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.

CARD*Shark: automated prioritization of literature curation for the Comprehensive Antibiotic Resistance Database
AbstractScientific literature is published at a rate that makes manual data extraction a highly time-consuming task. The Comprehensive Antibiotic Resistance Database (CARD) utilizes literature to curate information on antimicrobial resistance genes and to enable time-efficient triage of publications we have developed a classification algorithm for identifying publications describing first reports of new resistance genes. Trained on publications contained in the CARD, CARD*Shark downloads, processes and identifies publications recently added to PubMed that should be reviewed by biocurators. With CARD*Shark, we can minimize ...
Source: Database : The Journal of Biological Databases and Curation - April 20, 2023 Category: Databases & Libraries Source Type: research

Correction to: Standardized naming of microbiome samples in Genomes OnLine Database
(Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - April 20, 2023 Category: Databases & Libraries Source Type: research

NbThermo: a new thermostability database for nanobodies
We present NbThermo —a first-in-class database that collects melting temperatures (Tm), amino acid sequences and several other categories of useful data for hundreds of nanobodies (Nbs), compiled from an extensive literature search. This so-far unique database currently contains up-to-date, manually curated data for 564 Nbs. It represents a contribution to efforts aimed at developing new algorithms for reliableTm prediction to assist Nb engineering for a wide range of applications of these unique biomolecules. Nbs from the two most common source organisms —llama and camel—show similar distributions of melting tempera...
Source: Database : The Journal of Biological Databases and Curation - April 12, 2023 Category: Databases & Libraries Source Type: research

PurificationDB: database of purification conditions for proteins
AbstractThe isolation of proteins of interest from cell lysates is an integral step to study protein structure and function. Liquid chromatography is a technique commonly used for protein purification, where the separation is performed by exploiting the differences in physical and chemical characteristics of proteins. The complex nature of proteins requires researchers to carefully choose buffers that maintain stability and activity of the protein while also allowing for appropriate interaction with chromatography columns. To choose the proper buffer, biochemists often search for reports of successful purification in the l...
Source: Database : The Journal of Biological Databases and Curation - April 3, 2023 Category: Databases & Libraries Source Type: research

PDC: a highly compact file format to store protein 3D coordinates
AbstractRecent improvements in computational and experimental techniques for obtaining protein structures have resulted in an explosion of 3D coordinate data. To cope with the ever-increasing sizes of structure databases, this work proposes the Protein Data Compression (PDC) format, which compresses coordinates and temperature factors of full-atomic and C α-only protein structures. Without loss of precision, PDC results in 69% to 78% smaller file sizes than Protein Data Bank (PDB) and macromolecular Crystallographic Information File (mmCIF) files with standard GZIP compression. It uses ∼60% less space than existing comp...
Source: Database : The Journal of Biological Databases and Curation - April 3, 2023 Category: Databases & Libraries Source Type: research

Assessing the use of supplementary materials to improve genomic variant discovery
AbstractThe curation of genomic variants requires collecting evidence not only in variant knowledge bases but also in the literature. However, some variants result in no match when searched in the scientific literature. Indeed, it has been reported that a significant subset of information related to genomic variants are not reported in the full text, but only in the supplementary materials associated with a publication. In the study, we present an evaluation of the use of supplementary data (SD) to improve the retrieval of relevant scientific publications for variant curation. Our experiments show that searching SD enables...
Source: Database : The Journal of Biological Databases and Curation - March 31, 2023 Category: Databases & Libraries Source Type: research

Improved insights into the SABIO-RK database via visualization
AbstractSABIO-RK is a database for biochemical reactions and their kinetics. Data in SABIO-RK are inherently multidimensional and complex. The complex relationships between the data are often difficult to follow or even not represented when using standard tabular views. With an increasing number of data points the mismatch between tables and insights becomes more obvious, and getting an overview of the data becomes harder. Such complex data benefit from being presented using specially adapted visual tools. Visualization is a natural and user-friendly way to quickly get an overview of the data and to detect clusters and out...
Source: Database : The Journal of Biological Databases and Curation - March 31, 2023 Category: Databases & Libraries Source Type: research

A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade
AbstractThere is an urgent need for high-quality biodiversity data in the context of rapid environmental change. Nowhere is this need more urgent than in the deep ocean, with the possibility of seabed mining moving from exploration to exploitation, but where vast knowledge gaps persist. Regions of the seabed beyond national jurisdiction, managed by the International Seabed Authority (ISA), are undergoing intensive mining exploration, including the Clarion –Clipperton Zone (CCZ) in the Central Pacific. In 2019, the ISA launched its database ‘DeepData’, publishing environmental (including biological) data. Here, we exp...
Source: Database : The Journal of Biological Databases and Curation - March 30, 2023 Category: Databases & Libraries Source Type: research

FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes
AbstractProteins ’ molecular weight (MW) and isoelectric point (pI) are crucial for their subcellular localization and subsequent function. These are also useful in 2D gel electrophoresis, liquid chromatography –mass spectrometry and X-ray protein crystallography. Moreover, visualizations like a virtual 2D proteome map ofpI vs. MW are worthwhile to discuss the proteome diversity among different species. Although the genome sequence data of the fungi kingdom improved enormously, the proteomic details have been poorly elaborated. Therefore, we have calculated the MW andpI of the fungi proteins and reported them in, Fungi...
Source: Database : The Journal of Biological Databases and Curation - March 16, 2023 Category: Databases & Libraries Source Type: research

AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold
We report the results of AFTM together with those of UniProt, HTP, TmAlphaFold, PDBTM and Membranome in the online AFTM database compiled as a comprehensive resource of candidate human TMPs with structural models.Database URLhttp://conglab.swmed.edu/AFTM (Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - March 14, 2023 Category: Databases & Libraries Source Type: research

dbAQP-SNP: a database of missense single-nucleotide polymorphisms in human aquaporins
In this study, we have compiled 2798 SNPs that give rise to missense mutations in 13 human AQPs. To understand the nature of missense substitutions, we have systematically analyzed the pattern of substitutions. We found several examples in which substitutions could be considered as non-conservative that include small to big or hydrophobic to charged residues. We also analyzed these substitutions in the context of structure. We have identified SNPs that occur in NPA motifs or Ar/R SFs, and they will most certainly disrupt the structure and/or transport properties of human AQPs. We found 22 examples in which missense SNP sub...
Source: Database : The Journal of Biological Databases and Curation - March 13, 2023 Category: Databases & Libraries Source Type: research

Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII
AbstractThe BioCreative National Library of Medicine (NLM)-Chem track calls for a community effort to fine-tune automated recognition of chemical names in the biomedical literature. Chemicals are one of the most searched biomedical entities in PubMed, and —as highlighted during the coronavirus disease 2019 pandemic—their identification may significantly advance research in multiple biomedical subfields. While previous community challenges focused on identifying chemical names mentioned in titles and abstracts, the full text contains valuable addi tional detail. We, therefore, organized the BioCreative NLM-Chem track as...
Source: Database : The Journal of Biological Databases and Curation - March 7, 2023 Category: Databases & Libraries Source Type: research

lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs
AbstractLong non-coding ribonucleic acids (lncRNAs) account for the largest group of non-coding RNAs. However, knowledge about their function and regulation is limited. lncHUB2 is a web server database that provides known and inferred knowledge about the function of 18  705 human and 11 274 mouse lncRNAs. lncHUB2 produces reports that contain the secondary structure fold of the lncRNA, related publications, the most correlated coding genes, the most correlated lncRNAs, a network that visualizes the most correlated genes, predicted mouse phenotypes, predicted m embership in biological processes and pathways, predicted u...
Source: Database : The Journal of Biological Databases and Curation - March 4, 2023 Category: Databases & Libraries Source Type: research

WASP: the World Archives of Species Perception
AbstractWhile human perception can play a role in influencing public support for species conservation, the mechanisms underlying human perception remain poorly understood. Some previous studies on perception have focused on a few specific taxa, which makes the understanding of the public perception of species at large a resource- and time-intensive task. Here, we introduce the World Archives of Species Perception project that consists of an animal survey and a plant survey to construct the first systematic database to study the human perception of the floral and faunal diversity at a global scale. We provide a description ...
Source: Database : The Journal of Biological Databases and Curation - February 28, 2023 Category: Databases & Libraries Source Type: research

Assessing resource use: a case study with the Human Disease Ontology
AbstractAs a genomic resource provider, grappling with getting a handle on how your resource is utilized can be extremely challenging. At the same time, being able to thus document the plethora of use cases is vital to demonstrate sustainability. Herein, we describe a flexible workflow, built on readily available software, that the Human Disease Ontology (DO) project has utilized to transition to semi-automated methods to identify uses of the ontology in the published literature. The novel R package DO.utils (https://github.com/DiseaseOntology/DO.utils) has been devised with a small set of key functions to support our usag...
Source: Database : The Journal of Biological Databases and Curation - February 28, 2023 Category: Databases & Libraries Source Type: research