Database : The Journal of Biological Databases and Curation 
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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.AIMedGraph: a comprehensive multi-relational knowledge graph for precision medicine
AbstractThe development of high-throughput molecular testing techniques has enabled the large-scale exploration of the underlying molecular causes of diseases and the development of targeted treatment for specific genetic alterations. However, knowledge to interpret the impact of genetic variants on disease or treatment is distributed in different databases, scientific literature studies and clinical guidelines. AIMedGraph was designed to comprehensively collect and interrogate standardized information about genes, genetic alterations and their therapeutic and diagnostic relevance and build a multi-relational, evidence-bas...
Source: Database : The Journal of Biological Databases and Curation - February 28, 2023 Category: Databases & Libraries Source Type: research
Standardized naming of microbiome samples in Genomes OnLine Database
AbstractThe power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to c...
Source: Database : The Journal of Biological Databases and Curation - February 16, 2023 Category: Databases & Libraries Source Type: research
Coronavirus Immunotherapeutic Consortium Database
AbstractThe coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seen multiple anti-SARS-CoV-2 antibodies being generated globally. It is difficult, however, to assemble a useful compendium of these biological properties if they are derived from experimental measurements performed at different sites under different experimental conditions. The Coronavirus Immunotherapeutic Consortium (COVIC) circumvents these issues by experimentally testing blinded antibodies side by side for several functional activities. To collect these data in a consistent fashion ...
Source: Database : The Journal of Biological Databases and Curation - February 10, 2023 Category: Databases & Libraries Source Type: research
SalivaDB —a comprehensive database for salivary biomarkers in humans
AbstractSaliva as a non-invasive diagnostic fluid has immense potential as a tool for early diagnosis and prognosis of patients. The information about salivary biomarkers is broadly scattered across various resources and research papers. It is important to bring together all the information on salivary biomarkers to a single platform. This will accelerate research and development in non-invasive diagnosis and prognosis of complex diseases. We collected widespread information on five types of salivary biomarkers —proteins, metabolites, microbes, micro-ribonucleic acid (miRNA) and genes found in humans. This information wa...
Source: Database : The Journal of Biological Databases and Curation - February 7, 2023 Category: Databases & Libraries Source Type: research
Automatic Extraction of Medication Mentions from Tweets —Overview of the BioCreative VII Shared Task 3 Competition
This study presents the outcomes of the shared task competition BioCreative VII (Task 3) focusing on the extraction of medication names from a Twitter user ’s publicly available tweets (the user’s ‘timeline’). In general, detecting health-related tweets is notoriously challenging for natural language processing tools. The main challenge, aside from the informality of the language used, is that people tweet about any and all topics, and most of their tweets are not related to health. Thus, finding those tweets in a user’s timeline that mention specific health-related concepts such as medications requires addressin...
Source: Database : The Journal of Biological Databases and Curation - February 3, 2023 Category: Databases & Libraries Source Type: research
ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations
AbstractENCD (http://www.bio-server.cn/ENCD/) is a manually curated database that provides comprehensive experimentally supported associations among endocrine system diseases (ESDs) and long non-coding ribonucleic acid (lncRNAs). The incidence of ESDs has increased in recent years, often accompanying other chronic diseases, and can lead to disability. A growing body of research suggests that lncRNA plays an important role in the progression and metastasis of ESDs. However, there are no resources focused on collecting and integrating the latest and experimentally supported lncRNA –ESD associations. Hence, we developed an ...
Source: Database : The Journal of Biological Databases and Curation - January 19, 2023 Category: Databases & Libraries Source Type: research
New approaches in developing medicinal herbs databases
AbstractMedicinal herbs databases have become a crucial part of organizing new scientific literature generated in medicinal herbs field, as well as new drug discoveries in the information era. The aim of this review was to track the current status of medicinal herbs databases. Search for finding medicinal herbs databases was carried out via Google and PubMed. PubMed was searched for papers introducing medicinal herbs databases by the recruited search strategy. Papers with an active database on the web were included in the review. Google was also searched for medicinal herbs databases. Both retrieved papers and databases we...
Source: Database : The Journal of Biological Databases and Curation - January 10, 2023 Category: Databases & Libraries Source Type: research
Developing a disease-specific annotation protocol for VHL gene curation using Hypothes.is
AbstractVon Hippel –Lindau (VHL) disease is a rare, autosomal dominant disorder that predisposes individuals to developing tumors in many organs. There is significant phenotypic variability and genetic variants encountered within this syndrome, posing a considerable challenge to patient care. The lack ofVHL variant data sharing paired with the absence of aggregated genotype –phenotype information results in an arduous process, when characterizing genetic variants and predicting patient prognosis. To address these gaps in knowledge, the Clinical Genome Resource (ClinGen) VHL Variant Curation Expert Panel (VCEP) has been...
Source: Database : The Journal of Biological Databases and Curation - January 6, 2023 Category: Databases & Libraries Source Type: research
BCSCdb: a database of biomarkers of cancer stem cells
AbstractCancer stem cells (CSCs) are a small heterogeneous population present within the tumor cells exhibiting self-renewal properties. CSCs have been demonstrated to elicit an important role in cancer recurrence, metastasis and drug resistance. CSCs are distinguished from cancer cell populations based on their molecular profiling or expression of distinct CSC biomarker(s). Recently, a huge amount of omics data have been generated for the characterization of CSCs, which enables distinguishing CSCs in different cancers. Here, we report biomarkers of the Cancer Stem Cells database (BCSCdb), a repository of information about...
Source: Database : The Journal of Biological Databases and Curation - September 28, 2022 Category: Databases & Libraries Source Type: research
ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome
AbstractChemical probes are important tools to investigate the function of proteins, evaluate their potential as therapeutic targets and provide chemical starting points for drug discovery. As a result, a growing federation of scientists aims to generate chemical probes for all human druggable proteins. A diverse array of data typically guides target selection and chemical probe discovery: information on protein function can help prioritize targets, domain architecture can provide insight on druggability, structural data enables molecular design and existing chemical ligands can serve as foundation or inspiration for chemi...
Source: Database : The Journal of Biological Databases and Curation - September 27, 2022 Category: Databases & Libraries Source Type: research
DGPD: a knowledge database of dense granule proteins of the Apicomplexa
AbstractApicomplexan parasites cause severe diseases in human and livestock. Dense granule proteins (GRAs), specific to the Apicomplexa, participate in the maintenance of intracellular parasitism of host cells. GRAs have better immunogenicity and they can be emerged as important players in vaccine development. Although studies on GRAs have increased gradually in recent years, due to incompleteness and complexity of data collection, biologists have difficulty in the comprehensive utilization of information. Thus, there is a desperate need of user-friendly resource to integrate with existing GRAs. In this paper, we developed...
Source: Database : The Journal of Biological Databases and Curation - September 27, 2022 Category: Databases & Libraries Source Type: research
TFLink: an integrated gateway to access transcription factor –target gene interactions for multiple species
AbstractAnalysis of transcriptional regulatory interactions and their comparisons across multiple species are crucial for progress in various fields in biology, from functional genomics to the evolution of signal transduction pathways. However, despite the rapidly growing body of data on regulatory interactions in several eukaryotes, no databases exist to provide curated high-quality information on transcription factor –target gene interactions for multiple species. Here, we address this gap by introducing the TFLink gateway, which uniquely provides experimentally explored and highly accurate information on transcription...
Source: Database : The Journal of Biological Databases and Curation - September 16, 2022 Category: Databases & Libraries Source Type: research
COTTONOMICS: a comprehensive cotton multi-omics database
AbstractThe rapid advancement of sequencing technology, including next-generation sequencing (NGS), has greatly improved sequencing efficiency and decreased cost. Consequently, huge amounts of genomic, transcriptomic and epigenetic data concerning cotton species have been generated and released. These large-scale data provide immense opportunities for the study of cotton genomic structure and evolution, population genetic diversity and genome-wide mining of excellent genes for important traits. However, the complexity of NGS data also causes distress, as it cannot be utilized easily. Here, we presented the cotton omics dat...
Source: Database : The Journal of Biological Databases and Curation - September 12, 2022 Category: Databases & Libraries Source Type: research
AGODB: a comprehensive domain annotation database of argonaute proteins
AbstractArgonaute (Ago) proteins are widely expressed in almost all organisms. Eukaryotic Ago (eAgo) proteins bind small RNA guides forming RNA-induced silencing complex that silence gene expression, and prokaryotic Ago (pAgo) proteins defend against invading nucleic acids via binding small RNAs or DNAs. pAgo proteins have shown great potential as a candidate ‘scissors’ for gene editing. Protein domains are fundamental units of protein structure, function and evolution; however, the domains of Ago proteins are not well annotated/curated currently. Therefore, full functional domain annotation of Ago proteins is urgently...
Source: Database : The Journal of Biological Databases and Curation - September 7, 2022 Category: Databases & Libraries Source Type: research
CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota)
AbstractCarrotOmics (https://carrotomics.org/) is a comprehensive database for carrot (Daucus carota L.) breeding and research. CarrotOmics was developed using resources available at the MainLab Bioinformatics core (https://www.bioinfo.wsu.edu/) and is implemented using Tripal with Drupal modules. The database delivers access to download or visualize the carrot reference genome with gene predictions, gene annotations and sequence assembly. Other genomic resources include information for 11 224 genetic markers from 73 linkage maps or genotyping-by-sequencing and descriptions of 371 mapped loci. There are records for 1601...
Source: Database : The Journal of Biological Databases and Curation - September 7, 2022 Category: Databases & Libraries Source Type: research
