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Ontological knowledge

Cheleka A M Mpande, One B Dintwe, Munyaradzi Musvosvi, Simbarashe Mabwe, Nicole Bilek, Mark Hatherill, Elisa Nemes, Thomas J Scriba
Background: Maintenance of long-lasting immunity is thought to depend on stem cell memory T cells (TSCM ), which have superior self-renewing capacity, longevity and proliferative potential compared with central memory (TCM ) or effector (TEFF ) T cells. Our knowledge of TSCM derives primarily from studies of virus-specific CD8+ TSCM . We aimed to determine if infection with Mycobacterium tuberculosis ( M. tb ), the etiological agent of tuberculosis, generates antigen-specific CD4+ TSCM and to characterize their functional ontology...
2018: Frontiers in Immunology
Ellen V S Hessel, Yvonne C M Staal, Aldert H Piersma
Developmental neurotoxicity entails one of the most complex areas in toxicology. Animal studies provide only limited information as to human relevance. A multitude of alternative models have been developed over the years, providing insights into mechanisms of action. We give an overview of fundamental processes in neural tube formation, brain development and neural specification, aiming at illustrating complexity rather than comprehensiveness. We also give a flavor of the wealth of alternative methods in this area...
March 12, 2018: Toxicology and Applied Pharmacology
Mohammed Alsuhaibani, Danushka Bollegala, Takanori Maehara, Ken-Ichi Kawarabayashi
Methods for representing the meaning of words in vector spaces purely using the information distributed in text corpora have proved to be very valuable in various text mining and natural language processing (NLP) tasks. However, these methods still disregard the valuable semantic relational structure between words in co-occurring contexts. These beneficial semantic relational structures are contained in manually-created knowledge bases (KBs) such as ontologies and semantic lexicons, where the meanings of words are represented by defining the various relationships that exist among those words...
2018: PloS One
H-M Müller, K M Van Auken, Y Li, P W Sternberg
BACKGROUND: The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. RESULTS: We describe the next generation of the Textpresso information retrieval system, Textpresso Central (TPC). TPC builds on the strengths of the original system by expanding the full text corpus to include the PubMed Central Open Access Subset (PMC OA), as well as the WormBase C...
March 9, 2018: BMC Bioinformatics
Palle Duun Rohde, Solveig Østergaard, Torsten Nygaard Kristensen, Peter Sørensen, Volker Loeschcke, Trudy F C Mackay, Pernille Sarup
Understanding the genetic underpinnings of complex traits requires knowledge of the genetic variants that contribute to phenotypic variability. Reliable statistical approaches are needed to obtain such knowledge. In genome-wide association studies, variants are tested for association with trait variability to pinpoint loci that contribute to the quantitative trait. Because stringent genome-wide significance thresholds are applied to control the false positive rate, many true causal variants can remain undetected...
March 8, 2018: G3: Genes—Genomes—Genetics
Ricardo C Waldemarin, Cléver R G de Farias
A conceptual model abstractly defines a number of concepts and their relationships for the purposes of understanding and communication. Once a conceptual model is available, it can also be used as a starting point for the development of a software system. The development of conceptual models using the Unified Modeling Language (UML) facilitates the representation of modeled concepts and allows software developers to directly reuse these concepts in the design of a software system. The OBO Foundry represents the most relevant collaborative effort towards the development of ontologies in the biomedical domain...
February 26, 2018: Journal of Biomedical Informatics
Feixiang Xu, Xinhui Liu, Wei Chen, Chen Zhou, Bingwei Cao
This paper proposes an ontology-based fault diagnosis method which overcomes the difficulty of understanding complex fault diagnosis knowledge of loaders and offers a universal approach for fault diagnosis of all loaders. This method contains the following components: (1) An ontology-based fault diagnosis model is proposed to achieve the integrating, sharing and reusing of fault diagnosis knowledge for loaders; (2) combined with ontology, CBR (case-based reasoning) is introduced to realize effective and accurate fault diagnoses following four steps (feature selection, case-retrieval, case-matching and case-updating); and (3) in order to cover the shortages of the CBR method due to the lack of concerned cases, ontology based RBR (rule-based reasoning) is put forward through building SWRL (Semantic Web Rule Language) rules...
February 28, 2018: Sensors
Catherine Green
BACKGROUND: Today, when nurses are expected to manage large stores of data while providing precision care to individuals or groups of patients, it seems more important than ever that we understand the nature of nursing. Recently, there has been a renewed interest in examining what nursing is and how a clear understanding would impact nursing practice. OBJECTIVE: The goal of this article is to review an ontological account of nursing that seeks to understand the nature of nursing by showing the relation between the goal and structure of nursing care in association with the persons who are its recipients and practitioners...
March 2018: Nursing Research
Ilaria Cataldo, Atiqah Azhari, Gianluca Esposito
Oxytocin ( OXT ) and arginine-vasopressin ( AVP ) play a key regulatory part in social and affiliative behaviors; two aspects highly compromised in Autism Spectrum Disorder (ASD). Furthermore, variants in the adjacent oxytocin-vasopressin gene regions have been found to be associated with ASD diagnosis and endophenotypes. This review focuses mainly on common OXTr single nucleotide polymorphisms (SNPs), AVPR1a microsatellites and AVPR1b polymorphisms in relation to the development of autism. Although these genes did not surface in genome-wide association studies, evidence supports the hypothesis that these receptors and their polymorphisms are widely involved in the regulation of social behavior, and in modulating neural and physiological pathways contributing to the etiology of ASD...
2018: Frontiers in Molecular Neuroscience
Hongtao Liu, Li Jia, Wenfei Guo, Yingying Sun, Rining Zhu, Shuguang Li, Guanggang Qu, Hexiang Jiang, Junjie Wang, Jingmin Gu, Changjiang Sun, Xin Feng, Wenyu Han, Liancheng Lei
Streptococcus suis serotype 2 (SS2) is a zoonotic pathogen that can cause meningitis both in pigs and in human beings. However, the pathogenesis of central nervous system (CNS) infection caused by SS2 have not yet been elucidated. To find the key molecules in cerebrospinal fluid (CSF) needed for the pathogenesis, a SS2 meningoencephalitic pig model and a SS2 non-meningoencephalitic pig model were established in this study. CSF was collected from infected piglets, and protein profiling was performed with label-free proteomics technology...
2018: Frontiers in Cellular and Infection Microbiology
Antonio Cosma
Cell type classification and handling is a key issue for understanding biological systems. The advent of high multiplexing technologies increased the complexity of the classification process and new tools are needed to support the organization of this knowledge. I propose a classification based on both prime numbers and the fundamental theorem of arithmetic. As a not limiting example, I show the application of this method to unambiguously define any existing cell type using the CD nomenclature established by the Human Leukocyte Differentiation Antigens Workshops...
February 23, 2018: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
Chen Chu, Wu Chunshuai, Chen Jiajia, Zhang Jinlong, Xue Pengfei, Jiang Jiawei, Cui Zhiming
Circular RNAs are newly identified RNAs that regulate gene expression and execute various biological activities. Facet joint osteoarthritis (FJOA) is a severe facet joint cartilage degeneration disease that induces chronic low back pain to a larger population. The molecular mechanisms of FJOA, especially the presence and changes of circular RNAs in FJOA have not been investigated. In the current study, we analyzed RNA deep sequencing outcomes from healthy control group and FJOA group, identified and annotated circular RNAs, and determined the expressions of circular RNAs...
February 19, 2018: Biochemical and Biophysical Research Communications
Muhammad F Amith, Zhe He, Jiang Bian, Juan Antonio Lossio-Ventura, Cui Tao
With the proliferation of heterogeneous health care data in the last three decades, biomedical ontologies and controlled biomedical terminologies play a more and more important role in knowledge representation and management, data integration, natural language processing, as well as decision support for health information systems and biomedical research. Biomedical ontologies and controlled terminologies are intended to assure interoperability. Nevertheless, the quality of biomedical ontologies has hindered their applicability and subsequent adoption in real-world applications...
February 17, 2018: Journal of Biomedical Informatics
Jake R Saklatvala, Nick Dand, Michael A Simpson
The genetic diagnosis of rare monogenic diseases using exome/genome sequencing requires the true causal variant(s) to be identified from tens of thousands of observed variants. Typically a virtual gene panel approach is taken whereby only variants in genes known to cause phenotypes resembling the patient under investigation are considered. With the number of known monogenic gene-disease pairs exceeding 5000, manual curation of personalised virtual panels using exhaustive knowledge of the genetic basis of the human monogenic phenotypic spectrum is challenging...
February 20, 2018: Human Mutation
Jing Xia, Ling Kong, Li-Juan Zhou, Shui-Zhen Wu, Li-Jie Yao, Cheng He, Cynthia Y He, Hong-Juan Peng
Toxoplasma gondii rhoptry protein ROP18 ( Tg ROP18) is a key virulence factor secreted into the host cell during invasion, where it modulates the host cell response by interacting with its host targets. However, only a few Tg ROP18 targets have been identified. In this study, we applied a high-throughput protein-protein interaction (PPI) screening in human cells using bimolecular fluorescence complementation (BiFC) to identify the targets of Type I strain ROP18 (ROP18I ) and Type II strain ROP18 (ROP18II )...
2018: Frontiers in Immunology
Paul Denny, Marc Feuermann, David P Hill, Ruth C Lovering, Helene Plun-Favreau, Paola Roncaglia
Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular stresses and ridding cells of foreign material. Perturbations in autophagy have been implicated in a number of pathological conditions such as neurodegeneration, cardiac disease and cancer. The growing knowledge about autophagic mechanisms needs to be collected in a computable and shareable format to allow its use in data representation and interpretation...
February 17, 2018: Autophagy
Maureen E Pittman, Stephen W Edwards, Cataia Ives, Holly M Mortensen
The Adverse Outcome Pathway (AOP) framework describes the progression of a toxicity pathway from molecular perturbation to population-level outcome in a series of measurable, mechanistic responses. The controlled, computer-readable vocabulary that defines an AOP has the ability to, automatically and on a large scale, integrate AOP knowledge with publically available sources of biological high-throughput data and its derived associations. To support the discovery and development of putative (existing) and potential AOPs, we introduce the AOP-DB, an exploratory database resource that aggregates association relationships between genes and their related chemicals, diseases, pathways, species orthology information, ontologies, and gene interactions...
February 14, 2018: Toxicology and Applied Pharmacology
Mei-Hua Bao, Vivian Szeto, Burton B Yang, Shu-Zhen Zhu, Hong-Shuo Sun, Zhong-Ping Feng
Stroke is one of the leading causes of mortality and disability worldwide. Uncovering the cellular and molecular pathophysiological processes in stroke have been a top priority. Long non-coding (lnc) RNAs play critical roles in different kinds of diseases. In recent years, a bulk of aberrantly expressed lncRNAs have been screened out in ischemic stroke patients or ischemia insulted animals using new technologies such as RNA-seq, deep sequencing, and microarrays. Nine specific lncRNAs, antisense non-coding RNA in the INK4 locus (ANRIL), metastasis-associate lung adenocarcinoma transcript 1 (MALAT1), N1LR, maternally expressed gene 3 (MEG3), H19, CaMK2D-associated transcript 1 (C2dat1), Fos downstream transcript (FosDT), small nucleolar RNA host gene 14 (SNHG14), and taurine-upregulated gene 1 (TUG1), were found increased in cerebral ischemic animals and/or oxygen-glucose deprived (OGD) cells...
February 15, 2018: Cell Death & Disease
Ruth C Lovering, Paola Roncaglia, Douglas G Howe, Stanley J F Laulederkind, Varsha K Khodiyar, Tanya Z Berardini, Susan Tweedie, Rebecca E Foulger, David Osumi-Sutherland, Nancy H Campbell, Rachael P Huntley, Philippa J Talmud, Judith A Blake, Ross Breckenridge, Paul R Riley, Pier D Lambiase, Perry M Elliott, Lucie Clapp, Andrew Tinker, David P Hill
BACKGROUND: A systems biology approach to cardiac physiology requires a comprehensive representation of how coordinated processes operate in the heart, as well as the ability to interpret relevant transcriptomic and proteomic experiments. The Gene Ontology (GO) Consortium provides structured, controlled vocabularies of biological terms that can be used to summarize and analyze functional knowledge for gene products. METHODS AND RESULTS: In this study, we created a computational resource to facilitate genetic studies of cardiac physiology by integrating literature curation with attention to an improved and expanded ontological representation of heart processes in the Gene Ontology...
February 2018: Circ Genom Precis Med
Ying Shen, Kaiqi Yuan, Daoyuan Chen, Joël Colloc, Min Yang, Yaliang Li, Kai Lei
BACKGROUND: The available antibiotic decision-making systems were developed from a physician's perspective. However, because infectious diseases are common, many patients desire access to knowledge via a search engine. Although the use of antibiotics should, in principle, be subject to a doctor's advice, many patients take them without authorization, and some people cannot easily or rapidly consult a doctor. In such cases, a reliable antibiotic prescription support system is needed. METHODS AND RESULTS: This study describes the construction and optimization of the sensitivity and specificity of a decision support system named IDDAP, which is based on ontologies for infectious disease diagnosis and antibiotic therapy...
February 9, 2018: Artificial Intelligence in Medicine
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