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Journal of Biomedical Semantics

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https://www.readbyqxmd.com/read/28438189/modulated-evaluation-metrics-for-drug-based-ontologies
#1
Muhammad Amith, Cui Tao
BACKGROUND: Research for ontology evaluation is scarce. If biomedical ontological datasets and knowledgebases are to be widely used, there needs to be quality control and evaluation for the content and structure of the ontology. This paper introduces how to effectively utilize a semiotic-inspired approach to ontology evaluation, specifically towards drug-related ontologies hosted on the National Center for Biomedical Ontology BioPortal. RESULTS: Using the semiotic-based evaluation framework for drug-based ontologies, we adjusted the quality metrics based on the semiotic features of drug ontologies...
April 24, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28427468/learning-from-biomedical-linked-data-to-suggest-valid-pharmacogenes
#2
Kevin Dalleau, Yassine Marzougui, Sébastien Da Silva, Patrice Ringot, Ndeye Coumba Ndiaye, Adrien Coulet
BACKGROUND: A standard task in pharmacogenomics research is identifying genes that may be involved in drug response variability, i.e., pharmacogenes. Because genomic experiments tended to generate many false positives, computational approaches based on the use of background knowledge have been proposed. Until now, only molecular networks or the biomedical literature were used, whereas many other resources are available. METHOD: We propose here to consume a diverse and larger set of resources using linked data related either to genes, drugs or diseases...
April 20, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28412964/mesh-now-automatic-mesh-indexing-at-pubmed-scale-via-learning-to-rank
#3
Yuqing Mao, Zhiyong Lu
BACKGROUND: MeSH indexing is the task of assigning relevant MeSH terms based on a manual reading of scholarly publications by human indexers. The task is highly important for improving literature retrieval and many other scientific investigations in biomedical research. Unfortunately, given its manual nature, the process of MeSH indexing is both time-consuming (new articles are not immediately indexed until 2 or 3 months later) and costly (approximately ten dollars per article). In response, automatic indexing by computers has been previously proposed and attempted but remains challenging...
April 17, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28388928/snpphena-a-corpus-for-extracting-ranked-associations-of-single-nucleotide-polymorphisms-and-phenotypes-from-literature
#4
Behrouz Bokharaeian, Alberto Diaz, Nasrin Taghizadeh, Hamidreza Chitsaz, Ramyar Chavoshinejad
BACKGROUND: Single Nucleotide Polymorphisms (SNPs) are among the most important types of genetic variations influencing common diseases and phenotypes. Recently, some corpora and methods have been developed with the purpose of extracting mutations and diseases from texts. However, there is no available corpus, for extracting associations from texts, that is annotated with linguistic-based negation, modality markers, neutral candidates, and confidence level of associations. METHOD: In this research, different steps were presented so as to produce the SNPPhenA corpus...
April 7, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28298238/biofed-federated-query-processing-over-life-sciences-linked-open-data
#5
Ali Hasnain, Qaiser Mehmood, Syeda Sana E Zainab, Muhammad Saleem, Claude Warren, Durre Zehra, Stefan Decker, Dietrich Rebholz-Schuhmann
BACKGROUND: Biomedical data, e.g. from knowledge bases and ontologies, is increasingly made available following open linked data principles, at best as RDF triple data. This is a necessary step towards unified access to biological data sets, but this still requires solutions to query multiple endpoints for their heterogeneous data to eventually retrieve all the meaningful information. Suggested solutions are based on query federation approaches, which require the submission of SPARQL queries to endpoints...
March 15, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28288685/ontology-based-literature-mining-of-e-coli-vaccine-associated-gene-interaction-networks
#6
Junguk Hur, Arzucan Özgür, Yongqun He
BACKGROUND: Pathogenic Escherichia coli infections cause various diseases in humans and many animal species. However, with extensive E. coli vaccine research, we are still unable to fully protect ourselves against E. coli infections. To more rational development of effective and safe E. coli vaccine, it is important to better understand E. coli vaccine-associated gene interaction networks. METHODS: In this study, we first extended the Vaccine Ontology (VO) to semantically represent various E...
March 14, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28270198/large-scale-adverse-effects-related-to-treatment-evidence-standardization-laertes-an-open-scalable-system-for-linking-pharmacovigilance-evidence-sources-with-clinical-data
#7
(no author information available yet)
BACKGROUND: Integrating multiple sources of pharmacovigilance evidence has the potential to advance the science of safety signal detection and evaluation. In this regard, there is a need for more research on how to integrate multiple disparate evidence sources while making the evidence computable from a knowledge representation perspective (i.e., semantic enrichment). Existing frameworks suggest well-promising outcomes for such integration but employ a rather limited number of sources...
March 7, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28253937/therapeutic-indications-and-other-use-case-driven-updates-in-the-drug-ontology-anti-malarials-anti-hypertensives-opioid-analgesics-and-a-large-term-request
#8
William R Hogan, Josh Hanna, Amanda Hicks, Samira Amirova, Baxter Bramblett, Matthew Diller, Rodel Enderez, Timothy Modzelewski, Mirela Vasconcelos, Chris Delcher
BACKGROUND: The Drug Ontology (DrOn) is an OWL2-based representation of drug products and their ingredients, mechanisms of action, strengths, and dose forms. We originally created DrOn for use cases in comparative effectiveness research, primarily to identify historically complete sets of United States National Drug Codes (NDCs) that represent packaged drug products, by the ingredient(s), mechanism(s) of action, and so on contained in those products. Although we had designed DrOn from the outset to carefully distinguish those entities that have a therapeutic indication from those entities that have a molecular mechanism of action, we had not previously represented in DrOn any particular therapeutic indication...
March 3, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28253919/optimization-on-machine-learning-based-approaches-for-sentiment-analysis-on-hpv-vaccines-related-tweets
#9
Jingcheng Du, Jun Xu, Hsingyi Song, Xiangyu Liu, Cui Tao
BACKGROUND: Analysing public opinions on HPV vaccines on social media using machine learning based approaches will help us understand the reasons behind the low vaccine coverage and come up with corresponding strategies to improve vaccine uptake. OBJECTIVE: To propose a machine learning system that is able to extract comprehensive public sentiment on HPV vaccines on Twitter with satisfying performance. METHOD: We collected and manually annotated 6,000 HPV vaccines related tweets as a gold standard...
March 3, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28231809/12-years-on-is-the-nlm-medical-text-indexer-still-useful-and-relevant
#10
James Mork, Alan Aronson, Dina Demner-Fushman
BACKGROUND: Facing a growing workload and dwindling resources, the US National Library of Medicine (NLM) created the Indexing Initiative project in 1996. This cross-library team's mission is to explore indexing methodologies for ensuring quality and currency of NLM document collections. The NLM Medical Text Indexer (MTI) is the main product of this project and has been providing automated indexing recommendations since 2002. After all of this time, the questions arise whether MTI is still useful and relevant...
February 23, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28193260/evaluating-the-effect-of-annotation-size-on-measures-of-semantic-similarity
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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