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Ontological knowledge

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https://www.readbyqxmd.com/read/29352289/electroacupuncture-at-guanyuan-cv-4-zusanli-st-36-and-baihui-du-20-regulate-the-aging-related-changes-in-gene-expression-profile-of-the-hippocampus-in-sub-acutely-aging-rats
#1
Jianmin Liu, Jing Liu, Guang'an Wang, Guangya Liu, Huanjiao Zhou, Yun Fan, Fengxia Liang, Hua Wang
To investigate the molecular mechanisms of sub-acutely aging and demonstrate the effect of electroacupuncture (EA) at the Guanyuan (CV 4), Zusanli (ST 36) and Baihui (DU 20) acupoint on the sub-acutely aging brain, cDNA microarrays and bioinformatics analyses were carried out. Thirty Sprague-Dawley (SD) male rats were selected and randomly divided into three groups: the control group (C), the sub-acutely aging model group (M) and the electroacupuncture group (M+EA). Sub-acutely aging model rats were obtained by D-galactose s...
2018: PloS One
https://www.readbyqxmd.com/read/29347997/openbiodiv-o-ontology-of-the-openbiodiv-knowledge-management-system
#2
Viktor Senderov, Kiril Simov, Nico Franz, Pavel Stoev, Terry Catapano, Donat Agosti, Guido Sautter, Robert A Morris, Lyubomir Penev
BACKGROUND: The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowledge Management System. Our intent is to provide an ontology that fills the gaps between ontologies for biodiversity resources, such as DarwinCore-based ontologies, and semantic publishing ontologies, such as the SPAR Ontologies. We bridge this gap by providing an ontology focusing on biological taxonomy...
January 18, 2018: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29344252/itraq-based-quantitative-proteomic-analysis-and-bioinformatics-study-of-proteins-in-retinoblastoma
#3
Yong Cheng, Qingyu Meng, Lvzhen Huang, Xuan Shi, Jing Hou, Xiaoxin Li, Jianhong Liang
The aim of the present study was to analyze proteins in the aqueous humor (AH) of patients' retinoblastoma (RB), and investigate their potential role in RB using the comparative proteomic technique of isobaric tags for relative and absolute quantitation (iTRAQ) coupled with offline two-dimensional liquid chromatography-tandem mass spectrometry. A total of 0.1 ml AH was collected from 10 children with RB (mean age, 3.8 years; range, 2-5 years) and patients with senile cataracts (mean age, 70.4 years; range, 65-79 years), which was used as the control...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29335022/tackling-the-challenges-of-matching-biomedical-ontologies
#4
Daniel Faria, Catia Pesquita, Isabela Mott, Catarina Martins, Francisco M Couto, Isabel F Cruz
BACKGROUND: Biomedical ontologies pose several challenges to ontology matching due both to the complexity of the biomedical domain and to the characteristics of the ontologies themselves. The biomedical tracks in the Ontology Matching Evaluation Initiative (OAEI) have spurred the development of matching systems able to tackle these challenges, and benchmarked their general performance. In this study, we dissect the strategies employed by matching systems to tackle the challenges of matching biomedical ontologies and gauge the impact of the challenges themselves on matching performance, using the AgreementMakerLight (AML) system as the platform for this study...
January 15, 2018: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29332530/reconciliation-of-patient-doctor-vocabulary-in-a-structured-resource
#5
Mike Donald Tapi Nzali, Jérôme Aze, Sandra Bringay, Christian Lavergne, Caroline Mollevi, Thomas Optiz
Today, social media is increasingly used by patients to openly discuss their health. Mining automatically such data is a challenging task because of the non-structured nature of the text and the use of many abbreviations and the slang terms. Our goal is to use Patient Authored Text to build a French Consumer Health Vocabulary on breast cancer field, by collecting various kinds of non-experts' expressions that are related to their diseases and then compare them to biomedical terms used by health care professionals...
January 1, 2018: Health Informatics Journal
https://www.readbyqxmd.com/read/29330361/discovery-of-microrna-target-modules-of-african-rice-oryza-glaberrima-under-salinity-stress
#6
Tapan Kumar Mondal, Alok Kumar Panda, Hukam C Rawal, Tilak Raj Sharma
Oryza glaberrima is the second edible rice in the genus Oryza. It is grown in the African countries. miRNAs are regulatory molecules that are involved in every domains of gene expression including salinity stress response. Although several miRNAs have been reported from various species of Oryza, yet none of them are from this species. Salt treated (200 mM NaCl for 48 h) and control smallRNA libraries of RAM-100, a salt tolerant genotype, each with 2 replications generated 150 conserve and 348 novel miRNAs...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29329592/the-extensible-ontology-development-xod-principles-and-tool-implementation-to-support-ontology-interoperability
#7
REVIEW
Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A Overton, Edison Ong
Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles...
January 12, 2018: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29325989/proteomic-analysis-reveals-the-important-roles-of-alpha-5-collagen-and-atp5%C3%AE-during-skin-ulceration-syndrome-progression-of-sea-cucumber-apostichopus-japonicus
#8
Zelong Zhao, Jingwei Jiang, Yongjia Pan, Hongjuan Sun, Xiaoyan Guan, Shan Gao, Zhong Chen, Ying Dong, Zunchun Zhou
Apostichopus japonicus is one of the most important aquaculture species in China. Skin ulceration syndrome (SUS) of sea cucumber is a common and serious disease affected the development of A. japonicus culture industry. To better understand the response mechanisms of A. japonicus during SUS progression, the protein variations in the body wall of A. japonicus at different stages of SUS were investigated by a comparative proteomic approach based on isobaric tags for relative and absolute quantification. A total of 1449 proteins were identified from the samples at different SUS stages...
January 8, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29322916/cells-in-experimental-life-sciences-challenges-and-solution-to-the-rapid-evolution-of-knowledge
#9
EDITORIAL
Sirarat Sarntivijai, Alexander D Diehl, Yongqun He
Cell cultures used in biomedical experiments come in the form of both sample biopsy primary cells, and maintainable immortalised cell lineages. The rise of bioinformatics and high-throughput technologies has led us to the requirement of ontology representation of cell types and cell lines. The Cell Ontology (CL) and Cell Line Ontology (CLO) have long been established as reference ontologies in the OBO framework. We have compiled a series of the challenges and the proposals of solutions in this CELLS (Cells in ExperimentaL Life Sciences) thematic series that cover the grounds of standing issues and the directions, which were discussed in the First International Workshop on CELLS at the the International Conference on Biomedical Ontology (ICBO)...
December 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29322914/cell-ontology-in-an-age-of-data-driven-cell-classification
#10
David Osumi-Sutherland
BACKGROUND: Data-driven cell classification is becoming common and is now being implemented on a massive scale by projects such as the Human Cell Atlas. The scale of these efforts poses a challenge. How can the results be made searchable and accessible to biologists in general? How can they be related back to the rich classical knowledge of cell-types, anatomy and development? How will data from the various types of single cell analysis be made cross-searchable? Structured annotation with ontology terms provides a potential solution to these problems...
December 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29322912/usage-of-cell-nomenclature-in-biomedical-literature
#11
Şenay Kafkas, Sirarat Sarntivijai, Robert Hoehndorf
BACKGROUND: Cell lines and cell types are extensively studied in biomedical research yielding to a significant amount of publications each year. Identifying cell lines and cell types precisely in publications is crucial for science reproducibility and knowledge integration. There are efforts for standardisation of the cell nomenclature based on ontology development to support FAIR principles of the cell knowledge. However, it is important to analyse the usage of cell nomenclature in publications at a large scale for understanding the level of uptake of cell nomenclature in literature by scientists...
December 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29322305/construction-of-mammographic-examination-process-ontology-using-bottom-up-hierarchical-task-analysis
#12
Ayako Yagahara, Yuki Yokooka, Guoqian Jiang, Shintarou Tsuji, Akihisa Fukuda, Naoki Nishimoto, Kunio Kurowarabi, Katsuhiko Ogasawara
Describing complex mammography examination processes is important for improving the quality of mammograms. It is often difficult for experienced radiologic technologists to explain the process because their techniques depend on their experience and intuition. In our previous study, we analyzed the process using a new bottom-up hierarchical task analysis and identified key components of the process. Leveraging the results of the previous study, the purpose of this study was to construct a mammographic examination process ontology to formally describe the relationships between the process and image evaluation criteria to improve the quality of mammograms...
January 10, 2018: Radiological Physics and Technology
https://www.readbyqxmd.com/read/29316970/cuiless2016-a-clinical-corpus-applying-compositional-normalization-of-text-mentions
#13
John D Osborne, Matthew B Neu, Maria I Danila, Thamar Solorio, Steven J Bethard
BACKGROUND: Traditionally text mention normalization corpora have normalized concepts to single ontology identifiers ("pre-coordinated concepts"). Less frequently, normalization corpora have used concepts with multiple identifiers ("post-coordinated concepts") but the additional identifiers have been restricted to a defined set of relationships to the core concept. This approach limits the ability of the normalization process to express semantic meaning. We generated a freely available corpus using post-coordinated concepts without a defined set of relationships that we term "compositional concepts" to evaluate their use in clinical text...
January 10, 2018: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29302617/genetic-pathways-of-neuroregeneration-in-a-novel-mild-traumatic-brain-injury-model-in-adult-zebrafish
#14
Amanda L Maheras, Brian Dix, Olivia M S Carmo, Aleena E Young, Vanessa N Gill, Julia L Sun, Aleah R Booker, Helen A Thomason, Anastasia E Ibrahim, Lauren Stanislaw, Jennifer C Dallego, Cat N Ngo, Audrey Chen, Barbara K Fortini, Rory D Spence
Mild traumatic brain injuries (mTBIs) are one of the most prevalent neurological disorders, and humans are severely limited in their ability to repair and regenerate central nervous system (CNS) tissue postinjury. However, zebrafish (Danio rerio) maintain the remarkable ability to undergo complete and functional neuroregeneration as an adult. We wish to extend knowledge of the known mechanisms of neuroregeneration by analyzing the differentially expressed genes (DEGs) in a novel adult zebrafish model of mTBI...
January 2018: ENeuro
https://www.readbyqxmd.com/read/29299929/proteome-of-bovine-mitochondria-and-rod-outer-segment-disks-commonalities-and-differences
#15
Maurizio Bruschi, Andrea Petretto, Federico Caicci, Martina Bartolucci, Daniela Calzia, Laura Santucci, Lucia Manni, Luca A Ramenghi, Gian Marco Ghiggeri, Carlo E Traverso, Giovanni Candiano, Isabella Panfoli
The retinal rod outer segment (OS) is a stack of disks surrounded by the plasma membrane, housing proteins related to phototransduction, as well as mitochondrial proteins involved in oxidative phosphorylation (OxPhos). This prompted us to compare the proteome of bovine OS disks and mitochondria, to assess the significant top gene signatures of each sample. The two proteomes, obtained by LTQ-Orbitrap Velos mass spectrometry, were compared by statistical analyses. 4139 proteins were identified, 2045 of which overlapping in the two sets...
January 4, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29297309/identifying-term-relations-cross-different-gene-ontology-categories
#16
Jiajie Peng, Honggang Wang, Junya Lu, Weiwei Hui, Yadong Wang, Xuequn Shang
BACKGROUND: The Gene Ontology (GO) is a community-based bioinformatics resource that employs ontologies to represent biological knowledge and describes information about gene and gene product function. GO includes three independent categories: molecular function, biological process and cellular component. For better biological reasoning, identifying the biological relationships between terms in different categories are important. However, the existing measurements to calculate similarity between terms in different categories are either developed by using the GO data only or only take part of combined gene co-function network information...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29290766/integrated-analysis-of-long-non-coding-rna-and-mrna-expression-profile-in-pancreatic-cancer-derived-exosomes-treated-dendritic-cells-by-microarray-analysis
#17
Jionghuang Chen, Shaowen Wang, Shengnan Jia, Guoping Ding, Guixing Jiang, Liping Cao
Background: Pancreatic cancer is a devastating disease with a low five-year survival rate. Dendritic cells (DCs), which are the most potent antigen-presenting cells in the human body, play a pivotal role in the immune response. However, few studies have investigated the role of pancreatic cancer-derived exosomes (PEXs) in DC-meditated immune escape. The expression profiles of long noncoding RNAs (lncRNAs) and mRNAs of PEX-treated dendritic cells are unknown. Methods: We used integrated lncRNA and mRNA microarrays to determine the expression profiles of PEX-treated DCs and normal DCs derived from five healthy donors...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29284292/the-national-rare-diseases-registry-system-nrdrs-of-china-and-the-related-cohort-studies-vision-and-roadmap
#18
Shi Feng, Shuang Liu, Chong Zhu, Mengchun Gong, Yicheng Zhu, Shuyang Zhang
Rare diseases are major challenges in healthcare and medical research and have been involved in national development strategies in many countries. However, inadequate definition of rare diseases and lags in orphan drug development in China hinder rare diseases research. The first nationwide rare diseases registry system, National Rare Diseases Registry System of China (NRDRS) has been established and various cohort studies have been launched since 2016. More than 20 top academic institutions participate in this joint effort to carry out nationwide registration of rare diseases...
December 28, 2017: Human Gene Therapy
https://www.readbyqxmd.com/read/29283398/application-of-a-multimedia-service-and-resource-management-architecture-for-fault-diagnosis
#19
Alfonso Castro, Andrés A Sedano, Fco Javier García, Eduardo Villoslada, Víctor A Villagrá
Nowadays, the complexity of global video products has substantially increased. They are composed of several associated services whose functionalities need to adapt across heterogeneous networks with different technologies and administrative domains. Each of these domains has different operational procedures; therefore, the comprehensive management of multi-domain services presents serious challenges. This paper discusses an approach to service management linking fault diagnosis system and Business Processes for Telefónica's global video service...
December 28, 2017: Sensors
https://www.readbyqxmd.com/read/29277900/brain-maps-4-0-structure-of-the-rat-brain-an-open-access-atlas-with-global-nervous-system-nomenclature-ontology-and-flatmaps
#20
Larry W Swanson
The fourth edition (following editions in 1992, 1998, 2004) of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system. These tables constitute a global ontology for knowledge management systems dealing with neural circuitry...
December 26, 2017: Journal of Comparative Neurology
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