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Journal of Biomedical Semantics

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https://www.readbyqxmd.com/read/28069052/toward-a-comprehensive-drug-ontology-extraction-of-drug-indication-relations-from-diverse-information-sources
#1
Mark E Sharp
BACKGROUND: Drug ontologies could help pharmaceutical researchers overcome information overload and speed the pace of drug discovery, thus benefiting the industry and patients alike. Drug-disease relations, specifically drug-indication relations, are a prime candidate for representation in ontologies. There is a wealth of available drug-indication information, but structuring and integrating it is challenging. RESULTS: We created a drug-indication database (DID) of data from 12 openly available, commercially available, and proprietary information sources, integrated by terminological normalization to UMLS and other authorities...
January 10, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28049518/an-ontological-analysis-of-medical-bayesian-indicators-of-performance
#2
Adrien Barton, Jean-François Ethier, Régis Duvauferrier, Anita Burgun
BACKGROUND: Biomedical ontologies aim at providing the most exhaustive and rigorous representation of reality as described by biomedical sciences. A large part of medical reasoning deals with diagnosis and is essentially probabilistic. It would be an asset for biomedical ontologies to be able to support such a probabilistic reasoning and formalize Bayesian indicators of performance: sensitivity, specificity, positive predictive value and negative predictive value. In doing so, one has to consider that not only the positive and negative predictive values, but also sensitivity and specificity depend upon the group under consideration: this is the "spectrum effect"...
January 3, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28031037/tesa-a-distributional-measure-for-calculating-semantic-relatedness
#3
Maciej Rybinski, José Francisco Aldana-Montes
BACKGROUND: Semantic relatedness is a measure that quantifies the strength of a semantic link between two concepts. Often, it can be efficiently approximated with methods that operate on words, which represent these concepts. Approximating semantic relatedness between texts and concepts represented by these texts is an important part of many text and knowledge processing tasks of crucial importance in the ever growing domain of biomedical informatics. The problem of most state-of-the-art methods for calculating semantic relatedness is their dependence on highly specialized, structured knowledge resources, which makes these methods poorly adaptable for many usage scenarios...
December 28, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27955708/thematic-issue-of-the-second-combined-bio-ontologies-and-phenotypes-workshop
#4
Karin Verspoor, Anika Oellrich, Nigel Collier, Tudor Groza, Philippe Rocca-Serra, Larisa Soldatova, Michel Dumontier, Nigam Shah
This special issue covers selected papers from the 18th Bio-Ontologies Special Interest Group meeting and Phenotype Day, which took place at the Intelligent Systems for Molecular Biology (ISMB) conference in Dublin in 2015. The papers presented in this collection range from descriptions of software tools supporting ontology development and annotation of objects with ontology terms, to applications of text mining for structured relation extraction involving diseases and phenotypes, to detailed proposals for new ontologies and mapping of existing ontologies...
December 12, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27842607/the-flora-phenotype-ontology-flopo-tool-for-integrating-morphological-traits-and-phenotypes-of-vascular-plants
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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/27406187/the-ontology-of-medically-related-social-entities-recent-developments
#17
Amanda Hicks, Josh Hanna, Daniel Welch, Mathias Brochhausen, William R Hogan
BACKGROUND: The Ontology of Medically Related Social Entities (OMRSE) was initially developed in 2011 to provide a framework for modeling demographic data in Resource Description Framework/Web Ontology Language. It is built upon the Basic Formal Ontology and conforms to Open Biomedical Ontologies Foundry's best practices. DESCRIPTION: We report recent development of OMRSE which includes representations of organizations, roles, facilities, demographic data, enrollment in insurance plans, and data about socio-economic indicators...
July 12, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27392431/neurordf-semantic-integration-of-highly-curated-data-to-prioritize-biomarker-candidates-in-alzheimer-s-disease
#18
Anandhi Iyappan, Shweta Bagewadi Kawalia, Tamara Raschka, Martin Hofmann-Apitius, Philipp Senger
BACKGROUND: Neurodegenerative diseases are incurable and debilitating indications with huge social and economic impact, where much is still to be learnt about the underlying molecular events. Mechanistic disease models could offer a knowledge framework to help decipher the complex interactions that occur at molecular and cellular levels. This motivates the need for the development of an approach integrating highly curated and heterogeneous data into a disease model of different regulatory data layers...
July 8, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27377652/the-cell-ontology-2016-enhanced-content-modularization-and-ontology-interoperability
#19
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/27927232/publication-of-nuclear-magnetic-resonance-experimental-data-with-semantic-web-technology-and-the-application-thereof-to-biomedical-research-of-proteins
#20
Masashi Yokochi, Naohiro Kobayashi, Eldon L Ulrich, Akira R Kinjo, Takeshi Iwata, Yannis E Ioannidis, Miron Livny, John L Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara
BACKGROUND: The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. FINDINGS: To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data...
May 5, 2016: Journal of Biomedical Semantics
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