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MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences
AbstractNucleotide sequences reference collections or databases are fundamental components in DNA barcoding and metabarcoding data analyses pipelines. In such analyses, the accurate taxonomic assignment is a crucial aspect, relying directly on the availability of comprehensive and curated reference sequence collection and its taxonomy information. The currently wide use of the mitochondrial cytochrome oxidase subunit-I (COXI) as a standard DNA barcode marker in metazoan biodiversity studies highlights the need to shed light on the availability of the related relevant information from different data sources and their eventu...
Source: Database : The Journal of Biological Databases and Curation - February 5, 2022 Category: Databases & Libraries Source Type: research

Authors ’ attitude toward adopting a new workflow to improve the computability of phenotype publications
AbstractCritical to answering large-scale questions in biology is the integration of knowledge from different disciplines into a coherent, computable whole. Controlled vocabularies such as ontologies represent a clear path toward this goal. Using survey questionnaires, we examined the attitudes of biologists toward adopting controlled vocabularies in phenotype publications. Our questions cover current experience and overall attitude with controlled vocabularies, the awareness of the issues around ambiguity and inconsistency in phenotype descriptions and post-publication professional data curation, the preferred solutions a...
Source: Database : The Journal of Biological Databases and Curation - February 2, 2022 Category: Databases & Libraries Source Type: research

phytochemdb: a platform for virtual screening and computer-aided drug designing
AbstractThe phytochemicals of medicinal plants are regarded as a rich source of diverse chemical spaces that have been used as supplements and alternative medicines in the millennium. Even in this era of combinatorial chemical drugs, phytomedicines account for a large share of the statistics of newly approved drugs. In the field of computational aided and rational drug design, there is an urgent need to develop and build a useful phytochemical database management system with a user-friendly interface that allows proper data storage, retrieval and management. We showed ‘phytochemdb’, a manually managed database that com...
Source: Database : The Journal of Biological Databases and Curation - January 28, 2022 Category: Databases & Libraries Source Type: research

Automated extraction of genes associated with antibiotic resistance from the biomedical literature
AbstractThe detection of bacterial antibiotic resistance phenotypes is important when carrying out clinical decisions for patient treatment. Conventional phenotypic testing involves culturing bacteria which requires a significant amount of time and work. Whole-genome sequencing is emerging as a fast alternative to resistance prediction, by considering the presence/absence of certain genes. A lot of research has focused on determining which bacterial genes cause antibiotic resistance and efforts are being made to consolidate these facts in knowledge bases (KBs). KBs are usually manually curated by domain experts to be of th...
Source: Database : The Journal of Biological Databases and Curation - January 20, 2022 Category: Databases & Libraries Source Type: research

CATA: a comprehensive chromatin accessibility database for cancer
AbstractAccessible chromatin refers to the active regions of a chromosome that are bound by many transcription factors (TFs). Changes in chromatin accessibility play a critical role in tumorigenesis. With the emergence of novel methods like Assay for Transposase-accessible Chromatin Sequencing, a sequencing method that maps chromatin-accessible regions (CARs) and enables the computational analysis of TF binding at chromatin-accessible sites, the regulatory landscape in cancer can be dissected. Herein, we developed a comprehensive cancer chromatin accessibility database named CATA, which aims to provide available resources ...
Source: Database : The Journal of Biological Databases and Curation - January 17, 2022 Category: Databases & Libraries Source Type: research

PlantGF: an analysis and annotation platform for plant gene families
In this study, a comprehensive query and analysis platform of plant gene families, the Plant Gene Family Platform (PlantGF), was constructed. The platform is composed of four main parts: Search, Tools, Statistics and Auxiliary. A total of 2  909 580 gene family members were identified from 138 plant species in PlantGF. The data can be queried in the Search section through a user-friendly interface. A general process for gene family analysis, having nine steps, is provided. The platform also includes four online tools (HMM-Search, B LAST, MAFFT and HMMER) in the Tools section for useful additional analyses. The statisti...
Source: Database : The Journal of Biological Databases and Curation - January 17, 2022 Category: Databases & Libraries Source Type: research

SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data
AbstractIn recent years, efficient scRNA-seq methods have been developed, enabling the transcriptome profiling of single cells massively in parallel. Meanwhile, its high dimensionality and complexity bring challenges to the data analysis and require extensive collaborations between biologists and bioinformaticians and/or biostatisticians. The communication between these two units demands a platform for easy data sharing and exploration. Here we developed Single-Cell Transcriptomics Annotated Viewer (SCANNER), as a public web resource for the scientific community, for sharing and analyzing scRNA-seq data in a collaborative ...
Source: Database : The Journal of Biological Databases and Curation - January 17, 2022 Category: Databases & Libraries Source Type: research

PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1
AbstractThe characterization of subcellular protein localization provides a basis for further understanding cellular behaviors. A delineation of subcellular localization of proteins on cytosolic membrane-bound organelles in human liver cancer cell lines (hLCCLs) has yet to be performed. To obtain its proteome-wide view, we isolated and enriched six cytosolic membrane-bound organelles in one of the hLCCLs (SK_HEP1) and quantified their proteins using mass spectrometry. The vigorous selection of marker proteins and a machine-learning-based algorithm were implemented to localize proteins at cluster and neighborhood levels. We...
Source: Database : The Journal of Biological Databases and Curation - January 17, 2022 Category: Databases & Libraries Source Type: research

SITVITBovis —a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis
AbstractLimited data are available for bovine tuberculosis and the infections it can cause in humans and other mammals. We therefore constructed a publicly accessible SITVITBovis database that incorporates genotyping and epidemiological data onMycobacterium bovis. It also includes limited data onMycobacterium caprae (previously synonymous with the nameM. bovis subsp. Caprae) that can infect both animals and humans. SITVITBovis incorporates data on 25,741 isolates corresponding to 60 countries of origin (75 countries of isolation). It reports a total of 1000 spoligotype patterns: 537 spoligotype international types (SITs, c...
Source: Database : The Journal of Biological Databases and Curation - January 13, 2022 Category: Databases & Libraries Source Type: research

Prototheca-ID: a web-based application for molecular identification of Prototheca species
This report introduces the Prototheca-ID, a user-friendly, web-based application providing fast and reliable speciation ofPrototheca isolates. In addition, the application offers the users the possibility of depositing their sequences and associated metadata in a fully open Prototheca-ID database, developed to enhance research integrity and quality in the field of Protothecae and protothecosis.Database URL: The Prototheca-ID application is available athttps://prototheca-id.org (Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - November 13, 2021 Category: Databases & Libraries Source Type: research

HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure
AbstractAs the terminal clinical phenotype of almost all types of cardiovascular diseases, heart failure (HF) is a complex and heterogeneous syndrome leading to considerable morbidity and mortality. Existing HF-related omics studies mainly focus on case/control comparisons, small cohorts of special subtypes, etc., and a large amount of multi-omics data and knowledge have been generated. However, it is difficult for researchers to obtain biological and clinical insights from these scattered data and knowledge. In this paper, we built the Heart Failure Integrated Platform (HFIP) for data exploration, fusion analysis and visu...
Source: Database : The Journal of Biological Databases and Curation - November 13, 2021 Category: Databases & Libraries Source Type: research

DCMP: database of cancer mutant protein domains
In this study, the somatic mutations across 21 cancer types were mapped to the individual protein domains. To map the mutations to the domains, we employed the whole human proteome to predic t the domains in each protein sequence and recognized about 149 668 domains. A novel Perl-API program was developed to convert the protein domain positions into genomic positions, and users can freely access them through GitHub. We determined the distribution of protein domains across 23 chromosom es with the help of these genomic positions. Interestingly, chromosome 19 has more number of protein domains in comparison with other chro...
Source: Database : The Journal of Biological Databases and Curation - November 13, 2021 Category: Databases & Libraries Source Type: research

At-C-RNA database, a one-stop source for information on circRNAs in Arabidopsis thaliana in a unified format
AbstractCircular RNAs (circRNAs) are a large class of noncoding RNAs with functions that, in most cases, remain unknown. Recent genome-wide analysis of circRNAs using RNA-Seq has revealed that circRNAs are abundant and some of them conserved in plants. Furthermore, it has been shown that the expression of circRNAs in plants is regulated in a tissue-specific manner.Arabidopsis thaliana circular RNA database is a new resource designed to integrate and standardize the data available for circRNAs in a model plantA. thaliana, which is currently the best-characterized plant in terms of circRNAs. The resource integrates all appli...
Source: Database : The Journal of Biological Databases and Curation - November 11, 2021 Category: Databases & Libraries Source Type: research

JAMIR-eQTL: Japanese genome-wide identification of microRNA expression quantitative trait loci across dementia types
AbstractMicroRNAs (miRNAs) are small non-coding RNAs shown to regulate gene expression by binding to complementary transcripts. Genetic variants, including single-nucleotide polymorphisms and short insertions/deletions, contribute to traits and diseases by influencing miRNA expression. However, the association between genetic variation and miRNA expression remains to be elucidated. Here, by using genotype data and miRNA expression data from 3448 Japanese serum samples, we developed a computational pipeline to systematically identify genome-wide miRNA expression quantitative trait loci (miR-eQTLs). Not only did we identify ...
Source: Database : The Journal of Biological Databases and Curation - November 3, 2021 Category: Databases & Libraries Source Type: research

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies
AbstractBiological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies (OBO) Foundry was created to address this by facilitating the development, harmonization, application and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the OBO principles were not originally encoded in...
Source: Database : The Journal of Biological Databases and Curation - October 26, 2021 Category: Databases & Libraries Source Type: research