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.An optimized relational database for querying structural patterns in proteins
This article discusses the optimization of the GSP4PDB database by implementing two techniques: denormalization and indexing. The empirical evaluation described in the article shows that combining these techniques enhances the efficiency of the database when querying both real and artificial graph –based structural patterns. (Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - January 17, 2024 Category: Databases & Libraries Source Type: research
An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP)
We presented over 289 IBD-related genes based on the database collection in the gene section. We also obtained 153 manually curated IBD transcriptomics data, including 12 388 samples, on the Gene Expression Omnibus database. The sorted IBD-related m icrobiota data from three primary microbiome databases (GMrepo, gutMega and gutMDisorder) were available for download. We selected 23 149 IBD-related taxonomic records from these databases. Additionally, we collected 24 IBD metabolomics studies with 2896 participants in the metabolomics section. W e introduced two interactive single-cell data plug-in units that provided dat...
Source: Database : The Journal of Biological Databases and Curation - January 16, 2024 Category: Databases & Libraries Source Type: research
piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation
AbstractPIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly expressed and extensively studied from the germline. piRNAs associate with PIWI proteins to maintain DNA methylation for transposon silencing and transcriptional gene regulation for genomic stability. Mature germline piRNAs have distinct characteristics including a 24- to 32-nucleotide length and a 2 ʹ-O-methylation signature at the 3ʹ end. Although recent studies have identified piRNAs in somatic tissues, they remain poorly characterized. For example, we recently demonstrated notable expression of piRNA in the murine soma, and wh...
Source: Database : The Journal of Biological Databases and Curation - January 10, 2024 Category: Databases & Libraries Source Type: research
The African Human Microbiome Portal: a public web portal of curated metagenomic metadata
AbstractThere is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it is often challenging to extract accurate metadata from public repositories. Of particular concern is the metagenomic data related to African individuals, which often omit important information about the particular features of these populations. As part of a collaborative consortium, H3ABioNet, we created a web portal, namely the African Human Microbiome Portal (AHMP), exclusively dedicated to metadata related to African human microbiome samples. Metadata were collected from various...
Source: Database : The Journal of Biological Databases and Curation - January 10, 2024 Category: Databases & Libraries Source Type: research
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV
AbstractSerious illnesses caused by viruses are becoming the world ’s most critical public health issues and lead millions of deaths each year in the world. Thousands of studies confirmed that the plant-derived medicines could play positive therapeutic effects on the patients with viral diseases. Since thousands of antiviral phytochemicals have been identified as lifesaving drugs in medical research, a comprehensive database is highly desirable to integrate the medicinal plants with their different medicinal properties. Therefore, we provided a friendly antiviral phytochemical database AVPCD covering 2537 antiviral phyto...
Source: Database : The Journal of Biological Databases and Curation - August 18, 2023 Category: Databases & Libraries Source Type: research
Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish
AbstractThe lake sturgeon(Acipenser fulvescens) is an ancient, octoploid fish faced with conservation challenges across its range in North America, but a lack of genomic resources has hindered molecular research in the species. To support such research, we created a transcriptomic database from 13 tissues: brain, esophagus, gill, head kidney, heart, white muscle, liver, glandular stomach, muscular stomach, anterior intestine, pyloric cecum, spiral valve and rectum. The transcriptomes for each tissue were sequenced and assembled individually from a mean of 98.3 million ( ±38.9 million SD) reads each. In addition, an overal...
Source: Database : The Journal of Biological Databases and Curation - August 17, 2023 Category: Databases & Libraries Source Type: research
CCIDB: a manually curated cell –cell interaction database with cell context information
AbstractCell –cell interaction (CCI) is a crucial event in the development and function of multicellular organisms. The development of CCI databases is beneficial for researchers who want to analyze single-cell sequencing data or study CCI through molecular experiments. CCIs are known to act differently accord ing to cellular and biological contexts such as cell types, gene mutations or disease status; however, previous CCI databases do not completely provide this contextual information pertaining to CCIs. We constructed a cell-cell interaction database (CCIDB) containing the biological and clinical conte xts involved in...
Source: Database : The Journal of Biological Databases and Curation - August 11, 2023 Category: Databases & Libraries Source Type: research
The MetaGens algorithm for metagenomic database lossy compression and subject alignment
AbstractThe advancement of genetic sequencing techniques led to the production of a large volume of data. The extraction of genetic material from a sample is one of the early steps of the metagenomic study. With the evolution of the processes, the analysis of the sequenced data allowed the discovery of etiological agents and, by corollary, the diagnosis of infections. One of the biggest challenges of the technique is the huge volume of data generated with each new technology developed. To introduce an algorithm that may reduce the data volume, allowing faster DNA matching with the reference databases. Using techniques like...
Source: Database : The Journal of Biological Databases and Curation - August 11, 2023 Category: Databases & Libraries Source Type: research
MineProt: a stand-alone server for structural proteome curation
AbstractAlphaFold-like systems are rapidly expanding the scale of proteome structuring, and MineProt provides an effective solution for custom curation of these novel high-throughput data. It enables researchers to build their own server in simple steps, run almost out-of-the-box scripts to annotate and curate their proteins, analyze their data via a user-friendly online interface, and utilize plugins to extend the functionality of server. It is expected to support researcher productivity and facilitate data sharing in the new era of structural proteomics.Database URL MineProt is open-source software available athttps://gi...
Source: Database : The Journal of Biological Databases and Curation - August 10, 2023 Category: Databases & Libraries Source Type: research
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria
AbstractThe TRGdb database is a resource dedicated to taxonomically restricted genes (TRGs) in bacteria. It provides a comprehensive collection of genes that are specific to different genera and species, according to the latest release of bacterial taxonomy. The user interface allows for easy browsing and searching as well as sequence similarity exploration. The website also provides information on each TRG protein sequence, including its level of disorder, complexity and tendency to aggregate. TRGdb is a valuable resource for gaining a deeper understanding of the TRG-associated, unique features, and characteristics of bac...
Source: Database : The Journal of Biological Databases and Curation - August 8, 2023 Category: Databases & Libraries Source Type: research
CiliaMiner: an integrated database for ciliopathy genes and ciliopathies
AbstractCilia are found in eukaryotic species ranging from single-celled organisms, such asChlamydomonas reinhardtii, to humans, but not in plants. The ability to respond to repellents and/or attractants, regulate cell proliferation and differentiation and provide cellular mobility are just a few examples of how crucial cilia are to cells and organisms. Over 30 distinct rare disorders generally known as ciliopathy are caused by abnormalities or functional impairments in cilia and cilia-related compartments. Because of the complexity of ciliopathies and the rising number of ciliopathies and ciliopathy genes, a ciliopathy-or...
Source: Database : The Journal of Biological Databases and Curation - July 26, 2023 Category: Databases & Libraries Source Type: research
Biomedical relation extraction with knowledge base –refined weak supervision
AbstractBiomedical relation extraction (BioRE) is the task of automatically extracting and classifying relations between two biomedical entities in biomedical literature. Recent advances in BioRE research have largely been powered by supervised learning and large language models (LLMs). However, training of LLMs for BioRE with supervised learning requires human-annotated data, and the annotation process often accompanies challenging and expensive work. As a result, the quantity and coverage of annotated data are limiting factors for BioRE systems. In this paper, we present our system for the BioCreative VII challenge —Dr...
Source: Database : The Journal of Biological Databases and Curation - July 26, 2023 Category: Databases & Libraries Source Type: research
Unified and pluralistic ideals for data sharing and reuse in biodiversity
We describe and illustrate unified and pluralistic ideals for biodiversity data pooling and show how communities may advance toward these ideals using different heuristic strategies. We present evidence for the strengths and limitations of the unification and pluralistic ideals based on systemic relationships of power, responsibility and benefit they establish among stakeholders, and we conclude the pluralistic ideal is better suited for biodiversity data. (Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - July 18, 2023 Category: Databases & Libraries Source Type: research
AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence
AbstractThe increasing prevalence of diet-related diseases calls for an improvement in nutritional advice. Personalized nutrition aims to solve this problem by adapting dietary and lifestyle guidelines to the unique circumstances of each individual. With the latest advances in technology and data science, researchers can now automatically collect and analyze large amounts of data from a variety of sources, including wearable and smart devices. By combining these diverse data, more comprehensive insights of the human body and its diseases can be achieved. However, there are still major challenges to overcome, including the ...
Source: Database : The Journal of Biological Databases and Curation - July 18, 2023 Category: Databases & Libraries Source Type: research
APDB: a database on air pollutant characterization and similarity prediction
AbstractThe World Health Organization estimates that 9 out of 10 people worldwide breathe air containing high levels of pollutants. Long-term and chronic exposure to high concentrations of air pollutants is associated with deleterious effects on vital organs, including increased inflammation in the lungs, oxidative stress in the heart and disruption of the blood –brain barrier. For this reason, in an effort to find an association between exposure to pollutants and the toxicological effects observable on human health, an online resource collecting and characterizing in detail pollutant molecules could be helpful to invest...
Source: Database : The Journal of Biological Databases and Curation - July 14, 2023 Category: Databases & Libraries Source Type: research
