journal
MENU ▼
Read by QxMD icon Read
search

Journal of Biomedical Semantics

journal
https://www.readbyqxmd.com/read/28938912/semantic-annotation-in-biomedicine-the-current-landscape
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
journal
journal
43046
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"