, Elkin Peter & Barry Smith - 2016 - Proceedings of the Joint International Conference on Biological Ontology and Biocreative 1747.
    Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution grounded in formal ontology. Here, we present how (...)
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  17.  79
    Peer Review Report: Ontologies Relevant to Behaviour Change Interventions, Version 1.Robert M. Kelly, David Limbaugh & Barry Smith - 2020 - Human Behaviour Change Project.
    In “Ontologies Relevant to behaviour change interventions: A Method for their Development” Wright, et al. outline a step by step process for building ontologies of behaviour modification – what the authors call the Refined Ontology Developmental Method (RODM) – and demonstrate its use in the development of the Behaviour Change Intervention Ontology (BCIO). RODM is based on the principles of good ontology building used by the Open Biomedical Ontology (OBO) Foundry in addition to those outlined (...)
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  18. The Plant Ontology: A Common Reference Ontology for Plants.L. Walls Ramona, D. Cooper Laurel, Elser Justin, W. Stevenson Dennis, Barry Smith, Mungall Chris, A. Gandolfo Maria & Jaiswal Pankaj - 2010 - In Proceedings of the Workshop on Bio-Ontologies, ISMB, Boston, July, 2010.
    The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...)
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  19. SNOMED CT Standard Ontology Based on the Ontology for General Medical Science.Shaker El-Sappagh, Francesco Franda, Ali Farman & Kyung-Sup Kwak - 2018 - BMC Medical Informatics and Decision Making 76 (18):1-19.
    Background: Systematized Nomenclature of Medicine—Clinical Terms (SNOMED CT, hereafter abbreviated SCT) is acomprehensive medical terminology used for standardizing the storage, retrieval, and exchange of electronic healthdata. Some efforts have been made to capture the contents of SCT as Web Ontology Language (OWL), but theseefforts have been hampered by the size and complexity of SCT. Method: Our proposal here is to develop an upper-level ontology and to use it as the basis for defining the termsin SCT in a way that will (...)
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  20. The Infectious Disease Ontology in the Age of COVID-19.Shane Babcock, Lindsay G. Cowell, John Beverley & Barry Smith - 2021 - Journal of Biomedical Semantics 12 (13).
    The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper (...)
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  21. The Ontology of Biological and Clinical Statistics (OBCS) for Standardized and Reproducible Statistical Analysis.Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Lin Yu, Alfred Hero, Barry Smith & Yongqun He - 2016 - Journal of Biomedical Semantics 7 (53).
    Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...)
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