scholarly journals Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Diek W Wheeler ◽  
Charise M White ◽  
Christopher L Rees ◽  
Alexander O Komendantov ◽  
David J Hamilton ◽  
...  
Keyword(s):  
Knowledge Base ◽  
Hippocampal Formation ◽  
Literature Mining ◽  
Extensive Literature ◽  
Systematic Analysis ◽  
Synaptic Specificity ◽  
Formidable Challenge ◽  
Comprehensive Knowledge ◽  
User Friendly ◽  
Machine Readable

Hippocampome.org is a comprehensive knowledge base of neuron types in the rodent hippocampal formation (dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex). Although the hippocampal literature is remarkably information-rich, neuron properties are often reported with incompletely defined and notoriously inconsistent terminology, creating a formidable challenge for data integration. Our extensive literature mining and data reconciliation identified 122 neuron types based on neurotransmitter, axonal and dendritic patterns, synaptic specificity, electrophysiology, and molecular biomarkers. All ∼3700 annotated properties are individually supported by specific evidence (∼14,000 pieces) in peer-reviewed publications. Systematic analysis of this unprecedented amount of machine-readable information reveals novel correlations among neuron types and properties, the potential connectivity of the full hippocampal circuitry, and outstanding knowledge gaps. User-friendly browsing and online querying of Hippocampome.org may aid design and interpretation of both experiments and simulations. This powerful, simple, and extensible neuron classification endeavor is unique in its detail, utility, and completeness.

scholarly journals A comprehensive knowledge base of synaptic electrophysiology in the rodent hippocampal formation

2019 ◽  
Author(s):  
Keivan Moradi ◽  
Giorgio A. Ascoli
Keyword(s):  
Knowledge Base ◽  
Hippocampal Neurons ◽  
Large Scale ◽  
Hippocampal Formation ◽  
Neural System ◽  
Liquid Junction ◽  
Comprehensive Knowledge ◽  
General Rules ◽  
The Difference ◽  
Machine Readable

AbstractThe cellular and synaptic architecture of the rodent hippocampus has been described in thousands of peer-reviewed publications. However, no human- or machine-readable public catalog of synaptic electrophysiology data exists for this or any other neural system. Harnessing state of the art information technology, we have developed a cloud-based toolset for identifying empirical evidence from the scientific literature pertaining to synaptic electrophysiology, for extracting the experimental data of interest, and for linking each entry to relevant text or figure excerpts. Mining more than 1,200 published journal articles, we have identified eight different signal modalities quantified by 68 different methods to measure synaptic amplitude, kinetics, and plasticity in hippocampal neurons. We have designed a data structure that both reflects these variabilities and maintains the existing relations among experimental modalities. Moreover, we mapped every annotated experiment to identified “synapse types,” i.e. specific pairs of presynaptic and postsynaptic neuron types. To this aim, we leveraged Hippocampome.org, an open-access knowledge base of morphologically, electrophysiologically, and molecularly characterized neuron types in the rodent hippocampal formation. Specifically, we have implemented a computational pipeline to systematically translate neuron type properties into formal queries in order to find all compatible synapse types. With this system, we have collected nearly 40,000 synaptic data entities covering 88% of the 3,120 potential connections in Hippocampome.org. Correcting membrane potentials with respect to liquid junction potentials significantly reduced the difference between theoretical and experimental reversal potentials, thereby enabling the accurate conversion of all synaptic amplitudes to conductance. This dataset allows for large-scale hypothesis testing of the general rules governing synaptic signals. To illustrate these applications, we confirmed several expected correlations between synaptic measurements and their covariates while suggesting previously unreported ones. We release all data open source at Hippocampome.org in order to further research across disciplines.

scholarly journals CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Adriano Ferrasa ◽  
Mayara M Murata ◽  
Teresa D C G Cofre ◽  
Juliana S Cavallini ◽  
Gustavo Peron ◽  
...  
Keyword(s):  
Knowledge Base ◽  
Citrus Canker ◽  
Limited Information ◽  
Xanthomonas Citri ◽  
Comprehensive Knowledge ◽  
Genetic Mechanisms ◽  
Serious Disease ◽  
Canker Development ◽  
User Friendly

Abstract Citrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the CitrusKB knowledge base. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable resource of information on citrus and their interaction with the citrus canker bacterium X. citri. CitrusKB provides tools for a user-friendly web interface to let users search and analyse a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease, with controls and infected plants at different stages of infection by the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue over time by the incorporation of novel annotations and analysis tools. We expect that CitrusKB may substantially contribute to the field of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.

scholarly journals CitrusKB: A Comprehensive Knowledge Base for Transcriptome and Interactome of Citrus spp. Infected by Xanthomonas citri subsp. citri at Different Infection Stages

2020 ◽  
Author(s):  
Adriano Ferrasa ◽  
Mayara M. Murata ◽  
Teresa D. C. G. Cofre ◽  
Juliana S. Cavallini ◽  
Gustavo Peron ◽  
...  
Keyword(s):  
Knowledge Base ◽  
Citrus Canker ◽  
Limited Information ◽  
Xanthomonas Citri ◽  
Comprehensive Knowledge ◽  
Genetic Mechanisms ◽  
Serious Disease ◽  
Canker Development ◽  
User Friendly

AbstractCitrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the knowledge base for transcriptome of in vivo citrus interactome, the CitrusKB. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable source of information on citrus and their interaction with the citrus canker bacterium X. citri. The database provides tools for a user-friendly web interface to search and analyze a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease and their interaction, at different stages of infection, with the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue by incorporating annotations and analysis tools. We expect that CitrusKB may substantially contribute to the area of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.

scholarly journals Comprehensive knowledge base of two- and three-dimensional activity cliffs for medicinal and computational chemistry

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 168 ◽  
Author(s):  
Ye Hu ◽  
Norbert Furtmann ◽  
Dagmar Stumpfe ◽  
Jürgen Bajorath
Keyword(s):  
Knowledge Base ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Binding Modes ◽  
Activity Data ◽  
Systematic Analysis ◽  
Comprehensive Knowledge ◽  
Or Groups ◽  
2D And 3D ◽  
Activity Cliffs

Activity cliffs are formed by pairs or groups of structurally similar or analogous active compounds with large differences in potency. They can be defined in two or three dimensions by comparing graph-based molecular representations or compound binding modes, respectively. Through systematic analysis of publicly available compound activity data and ligand-target X-ray structures we have in a series of studies determined all currently available two- and three-dimensional activity cliffs (2D- and 3D-cliffs, respectively). Furthermore, we have systematically searched for 2D extensions of 3D-cliffs. Herein, we specify different categories of activity cliffs we have explored and introduce an open access data deposition in ZENODO (doi: 10.5281/zenodo.18490) that makes the entire knowledge base of current activity cliffs freely available in an organized form.

Psychological Capital and Work Attitudes: A Conceptual Analysis

2015 ◽  
Vol 4 (2and3) ◽  
Author(s):  
Bharat Chandra Sahoo ◽  
Surendra Kumar Sia ◽  
Niranjan Sahu ◽  
Aneesh V. Appu
Keyword(s):  
Job Satisfaction ◽  
Organizational Commitment ◽  
Organizational Development ◽  
Turnover Intention ◽  
Psychological Capital ◽  
Practical Implication ◽  
Job Involvement ◽  
Work Attitudes ◽  
Extensive Literature ◽  
Systematic Analysis

The major thrust of the present paper, pertaining to employees growth and development at work, attempts a systematic analysis of attitudinal outcomes and performance improvement due to psychological capital. The constructs, namely psychological capital, and work attitudes like job involvement, job satisfaction, organizational commitment, cynicism, and turnover intention have been described. Based on far reaching Indian as well as western literature and findings, it is suggested that psychological capital would be positively related to desirable attitudes like job satisfaction, organizational commitment, and job involvement whereas negatively related to undesirable attitudes like organizational cynicisms and turnover intention. Through extensive literature and findings, the researcher is aiming to formulate a conceptual model of psychological capital based on propositions and to show how psychological capital is related to job attitudes. With respect to organizational development, this paper also covers practical implication where systematic intervention of psychological capital is given utmost priority. With reference to various organizations and workplaces, how psychological capital can be applied in a scientific direction through proper training, workshop, and web-based programme in order to promote healthy and balanced life.

scholarly journals Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Chris Bauer ◽  
Ralf Herwig ◽  
Matthias Lienhard ◽  
Paul Prasse ◽  
Tobias Scheffer ◽  
...  
Keyword(s):  
Text Mining ◽  
Knowledge Base ◽  
Survival Data ◽  
Scientific Literature ◽  
Entity Recognition ◽  
Literature Mining ◽  
Cancer Drugs ◽  
Classical Text ◽  
Anti Cancer ◽  
Cancer Types

Abstract Background There is a huge body of scientific literature describing the relation between tumor types and anti-cancer drugs. The vast amount of scientific literature makes it impossible for researchers and physicians to extract all relevant information manually. Methods In order to cope with the large amount of literature we applied an automated text mining approach to assess the relations between 30 most frequent cancer types and 270 anti-cancer drugs. We applied two different approaches, a classical text mining based on named entity recognition and an AI-based approach employing word embeddings. The consistency of literature mining results was validated with 3 independent methods: first, using data from FDA approvals, second, using experimentally measured IC-50 cell line data and third, using clinical patient survival data. Results We demonstrated that the automated text mining was able to successfully assess the relation between cancer types and anti-cancer drugs. All validation methods showed a good correspondence between the results from literature mining and independent confirmatory approaches. The relation between most frequent cancer types and drugs employed for their treatment were visualized in a large heatmap. All results are accessible in an interactive web-based knowledge base using the following link: https://knowledgebase.microdiscovery.de/heatmap. Conclusions Our approach is able to assess the relations between compounds and cancer types in an automated manner. Both, cancer types and compounds could be grouped into different clusters. Researchers can use the interactive knowledge base to inspect the presented results and follow their own research questions, for example the identification of novel indication areas for known drugs.

COMPARATIVE ANALYSIS OF CUSTOMER SATISFACTION OF TELECOM SERVICE PROVIDERS IN HARYANA

2021 ◽  
Vol 9 (1) ◽  
pp. 709-719
Author(s):  
RAMESH C. HOODA, DR. VIKAS TYAGI
Keyword(s):  
Comparative Analysis ◽  
Customer Satisfaction ◽  
Mobile Networks ◽  
Research Study ◽  
Service Providers ◽  
Advanced Technology ◽  
Survey Method ◽  
Extensive Literature ◽  
Systematic Analysis ◽  
Telecom Service

Objective of the study is to make a comparative analysis of customer satisfaction of different Telecom Service Providers in Haryana along with identification of factors which influence customer satisfaction. After completing extensive literature review, eight attributes  namely ‘attractive offers’, ‘using advanced technology’, ‘mobile provider being friendly’, ‘reliability’, ‘promptness of response’,  ‘it delivers promises, it makes’, ‘availability’ and ‘network’ are identified influencing customers satisfaction. Survey method was adopted for the study. 250 respondents of different TSP’s covering all Telecom Districts in Haryana. SPSS 21.0 was applied for analysis of the collected data. Statistical tools namely Descriptive Analysis, Frequency Analysis, Cross-Tabs Analysis and One Way ANOVA were used in the research study. After systematic analysis and findings of the study, it is found that highest percentage of respondents are satisfied with the attributes namely ‘attractive offers’, ‘mobile provider being friendly’, ‘availability’ and ‘network’ of Airtel along with ‘reliability’ and ‘it delivers promises, it makes’ of Vodafone-Idea, ‘promptness of response’ of BSNL and ‘using advanced technology’ of Reliance-Jio. It is also revealed from the study that Airtel is required to improve ‘reliability’ and ‘availability’ of its mobile networks. Vodafone-Idea needs to improve upon the attributes ‘attractive offers’, ‘using advanced technology’, ‘mobile provider being friendly’ and ‘network’. BSNL may further improve ‘promptness of response’ and Reliance-Jio needs to show improvement about ‘it delivers promises, it makes’. It is concluded from the research study that services of Airtel are preferred by maximum percentage of respondents.

scholarly journals MIKB: A Manually Curated and Comprehensive Knowledge Base for Myocardial Infarction

2021 ◽  
Author(s):  
Chaoying Zhan ◽  
Yingbo Zhang ◽  
Xingyun Liu ◽  
Rongrong Wu ◽  
Ke Zhang ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Knowledge Base ◽  
Comprehensive Knowledge

scholarly journals ONTOLOGY-BASED WEB TOOLS FOR RETRIEVING PHOTOGRAMMETRIC CULTURAL HERITAGE MODELS

2019 ◽  
Vol XLII-2/W10 ◽  
pp. 31-38 ◽  
Author(s):  
M. Ben Ellefi ◽  
P. Drap ◽  
O. Papini ◽  
D. Merad ◽  
J. P. Royer ◽  
...  
Keyword(s):  
Cultural Heritage ◽  
Specific Knowledge ◽  
Domain Specific ◽  
Knowledge Based ◽  
Web Tools ◽  
Domain Specific Knowledge ◽  
Visualization Systems ◽  
User Friendly ◽  
Machine Readable ◽  
Associated Knowledge

<p><strong>Abstract.</strong> A key challenge in cultural heritage (CH) sites visualization is to provide models and tools that effectively integrate the content of a CH data with domain-specific knowledge so that the users can query, interpret and consume the visualized information. Moreover, it is important that the intelligent visualization systems are interoperable in the semantic web environment and thus, capable of establishing a methodology to acquire, integrate, analyze, generate and share numeric contents and associated knowledge in human and machine-readable Web. In this paper, we present a model, a methodology and a software Web-tools that support the coupling of the 2D/3D Web representation with the knowledge graph database of <i>Xlendi</i> shipwreck. The Web visualization tools and the knowledge-based techniques are married into a photogrammetry driven ontological model while at the same time, user-friendly web tools for querying and semantic consumption of the shipwreck information are introduced.</p>

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