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Journal of Biomedical Semantics

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https://www.readbyqxmd.com/read/29132408/using-semantics-for-representing-experimental-protocols
#1
Olga Giraldo, Alexander García, Federico López, Oscar Corcho
BACKGROUND: An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory...
November 13, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29122012/drug-target-ontology-to-classify-and-integrate-drug-discovery-data
#2
Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J Yang, Cristian G Bologa, Tudor I Oprea, Stephan C Schürer
BACKGROUND: One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome...
November 9, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29122011/entity-recognition-in-the-biomedical-domain-using-a-hybrid-approach
#3
Marco Basaldella, Lenz Furrer, Carlo Tasso, Fabio Rinaldi
BACKGROUND: This article describes a high-recall, high-precision approach for the extraction of biomedical entities from scientific articles. METHOD: The approach uses a two-stage pipeline, combining a dictionary-based entity recognizer with a machine-learning classifier. First, the OGER entity recognizer, which has a bias towards high recall, annotates the terms that appear in selected domain ontologies. Subsequently, the Distiller framework uses this information as a feature for a machine learning algorithm to select the relevant entities only...
November 9, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28982381/querying-clinical-data-in-hl7-rim-based-relational-model-with-morph-rdb
#4
Freddy Priyatna, Raul Alonso-Calvo, Sergio Paraiso-Medina, Oscar Corcho
BACKGROUND: Semantic interoperability is essential when carrying out post-genomic clinical trials where several institutions collaborate, since researchers and developers need to have an integrated view and access to heterogeneous data sources. One possible approach to accommodate this need is to use RDB2RDF systems that provide RDF datasets as the unified view. These RDF datasets may be materialized and stored in a triple store, or transformed into RDF in real time, as virtual RDF data sources...
October 5, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28978337/towards-refactoring-the-molecular-function-ontology-with-a-uml-profile-for-function-modeling
#5
Patryk Burek, Frank Loebe, Heinrich Herre
BACKGROUND: Gene Ontology (GO) is the largest resource for cataloging gene products. This resource grows steadily and, naturally, this growth raises issues regarding the structure of the ontology. Moreover, modeling and refactoring large ontologies such as GO is generally far from being simple, as a whole as well as when focusing on certain aspects or fragments. It seems that human-friendly graphical modeling languages such as the Unified Modeling Language (UML) could be helpful in connection with these tasks...
October 4, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28969675/a-histological-ontology-of-the-human-cardiovascular-system
#6
Claudia Mazo, Liliana Salazar, Oscar Corcho, Maria Trujillo, Enrique Alegre
BACKGROUND: In this paper, we describe a histological ontology of the human cardiovascular system developed in collaboration among histology experts and computer scientists. RESULTS: The histological ontology is developed following an existing methodology using Conceptual Models (CMs) and validated using OOPS!, expert evaluation with CMs, and how accurately the ontology can answer the Competency Questions (CQ). It is publicly available at http://bioportal.bioontology...
October 2, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28962670/analysis-and-visualization-of-disease-courses-in-a-semantically-enabled-cancer-registry
#7
Angel Esteban-Gil, Jesualdo Tomás Fernández-Breis, Martin Boeker
BACKGROUND: Regional and epidemiological cancer registries are important for cancer research and the quality management of cancer treatment. Many technological solutions are available to collect and analyse data for cancer registries nowadays. However, the lack of a well-defined common semantic model is a problem when user-defined analyses and data linking to external resources are required. The objectives of this study are: (1) design of a semantic model for local cancer registries; (2) development of a semantically-enabled cancer registry based on this model; and (3) semantic exploitation of the cancer registry for analysing and visualising disease courses...
September 29, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28962645/simplifying-drug-package-leaflets-written-in-spanish-by-using-word-embedding
#8
Isabel Segura-Bedmar, Paloma Martínez
BACKGROUND: Drug Package Leaflets (DPLs) provide information for patients on how to safely use medicines. Pharmaceutical companies are responsible for producing these documents. However, several studies have shown that patients usually have problems in understanding sections describing posology (dosage quantity and prescription), contraindications and adverse drug reactions. An ultimate goal of this work is to provide an automatic approach that helps these companies to write drug package leaflets in an easy-to-understand language...
September 29, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28938912/semantic-annotation-in-biomedicine-the-current-landscape
#9
REVIEW
Jelena Jovanović, Ebrahim Bagheri
The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such texts. Annotation of biomedical documents with machine intelligible semantics facilitates advanced, semantics-based text management, curation, indexing, and search. This paper focuses on annotation of biomedical entity mentions with concepts from relevant biomedical knowledge bases such as UMLS. As a result, the meaning of those mentions is unambiguously and explicitly defined, and thus made readily available for automated processing...
September 22, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28938902/large-scale-online-semantic-indexing-of-biomedical-articles-via-an-ensemble-of-multi-label-classification-models
#10
Yannis Papanikolaou, Grigorios Tsoumakas, Manos Laliotis, Nikos Markantonatos, Ioannis Vlahavas
BACKGROUND: In this paper we present the approach that we employed to deal with large scale multi-label semantic indexing of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge (2013-2017), a challenge concerned with biomedical semantic indexing and question answering. METHODS: Our main contribution is a MUlti-Label Ensemble method (MULE) that incorporates a McNemar statistical significance test in order to validate the combination of the constituent machine learning algorithms...
September 22, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28931422/pibas-fedsparql-a-web-based-platform-for-integration-and-exploration-of-bioinformatics-datasets
#11
Marija Djokic-Petrovic, Vladimir Cvjetkovic, Jeremy Yang, Marko Zivanovic, David J Wild
BACKGROUND: There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semantic technologies offer the ability to create links and mappings across datasets and manage them as a single, linked network so that searching can be carried out across datasets, independently of the source. We have developed an application called PIBAS FedSPARQL that uses semantic technologies to allow researchers to carry out such searching across a vast array of data sources...
September 20, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28927463/towards-precision-medicine-discovering-novel-gynecological-cancer-biomarkers-and-pathways-using-linked-data
#12
Alokkumar Jha, Yasar Khan, Muntazir Mehdi, Md Rezaul Karim, Qaiser Mehmood, Achille Zappa, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
BACKGROUND: Next Generation Sequencing (NGS) is playing a key role in therapeutic decision making for the cancer prognosis and treatment. The NGS technologies are producing a massive amount of sequencing datasets. Often, these datasets are published from the isolated and different sequencing facilities. Consequently, the process of sharing and aggregating multisite sequencing datasets are thwarted by issues such as the need to discover relevant data from different sources, built scalable repositories, the automation of data linkage, the volume of the data, efficient querying mechanism, and information rich intuitive visualisation...
September 19, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28927443/towards-achieving-semantic-interoperability-of-clinical-study-data-with-fhir
#13
Hugo Leroux, Alejandro Metke-Jimenez, Michael J Lawley
BACKGROUND: Observational clinical studies play a pivotal role in advancing medical knowledge and patient healthcare. To lessen the prohibitive costs of conducting these studies and support evidence-based medicine, results emanating from these studies need to be shared and compared to one another. Current approaches for clinical study management have limitations that prohibit the effective sharing of clinical research data. METHODS: The objective of this paper is to present a proposal for a clinical study architecture to not only facilitate the communication of clinical study data but also its context so that the data that is being communicated can be unambiguously understood at the receiving end...
September 19, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28915930/predicting-activities-of-daily-living-for-cancer-patients-using-an-ontology-guided-machine-learning-methodology
#14
Hua Min, Hedyeh Mobahi, Katherine Irvin, Sanja Avramovic, Janusz Wojtusiak
BACKGROUND: Bio-ontologies are becoming increasingly important in knowledge representation and in the machine learning (ML) fields. This paper presents a ML approach that incorporates bio-ontologies and its application to the SEER-MHOS dataset to discover patterns of patient characteristics that impact the ability to perform activities of daily living (ADLs). Bio-ontologies are used to provide computable knowledge for ML methods to "understand" biomedical data. RESULTS: This retrospective study included 723 cancer patients from the SEER-MHOS dataset...
September 16, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28893314/design-of-an-extensive-information-representation-scheme-for-clinical-narratives
#15
Louise Deléger, Leonardo Campillos, Anne-Laure Ligozat, Aurélie Névéol
BACKGROUND: Knowledge representation frameworks are essential to the understanding of complex biomedical processes, and to the analysis of biomedical texts that describe them. Combined with natural language processing (NLP), they have the potential to contribute to retrospective studies by unlocking important phenotyping information contained in the narrative content of electronic health records (EHRs). This work aims to develop an extensive information representation scheme for clinical information contained in EHR narratives, and to support secondary use of EHR narrative data to answer clinical questions...
September 11, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28877732/ontology-based-specification-identification-and-analysis-of-perioperative-risks
#16
Alexandr Uciteli, Juliane Neumann, Kais Tahar, Kutaiba Saleh, Stephan Stucke, Sebastian Faulbrück-Röhr, André Kaeding, Martin Specht, Tobias Schmidt, Thomas Neumuth, Andreas Besting, Dominik Stegemann, Frank Portheine, Heinrich Herre
BACKGROUND: Medical personnel in hospitals often works under great physical and mental strain. In medical decision-making, errors can never be completely ruled out. Several studies have shown that between 50 and 60% of adverse events could have been avoided through better organization, more attention or more effective security procedures. Critical situations especially arise during interdisciplinary collaboration and the use of complex medical technology, for example during surgical interventions and in perioperative settings (the period of time before, during and after surgical intervention)...
September 6, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28870259/rdfio-extending-semantic-mediawiki-for-interoperable-biomedical-data-management
#17
Samuel Lampa, Egon Willighagen, Pekka Kohonen, Ali King, Denny Vrandečić, Roland Grafström, Ola Spjuth
BACKGROUND: Biological sciences are characterised not only by an increasing amount but also the extreme complexity of its data. This stresses the need for efficient ways of integrating these data in a coherent description of biological systems. In many cases, biological data needs organization before integration. This is not seldom a collaborative effort, and it is thus important that tools for data integration support a collaborative way of working. Wiki systems with support for structured semantic data authoring, such as Semantic MediaWiki, provide a powerful solution for collaborative editing of data combined with machine-readability, so that data can be handled in an automated fashion in any downstream analyses...
September 4, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28830518/discovering-associations-between-adverse-drug-events-using-pattern-structures-and-ontologies
#18
Gabin Personeni, Emmanuel Bresso, Marie-Dominique Devignes, Michel Dumontier, Malika Smaïl-Tabbone, Adrien Coulet
BACKGROUND: Patient data, such as electronic health records or adverse event reporting systems, constitute an essential resource for studying Adverse Drug Events (ADEs). We explore an original approach to identify frequently associated ADEs in subgroups of patients. RESULTS: Because ADEs have complex manifestations, we use formal concept analysis and its pattern structures, a mathematical framework that allows generalization using domain knowledge formalized in medical ontologies...
August 22, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28764813/an-ontology-driven-tool-for-structured-data-acquisition-using-web-forms
#19
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
#20
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
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