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Journal of Biomedical Semantics

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https://www.readbyqxmd.com/read/28764813/an-ontology-driven-tool-for-structured-data-acquisition-using-web-forms
#1
Rafael S Gonçalves, Samson W Tu, Csongor I Nyulas, Michael J Tierney, Mark A Musen
BACKGROUND: Structured data acquisition is a common task that is widely performed in biomedicine. However, current solutions for this task are far from providing a means to structure data in such a way that it can be automatically employed in decision making (e.g., in our example application domain of clinical functional assessment, for determining eligibility for disability benefits) based on conclusions derived from acquired data (e.g., assessment of impaired motor function). To use data in these settings, we need it structured in a way that can be exploited by automated reasoning systems, for instance, in the Web Ontology Language (OWL); the de facto ontology language for the Web...
August 1, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28750648/towards-a-more-molecular-taxonomy-of-disease
#2
Jisoo Park, Benjamin J Hescott, Donna K Slonim
BACKGROUND: Disease taxonomies have been designed for many applications, but they tend not to fully incorporate the growing amount of molecular-level knowledge of disease processes, inhibiting research efforts. Understanding the degree to which we can infer disease relationships from molecular data alone may yield insights into how to ultimately construct more modern taxonomies that integrate both physiological and molecular information. RESULTS: We introduce a new technique we call Parent Promotion to infer hierarchical relationships between disease terms using disease-gene data...
July 27, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28651634/data-and-expert-driven-rule-induction-and-filtering-framework-for-functional-interpretation-and-description-of-gene-sets
#3
Aleksandra Gruca, Marek Sikora
BACKGROUND: High-throughput methods in molecular biology provided researchers with abundance of experimental data that need to be interpreted in order to understand the experimental results. Manual methods of functional gene/protein group interpretation are expensive and time-consuming; therefore, there is a need to develop new efficient data mining methods and bioinformatics tools that could support the expert in the process of functional analysis of experimental results. RESULTS: In this study, we propose a comprehensive framework for the induction of logical rules in the form of combinations of Gene Ontology (GO) terms for functional interpretation of gene sets...
June 26, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28651575/ontological-interpretation-of-biomedical-database-content
#4
Filipe Santana da Silva, Ludger Jansen, Fred Freitas, Stefan Schulz
BACKGROUND: Biological databases store data about laboratory experiments, together with semantic annotations, in order to support data aggregation and retrieval. The exact meaning of such annotations in the context of a database record is often ambiguous. We address this problem by grounding implicit and explicit database content in a formal-ontological framework. METHODS: By using a typical extract from the databases UniProt and Ensembl, annotated with content from GO, PR, ChEBI and NCBI Taxonomy, we created four ontological models (in OWL), which generate explicit, distinct interpretations under the BioTopLite2 (BTL2) upper-level ontology...
June 26, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28629436/disease-compass-a-navigation-system-for-disease-knowledge-based-on-ontology-and-linked-data-techniques
#5
Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe
BACKGROUND: Medical ontologies are expected to contribute to the effective use of medical information resources that store considerable amount of data. In this study, we focused on disease ontology because the complicated mechanisms of diseases are related to concepts across various medical domains. The authors developed a River Flow Model (RFM) of diseases, which captures diseases as the causal chains of abnormal states. It represents causes of diseases, disease progression, and downstream consequences of diseases, which is compliant with the intuition of medical experts...
June 19, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28592275/ncbo-ontology-recommender-2-0-an-enhanced-approach-for-biomedical-ontology-recommendation
#6
Marcos Martínez-Romero, Clement Jonquet, Martin J O'Connor, John Graybeal, Alejandro Pazos, Mark A Musen
BACKGROUND: Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms...
June 7, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28587637/literature-evidence-in-open-targets-a-target-validation-platform
#7
Şenay Kafkas, Ian Dunham, Johanna McEntyre
BACKGROUND: We present the Europe PMC literature component of Open Targets - a target validation platform that integrates various evidence to aid drug target identification and validation. The component identifies target-disease associations in documents and ranks the documents based on their confidence from the Europe PMC literature database, by using rules utilising expert-provided heuristic information. The confidence score of a given document represents how valuable the document is in the scope of target validation for a given target-disease association by taking into account the credibility of the association based on the properties of the text...
June 6, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28583204/building-a-semantic-web-based-metadata-repository-for-facilitating-detailed-clinical-modeling-in-cancer-genome-studies
#8
Deepak K Sharma, Harold R Solbrig, Cui Tao, Chunhua Weng, Christopher G Chute, Guoqian Jiang
BACKGROUND: Detailed Clinical Models (DCMs) have been regarded as the basis for retaining computable meaning when data are exchanged between heterogeneous computer systems. To better support clinical cancer data capturing and reporting, there is an emerging need to develop informatics solutions for standards-based clinical models in cancer study domains. The objective of the study is to develop and evaluate a cancer genome study metadata management system that serves as a key infrastructure in supporting clinical information modeling in cancer genome study domains...
June 5, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28583177/dead-simple-owl-design-patterns
#9
David Osumi-Sutherland, Melanie Courtot, James P Balhoff, Christopher Mungall
BACKGROUND: Bio-ontologies typically require multiple axes of classification to support the needs of their users. Development of such ontologies can only be made scalable and sustainable by the use of inference to automate classification via consistent patterns of axiomatization. Many bio-ontologies originating in OBO or OWL follow this approach. These patterns need to be documented in a form that requires minimal expertise to understand and edit and that can be validated and applied using any of the various programmatic approaches to working with OWL ontologies...
June 5, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28438189/modulated-evaluation-metrics-for-drug-based-ontologies
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
(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
#17
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
#18
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
#19
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
#20
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
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