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Ontological knowledge

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The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools...
November 29, 2016: Nucleic Acids Research
Ling Zhou, Longhai Luo, Jian-Fang Zuo, Linfeng Yang, Li Zhang, Xuanmin Guang, Yuan Niu, Jianbo Jian, Qing-Chun Geng, Liping Liang, Qijian Song, Jim M Dunwell, Zhenzhen Wu, Jia Wen, Yu-Qin Liu, Yuan-Ming Zhang
Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses...
July 2016: Plant Genome
Lei Cui, Hongtao Hu, Wei Wei, Weimin Wang, Hong Liu
MicroRNAs (miRNAs) are small RNA molecules that play key roles in regulation of various biological processes. In order to better understand the biological significance of miRNAs in the context of Aeromonas hydrophila infection in Megalobrama amblycephala, small RNA libraries obtained from fish liver at 0 (non-infection), 4, and 24 h post infection (poi) were sequenced using Illumina deep sequencing technology. A total of 11,244,207, 9,212,958, and 7,939,157 clean reads were obtained from these three RNA libraries, respectively...
November 25, 2016: International Journal of Molecular Sciences
Frank Kramer, Tim Beißbarth
Ontologies are powerful and popular tools to encode data in a structured format and manage knowledge. A large variety of existing ontologies offer users access to biomedical knowledge. This chapter contains a short theoretical background of ontologies and introduces two notable examples: The Gene Ontology and the ontology for Biological Pathways Exchange. For both ontologies a short overview and working bioinformatic applications, i.e., Gene Ontology enrichment analyses and pathway data visualization, are provided...
2017: Methods in Molecular Biology
Sophie Hill
BACKGROUND: Curriculum documents identify key concepts within learning prosthetics. Threshold concepts provide an alternative way of viewing the curriculum, focussing on the ways of thinking and practicing within prosthetics. Threshold concepts can be described as an opening to a different way of viewing a concept. This article forms part of a larger study exploring what students and staff experience as difficult in learning about prosthetics. OBJECTIVES: To explore possible threshold concepts within prosthetics...
November 24, 2016: Prosthetics and Orthotics International
Golnaz Bahramali, Bahram Goliaei, Zarrin Minuchehr, Sayed-Amir Marashi
Chameleon proteins are proteins which include sequences that can adopt α-helix-β-strand (HE-chameleon) or α-helix-coil (HC-chameleon) or β-strand-coil (CE-chameleon) structures to operate their crucial biological functions. In this study, using a network-based approach, we examined the chameleon proteins to give a better knowledge on these proteins. We focused on proteins with identical chameleon sequences with more than or equal to seven residues long in different PDB entries, which adopt HE-chameleon, HC-chameleon, and CE-chameleon structures in the same protein...
November 24, 2016: Amino Acids
Irina Matetovici, Guy Caljon, Jan Van Den Abbeele
BACKGROUND: For their transmission, African trypanosomes rely on their blood feeding insect vector, the tsetse fly (Glossina sp.). The ingested Trypanosoma brucei parasites have to overcome a series of barriers in the tsetse fly alimentary tract to finally develop into the infective metacyclic forms in the salivary glands that are transmitted to a mammalian host by the tsetse bite. The parasite population in the salivary gland is dense with a significant number of trypanosomes tightly attached to the epithelial cells...
November 25, 2016: BMC Genomics
Yong Zeng, Fei-Yan Deng, Wei Zhu, Lan Zhang, Hao He, Chao Xu, Qing Tian, Ji-Gang Zhang, Li-Shu Zhang, Hong-Gang Hu, Hong-Wen Deng
Human monocyte is an important cell type which is involved in various complex human diseases. To better understand the biology of human monocytes and facilitate further studies, we developed the first comprehensive proteome knowledge base specifically for human monocytes by integrating both in vivo and in vitro datasets. The top 2000 expressed genes from in vitro datasets and 779 genes from in vivo experiments were integrated into this study. Altogether, a total of 2237 unique monocyte-expressed genes were cataloged...
November 22, 2016: Protein & Cell
Liqin Wang, Guilherme Del Fiol, Bruce E Bray, Peter J Haug
OBJECTIVE: Healthcare communities have identified a significant need for disease-specific information. Disease-specific ontologies are useful in assisting the retrieval of disease-relevant information from various sources. However, building these ontologies is labor intensive. Our goal is to develop a system for an automated generation of disease-pertinent concepts from a popular knowledge resource for the building of disease-specific ontologies. METHODS: A pipeline system was developed with an initial focus of generating disease-specific treatment vocabularies...
November 16, 2016: Journal of Biomedical Informatics
Antonio Aledo-Tur, J Andrés Domínguez-Gómez
The literature specialized in Social Impact Assessment (SIA) concurs that there is still much work to do in the discussion and thorough grounding of its theories and conceptual bases. The authors of this paper consider that the understanding of SIA as a paradigm may prove useful as a foundation on which more robust and better grounded SIA knowledge production may be built. Further, we suggest that the application of the concept of the paradigm in the terms expressed here may offer a comprehensive guide to practice in SIA studies...
November 8, 2016: Journal of Environmental Management
L F Soualmia, J Charlet
OBJECTIVES: To summarize excellent current research in the field of Knowledge Representation and Management (KRM) within the health and medical care domain. METHOD: We provide a synopsis of the 2016 IMIA selected articles as well as a related synthetic overview of the current and future field activities. A first step of the selection was performed through MEDLINE querying with a list of MeSH descriptors completed by a list of terms adapted to the KRM section. The second step of the selection was completed by the two section editors who separately evaluated the set of 1,432 articles...
November 10, 2016: Yearbook of Medical Informatics
M Barros, F M Couto
INTRODUCTION: Biomedical research is increasingly becoming a data-intensive science in several areas, where prodigious amounts of data is being generated that has to be stored, integrated, shared and analyzed. In an effort to improve the accessibility of data and knowledge, the Linked Data initiative proposed a well-defined set of recommendations for exposing, sharing and integrating data, information and knowledge, using semantic web technologies. OBJECTIVE: The main goal of this paper is to identify the current status and future trends of knowledge representation and management in Life and Health Sciences, mostly with regard to linked data technologies...
November 10, 2016: Yearbook of Medical Informatics
Suyu Mei, Kun Zhang
Protein-protein interaction (PPI) networks are naturally viewed as infrastructure to infer signalling pathways. The descriptors of signal events between two interacting proteins such as upstream/downstream signal flow, activation/inhibition relationship and protein modification are indispensable for inferring signalling pathways from PPI networks. However, such descriptors are not available in most cases as most PPI networks are seldom semantically annotated. In this work, we extend ℓ2-regularized logistic regression to the scenario of multi-label learning for predicting the activation/inhibition relationships in human PPI networks...
November 7, 2016: Scientific Reports
Luis Isaí Gonzalez Echeverria, Angélica Aguirre Pizarro, Romina Kraunik Ramirez, Rebeca Palacios Pinto, Paula Sepúlveda Barra, María-Eugenia Rapiman
INTRODUCTION: Little research has been done on elderly adults from an optimistic perspective. What is it like to be a happy elderly person who is moving toward death? How can we approach their health promotion? This study aimed at exploring ways of being happy in older adults in Chile. METHODS: We used a phenomenological approach, using Martin Heidegger’s philosophical frame. Participants were chosen after applying the Lyubomirski scale – those who fell into the “happy” category were invited to a semi-structured interview...
October 12, 2016: Medwave
Suzanna E Lewis
The overarching goal of the Gene Ontology (GO) Consortium is to provide researchers in biology and biomedicine with all current functional information concerning genes and the cellular context under which these occur. When the GO was started in the 1990s surprisingly little attention had been given to how functional information about genes was to be uniformly captured, structured in a computable form, and made accessible to biologists. Because knowledge of gene, protein, ncRNA, and molecular complex roles is continuously accumulating and changing, the GO needed to be a dynamic resource, accurately tracking ongoing research results over time...
2017: Methods in Molecular Biology
Spiros C Denaxas
Electronic Health Records (EHR) are inherently complex and diverse and cannot be readily integrated and analyzed. Analogous to the Gene Ontology, controlled clinical terminologies were created to facilitate the standardization and integration of medical concepts and knowledge and enable their subsequent use for translational research, official statistics and medical billing. This chapter will introduce several of the main controlled clinical terminologies used to record diagnoses, surgical procedures, laboratory results and medications...
2017: Methods in Molecular Biology
Rachael P Huntley, Ruth C Lovering
The specificity of knowledge that Gene Ontology (GO) annotations currently can represent is still restricted by the legacy format of the GO annotation file, a format intentionally designed for simplicity to keep the barriers to entry low and thus encourage initial adoption. Historically, the information that could be captured in a GO annotation was simply the role or location of a gene product, although genetically interacting or binding partners could be specified. While there was no mechanism within the original GO annotation format for capturing additional information about the context of a GO term, such as the target gene of an activity or the location of a molecular function, the long-term vision for the GO Consortium was to provide greater expressivity in its annotations to capture physiologically relevant information...
2017: Methods in Molecular Biology
Sebastian Bauer
Gene-category analysis is one important knowledge integration approach in biomedical sciences that combines knowledge bases such as Gene Ontology with lists of genes or their products, which are often the result of high-throughput experiments, gained from either wet-lab or synthetic experiments. In this chapter, we will motivate this class of analyses and describe an often used variant that is based on Fisher's exact test. We show that this approach has some problems in the context of Gene Ontology of which users should be aware...
2017: Methods in Molecular Biology
Sylvain Poux, Pascale Gaudet
The Gene Ontology (GO) is a framework designed to represent biological knowledge about gene products' biological roles and the cellular location in which they act. Biocuration is a complex process: the body of scientific literature is large and selection of appropriate GO terms can be challenging. Both these issues are compounded by the fact that our understanding of biology is still incomplete; hence it is important to appreciate that GO is inherently an evolving model. In this chapter, we describe how biocurators create GO annotations from experimental findings from research articles...
2017: Methods in Molecular Biology
Chunjiang Yu, Bairong Shen
The development of information technology has resulted in its penetration into every area of clinical research. Various clinical systems have been developed, which produce increasing volumes of clinical data. However, saving, exchanging, querying, and exploiting these data are challenging issues. The development of Extensible Markup Language (XML) has allowed the generation of flexible information formats to facilitate the electronic sharing of structured data via networks, and it has been used widely for clinical data processing...
2016: Advances in Experimental Medicine and Biology
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