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https://www.readbyqxmd.com/read/27899668/cyanobase-%C3%A2-a-large-scale-update-on-its-20th-anniversary
#1
Takatomo Fujisawa, Rei Narikawa, Shin-Ichi Maeda, Satoru Watanabe, Yu Kanesaki, Koichi Kobayashi, Jiro Nomata, Mitsumasa Hanaoka, Mai Watanabe, Shigeki Ehira, Eiji Suzuki, Koichiro Awai, Yasukazu Nakamura
The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase (http://genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently. Since then, CyanoBase has constantly been extended and has received several updates. Here, we describe a new large-scale update of the database, which coincides with its 20th anniversary. We have expanded the number of cyanobacterial genomic sequences from 39 to 376 species, which consists of 86 complete and 290 draft genomes...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899649/protein-ontology-pro-enhancing-and-scaling-up-the-representation-of-protein-entities
#2
Darren A Natale, Cecilia N Arighi, Judith A Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R Christie, Julie Cowart, Peter D'Eustachio, Alexander D Diehl, Harold J Drabkin, William D Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed, Cathy H Wu
The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899636/the-monarch-initiative-an-integrative-data-and-analytic-platform-connecting-phenotypes-to-genotypes-across-species
#3
Christopher J Mungall, Julie A McMurry, Sebastian Köhler, James P Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J P Gourdine, Julius O B Jacobsen, Dan Keith, Bryan Laraway, Suzanna E Lewis, Jeremy NguyenXuan, Kent Shefchek, Nicole Vasilevsky, Zhou Yuan, Nicole Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N Robinson, Melissa A Haendel
The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27875201/categorical-colormap-optimization-with-visualization-case-studies
#4
H Fang, S Walton, E Delahaye, J Harris, D A Storchak, M Chen
Mapping a set of categorical values to different colors is an elementary technique in data visualization. Users of visualization software routinely rely on the default colormaps provided by a system, or colormaps suggested by software such as ColorBrewer. In practice, users often have to select a set of colors in a semantically meaningful way (e.g., based on conventions, color metaphors, and logological associations), and consequently would like to ensure their perceptual differentiation is optimized. In this paper, we present an algorithmic approach for maximizing the perceptual distances among a set of given colors...
January 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/27861505/content-based-discovery-for-web-map-service-using-support-vector-machine-and-user-relevance-feedback
#5
Kai Hu, Zhipeng Gui, Xiaoqiang Cheng, Kunlun Qi, Jie Zheng, Lan You, Huayi Wu
Many discovery methods for geographic information services have been proposed. There are approaches for finding and matching geographic information services, methods for constructing geographic information service classification schemes, and automatic geographic information discovery. Overall, the efficiency of the geographic information discovery keeps improving., There are however, still two problems in Web Map Service (WMS) discovery that must be solved. Mismatches between the graphic contents of a WMS and the semantic descriptions in the metadata make discovery difficult for human users...
2016: PloS One
https://www.readbyqxmd.com/read/27853445/semantic-differential-scale-method-can-reveal-multi-dimensional-aspects-of-mind-perception
#6
Hideyuki Takahashi, Midori Ban, Minoru Asada
As humans, we tend to perceive minds in both living and non-living entities, such as robots. From a questionnaire developed in a previous mind perception study, authors found that perceived minds could be located on two dimensions "experience" and "agency." This questionnaire allowed the assessment of how we perceive minds of various entities from a multi-dimensional point of view. In this questionnaire, subjects had to evaluate explicit mental capacities of target characters (e.g., capacity to feel hunger)...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27849523/videostory-embeddings-recognize-events-when-examples-are-scarce
#7
Amirhossein Habibian, Thomas Mensink, Cees G M Snoek
This paper aims for event recognition when video examples are scarce or even completely absent. The key in such a challenging setting is a semantic video representation. Rather than building the representation from individual attribute detectors and their annotations, we propose to learn the entire representation from freely available web videos and their descriptions using an embedding between video features and term vectors. In our proposed embedding, which we call Video2vec, the correlations between the words are utilized to learn a more effective representation by optimizing a joint objective balancing descriptiveness and predictability...
November 10, 2016: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/27830249/efficient-results-in-semantic-interoperability-for-health-care-findings-from-the-section-on-knowledge-representation-and-management
#8
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
https://www.readbyqxmd.com/read/27830248/knowledge-representation-and-management-a-linked-data-perspective
#9
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
https://www.readbyqxmd.com/read/27815682/amyloid-pet-in-primary-progressive-aphasia-case-series-and-systematic-review-of-the-literature
#10
Alberto Villarejo-Galende, Sara Llamas-Velasco, Adolfo Gómez-Grande, Verónica Puertas-Martín, Israel Contador, Pilar Sarandeses, Marta González-Sánchez, Rocío Trincado, Patrick Pilkington, Sebastián Ruiz-Solis, David A Pérez-Martínez, Alejandro Herrero-San Martín
Primary progressive aphasia (PPA) is considered a heterogeneous syndrome, with different clinical subtypes and neuropathological causes. Novel PET biomarkers may help to predict the underlying neuropathology, but many aspects remain unclear. We studied the relationship between amyloid PET and PPA variant in a clinical series of PPA patients. A systematic review of the literature was performed. Patients with PPA were assessed over a 2-year period and classified based on language testing and the International Consensus Criteria as non-fluent/agrammatic (nfvPPA), semantic (svPPA), logopenic variant (lvPPA) or as unclassifiable (ucPPA)...
November 4, 2016: Journal of Neurology
https://www.readbyqxmd.com/read/27814769/somatic-cancer-variant-curation-and-harmonization-through-consensus-minimum-variant-level-data
#11
Deborah I Ritter, Sameek Roychowdhury, Angshumoy Roy, Shruti Rao, Melissa J Landrum, Dmitriy Sonkin, Mamatha Shekar, Caleb F Davis, Reece K Hart, Christine Micheel, Meredith Weaver, Eliezer M Van Allen, Donald W Parsons, Howard L McLeod, Michael S Watson, Sharon E Plon, Shashikant Kulkarni, Subha Madhavan
BACKGROUND: To truly achieve personalized medicine in oncology, it is critical to catalog and curate cancer sequence variants for their clinical relevance. The Somatic Working Group (WG) of the Clinical Genome Resource (ClinGen), in cooperation with ClinVar and multiple cancer variant curation stakeholders, has developed a consensus set of minimal variant level data (MVLD). MVLD is a framework of standardized data elements to curate cancer variants for clinical utility. With implementation of MVLD standards, and in a working partnership with ClinVar, we aim to streamline the somatic variant curation efforts in the community and reduce redundancy and time burden for the interpretation of cancer variants in clinical practice...
November 4, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27814027/harnessing-big-data-for-systems-pharmacology
#12
Lei Xie, Eli J Draizen, Philip E Bourne
Systems pharmacology aims to holistically understand mechanisms of drug actions to support drug discovery and clinical practice. Systems pharmacology modeling (SPM) is data driven. It integrates an exponentially growing amount of data at multiple scales (genetic, molecular, cellular, organismal, and environmental). The goal of SPM is to develop mechanistic or predictive multiscale models that are interpretable and actionable. The current explosions in genomics and other omics data, as well as the tremendous advances in big data technologies, have already enabled biologists to generate novel hypotheses and gain new knowledge through computational models of genome-wide, heterogeneous, and dynamic data sets...
October 13, 2016: Annual Review of Pharmacology and Toxicology
https://www.readbyqxmd.com/read/27797761/isomorphic-semantic-mapping-of-variant-call-format-vcf2rdf
#13
Emanuel Diego S Penha, Egiebade Iriabho, Alex Dussaq, Diana Magalhães de Oliveira, Jonas S Almeida
: The move of computational genomics workflows to Cloud Computing platforms is associated with a new level of integration and interoperability that challenges existing data representation formats. The Variant Calling Format (VCF) is in a particularly sensitive position in that regard, with both clinical and consumer-facing analysis tools relying on this self-contained description of genomic variation in Next Generation Sequencing (NGS) results. In this report we identify an isomorphic map between VCF and the reference Resource Description Framework...
October 25, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27785153/developing-a-modular-architecture-for-creation-of-rule-based-clinical-diagnostic-criteria
#14
Na Hong, Jyotishman Pathak, Christopher G Chute, Guoqian Jiang
BACKGROUND: With recent advances in computerized patient records system, there is an urgent need for producing computable and standards-based clinical diagnostic criteria. Notably, constructing rule-based clinical diagnosis criteria has become one of the goals in the International Classification of Diseases (ICD)-11 revision. However, few studies have been done in building a unified architecture to support the need for diagnostic criteria computerization. In this study, we present a modular architecture for enabling the creation of rule-based clinical diagnostic criteria leveraging Semantic Web technologies...
2016: BioData Mining
https://www.readbyqxmd.com/read/27766940/prioritization-clustering-and-functional-annotation-of-micrornas-using-latent-semantic-indexing-of-medline-abstracts
#15
Sujoy Roy, Brandon C Curry, Behrouz Madahian, Ramin Homayouni
BACKGROUND: The amount of scientific information about MicroRNAs (miRNAs) is growing exponentially, making it difficult for researchers to interpret experimental results. In this study, we present an automated text mining approach using Latent Semantic Indexing (LSI) for prioritization, clustering and functional annotation of miRNAs. RESULTS: For approximately 900 human miRNAs indexed in miRBase, text documents were created by concatenating titles and abstracts of MEDLINE citations which refer to the miRNAs...
October 6, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27750378/pophr-a-knowledge-based-platform-to-support-integration-analysis-and-visualization-of-population-health-data
#16
Arash Shaban-Nejad, Maxime Lavigne, Anya Okhmatovskaia, David L Buckeridge
Population health decision makers must consider complex relationships between multiple concepts measured with differential accuracy from heterogeneous data sources. Population health information systems are currently limited in their ability to integrate data and present a coherent portrait of population health. Consequentially, these systems can provide only basic support for decision makers. The Population Health Record (PopHR) is a semantic web application that automates the integration and extraction of massive amounts of heterogeneous data from multiple distributed sources (e...
October 17, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27731860/semantic-indexing-of-medical-learning-objects-medical-students-usage-of-a-semantic-network
#17
Nadine Tix, Paul Gießler, Ursula Ohnesorge-Radtke, Cord Spreckelsen
BACKGROUND: The Semantically Annotated Media (SAM) project aims to provide a flexible platform for searching, browsing, and indexing medical learning objects (MLOs) based on a semantic network derived from established classification systems. Primarily, SAM supports the Aachen emedia skills lab, but SAM is ready for indexing distributed content and the Simple Knowledge Organizing System standard provides a means for easily upgrading or even exchanging SAM's semantic network. There is a lack of research addressing the usability of MLO indexes or search portals like SAM and the user behavior with such platforms...
November 11, 2015: JMIR Medical Education
https://www.readbyqxmd.com/read/27723603/inferring-unknown-biological-functions-by-integration-of-go-annotations-and-gene-expression-data
#18
Guillermo Leale, Ariel Baya, Diego Milone, Pablo Granitto, Georgina Stegmayer
Characterizing genes with semantic information is an important process regarding the description of gene products. In spite that complete genomes of many organisms have been already sequenced, the biological functions of all of their genes are still unknown. Since experimentally studying the functions of those genes, one by one, would be unfeasible, new computational methods for gene functions inference are needed. We present here a novel computational approach for inferring biological function for a set of genes with previously unknown function, given a set of genes with well-known information...
October 7, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27716781/cross-species-analysis-of-gene-expression-and-function-in-prefrontal-cortex-hippocampus-and-striatum
#19
Wei Chen, Xiayu Xia, Nan Song, Ying Wang, Hua Zhu, Wei Deng, Qi Kong, Xianmin Pan, Chuan Qin
BACKGROUND: Mouse has been extensively used as a tool for investigating the onset and development of human neurological disorders. As a first step to construct a transgenic mouse model of human brain lesions, it is of fundamental importance to clarify the similarity and divergence of genetic background between non-diseased human and mouse brain tissues. METHODS: We systematically compared, based on large scale integrated microarray data, the transcriptomes of three anatomically distinct brain regions; prefrontal cortex (PFC), hippocampus (HIP) and striatum (STR), across human and mouse...
2016: PloS One
https://www.readbyqxmd.com/read/27705859/web-video-event-recognition-by-semantic-analysis-from-ubiquitous-documents
#20
Litao Yu, Yang Yang, Zi Huang, Peng Wang, Jingkuan Song, Heng Tao Shen
In recent years, the task of event recognition from videos has attracted increasing interest in multimedia area. While most of the existing research was mainly focused on exploring visual cues to handle relatively small-granular events, it is difficult to directly analyze video content without any prior knowledge. Therefore, synthesizing both the visual and semantic analysis is a natural way for video event understanding. In this paper, we study the problem of Web video event recognition, where Web videos often describe large-granular events and carry limited textual information...
December 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
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