scholarly journals ThRSDB: a database of Thai rice starch composition, molecular structure and functionality

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Kwanjeera Wanichthanarak ◽  
Maysaya Thitisaksakul
Keyword(s):  
Molecular Structure ◽  
Rice Starch ◽  
Original Research ◽  
Rice Cultivars ◽  
Web Interface ◽  
High Demand ◽  
Starch Properties ◽  
Visualization Tools ◽  
Starch Composition ◽  
User Friendly

Abstract As starch properties can affect end product quality in many ways, rice starch from Thai domesticated cultivars and landraces has been the focus of increasing research interest. Increasing knowledge in this area creates a high demand from the research community for better organized information. The Thai Rice Starch Database (ThRSDB) is an online database containing data extensively curated from original research articles on Thai rice starch composition, molecular structure and functionality. The key aim of the ThRSDB is to facilitate accessibility to dispersed rice starch information for, but not limited to, both research and industrial users. Currently, 373 samples from 191 different Thai rice cultivars have been collected from 39 published articles. The ThRSDB includes the search functions necessary for accessing data together with a user-friendly web interface and interactive visualization tools. We have also demonstrated how the collected data can be efficiently used to observe the relationships between starch parameters and rice cultivars through correlation analysis and Partial Least Squares Discriminant Analysis. Database URL: http://thairicestarch.kku.ac.th

Natural variation in rice starch synthase IIa affects enzyme and starch properties

2004 ◽  
Vol 31 (7) ◽  
pp. 671 ◽  
Author(s):  
Takayuki Umemoto ◽  
Noriaki Aoki ◽  
Hongxuan Lin ◽  
Yasunori Nakamura ◽  
Naoyoshi Inouchi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Natural Variation ◽  
Oryza Sativa L ◽  
Length Distribution ◽  
Starch Synthase ◽  
Rice Starch ◽  
Nucleotide Polymorphisms ◽  
Cultivated Rice ◽  
Chain Length Distribution ◽  
Starch Properties

The natural variation in starch synthase IIa (SSIIa) of rice (Oryza sativa L.) was characterised using near-isogenic lines (NILs). SSIIa is a candidate for the alk gene regulating the alkali disintegration of rice grains, since both genes are genetically mapped at the same position on chromosome 6 and related to starch properties. In this study, we report that the alkali-susceptible cultivar Nipponbare lacked SSIIa activity in endosperm. However, the activity was detected with NILs having the alk allele of alkali-tolerant Kasalath. SSIIa protein was present even in Nipponbare endosperm, but it was not associated with starch granules at the milky stage of endosperm. Three single-nucleotide polymorphisms (SNPs) predicting amino acid substitutions existed between the cDNA sequences of SSIIa of Nipponbare and Kasalath were genotyped with 65 rice cultivars and four wild relatives of cultivated rice. The results obtained explain the potential importance of two of the amino acid residues for starch association of rice SSIIa. An analysis of the chain-length distribution of β-limit dextrin of amylopectin showed that without SSIIa activity, the relative number of A-chains (the short chains without branches) increased and that of B1-chains (the short chains with branches) decreased. This suggests that, given the SSIIa defect, short A-chains could not reach a sufficient length for branching enzymes to act on them to produce B1-chains.

MetaADEDB 2.0: a comprehensive database on adverse drug events

2020 ◽  
Author(s):  
Zhuohang Yu ◽  
Zengrui Wu ◽  
Weihua Li ◽  
Guixia Liu ◽  
Yun Tang
Keyword(s):  
Safety Assessment ◽  
Adverse Drug Events ◽  
Adverse Event Reporting System ◽  
Adverse Event Reporting ◽  
Supplementary Information ◽  
Online Database ◽  
Web Interface ◽  
Drug Discovery And Development ◽  
Comprehensive Information ◽  
User Friendly

Abstract Summary MetaADEDB is an online database we developed to integrate comprehensive information on adverse drug events (ADEs). The first version of MetaADEDB was released in 2013 and has been widely used by researchers. However, it has not been updated for more than seven years. Here, we reported its second version by collecting more and newer data from the U.S. FDA Adverse Event Reporting System (FAERS) and Canada Vigilance Adverse Reaction Online Database, in addition to the original three sources. The new version consists of 744 709 drug–ADE associations between 8498 drugs and 13 193 ADEs, which has an over 40% increase in drug–ADE associations compared to the previous version. Meanwhile, we developed a new and user-friendly web interface for data search and analysis. We hope that MetaADEDB 2.0 could provide a useful tool for drug safety assessment and related studies in drug discovery and development. Availability and implementation The database is freely available at: http://lmmd.ecust.edu.cn/metaadedb/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals SSFinder: High Throughput CRISPR-Cas Target Sites Prediction Tool

2014 ◽  
Vol 2014 ◽  
pp. 1-4 ◽  
Author(s):  
Santosh Kumar Upadhyay ◽  
Shailesh Sharma
Keyword(s):  
Operating Systems ◽  
High Throughput ◽  
Genomic Data ◽  
Prediction Tool ◽  
High Demand ◽  
Specific Target ◽  
Target Sites ◽  
High Throughput Detection ◽  
User Friendly

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system facilitates targeted genome editing in organisms. Despite high demand of this system, finding a reliable tool for the determination of specific target sites in large genomic data remained challenging. Here, we report SSFinder, a python script to perform high throughput detection of specific target sites in large nucleotide datasets. The SSFinder is a user-friendly tool, compatible with Windows, Mac OS, and Linux operating systems, and freely available online.

scholarly journals VIP-HL: Semi-automated ACMG/AMP variant interpretation platform for genetic hearing loss

2020 ◽  
Author(s):  
Jiguang Peng ◽  
Jiale Xiang ◽  
Xiangqian Jin ◽  
Junhua Meng ◽  
Nana Song ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Expert Panel ◽  
Sequence Variant ◽  
Variant Interpretation ◽  
Web Interface ◽  
Online Tool ◽  
Genetic Hearing Loss ◽  
Genetics And Genomics ◽  
Evidence Based Guidelines ◽  
User Friendly

The American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG/AMP) have proposed a set of evidence-based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL-EP) introduced further specifications into the ACMG/AMP framework for genetic hearing loss. This study developed a tool named VIP-HL, aiming to semi-automate the HL ACMG/AMP rules. VIP-HL aggregates information from external databases to automate 13 out of 24 ACMG/AMP rules specified by HL-EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7. We benchmarked VIP-HL using 50 variants where 83 rules were activated by the ClinGen HL-EP. VIP-HL concordantly activated 96% (80/83) rules, significantly higher than that of by InterVar (47%; 39/83). Of 4948 ClinVar star 2+ variants from 142 deafness-related genes, VIP-HL achieved an overall variant interpretation concordance in 88.0% (4353/4948). VIP-HL is an integrated online tool for reliable automated variant classification in hearing loss genes. It assists curators in variant interpretation and provides a platform for users to share classifications with each other. VIP-HL is available with a user-friendly web interface at http://hearing.genetics.bgi.com/.

scholarly journals The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics

2018 ◽  
Vol 2 ◽  
pp. 3 ◽  
Author(s):  
Heba Shaaban ◽  
David A. Westfall ◽  
Rawhi Mohammad ◽  
David Danko ◽  
Daniela Bezdan ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Large Scale ◽  
Research Effort ◽  
Gram Stain ◽  
Web Interface ◽  
Ongoing Effort ◽  
Student Researchers ◽  
User Friendly ◽  
Optimal Ph ◽  
Online Web

The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes’ characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY—Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism’s taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart (https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe.

scholarly journals COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints

2021 ◽  
Author(s):  
Lisa Langnickel ◽  
Roman Baum ◽  
Johannes Darms ◽  
Sumit Madan ◽  
Juliane Fluck
Keyword(s):  
Search Engine ◽  
Access Point ◽  
Semantic Search ◽  
Web Interface ◽  
Disease Trajectory ◽  
Human Genes ◽  
Central Access ◽  
Semantic Information Retrieval ◽  
User Friendly ◽  
Semantic Search Engine

During the current COVID-19 pandemic, the rapid availability of profound information is crucial in order to derive information about diagnosis, disease trajectory, treatment or to adapt the rules of conduct in public. The increased importance of preprints for COVID-19 research initiated the design of the preprint search engine preVIEW. Conceptually, it is a lightweight semantic search engine focusing on easy inclusion of specialized COVID-19 textual collections and provides a user friendly web interface for semantic information retrieval. In order to support semantic search functionality, we integrated a text mining workflow for indexing with relevant terminologies. Currently, diseases, human genes and SARS-CoV-2 proteins are annotated, and more will be added in future. The system integrates collections from several different preprint servers that are used in the biomedical domain to publish non-peer-reviewed work, thereby enabling one central access point for the users. In addition, our service offers facet searching, export functionality and an API access. COVID-19 preVIEW is publicly available at https://preview.zbmed.de.

scholarly journals KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Hugo Mochão ◽  
Pedro Barahona ◽  
Rafael S Costa
Keyword(s):  
Experimental Data ◽  
Metabolic Networks ◽  
Model Simulation ◽  
Web Interface ◽  
Concentration Data ◽  
Web Based ◽  
Share Data ◽  
Visualization Tools ◽  
Filter Mechanism ◽  
Machine Readable

Abstract The KiMoSys (https://kimosys.org), launched in 2014, is a public repository of published experimental data, which contains concentration data of metabolites, protein abundances and flux data. It offers a web-based interface and upload facility to share data, making it accessible in structured formats, while also integrating associated kinetic models related to the data. In addition, it also supplies tools to simplify the construction process of ODE (Ordinary Differential Equations)-based models of metabolic networks. In this release, we present an update of KiMoSys with new data and several new features, including (i) an improved web interface, (ii) a new multi-filter mechanism, (iii) introduction of data visualization tools, (iv) the addition of downloadable data in machine-readable formats, (v) an improved data submission tool, (vi) the integration of a kinetic model simulation environment and (vii) the introduction of a unique persistent identifier system. We believe that this new version will improve its role as a valuable resource for the systems biology community. Database URL:  www.kimosys.org

scholarly journals Arabic-English Parallel Corpus: A New Resource for Translation Training and Language Teaching

2017 ◽  
Author(s):  
Arab World English Journal ◽  
Hind M. Alotaibi
Keyword(s):  
Language Teaching ◽  
Data Driven ◽  
Text Segmentation ◽  
Web Interface ◽  
King Saud University ◽  
Parallel Corpora ◽  
Parallel Corpus ◽  
Source Language ◽  
User Friendly ◽  
Ongoing Project

Parallel corpora can be defined as collections of aligned, translated texts of two or more languages. They play a major role in translation and contrastive studies, and are also becoming popular in translation training and language teaching, with the advent of the data-driven learning (DDL) approach. Despite their significance, however, Arabic seems to lack a satisfactory general-use parallel corpus resource. The literature describes few Arabic–English parallel corpora, and these few are usually inaccurate and/or expensive. Some are small in size, while others are restricted in terms of genre, failing to meet the requirements of many academics and researchers. This paper describes an ongoing project at the College of Languages and Translation, King Saud University, to compile a 10-million-word Arabic–English parallel corpus to be used as a resource for translation training and language teaching. The bidirectional corpus can be used to compare translated and source language and identify differences. The corpus has been manually verified at different stages, including translation, text segmentation, alignment, and file preparation; it is available as full-text in XML format and through a user-friendly web interface that provides a concordancer to support bilingual search queries and several filtering options.

TRIANGLE Portal: An User-Friendly Web Interface for Remote Experimentation

2018 ◽  
pp. 110-117 ◽  
Author(s):  
Almudena Díaz-Zayas ◽  
Alberto Salmerón Moreno ◽  
Gustavo García Pascual ◽  
Pedro Merino Gómez
Keyword(s):  
Web Interface ◽  
User Friendly ◽  
Remote Experimentation
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