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.

Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine
AbstractA timely understanding of the biological secrets of complex diseases will ultimately benefit millions of individuals by reducing the high risks for mortality and improving the quality of life with personalized diagnoses and treatments. Due to the advancements in sequencing technologies and reduced cost, genomics data are developing at an unmatched pace and levels to foster translational research and precision medicine. Over 10 million genomics datasets have been produced and publicly shared in 2022. Diverse and high-volume genomics and clinical data have the potential to broaden the scope of biological discoveries ...
Source: Database : The Journal of Biological Databases and Curation - May 17, 2023 Category: Databases & Libraries Source Type: research

scBrainMap: a landscape for cell types and associated genetic markers in the brain
AbstractThe great variety of brain cell types is a fundamental element for neuronal circuits. One major goal of modern neuroscience is to decipher the various types of cellular composition and characterize their properties. Due to the high heterogeneity of neuronal cells, until recently, it was not possible to group brain cell types at high resolution. Thanks to the single-cell transcriptome technology, a dedicated database of brain cell types across species has been established. Here, we developedscBrainMap, a database for brain cell types and associated genetic markers for several species. The currentscBrainMap database ...
Source: Database : The Journal of Biological Databases and Curation - May 17, 2023 Category: Databases & Libraries Source Type: research

SmartWoodID —an image collection of large end-grain surfaces to support wood identification systems
AbstractWood identification is a key step in the enforcement of laws and regulations aimed at combatting illegal timber trade. Robust wood identification tools, capable of distinguishing a large number of timbers, depend on a solid database of reference material. Reference material for wood identification is typically curated in botanical collections dedicated to wood consisting of samples of secondary xylem of lignified plants. Specimens from the Tervuren Wood Collection, one of the large institutional wood collections around the world, are used as a source of tree species data with potential application as timber. Here, ...
Source: Database : The Journal of Biological Databases and Curation - May 13, 2023 Category: Databases & Libraries Source Type: research

CaviDB: a database of cavities and their features in the structural and conformational space of proteins
AbstractProteins are the structural, functional and evolutionary units of cells. On their surface, proteins are shaped into numerous depressions and protrusions that provide unique microenvironments for ligand binding and catalysis. The dynamics, size and chemical properties of these cavities are essential for a mechanistic understanding of protein function. Here, we present CaviDB, a novel database of cavities and their features in known protein structures. It integrates the results of commonly used cavity detection software with protein features derived from sequence, structural and functional analyses. Each protein in C...
Source: Database : The Journal of Biological Databases and Curation - May 10, 2023 Category: Databases & Libraries Source Type: research

OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology
AbstractNumerous studies have been published which, separately, investigate the influence of molecular features on oncological and cardiac pathologies. Nevertheless, the relationship between both families of diseases at the molecular level is an emerging area within onco-cardiology/cardio-oncology. This paper presents a new open-source database that aims to organize the curated information concerning the molecular features validated in patients involved in both cancer and cardiovascular diseases. Entities like gene, variation, drug, study and others are modelled as objects of a database which is populated with curated info...
Source: Database : The Journal of Biological Databases and Curation - May 9, 2023 Category: Databases & Libraries Source Type: research

SyntenyViewer: a comparative genomics-driven translational research tool
AbstractSyntenyViewer is a public web-based tool relying on a relational database available athttps://urgi.versailles.inrae.fr/synteny delivering comparative genomics data and associated reservoir of conserved genes between angiosperm species for both fundamental (evolutionary studies) and applied (translational research) applications. SyntenyViewer is made available for (i) providing comparative genomics data for seven major botanical families of flowering plants, (ii) delivering a robust catalog of 103  465 conserved genes between 44 species and inferred ancestral genomes, (iii) allowing us to investigate the evolution...
Source: Database : The Journal of Biological Databases and Curation - May 9, 2023 Category: Databases & Libraries Source Type: research

TRSRD: a database for research on risky substances in tea using natural language processing and knowledge graph-based techniques
AbstractDuring the production and processing of tea, harmful substances are often introduced. However, they have never been systematically integrated, and it is impossible to understand the harmful substances that may be introduced during tea production and their related relationships when searching for papers. To address these issues, a database on tea risk substances and their research relationships was constructed. These data were correlated by knowledge mapping techniques, and a Neo4j graph database centered on tea risk substance research was constructed, containing 4189 nodes and 9400 correlations (e.g. research categ...
Source: Database : The Journal of Biological Databases and Curation - May 9, 2023 Category: Databases & Libraries Source Type: research

MantaID: a machine learning –based tool to automate the identification of biological database IDs
AbstractThe number of biological databases is growing rapidly, but different databases use different identifiers (IDs) to refer to the same biological entity. The inconsistency in IDs impedes the integration of various types of biological data. To resolve the problem, we developed MantaID, a data-driven, machine learning –based approach that automates identifying IDs on a large scale. The MantaID model’s prediction accuracy was proven to be 99%, and it correctly and effectively predicted 100,000 ID entries within 2 min. MantaID supports the discovery and exploitation of ID from large quantities of databases (e .g. up...
Source: Database : The Journal of Biological Databases and Curation - May 9, 2023 Category: Databases & Libraries Source Type: research

PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes
We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family —pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization—including quantitative evaluation of allosteric regulation—of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predic...
Source: Database : The Journal of Biological Databases and Curation - May 3, 2023 Category: Databases & Libraries Source Type: research

The landscape of health disparities in the UK Biobank
AbstractThe UK Biobank (UKB), a large-scale biomedical database that includes demographic and electronic health record data for more than half a million ethnically diverse participants, is a potentially valuable resource for the study of health disparities. However, publicly accessible databases that catalog health disparities in the UKB do not exist. We developed the UKB Health Disparities Browser with the aims of (i) facilitating the exploration of the landscape of health disparities in the UK and (ii) directing the attention to areas of disparities research that might have the greatest public health impact. Health dispa...
Source: Database : The Journal of Biological Databases and Curation - April 26, 2023 Category: Databases & Libraries Source Type: research

Semi-automatic translation of medicine usage data (in Dutch, free-text) from Lifelines COVID-19 questionnaires to ATC codes
AbstractThe mapping of human-entered data to codified data formats that can be analysed is a common problem across medical research and health care. To identify risk and protective factors for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) susceptibility and coronavirus disease 2019 (COVID-19) severity, frequent questionnaires were sent out to participants of the Lifelines Cohort Study starting 30 March 2020. Because specific drugs were suspected COVID-19 risk factors, the questionnaires contained multiple-choice questions about commonly used drugs and open-ended questions to capture all other drugs used. To ...
Source: Database : The Journal of Biological Databases and Curation - April 26, 2023 Category: Databases & Libraries Source Type: research

Review of databases for experimentally validated human microRNA –mRNA interactions
AbstractMicroRNAs (miRs) may contribute to disease etiology by influencing gene expression. Numerous databases are available for miR target prediction and validation, but their functionality is varied, and outputs are not standardized. The purpose of this review is to identify and describe databases for cataloging validated miR targets. Using Tools4miRs and PubMed, we identified databases with experimentally validated targets, human data, and a focus on miR –messenger RNA (mRNA) interactions. Data were extracted about the number of times each database was cited, the number of miRs, the target genes, the interactions per ...
Source: Database : The Journal of Biological Databases and Curation - April 25, 2023 Category: Databases & Libraries Source Type: research

RNA-Chrom: a manually curated analytical database of RNA –chromatin interactome
AbstractEvery year there is more and more evidence that non-coding RNAs play an important role in biological processes affecting various levels of organization of living systems: from the cellular (regulation of gene expression, remodeling and maintenance of chromatin structure, co-transcriptional suppression of transposons, splicing, post-transcriptional RNA modifications, etc.) to cell populations and even organismal ones (development, aging, cancer, cardiovascular and many other diseases). The development and creation of mutually complementary databases that will aggregate, unify and structure different types of data ca...
Source: Database : The Journal of Biological Databases and Curation - April 24, 2023 Category: Databases & Libraries Source Type: research

MBS: a genome browser annotation track for high-confident microRNA binding sites in whole human transcriptome
AbstractMicroRNAs (miRNAs) are small non-coding ribonucleic acids (RNAs) that play a role in many regulatory pathways in eukaryotes. They usually exert their functions by binding mature messenger RNAs. The prediction of the binding targets of the endogenous miRNAs is crucial to unravel the processes they are involved in. In this work, we performed an extensive miRNA binding sites (MBS) prediction over all the annotated transcript sequences and made them available through an UCSC track. MBS annotation track allows to study and visualize the human miRNA binding sites transcriptome-wide in a genome browser, together with any ...
Source: Database : The Journal of Biological Databases and Curation - April 22, 2023 Category: Databases & Libraries Source Type: research

A combinatorial approach implementing new database structures to facilitate practical data curation management of QTL, association, correlation and heritability data on trait variants
AbstractA precise description of traits is essential in genetics and genomics studies to facilitate comparative genetics and meta-analyses. It is an ongoing challenge in research and production environments to unambiguously and consistently compare traits of interest from data collected under various conditions. Despite previous efforts to standardize trait nomenclature, it remains a challenge to fully and accurately capture trait nomenclature granularity in a way that ensures long-term data sustainability in terms of the data curation processes, data management logistics and the ability to make meaningful comparisons acro...
Source: Database : The Journal of Biological Databases and Curation - April 21, 2023 Category: Databases & Libraries Source Type: research