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.

The importance of  graph databases and graph learning for clinical applications
AbstractThe increasing amount and complexity of clinical data require an appropriate way of storing and analyzing those data. Traditional approaches use a tabular structure (relational databases) for storing data and thereby complicate storing and retrieving interlinked data from the clinical domain. Graph databases provide a great solution for this by storing data in a graph as nodes (vertices) that are connected by edges (links). The underlying graph structure can be used for the subsequent data analysis (graph learning). Graph learning consists of two parts: graph representation learning and graph analytics. Graph repre...
Source: Database : The Journal of Biological Databases and Curation - July 10, 2023 Category: Databases & Libraries Source Type: research

VariantHunter: a method and  tool for fast detection of emerging SARS-CoV-2 variants
AbstractWith the progression of the COVID-19 pandemic, large datasets of SARS-CoV-2 genome sequences were collected to closely monitor the evolution of the virus and identify the novel variants/strains. By analyzing genome sequencing data, health authorities can ‘hunt’ novel emerging variants of SARS-CoV-2 as early as possible, and then monitor their evolution and spread. We designed VariantHunter, a highly flexible and user-friendly tool for systematically monitoring the evolution of SARS-CoV-2 at global and regional levels. In VariantHunter, amino aci d changes are analyzed over an interval of 4 weeks in an arbitra...
Source: Database : The Journal of Biological Databases and Curation - July 6, 2023 Category: Databases & Libraries Source Type: research

PearMODB: a multiomics database for  pear (Pyrus) genomics, genetics and breeding study
AbstractPear (Pyrus ssp.) belongs to Rosaceae and is an important fruit tree widely cultivated around the world. Currently, challenges to cope with the burgeoning sets of multiomics data are rapidly increasing. Here, we constructed the Pear Multiomics Database (PearMODB) by integrating genome, transcriptome, epigenome and population variation data, and aimed to provide a portal for accessing and analyzing pear multiomics data. A variety of online tools were built including gene search, BLAST, JBrowse, expression heatmap, synteny analysis and primer design. The information of DNA methylation sites and single-nucleotide poly...
Source: Database : The Journal of Biological Databases and Curation - July 6, 2023 Category: Databases & Libraries Source Type: research

Correction to: RNA-Chrom: a manually curated analytical database of  RNA–chromatin interactome
(Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - July 1, 2023 Category: Databases & Libraries Source Type: research

CropGF: a comprehensive visual platform for  crop gene family mining and analysis
AbstractA gene family refers to a group of genes that share a common ancestry and encode proteins or RNA molecules with similar functions or structural features. Gene families play a crucial role in determining the traits of plants and can be utilized to develop new crop varieties. Therefore, a comprehensive database of gene family is significant for gaining deep insight into crops. To address this need, we have developed CropGF (https://bis.zju.edu.cn/cropgf), a comprehensive visual platform that encompasses six important crops (rice, wheat, maize, barley, sorghum and foxtail millet) and one model plant (Arabidopsis), as ...
Source: Database : The Journal of Biological Databases and Curation - July 1, 2023 Category: Databases & Libraries Source Type: research

GeniePool: genomic database with corresponding annotated samples based on  a cloud data lake architecture
AbstractIn recent years, there are a huge influx of genomic data and a growing need for its phenotypic correlations, yet existing genomic databases do not allow easy storage and accessibility to the combined phenotypic –genotypic information. Freely accessible allele frequency (AF) databases, such as gnomAD, are crucial for evaluating variants but lack correlated phenotype data. The Sequence Read Archive (SRA) accumulates hundreds of thousands of next-generation sequencing (NGS) samples tagged by their submitter s and various attributes. However, samples are stored in large raw format files, inaccessible for a common use...
Source: Database : The Journal of Biological Databases and Curation - June 13, 2023 Category: Databases & Libraries Source Type: research

Neodb: a comprehensive neoantigen database and  discovery platform for cancer immunotherapy
AbstractNeoantigens derived from somatic deoxyribonucleic acid alterations are ideal cancer-specific targets. However, integrated platform for neoantigen discovery is urgently needed. Recently, many scattered experimental evidences suggest that some neoantigens are immunogenic, and comprehensive collection of these experimentally validated neoantigens is still lacking. Here, we have integrated the commonly used tools in the current neoantigen discovery process to form a comprehensive web-based analysis platform. To identify experimental evidences supporting the immunogenicity of neoantigens, we performed comprehensive lite...
Source: Database : The Journal of Biological Databases and Curation - June 13, 2023 Category: Databases & Libraries Source Type: research

PETCH-DB: a Portal for  Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines
AbstractEpigenetic modifications play critical roles in gene regulation and disease pathobiology. Highly sensitive enabling technologies, including microarray- and sequencing-based approaches have allowed genome-wide profiling of cytosine modifications in DNAs in clinical samples to facilitate discovery of epigenetic biomarkers for disease diagnosis and prognosis. Historically, many previous studies, however, did not distinguish the most investigated 5-methylcytosines (5mC) from other modified cytosines, especially the biochemically stable  5-hydroxymethylcytosines (5hmC), which have been shown to have a distinct genomic ...
Source: Database : The Journal of Biological Databases and Curation - June 10, 2023 Category: Databases & Libraries Source Type: research

PLBD: protein –ligand binding database of thermodynamic and kinetic intrinsic parameters
AbstractWe introduce a protein –ligand binding database (PLBD) that presents thermodynamic and kinetic data of reversible protein interactions with small molecule compounds. The manually curated binding data are linked to protein–ligand crystal structures, enabling structure–thermodynamics correlations to be determined. The database contains over 5500 binding datasets of 556 sulfonamide compound interactions with the 12 catalytically active human carbonic anhydrase isozymes defined by fluorescent thermal shift assay, isothermal titration calorimetry, inhibition of enzymatic activity and surface plasmon resonance. In ...
Source: Database : The Journal of Biological Databases and Curation - June 8, 2023 Category: Databases & Libraries Source Type: research

IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2)
AbstractIndian Himalayan metagenome database (IHM-DB) is a web-based database consisting of information on metagenomic datasets from various databases and publications that are specifically reported from the Indian Himalayan Region (IHR). The online interface allows users to view or download the dataset-specific information for the respective states, category-wise, or according to the hypervariable region. The IHM-DB also provides an opportunity for the users to access the metagenomic publications from the IHR as well as upload their microbiome information to the website. Additionally, an open-source 16S rRNA amplicon-base...
Source: Database : The Journal of Biological Databases and Curation - June 3, 2023 Category: Databases & Libraries Source Type: research

ChagasDB: 80 years of publicly available data on the molecular host response to Trypanosoma cruzi infection in a single database
AbstractChagas disease is a parasitical disease caused byTrypanosoma cruzi which affects ∼7 million people worldwide. Per year, ∼10 000 people die from this pathology. Indeed, ∼30% of humans develop severe chronic forms, including cardiac, digestive or neurological disorders, for which there is still no treatment. In order to facilitate research on Chagas disease, a manual curat ion of all papers corresponding to ‘Chagas disease’ referenced on PubMed has been performed. All deregulated molecules in hosts (all mammals, humans, mice or others) followingT. cruzi infection were retrieved and included in a database,...
Source: Database : The Journal of Biological Databases and Curation - May 26, 2023 Category: Databases & Libraries Source Type: research

CIGAF —a database and interactive platform for insect-associated trichomycete fungi
We present CIGAF (short for Collections of Insect Gut –Associated Fungi), a trichomycetes-focused digital database with interactive visualization functions enabled by the R Shiny web application. CIGAF curated 3120 collection records of trichomycetes across the globe, spanning from 1929 to 2022. CIGAF allows the exploration of nearly 100 years of f ield collection data through the web interface, including primary published data such as insect host information, collection site coordinates, descriptions and date of collection. When possible, specimen records are supplemented with climatic measures at collection sites. As...
Source: Database : The Journal of Biological Databases and Curation - May 23, 2023 Category: Databases & Libraries Source Type: research

BLAB2CancerKD: a knowledge graph database focusing on the association between lactic acid bacteria and cancer, but beyond
AbstractIn a broad sense, lactic acid bacteria (LAB) is a general term for Gram-positive bacteria that can produce lactic acid by utilizing fermentable carbohydrates. It is widely used in essential fields such as industry, agriculture, animal husbandry and medicine. At the same time, LAB are closely related to human health. They can regulate human intestinal flora and improve gastrointestinal function and body immunity. Cancer, a disease in which some cells grow out of control and spread to other body parts, is one of the leading causes of human death worldwide. In recent years, the potential of LAB in cancer treatment has...
Source: Database : The Journal of Biological Databases and Curation - May 23, 2023 Category: Databases & Libraries Source Type: research

CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines
AbstractEnhancers, which are key tumorigenic factors with wide applications for subtyping, diagnosis and treatment of cancer, are attracting increasing attention in the cancer research. However, systematic analysis of cancer enhancers poses a challenge due to the lack of integrative data resources, especially those from tumor primary tissues. To provide a comprehensive enhancer profile across cancer types, we developed a cancer enhancer database CenhANCER by curating public resources including all the public H3K27ac ChIP-Seq data from 805 primary tissue samples and 671 cell line samples across 41 cancer types. In total, 57...
Source: Database : The Journal of Biological Databases and Curation - May 18, 2023 Category: Databases & Libraries Source Type: research

Developing TeroENZ and TeroMAP modules for the terpenome research platform TeroKit
AbstractTerpenoids and their derivatives are collectively known as the terpenome and are the largest class of natural products, whose biosynthesis refers to various kinds of enzymes. To date, there is no terpenome-related enzyme database, which is a desire for enzyme mining, metabolic engineering and discovery of new natural products related to terpenoids. In this work, we have constructed a comprehensive database called TeroENZ (http://terokit.qmclab.com/browse_enz.html) containing 13  462 enzymes involved in the terpenoid biosynthetic pathway, covering 2541 species and 4293 reactions reported in the literature and publ...
Source: Database : The Journal of Biological Databases and Curation - May 18, 2023 Category: Databases & Libraries Source Type: research