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Ontological knowledge

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https://www.readbyqxmd.com/read/28929028/fish-ontology-framework-for-taxonomy-based-fish-recognition
#1
Najib M Ali, Haris A Khan, Amy Y-Hui Then, Chong Ving Ching, Manas Gaur, Sarinder Kaur Dhillon
Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval...
2017: PeerJ
https://www.readbyqxmd.com/read/28923703/transcriptome-analysis-of-three-critical-periods-of-ovarian-development-in-yellow-river-carp-cyprinus-carpio
#2
Yongfang Jia, Ping Nan, Wanwan Zhang, Fang Wang, Ruihua Zhang, Tingting Liang, Xiaolin Ji, Qiyan Du, Zhongjie Chang
Ovary development is a complex process involving numerous genes; the molecular mechanism underlying the ovary development of carp is still unknown. Here we used Illumina HiSeq™ 2500 to explore the transcriptome of undifferentiated gland (PG), juvenile ovary (OJ) and adult ovary (OA) of Yellow River carp (Cyprinus carpio). A total of 58,749 unigenes were obtained, comprising 45,707 known genes and 13,042 new genes. We identified differentially-expressed genes (DEGs) during development and characterized the functional properties of DEGs by comparison with the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes databases...
September 9, 2017: Theriogenology
https://www.readbyqxmd.com/read/28916330/brains-language-and-the-argumentative-mind-in-western-and-eastern-societies-the-fertile-differences-between-western-eastern-argumentative-traditions
#3
REVIEW
Jordi Vallverdú
The philosophical differences between Western and Eastern philosophy not only derive from general cultural ideas about reality, but as Nisbet writes (2003), are also methodological, ontological, and cognitively driven. Thus, we can see that strategies of thought and theory-generation are constrained and enabled by conceptual levels, and that the existence of differences and within these levels may be pragmatically combined in fruitful ways. At this point, I remark that there is not a single way to connect biology and culture, but at least we need to admit that brains allow the existence of minds and that these create languages, which also organize the world symbolically following a long set of (sometimes interconnected) heuristics...
September 12, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28915930/predicting-activities-of-daily-living-for-cancer-patients-using-an-ontology-guided-machine-learning-methodology
#4
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/28887142/marriages-of-mathematics-and-physics-a-challenge-for-biology
#5
REVIEW
Arezoo Islami, Giuseppe Longo
The human attempts to access, measure and organize physical phenomena have led to a manifold construction of mathematical and physical spaces. We will survey the evolution of geometries from Euclid to the Algebraic Geometry of the 20th century. The role of Persian/Arabic Algebra in this transition and its Western symbolic development is emphasized. In this relation, we will also discuss changes in the ontological attitudes toward mathematics and its applications. Historically, the encounter of geometric and algebraic perspectives enriched the mathematical practices and their foundations...
September 5, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28885592/a-tailored-ontology-supporting-sensor-implementation-for-the-maintenance-of-industrial-machines
#6
Elaheh Maleki, Farouk Belkadi, Mathieu Ritou, Alain Bernard
The longtime productivity of an industrial machine is improved by condition-based maintenance strategies. To do this, the integration of sensors and other cyber-physical devices is necessary in order to capture and analyze a machine's condition through its lifespan. Thus, choosing the best sensor is a critical step to ensure the efficiency of the maintenance process. Indeed, considering the variety of sensors, and their features and performance, a formal classification of a sensor's domain knowledge is crucial...
September 8, 2017: Sensors
https://www.readbyqxmd.com/read/28883194/light-weighted-automatic-import-of-standardized-ontologies-into-the-content-management-system-drupal
#7
Christoph Beger, Alexandr Uciteli, Heinrich Herre
The amount of ontologies, which are utilizable for widespread domains, is growing steadily. BioPortal alone, embraces over 500 published ontologies with nearly 8 million classes. In contrast, the vast informative content of these ontologies is only directly intelligible by experts. To overcome this deficiency it could be possible to represent ontologies as web portals, which does not require knowledge about ontologies and their semantics, but still carries as much information as possible to the end-user. Furthermore, the conception of a complex web portal is a sophisticated process...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28883193/expert2owl-a-methodology-for-pattern-based-ontology-development
#8
Kais Tahar, Jie Xu, Heinrich Herre
The formalization of expert knowledge enables a broad spectrum of applications employing ontologies as underlying technology. These include eLearning, Semantic Web and expert systems. However, the manual construction of such ontologies is time-consuming and thus expensive. Moreover, experts are often unfamiliar with the syntax and semantics of formal ontology languages such as OWL and usually have no experience in developing formal ontologies. To overcome these barriers, we developed a new method and tool, called Expert2OWL that provides efficient features to support the construction of OWL ontologies using GFO (General Formal Ontology) as a top-level ontology...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28881973/biosses-a-semantic-sentence-similarity-estimation-system-for-the-biomedical-domain
#9
Gizem Sogancioglu, Hakime Öztürk, Arzucan Özgür
Motivation: The amount of information available in textual format is rapidly increasing in the biomedical domain. Therefore, natural language processing (NLP) applications are becoming increasingly important to facilitate the retrieval and analysis of these data. Computing the semantic similarity between sentences is an important component in many NLP tasks including text retrieval and summarization. A number of approaches have been proposed for semantic sentence similarity estimation for generic English...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28881636/the-landscape-of-dna-methylation-mediated-regulation-of-long-non-coding-rnas-in-breast-cancer
#10
Chunlong Zhang, Xinyu Wang, Xuecang Li, Ning Zhao, Yihan Wang, Xiaole Han, Ce Ci, Jian Zhang, Meng Li, Yan Zhang
Although systematic studies have identified a host of long non-coding RNAs (lncRNAs) which are involved in breast cancer, the knowledge about the methyla-tion-mediated dysregulation of those lncRNAs remains limited. Here, we integrated multi-omics data to analyze the methylated alteration of lncRNAs in breast invasive carcinoma (BRCA). We found that lncRNAs showed diverse methylation patterns on promoter regions in BRCA. LncRNAs were divided into two categories and four subcategories based on their promoter methylation patterns and expression levels be-tween tumor and normal samples...
August 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28870170/analysis-of-the-genome-sequence-of-phomopsis-longicolla-a-fungal-pathogen-causing-phomopsis-seed-decay-in-soybean
#11
Shuxian Li, Omar Darwish, Nadim W Alkharouf, Bryan Musungu, Benjamin F Matthews
BACKGROUND: Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is a seed-borne fungus causing Phomopsis seed decay in soybean. This disease is one of the most devastating diseases reducing soybean seed quality worldwide. To facilitate investigation of the genomic basis of pathogenicity and to understand the mechanism of the disease development, the genome of an isolate, MSPL10-6, from Mississippi, USA was sequenced, de novo assembled, and analyzed. RESULTS: The genome of MSPL 10-6 was estimated to be approximately 62 Mb in size with an overall G + C content of 48...
September 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28854641/conserved-transcription-factors-steer-growth-related-genomic-programs-in-daphnia
#12
Katina I Spanier, Mieke Jansen, Ellen Decaestecker, Gert Hulselmans, Dörthe Becker, John K Colbourne, Luisa Orsini, Luc De Meester, Stein Aerts
Ecological genomics aims to understand the functional association between environmental gradients and the genes underlying adaptive traits. Many genes that are identified by genome-wide screening in ecologically relevant species lack functional annotations. Although gene functions can be inferred from sequence homology, such approaches have limited power. Here, we introduce ecological regulatory genomics by presenting an ontology-free gene prioritization method. Specifically, our method combines transcriptome profiling with high-throughput cis-regulatory sequence analysis in the water fleas Daphnia pulex and Daphnia magna...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28843533/the-molecular-mechanism-and-post-transcriptional-regulation-characteristic-of-tetragenococcus-halophilus-acclimation-to-osmotic-stress-revealed-by-quantitative-proteomics
#13
Jieting Lin, Hebin Liang, Junwei Yan, Lixin Luo
Tetragenococcus halophilus is a moderate halophilic bacterium which was widely used in fermentation processes, growing in a broad range of salinity conditions, and can survive a saturated 26.47% w/w NaCl concentration. However, the mechanism of this outstanding ability to acclimate to extracellular osmotic stress still remains unknown. The current study firstly conducted a quantitative proteomic analysis to identify alterations of the cellular proteome under both hypo-osmotic and hyper-osmotic stress conditions...
August 24, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28830518/discovering-associations-between-adverse-drug-events-using-pattern-structures-and-ontologies
#14
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/28818520/owlready-ontology-oriented-programming-in-python-with-automatic-classification-and-high-level-constructs-for-biomedical-ontologies
#15
Jean-Baptiste Lamy
OBJECTIVE: Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies...
July 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28815127/a-knowledge-based-system-for-intelligent-support-in-pharmacogenomics-evidence-assessment-ontology-driven-evidence-representation-and-retrieval
#16
Chia-Ju Lee, Beth Devine, Peter Tarczy-Hornoch
Pharmacogenomics holds promise as a critical component of precision medicine. Yet, the use of pharmacogenomics in routine clinical care is minimal, partly due to the lack of efficient and effective use of existing evidence. This paper describes the design, development, implementation and evaluation of a knowledge-based system that fulfills three critical features: a) providing clinically relevant evidence, b) applying an evidence-based approach, and c) using semantically computable formalism, to facilitate efficient evidence assessment to support timely decisions on adoption of pharmacogenomics in clinical care...
2017: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/28814335/comparative-transcriptome-analysis-of-second-and-third-generation-merozoites-of-eimeria-necatrix
#17
Shijie Su, Zhaofeng Hou, Dandan Liu, Chuanli Jia, Lele Wang, Jinjun Xu, Jianping Tao
BACKGROUND: Eimeria is a common genus of apicomplexan parasites that infect diverse vertebrates, most notably poultry, causing serious disease and economic losses. Eimeria species have complex life-cycles consisting of three developmental stages. However, the molecular basis of the Eimeria reproductive mode switch remains an enigma. METHODS: Total RNA extracted from second- (MZ-2) and third-generation merozoites (MZ-3) of Eimeria necatrix was subjected to transcriptome analysis using RNA sequencing (RNA-seq) followed by qRT-PCR validation...
August 16, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28797230/use-of-biological-priors-enhances-understanding-of-genetic-architecture-and-genomic-prediction-of-complex-traits-within-and-between-dairy-cattle-breeds
#18
Lingzhao Fang, Goutam Sahana, Peipei Ma, Guosheng Su, Ying Yu, Shengli Zhang, Mogens Sandø Lund, Peter Sørensen
BACKGROUND: A better understanding of the genetic architecture underlying complex traits (e.g., the distribution of causal variants and their effects) may aid in the genomic prediction. Here, we hypothesized that the genomic variants of complex traits might be enriched in a subset of genomic regions defined by genes grouped on the basis of "Gene Ontology" (GO), and that incorporating this independent biological information into genomic prediction models might improve their predictive ability...
August 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28797229/odg-omics-database-generator-a-tool-for-generating-querying-and-analyzing-multi-omics-comparative-databases-to-facilitate-biological-understanding
#19
Joseph Guhlin, Kevin A T Silverstein, Peng Zhou, Peter Tiffin, Nevin D Young
BACKGROUND: Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotated datasets available on the web with few ways to link them to in-lab datasets. With so many research groups generating their own data, the ability to relate it to the larger genomic and comparative genomic context is becoming increasingly crucial to make full use of the data...
August 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28794902/generic-distributed-framework-for-cloud-services-marketplace-based-on-unified-ontology
#20
Samer Hasan, V Valli Kumari
Cloud computing is a pattern for delivering ubiquitous and on demand computing resources based on pay-as-you-use financial model. Typically, cloud providers advertise cloud service descriptions in various formats on the Internet. On the other hand, cloud consumers use available search engines (Google and Yahoo) to explore cloud service descriptions and find the adequate service. Unfortunately, general purpose search engines are not designed to provide a small and complete set of results, which makes the process a big challenge...
November 2017: Journal of Advanced Research
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