Database : The Journal of Biological Databases and Curation Database : The Journal of Biological Databases and Curation RSS feedThis 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.

A curated database reveals trends in single-cell transcriptomics
AbstractThe more than 1000 single-cell transcriptomics studies that have been published to date constitute a valuable and vast resource for biological discovery. While various ‘atlas’ projects have collated some of the associated datasets, most questions related to specific tissue types, species or other attributes of studies require identifying papers through manual and challenging literature search. To facilitate discovery with published single-cell transcriptomics data, we have assembled a near exhaustive, manually curated database of single-cell transcriptomics studies with key information: descriptions of the type...
Source: Database : The Journal of Biological Databases and Curation - November 28, 2020 Category: Databases & Libraries Source Type: research

OGDA: a comprehensive organelle genome database for algae
AbstractAlgae are the oldest taxa on Earth, with an evolutionary relationship that spans prokaryotes (Cyanobacteria) and eukaryotes. A long evolutionary history has led to high algal diversity. Their organelle DNAs are characterized by uniparental inheritance and a compact genome structure compared with nuclear genomes; thus, they are efficient molecular tools for the analysis of gene structure, genome structure, organelle function and evolution. However, an integrated organelle genome database for algae, which could enable users to both examine and use relevant data, has not previously been developed. Therefore, to provid...
Source: Database : The Journal of Biological Databases and Curation - November 28, 2020 Category: Databases & Libraries Source Type: research

An informatics research platform to make public gene expression time-course datasets reusable for more scientific discoveries
AbstractThe exponential growth of genomic/genetic data in the era of Big Data demands new solutions for making these data findable, accessible, interoperable and reusable. In this article, we present a web-based platform named Gene Expression Time-Course Research (GETc) Platform that enables the discovery and visualization of time-course gene expression data and analytical results from the NIH/NCBI-sponsored Gene Expression Omnibus (GEO). The analytical results are produced from an analytic pipeline based on the ordinary differential equation model. Furthermore, in order to extract scientific insights from these results an...
Source: Database : The Journal of Biological Databases and Curation - November 28, 2020 Category: Databases & Libraries Source Type: research

VarStack: a web tool for data retrieval to interpret somatic variants in cancer
AbstractAdvances in tumor genome sequencing created an urgent need for bioinformatics tools to support the interpretation of the clinical significance of the variants detected. VarStack is a web tool which is a base to retrieve somatic variant data relating to cancer from existing databases. VarStack incorporates data from several publicly available databases and presents them with an easy-to-navigate user interface. It currently supports data from the Catalogue of Somatic Mutations in Cancer, gnomAD, cBioPortal, ClinVar, OncoKB, CiViC and UCSC Genome Browser. It retrieves the data from these databases and returns them bac...
Source: Database : The Journal of Biological Databases and Curation - November 28, 2020 Category: Databases & Libraries Source Type: research

RecipeDB: a resource for exploring recipes
AbstractCooking is the act of turning nature into the culture, which has enabled the advent of the omnivorous human diet. The cultural wisdom of processing raw ingredients into delicious dishes is embodied in their cuisines. Recipes thus are the cultural capsules that encode elaborate cooking protocols for evoking sensory satiation as well as providing nourishment. As we stand on the verge of an epidemic of diet-linked disorders, it is eminently important to investigate the culinary correlates of recipes to probe their association with sensory responses as well as consequences for nutrition and health.RecipeDB (https://cos...
Source: Database : The Journal of Biological Databases and Curation - November 25, 2020 Category: Databases & Libraries Source Type: research

Siberian sturgeon multi-tissue reference transcriptome database
We present here a high-quality transcriptome assembly database built using RNA-seq reads coming from brain, pituitary, gonadal, liver, stomach, kidney, anterior kidney, heart, embryonic and pre-larval tissues. It will facilitate crucial research on topics such as puberty, reproduction, growth, food intake and immunology. This database represents a major contribution to the publicly available sturgeon transcriptome reference datasets.Availability: The database is publicly available athttp://siberiansturgeontissuedb.sigenae.orgSupplementary information: Supplementary dataSupplementary data are available atDatabase online. (...
Source: Database : The Journal of Biological Databases and Curation - November 25, 2020 Category: Databases & Libraries Source Type: research

MetaTropismDB: a database of organ-specific metastasis induced by human cancer cell lines in mouse models
AbstractThe organotropism is the propensity of metastatic cancer cells to colonize preferably certain distant organs, resulting in a non-random distribution of metastases. In order to shed light on this behaviour, several studies were performed by the injection of human cancer cell lines into immunocompromised mouse models. However, the information about these experiments is spread in the literature. For each xenograft experiment reported in the literature, we annotated both the experimental conditions and outcomes, including details on inoculated human cell lines, mouse models, injection methods, sites of metastasis, orga...
Source: Database : The Journal of Biological Databases and Curation - November 25, 2020 Category: Databases & Libraries Source Type: research

DPL: a comprehensive database on sequences, structures, sources and functions of peptide ligands
In conclusion, DPL is a unique resource, which allows users easily to explore the targets, different structures as well as properties of peptides. (Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - November 20, 2020 Category: Databases & Libraries Source Type: research

STOREFISH 2.0: a database on the reproductive strategies of teleost fishes
AbstractTeleost fishes show the most outstanding reproductive diversity of all vertebrates. Yet to date, no one has been able to decisively explain this striking variability nor to perform large-scale phylogenetic analyses of reproductive modes. Here, we describe STrategies Of REproduction in FISH (STOREFISH) 2.0, an online database easing the sharing of an original data set on reproduction published in 2007, enriched with automated data extraction and presentation to display the knowledge acquired on temperate freshwater fish species. STOREFISH 2.0 contains the information for 80 freshwater fish species and 50 traits from...
Source: Database : The Journal of Biological Databases and Curation - November 20, 2020 Category: Databases & Libraries Source Type: research

GPCR-PEnDB: a database of protein sequences and derived features to facilitate prediction and classification of G protein-coupled receptors
We present examples of using this database along with its graphical user inter face, to query for GPCRs with specific sequence properties and to compare the accuracies of five tools for GPCR prediction. This initial version of GPCR-PEnDB will provide a framework for future extensions to include additional sequence and feature data to facilitate the design and assessment of sof tware tools and experimental studies to help understand the functional roles of GPCRs.Database URL:gpcr.utep.edu/database (Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - November 20, 2020 Category: Databases & Libraries Source Type: research

Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes
AbstractTo use published phenotype information in computational analyses, there have been efforts to convert descriptions of phenotype characters from human languages to ontologized statements. This postpublication curation process is not only slow and costly, it is also burdened with significant intercurator variation (including curator –author variation), due to different interpretations of a character by various individuals. This problem is inherent in any human-based intellectual activity. To address this problem, making scientific publications semantically clear (i.e. computable) by the authors at the time of public...
Source: Database : The Journal of Biological Databases and Curation - November 20, 2020 Category: Databases & Libraries Source Type: research

Predicted rat interactome database and gene set linkage analysis
AbstractRattus norvegicus, or the rat, has been widely used as animal models for a diversity of human diseases in the last 150 years. The rat, as a disease model, has the advantage of relatively large body size and highly similar physiology to humans. In drug discovery, rat models are routinely used in drug efficacy and toxicity assessments. To facilitate molecular pharmacology studies in rats, we present the predicted rat interactome database (PRID), which is a database of high-quality predicted functional gene interactions with balanced sensitivity and specificity. PRID integrates functional gene association data from 10...
Source: Database : The Journal of Biological Databases and Curation - November 20, 2020 Category: Databases & Libraries Source Type: research

EukRef-excavates: seven curated SSU ribosomal RNA gene databases
AbstractThe small subunit ribosomal RNA (SSU rRNA) gene is a widely used molecular marker to study the diversity of life. Sequencing of SSU rRNA gene amplicons has become a standard approach for the investigation of the ecology and diversity of microbes. However, a well-curated database is necessary for correct classification of these data. While available for many groups of Bacteria and Archaea, such reference databases are absent for most eukaryotes. The primary goal of the EukRef project (eukref.org) is to close this gap and generate well-curated reference databases for major groups of eukaryotes, especially protists. H...
Source: Database : The Journal of Biological Databases and Curation - November 20, 2020 Category: Databases & Libraries Source Type: research

WCSdb: a database of wild Coffea species
The objective of this database is to better understand and characterize the species (identification, morphology, biochemical compounds, genetic diversity and sequence data) in order to better protect and promote them.Database URLhttp://publish.plantnet-project.org/project/wildcofdb_en (Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - November 20, 2020 Category: Databases & Libraries Source Type: research

CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats
AbstractThe genomics era is resulting in the generation of a plethora of biological sequences that are usually stored in public databases. There are many computational tools that facilitate the annotation of these sequences, but sometimes they produce mistakes that enter the databases and can be propagated when erroneous data are used for secondary analyses, such as gene prediction or homology searching. While developing a computational gene finder based on protein-coding sequences, we discovered that the reference UniProtKB protein database is contaminated with some spurious sequences translated from DNA containing cluste...
Source: Database : The Journal of Biological Databases and Curation - November 18, 2020 Category: Databases & Libraries Source Type: research