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Ontological knowledge

Flavio E Spetale, Debora Arce, Flavia Krsticevic, Pilar Bulacio, Elizabeth Tapia
The GO-Cellular Component (GO-CC) ontology provides a controlled vocabulary for the consistent description of the subcellular compartments or macromolecular complexes where proteins may act. Current machine learning-based methods used for the automated GO-CC annotation of proteins suffer from the inconsistency of individual GO-CC term predictions. Here, we present FGGA-CC+ , a class of hierarchical graph-based classifiers for the consistent GO-CC annotation of protein coding genes at the subcellular compartment or macromolecular complex levels...
May 17, 2018: Scientific Reports
Youngmin Park, Sangwoo Kang, Jungyun Seo
In recent times, with the increasing interest in conversational agents for smart homes, task-oriented dialog systems are being actively researched. However, most of these studies are focused on the individual modules of such a system, and there is an evident lack of research on a dialog framework that can integrate and manage the entire dialog system. Therefore, in this study, we propose a framework that enables the user to effectively develop an intelligent dialog system. The proposed framework ontologically expresses the knowledge required for the task-oriented dialog system's process and can build a dialog system by editing the dialog knowledge...
May 16, 2018: Sensors
Anil Pacaci, Suat Gonul, A Anil Sinaci, Mustafa Yuksel, Gokce B Laleci Erturkmen
Background: Utilization of the available observational healthcare datasets is key to complement and strengthen the postmarketing safety studies. Use of common data models (CDM) is the predominant approach in order to enable large scale systematic analyses on disparate data models and vocabularies. Current CDM transformation practices depend on proprietarily developed Extract-Transform-Load (ETL) procedures, which require knowledge both on the semantics and technical characteristics of the source datasets and target CDM...
2018: Frontiers in Pharmacology
Stefan Kropf, Alexandr Uciteli, Katrin Schierle, Peter Krücken, Kerstin Denecke, Heinrich Herre
BACKGROUND: Legacy data and new structured data can be stored in a standardized format as XML-based EHRs on XML databases. Querying documents on these databases is crucial for answering research questions. Instead of using free text searches, that lead to false positive results, the precision can be increased by constraining the search to certain parts of documents. METHODS: A search ontology-based specification of queries on XML documents defines search concepts and relates them to parts in the XML document structure...
May 11, 2018: Journal of Biomedical Semantics
Xin Qian, Zhiming Zhao, Wei Shang, Zhihan Xu, Beibei Zhang, Hui Cai
Rheumatoid arthritis (RA) is an autoimmune disease, which is characterized by inflammatory synovitis, and the subsequent destruction of articular cartilage and bone. Sinomenine is a traditional Chinese medicine, which has been employed as a clinical treatment for RA for several years in China. The present study investigated the anti‑arthritic effects of sinomenine on Sprague‑Dawley rats with collagen‑induced arthritis (CIA). The differentially expressed proteins in serum were measured by proteomic analysis in order to generate a differentially expressed protein network...
May 3, 2018: Molecular Medicine Reports
John Judkins, Jessica Tay-Sontheimer, Richard D Boyce, Mathias Brochhausen
BACKGROUND: Prompted by the frequency of concomitant use of prescription drugs with natural products, and the lack of knowledge regarding the impact of pharmacokinetic-based natural product-drug interactions (PK-NPDIs), the United States National Center for Complementary and Integrative Health has established a center of excellence for PK-NPDI. The Center is creating a public database to help researchers (primarly pharmacologists and medicinal chemists) to share and access data, results, and methods from PK-NPDI studies...
May 9, 2018: Journal of Biomedical Semantics
David Anton, Idoia Berges, Jesús Bermúdez, Alfredo Goñi, Arantza Illarramendi
Telerehabilitation systems that support physical therapy sessions anywhere can help save healthcare costs while also improving the quality of life of the users that need rehabilitation. The main contribution of this paper is to present, as a whole, all the features supported by the innovative Kinect-based Telerehabilitation System (KiReS). In addition to the functionalities provided by current systems, it handles two new ones that could be incorporated into them, in order to give a step forward towards a new generation of telerehabilitation systems...
May 8, 2018: Sensors
Lars Marcus
The world is witnessing unprecedented urbanization, bringing extreme challenges to contemporary practices in urban planning and design. This calls for improved urban models that can generate new knowledge and enhance practical skill. Importantly, any urban model embodies a conception of the relation between humans and the physical environment. In urban modeling this is typically conceived of as a relation between human subjects and an environmental object, thereby reproducing a humans-environment dichotomy...
2018: Frontiers in Psychology
Paolo Uva, Paolo Cossu-Rocca, Federica Loi, Giovanna Pira, Luciano Murgia, Sandra Orrù, Matteo Floris, Maria Rosaria Muroni, Francesca Sanges, Ciriaco Carru, Andrea Angius, Maria Rosaria De Miglio
The clinical and genetic heterogeneity of Triple Negative Breast Cancer (TNBC) and the lack of unambiguous molecular targets contribute to the inadequacy of current therapeutic options for these variants. MicroRNAs (miRNA) are a class of small highly conserved regulatory endogenous non-coding RNA, which can alter the expression of genes encoding proteins and may play a role in the dysregulation of cellular pathways. Our goal was to improve the knowledge of the molecular pathogenesis of TNBC subgroups analyzing the miRNA expression profile, and to identify new prognostic and predictive biomarkers...
2018: International Journal of Medical Sciences
Yang Yang, Xiaofeng Fu, Wenhao Qu, Yiqun Xiao, Hong-Bin Shen
Motivation: Benefiting from high-throughput experimental technologies, whole-genome analysis of microRNAs (miRNAs) has been more and more common to uncover important regulatory roles of miRNAs and identify miRNA biomarkers for disease diagnosis. As a complementary information to the high-throughput experimental data, domain knowledge like the Gene Ontology and KEGG pathway is usually used to guide gene function analysis. However, functional annotation for miRNAs is scarce in the public databases...
April 27, 2018: Bioinformatics
Ken McGarry, Sharon McDonald
In this work we use complex network theory to provide a statistical model of the connectivity patterns of human proteins and their interaction partners. Our intention is to identify important proteins that may be predisposed to be potential candidates as drug targets for therapeutic interventions. Target proteins usually have more interaction partners than non-target proteins, but there are no hard-and-fast rules for defining the actual number of interactions. We devise a statistical measure for identifying hub proteins, we score our target proteins with gene ontology annotations...
April 26, 2018: Computers in Biology and Medicine
Karen R Christie, Judith A Blake
Background: Cilia are specialized, hair-like structures that project from the cell bodies of eukaryotic cells. With increased understanding of the distribution and functions of various types of cilia, interest in these organelles is accelerating. To effectively use this great expansion in knowledge, this information must be made digitally accessible and available for large-scale analytical and computational investigation. Capture and integration of knowledge about cilia into existing knowledge bases, thus providing the ability to improve comparative genomic data analysis, is the objective of this work...
2018: Cilia
Liang-Chin Huang, Karen E Ross, Timothy R Baffi, Harold Drabkin, Krzysztof J Kochut, Zheng Ruan, Peter D'Eustachio, Daniel McSkimming, Cecilia Arighi, Chuming Chen, Darren A Natale, Cynthia Smith, Pascale Gaudet, Alexandra C Newton, Cathy Wu, Natarajan Kannan
Many bioinformatics resources with unique perspectives on the protein landscape are currently available. However, generating new knowledge from these resources requires interoperable workflows that support cross-resource queries. In this study, we employ federated queries linking information from the Protein Kinase Ontology, iPTMnet, Protein Ontology, neXtProt, and the Mouse Genome Informatics to identify key knowledge gaps in the functional coverage of the human kinome and prioritize understudied kinases, cancer variants and post-translational modifications (PTMs) for functional studies...
April 25, 2018: Scientific Reports
Vibeke Bruun Lorentsen, Dagfinn Nåden, Berit Sæteren
BACKGROUND: People with progressive cancer experience that their bodies change due to disease and/or treatment. The body is integral to the unity of the human being, a unity that must be perceived as whole if dignity shall be experienced. Relatives are in touch with the suffering bodies of their dear ones, physically, socially, mentally, and existentially, and thus the relatives' experiences of the bodies of their dear ones might yield insight into the concept of dignity. AIM: The aim of this study is to explore relatives' experiences of the patients' bodily changes from a perspective of dignity...
January 1, 2018: Nursing Ethics
Bi Yao Mo, Xing Hua Guo, Meng Ru Yang, Fang Liu, Xuan Bi, Yan Liu, Lin Kai Fang, Xi Qing Luo, Julie Wang, Joseph A Bellanti, Yun Feng Pan, Song Guo Zheng
Rapidly accumulating evidence has now suggested that the long non-coding RNAs (LncRNAs), a large and diverse class of non-coding transcribed RNA molecules with diverse functional roles and mechanisms, play a major role in the pathogenesis of many human inflammatory diseases. Although some LncRNAs are overexpressed in plasma, T cell, and synovial tissues of patients with rheumatoid arthritis (RA), there is a dearth of knowledge in what role these transcripts play in fibroblast-like synoviocytes (FLSs) of these patients...
2018: Frontiers in Immunology
Kleanthi Lakiotaki, Nikolaos Vorniotakis, Michail Tsagris, Georgios Georgakopoulos, Ioannis Tsamardinos
Biotechnology revolution generates a plethora of omics data with an exponential growth pace. Therefore, biological data mining demands automatic, 'high quality' curation efforts to organize biomedical knowledge into online databases. BioDataome is a database of uniformly preprocessed and disease-annotated omics data with the aim to promote and accelerate the reuse of public data. We followed the same preprocessing pipeline for each biological mart (microarray gene expression, RNA-Seq gene expression and DNA methylation) to produce ready for downstream analysis datasets and automatically annotated them with disease-ontology terms...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Randi Vita, James A Overton, Christopher J Mungall, Alessandro Sette, Bjoern Peters
The Immune Epitope Database (IEDB), at, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Violeta García-Hernández, Carmen Sánchez-Bernal, Domitille Schvartz, José J Calvo, Jean-Charles Sanchez, Jesús Sánchez-Yagüe
Changes in the protein expression occurring within the initiation phase of acute pancreatitis (AP) might be vital in the development of this complex disease. However, the exact mechanisms involved in the onset of AP remains elusive and most of our knowledge about the pathobiology of AP comes from animal models. We performed in a rat pancreatitic model a high-throughput shotgun proteomic profiling of the soluble and whole membrane fractions from the pancreas during the early phase of cerulein (Cer)-induced AP...
April 17, 2018: Journal of Proteomics
Jacques Bouaud, Gilles Guézennec, Brigitte Séroussi
The integration of clinical information models and termino-ontological models into a unique ontological framework is highly desirable for it facilitates data integration and management using the same formal mechanisms for both data concepts and information model components. This is particularly true for knowledge-based decision support tools that aim to take advantage of all facets of semantic web technologies in merging ontological reasoning, concept classification, and rule-based inferences. We present an ontology template that combines generic data model components with (parts of) existing termino-ontological resources...
2018: Studies in Health Technology and Informatics
Retno Vinarti, Lucy Hederman
We present a knowledge-base to represent collated infectious disease risk (IDR) knowledge. The knowledge is about personal and contextual risk of contracting an infectious disease obtained from declarative sources (e.g. Atlas of Human Infectious Diseases). Automated prediction requires encoding this knowledge in a form that can produce risk probabilities (e.g. Bayesian Network - BN). The knowledge-base presented in this paper feeds an algorithm that can auto-generate the BN. The knowledge from 234 infectious diseases was compiled...
2018: Studies in Health Technology and Informatics
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