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Journal of Biomedical Semantics

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https://www.readbyqxmd.com/read/28193260/evaluating-the-effect-of-annotation-size-on-measures-of-semantic-similarity
#1
Maxat Kulmanov, Robert Hoehndorf
BACKGROUND: Ontologies are widely used as metadata in biological and biomedical datasets. Measures of semantic similarity utilize ontologies to determine how similar two entities annotated with classes from ontologies are, and semantic similarity is increasingly applied in applications ranging from diagnosis of disease to investigation in gene networks and functions of gene products. RESULTS: Here, we analyze a large number of semantic similarity measures and the sensitivity of similarity values to the number of annotations of entities, difference in annotation size and to the depth or specificity of annotation classes...
February 13, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28173841/building-a-model-for-disease-classification-integration-in-oncology-an-approach-based-on-the-national-cancer-institute-thesaurus
#2
Vianney Jouhet, Fleur Mougin, Bérénice Bréchat, Frantz Thiessard
BACKGROUND: Identifying incident cancer cases within a population remains essential for scientific research in oncology. Data produced within electronic health records can be useful for this purpose. Due to the multiplicity of providers, heterogeneous terminologies such as ICD-10 and ICD-O-3 are used for oncology diagnosis recording purpose. To enable disease identification based on these diagnoses, there is a need for integrating disease classifications in oncology. Our aim was to build a model integrating concepts involved in two disease classifications, namely ICD-10 (diagnosis) and ICD-O-3 (topography and morphology), despite their structural heterogeneity...
February 7, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28148277/safe-sparql-federation-over-rdf-data-cubes-with-access-control
#3
Yasar Khan, Muhammad Saleem, Muntazir Mehdi, Aidan Hogan, Qaiser Mehmood, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
BACKGROUND: Several query federation engines have been proposed for accessing public Linked Open Data sources. However, in many domains, resources are sensitive and access to these resources is tightly controlled by stakeholders; consequently, privacy is a major concern when federating queries over such datasets. In the Healthcare and Life Sciences (HCLS) domain real-world datasets contain sensitive statistical information: strict ownership is granted to individuals working in hospitals, research labs, clinical trial organisers, etc...
February 1, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28137311/developing-a-knowledge-base-to-support-the-annotation-of-ultrasound-images-of-ectopic-pregnancy
#4
Ferdinand Dhombres, Paul Maurice, Stéphanie Friszer, Lucie Guilbaud, Nathalie Lelong, Babak Khoshnood, Jean Charlet, Nicolas Perrot, Eric Jauniaux, Davor Jurkovic, Jean-Marie Jouannic
BACKGROUND: Ectopic pregnancy is a frequent early complication of pregnancy associated with significant rates of morbidly and mortality. The positive diagnosis of this condition is established through transvaginal ultrasound scanning. The timing of diagnosis depends on the operator expertise in identifying the signs of ectopic pregnancy, which varies dramatically among medical staff with heterogeneous training. Developing decision support systems in this context is expected to improve the identification of these signs and subsequently improve the quality of care...
January 31, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28109310/consolidating-drug-data-on-a-global-scale-using-linked-data
#5
Milos Jovanovik, Dimitar Trajanov
BACKGROUND: Drug product data is available on the Web in a distributed fashion. The reasons lie within the regulatory domains, which exist on a national level. As a consequence, the drug data available on the Web are independently curated by national institutions from each country, leaving the data in varying languages, with a varying structure, granularity level and format, on different locations on the Web. Therefore, one of the main challenges in the realm of drug data is the consolidation and integration of large amounts of heterogeneous data into a comprehensive dataspace, for the purpose of developing data-driven applications...
January 21, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28069052/toward-a-comprehensive-drug-ontology-extraction-of-drug-indication-relations-from-diverse-information-sources
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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