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Journal of Biomedical Semantics

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https://www.readbyqxmd.com/read/27842607/the-flora-phenotype-ontology-flopo-tool-for-integrating-morphological-traits-and-phenotypes-of-vascular-plants
#1
Robert Hoehndorf, Mona Alshahrani, Georgios V Gkoutos, George Gosline, Quentin Groom, Thomas Hamann, Jens Kattge, Sylvia Mota de Oliveira, Marco Schmidt, Soraya Sierra, Erik Smets, Rutger A Vos, Claus Weiland
BACKGROUND: The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on...
November 14, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27842575/tnm-o-ontology-support-for-staging-of-malignant-tumours
#2
Martin Boeker, Fábio França, Peter Bronsert, Stefan Schulz
BACKGROUND: Objectives of this work are to (1) present an ontological framework for the TNM classification system, (2) exemplify this framework by an ontology for colon and rectum tumours, and (3) evaluate this ontology by assigning TNM classes to real world pathology data. METHODS: The TNM ontology uses the Foundational Model of Anatomy for anatomical entities and BioTopLite 2 as a domain top-level ontology. General rules for the TNM classification system and the specific TNM classification for colorectal tumours were axiomatised in description logic...
November 14, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27751176/supporting-the-analysis-of-ontology-evolution-processes-through-the-combination-of-static-and-dynamic-scaling-functions-in-oquare
#3
Astrid Duque-Ramos, Manuel Quesada-Martínez, Miguela Iniesta-Moreno, Jesualdo Tomás Fernández-Breis, Robert Stevens
BACKGROUND: The biomedical community has now developed a significant number of ontologies. The curation of biomedical ontologies is a complex task and biomedical ontologies evolve rapidly, so new versions are regularly and frequently published in ontology repositories. This has the implication of there being a high number of ontology versions over a short time span. Given this level of activity, ontology designers need to be supported in the effective management of the evolution of biomedical ontologies as the different changes may affect the engineering and quality of the ontology...
October 17, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27737720/dione-an-owl-representation-of-icd-10-cm-for-classifying-patients-diseases
#4
María Del Mar Roldán-García, María Jesús García-Godoy, José F Aldana-Montes
BACKGROUND: Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) has been designed as standard clinical terminology for annotating Electronic Health Records (EHRs). EHRs textual information is used to classify patients' diseases into an International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) category (usually by an expert). Improving the accuracy of classification is the main purpose of using ontologies and OWL representations at the core of classification systems...
October 13, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27717403/the-early-bird-catches-the-term-combining-twitter-and-news-data-for-event-detection-and-situational-awareness
#5
Nicholas Thapen, Donal Simmie, Chris Hankin
BACKGROUND: Twitter updates now represent an enormous stream of information originating from a wide variety of formal and informal sources, much of which is relevant to real-world events. They can therefore be highly useful for event detection and situational awareness applications. RESULTS: In this paper we apply customised filtering techniques to existing bio-surveillance algorithms to detect localised spikes in Twitter activity, showing that these correspond to real events with a high level of confidence...
October 7, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27716359/trhont-building-an-ontology-to-assist-rehabilitation-processes
#6
Idoia Berges, David Antón, Jesús Bermúdez, Alfredo Goñi, Arantza Illarramendi
BACKGROUND: One of the current research efforts in the area of biomedicine is the representation of knowledge in a structured way so that reasoning can be performed on it. More precisely, in the field of physiotherapy, information such as the physiotherapy record of a patient or treatment protocols for specific disorders must be adequately modeled, because they play a relevant role in the management of the evolutionary recovery process of a patient. In this scenario, we introduce TRHONT, an application ontology that can assist physiotherapists in the management of the patients' evolution via reasoning supported by semantic technology...
October 4, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27678076/a-drug-target-slim-using-gene-ontology-and-gene-ontology-annotations-to-navigate-protein-ligand-target-space-in-chembl
#7
Prudence Mutowo, A Patrícia Bento, Nathan Dedman, Anna Gaulton, Anne Hersey, Jane Lomax, John P Overington
BACKGROUND: The process of discovering new drugs is a lengthy, time-consuming and expensive process. Modern day drug discovery relies heavily on the rapid identification of novel 'targets', usually proteins that can be modulated by small molecule drugs to cure or minimise the effects of a disease. Of the 20,000 proteins currently reported as comprising the human proteome, just under a quarter of these can potentially be modulated by known small molecules Storing information in curated, actively maintained drug discovery databases can help researchers access current drug discovery information quickly...
September 27, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27671202/expansion-of-medical-vocabularies-using-distributional-semantics-on-japanese-patient-blogs
#8
Magnus Ahltorp, Maria Skeppstedt, Shiho Kitajima, Aron Henriksson, Rafal Rzepka, Kenji Araki
BACKGROUND: Research on medical vocabulary expansion from large corpora has primarily been conducted using text written in English or similar languages, due to a limited availability of large biomedical corpora in most languages. Medical vocabularies are, however, essential also for text mining from corpora written in other languages than English and belonging to a variety of medical genres. The aim of this study was therefore to evaluate medical vocabulary expansion using a corpus very different from those previously used, in terms of grammar and orthographics, as well as in terms of text genre...
September 26, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27664130/the-environment-ontology-in-2016-bridging-domains-with-increased-scope-semantic-density-and-interoperation
#9
Pier Luigi Buttigieg, Evangelos Pafilis, Suzanna E Lewis, Mark P Schildhauer, Ramona L Walls, Christopher J Mungall
BACKGROUND: The Environment Ontology (ENVO; http://www.environmentontology.org/ ), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description...
September 23, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27633888/diagnosis-misdiagnosis-lucky-guess-hearsay-and-more-an-ontological-analysis
#10
William R Hogan, Werner Ceusters
BACKGROUND: Disease and diagnosis have been the subject of much ontological inquiry. However, the insights gained therein have not yet been well enough applied to the study, management, and improvement of data quality in electronic health records (EHR) and administrative systems. Data in these systems suffer from workarounds clinicians are forced to apply due to limitations in the current state-of-the art in system design which ignore the various types of entities that diagnoses as information content entities can be and are about...
September 15, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27627881/the-ontology-of-biological-and-clinical-statistics-obcs-for-standardized-and-reproducible-statistical-analysis
#11
Jie Zheng, Marcelline R Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith, Yongqun He
BACKGROUND: 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. RESULTS: The terms in OBCS including 'data collection', 'data transformation in statistics', 'data visualization', 'statistical data analysis', and 'drawing a conclusion based on data', cover the major types of statistical processes used in basic biological research and clinical outcome studies...
September 14, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27613112/gene-ontology-synonym-generation-rules-lead-to-increased-performance-in-biomedical-concept-recognition
#12
Christopher S Funk, K Bretonnel Cohen, Lawrence E Hunter, Karin M Verspoor
BACKGROUND: Gene Ontology (GO) terms represent the standard for annotation and representation of molecular functions, biological processes and cellular compartments, but a large gap exists between the way concepts are represented in the ontology and how they are expressed in natural language text. The construction of highly specific GO terms is formulaic, consisting of parts and pieces from more simple terms. RESULTS: We present two different types of manually generated rules to help capture the variation of how GO terms can appear in natural language text...
September 9, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27377652/the-cell-ontology-2016-enhanced-content-modularization-and-ontology-interoperability
#13
Alexander D Diehl, Terrence F Meehan, Yvonne M Bradford, Matthew H Brush, Wasila M Dahdul, David S Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E Van Slyke, Nicole A Vasilevsky, Melissa A Haendel, Judith A Blake, Christopher J Mungall
BACKGROUND: The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. CONSTRUCTION AND CONTENT: Recent work on the CL has focused on extending the representation of various cell types, and developing new modules in the CL itself, and in related ontologies in coordination with the CL...
July 4, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27765065/extending-gene-ontology-in-the-context-of-extracellular-rna-and-vesicle-communication
#14
Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B Gerstein, Andrew F Hill, Robert R Kitchen, Jan Lötvall, Tushar Patel, Dena C Procaccini, Peter Quesenberry, Joel Rozowsky, Robert L Raffai, Aleksandra Shypitsyna, Andrew I Su, Clotilde Théry, Kasey Vickers, Marca H M Wauben, Suresh Mathivanan, Aleksandar Milosavljevic, Louise C Laurent
BACKGROUND: To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research. METHODS: By following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO...
April 12, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27655655/can-snomed-ct-be-squeezed-without-losing-its-shape
#15
Pablo López-García, Stefan Schulz
BACKGROUND: In biomedical applications where the size and complexity of SNOMED CT become problematic, using a smaller subset that can act as a reasonable substitute is usually preferred. In a special class of use cases-like ontology-based quality assurance, or when performing scaling experiments for real-time performance-it is essential that modules show a similar shape than SNOMED CT in terms of concept distribution per sub-hierarchy. Exactly how to extract such balanced modules remains unclear, as most previous work on ontology modularization has focused on other problems...
2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27637866/making-adjustments-to-event-annotations-for-improved-biological-event-extraction
#16
Seung-Cheol Baek, Jong C Park
BACKGROUND: Current state-of-the-art approaches to biological event extraction train statistical models in a supervised manner on corpora annotated with event triggers and event-argument relations. Inspecting such corpora, we observe that there is ambiguity in the span of event triggers (e.g., "transcriptional activity" vs. 'transcriptional'), leading to inconsistencies across event trigger annotations. Such inconsistencies make it quite likely that similar phrases are annotated with different spans of event triggers, suggesting the possibility that a statistical learning algorithm misses an opportunity for generalizing from such event triggers...
2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27608917/information-and-organization-in-public-health-institutes-an-ontology-based-modeling-of-the-entities-in-the-reception-analysis-report-phases
#17
Giandomenico Pozza, Stefano Borgo, Alessandro Oltramari, Laura Contalbrigo, Stefano Marangon
BACKGROUND: Ontologies are widely used both in the life sciences and in the management of public and private companies. Typically, the different offices in an organization develop their own models and related ontologies to capture specific tasks and goals. Although there might be an overall coordination, the use of distinct ontologies can jeopardize the integration of data across the organization since data sharing and reusability are sensitive to modeling choices. RESULTS: The paper provides a study of the entities that are typically found at the reception, analysis and report phases in public institutes in the life science domain...
2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27538448/the-apollo-structured-vocabulary-an-owl2-ontology-of-phenomena-in-infectious-disease-epidemiology-and-population-biology-for-use-in-epidemic-simulation
#18
William R Hogan, Michael M Wagner, Mathias Brochhausen, John Levander, Shawn T Brown, Nicholas Millett, Jay DePasse, Josh Hanna
BACKGROUND: We developed the Apollo Structured Vocabulary (Apollo-SV)-an OWL2 ontology of phenomena in infectious disease epidemiology and population biology-as part of a project whose goal is to increase the use of epidemic simulators in public health practice. Apollo-SV defines a terminology for use in simulator configuration. Apollo-SV is the product of an ontological analysis of the domain of infectious disease epidemiology, with particular attention to the inputs and outputs of nine simulators...
2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27502585/using-aberowl-for-fast-and-scalable-reasoning-over-bioportal-ontologies
#19
Luke Slater, Georgios V Gkoutos, Paul N Schofield, Robert Hoehndorf
BACKGROUND: Reasoning over biomedical ontologies using their OWL semantics has traditionally been a challenging task due to the high theoretical complexity of OWL-based automated reasoning. As a consequence, ontology repositories, as well as most other tools utilizing ontologies, either provide access to ontologies without use of automated reasoning, or limit the number of ontologies for which automated reasoning-based access is provided. METHODS: We apply the AberOWL infrastructure to provide automated reasoning-based access to all accessible and consistent ontologies in BioPortal (368 ontologies)...
2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27502477/towards-natural-language-question-generation-for-the-validation-of-ontologies-and-mappings
#20
Asma Ben Abacha, Julio Cesar Dos Reis, Yassine Mrabet, Cédric Pruski, Marcos Da Silveira
BACKGROUND: The increasing number of open-access ontologies and their key role in several applications such as decision-support systems highlight the importance of their validation. Human expertise is crucial for the validation of ontologies from a domain point-of-view. However, the growing number of ontologies and their fast evolution over time make manual validation challenging. METHODS: We propose a novel semi-automatic approach based on the generation of natural language (NL) questions to support the validation of ontologies and their evolution...
2016: Journal of Biomedical Semantics
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