Database : The Journal of Biological Databases and Curation This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Creating a Metabolic Syndrome Research Resource using the National Health and Nutrition Examination Survey
AbstractMetabolic syndrome (MetS) is multifaceted. Risk factors include visceral adiposity, dyslipidemia, hyperglycemia, hypertension and environmental stimuli. MetS leads to an increased risk of cardiovascular disease, type 2 diabetes and stroke. Comparative studies, however, have identified heterogeneity in the pathology of MetS across groups though the etiology of these differences has yet to be elucidated. The Metabolic Syndrome Research Resource (MetSRR) described in this report is a curated database that provides access to MetS-associated biological and ancillary data and pools current and potential biomarkers of Met...
Source: Database : The Journal of Biological Databases and Curation - December 31, 2020 Category: Databases & Libraries Source Type: research

MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle
AbstractMuscleAtlasExplorer is a freely available web application that allows for the exploration of gene expression data from human skeletal muscle. It draws from an extensive publicly available dataset of 1654 skeletal muscle expression microarray samples. Detailed, manually curated, patient phenotype data, with information such as age, sex, BMI and disease status, are combined with skeletal muscle gene expression to provide insights into gene function in skeletal muscle. It aims to facilitate easy exploration of the data using powerful data visualization functions, while allowing for sample selection, in-depth inspectio...
Source: Database : The Journal of Biological Databases and Curation - December 18, 2020 Category: Databases & Libraries Source Type: research

Novel methods included in SpolLineages tool for fast and precise prediction of Mycobacterium tuberculosis complex spoligotype families
In this study, we present two complementary data-driven approaches allowing fast and precise family prediction from spoligotyping patterns. The first one is based on data transformation and the use of decision tree classifiers. In contrast, the second one searches for a set of simple rules using binary mask s through a specifically designed evolutionary algorithm. The comparison with the three main approaches in the field highlighted the good performances of our contributions and the significant runtime gain. Finally, we propose the ‘SpolLineages’ software tool (https://github.com/dcouvin/SpolLineages), which implement...
Source: Database : The Journal of Biological Databases and Curation - December 15, 2020 Category: Databases & Libraries Source Type: research

Knowledge extraction for assisted curation of summaries of bacterial transcription factor properties
AbstractTranscription factors (TFs) play a main role in transcriptional regulation of bacteria, as they regulate transcription of the genetic information encoded in DNA. Thus, the curation of the properties of these regulatory proteins is essential for a better understanding of transcriptional regulation. However, traditional manual curation of article collections to compile descriptions of TF properties takes significant time and effort due to the overwhelming amount of biomedical literature, which increases every day. The development of automatic approaches for knowledge extraction to assist curation is therefore critica...
Source: Database : The Journal of Biological Databases and Curation - December 11, 2020 Category: Databases & Libraries Source Type: research

Applying graph database technology for analyzing perturbed co-expression networks in cancer
AbstractGraph representations provide an elegant solution to capture and analyze complex molecular mechanisms in the cell. Co-expression networks are undirected graph representations of transcriptional co-behavior indicating (co-)regulations, functional modules or even physical interactions between the corresponding gene products. The growing avalanche of available RNA sequencing (RNAseq) data fuels the construction of such networks, which are usually stored in relational databases like most other biological data. Inferring linkage by recursive multiple-join statements, however, is computationally expensive and complex to ...
Source: Database : The Journal of Biological Databases and Curation - December 11, 2020 Category: Databases & Libraries Source Type: research

CEG 2.0: an updated database of clusters of essential genes including eukaryotic organisms
AbstractEssential genes are key elements for organisms to maintain their living. Building databases that store essential genes in the form of homologous clusters, rather than storing them as a singleton, can provide more enlightening information such as the general essentiality of homologous genes in multiple organisms. In 2013, the first database to store prokaryotic essential genes in clusters, CEG (Clusters of Essential Genes), was constructed. Afterward, the amount of available data for essential genes increased by a factor>3 since the last revision. Herein, we updated CEG to version 2, including more prokaryotic es...
Source: Database : The Journal of Biological Databases and Curation - December 11, 2020 Category: Databases & Libraries Source Type: research

CamRegBase: a gene regulation database for the biofuel crop, Camelina sativa
AbstractCamelina is an annual oilseed plant from the Brassicaceae family that is gaining momentum as a biofuel winter cover crop. However, a significant limitation in further enhancing its utility as a producer of oils that can be used as biofuels, jet fuels or bio-based products is the absence of a repository for all the gene expression and regulatory information that is being rapidly generated by the community. Here, we provide CamRegBase (https://camregbase.org/) as a one-stop resource to access Camelina information on gene expression and co-expression, transcription factors, lipid associated genes and genome-wide ortho...
Source: Database : The Journal of Biological Databases and Curation - December 11, 2020 Category: Databases & Libraries Source Type: research

NPBS database: a chemical data resource with relational data between natural products and biological sources
AbstractNPBS (Natural Products& Biological Sources) database is a chemical data resource with relational data between natural products and biological sources, manually curated from literatures of natural product researches. The relational data link a specific species and all the natural products derived from it and contrarily link a specific natural product and all the biological sources. The biological sources cover diverse species of plant, bacterial, fungal and marine organisms; the natural molecules have proper chemical structure data and computable molecular properties and all the relational data have correspondin...
Source: Database : The Journal of Biological Databases and Curation - December 11, 2020 Category: Databases & Libraries Source Type: research

HAHmiR.DB: a server platform for high-altitude human miRNA –gene coregulatory networks and associated regulatory circuits
AbstractAround 140 million people live in high-altitude (HA) conditions! and even a larger number visit such places for tourism, adventure-seeking or sports training. Rapid ascent to HA can cause severe damage to the body organs and may lead to many fatal disorders. During induction to HA, human body undergoes various physiological, biochemical, hematological and molecular changes to adapt to the extreme environmental conditions. Several literature references hint that gene-expression-regulation and regulatory molecules like miRNAs and transcription factors (TFs) control adaptive responses during HA stress. These biomolecu...
Source: Database : The Journal of Biological Databases and Curation - December 1, 2020 Category: Databases & Libraries Source Type: research

ThRSDB: a database of Thai rice starch composition, molecular structure and functionality
AbstractAs 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 re...
Source: Database : The Journal of Biological Databases and Curation - December 1, 2020 Category: Databases & Libraries Source Type: research

RegulomePA: a database of transcriptional regulatory interactions in Pseudomonas aeruginosa PAO1
We present RegulomePA, a database that contains biological information on regulatory interactions between transcription factors (TFs), sigma factor (SFs) and target genes inPseudomonas aeruginosa PAO1. RegulomePA consists of 4827 regulatory interactions between 2831 nodes, which represent the interactions of TFs and SFs with their target genes, from the total of predicted RegulomePA including 27.27% of the TFs, 54.16% of SFs and 50.8% of the total genes. Each entry in the database corresponds to one node in the network and provides comprehensive details about the gene and its regulatory interactions such as gene descriptio...
Source: Database : The Journal of Biological Databases and Curation - December 1, 2020 Category: Databases & Libraries Source Type: research

A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing
AbstractBiomedical relation extraction (RE) datasets are vital in the construction of knowledge bases and to potentiate the discovery of new interactions. There are several ways to create biomedical RE datasets, some more reliable than others, such as resorting to domain expert annotations. However, the emerging use of crowdsourcing platforms, such as Amazon Mechanical Turk (MTurk), can potentially reduce the cost of RE dataset construction, even if the same level of quality cannot be guaranteed. There is a lack of power of the researcher to control who, how and in what context workers engage in crowdsourcing platforms. He...
Source: Database : The Journal of Biological Databases and Curation - December 1, 2020 Category: Databases & Libraries Source Type: research

ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls
AbstractVariants within the non-coding genome are frequently associated with phenotypes in genome-wide association studies. These non-coding regions may be involved in the regulation of gene expression, encode functional non-coding RNAs, or influence splicing and other cellular functions. We have curated a list of characterized non-coding human genome variants based on the published evidence that indicates phenotypic consequences of the variation. In order to minimize annotation errors, two curators have independently verified the supporting evidence for pathogenicity of each non-coding variant in the published literature....
Source: Database : The Journal of Biological Databases and Curation - December 1, 2020 Category: Databases & Libraries Source Type: research

KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling
AbstractThe 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 ...
Source: Database : The Journal of Biological Databases and Curation - November 28, 2020 Category: Databases & Libraries Source Type: research

BarleyVarDB: a database of barley genomic variation
AbstractBarley (Hordeum vulgare L.) is one of the first domesticated grain crops and represents the fourth most important cereal source for human and animal consumption. BarleyVarDB is a database of barley genomic variation. It can be publicly accessible through the website athttp://146.118.64.11/BarleyVar. This database mainly provides three sets of information. First, there are 57  754 224 single nuclear polymorphisms (SNPs) and 3 600 663 insertions or deletions (InDels) included in BarleyVarDB, which were identified from high-coverage whole genome sequencing of 21 barley germplasm, including 8 wild barley access...
Source: Database : The Journal of Biological Databases and Curation - November 28, 2020 Category: Databases & Libraries Source Type: research