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.

Gene Ontology curation of the blood –brain barrier to improve the analysis of Alzheimer’s and other neurological diseases
AbstractThe role of the blood –brain barrier (BBB) in Alzheimer’s and other neurodegenerative diseases is still the subject of many studies. However, those studies using high-throughput methods have been compromised by the lack of Gene Ontology (GO) annotations describing the role of proteins in the normal function of the BB B. The GO Consortium provides a gold-standard bioinformatics resource used for analysis and interpretation of large biomedical data sets. However, the GO is also used by other research communities and, therefore, must meet a variety of demands on the breadth and depth of information that is provide...
Source: Database : The Journal of Biological Databases and Curation - October 26, 2021 Category: Databases & Libraries Source Type: research

Mining drug –target and drug–adverse drug reaction databases to identify target–adverse drug reaction relationships
AbstractThe level of attrition on drug discovery, particularly at advanced stages, is very high due to unexpected adverse drug reactions (ADRs) caused by drug candidates, and thus, being able to predict undesirable responses when modulating certain protein targets would contribute to the development of safer drugs and have important economic implications. On the one hand, there are a number of databases that compile information of drug –target interactions. On the other hand, there are a number of public resources that compile information on drugs and ADR. It is therefore possible to link target and ADRs using drug entit...
Source: Database : The Journal of Biological Databases and Curation - October 22, 2021 Category: Databases & Libraries Source Type: research

MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses
AbstractThe recent viral outbreaks and the current pandemic situation urges us to timely address any emerging viral infections by designing therapeutic strategies. Multi-omics and therapeutic data are of great interest to develop early remedial interventions. This work provides a therapeutic data platform (Mammarenavirus (MMV)-db) for pathogenic mammarenaviruses with potential catastrophic effects on human health around the world. The database integrates vaccinomics and RNA-based therapeutics data for seven human pathogenic MMVs associated with severe viral hemorrhagic fever and lethality in humans. Protein-specific cytoto...
Source: Database : The Journal of Biological Databases and Curation - October 22, 2021 Category: Databases & Libraries Source Type: research

The World Spider Trait database: a centralized global open repository for curated data on spider traits
AbstractSpiders are a highly diversified group of arthropods and play an important role in terrestrial ecosystems as ubiquitous predators, which makes them a suitable group to test a variety of eco-evolutionary hypotheses. For this purpose, knowledge of a diverse range of species traits is required. Until now, data on spider traits have been scattered across thousands of publications produced for over two centuries and written in diverse languages. To facilitate access to such data, we developed an online database for archiving and accessing spider traits at a global scale. The database has been designed to accommodate a g...
Source: Database : The Journal of Biological Databases and Curation - October 15, 2021 Category: Databases & Libraries Source Type: research

https://botryosphaeriales.org/, an online platform for up-to-date classification and account of taxa of Botryosphaeriales
AbstractFungi are eukaryotes that inhabit various ecosystems worldwide and have a decomposing effect that other organisms cannot replace. Fungi are divided into two main groups depending on how their sexual spores are formed, viz. Ascomycota and Basidiomycota. The members of Botryosphaeriales (Dothideomycetes, Ascomycota) are ubiquitous. They are pathogenic on a wide range of hosts, causing diverse diseases including dieback, canker, leaf spots and root rots and are also reported as saprobes and endophytes worldwide. As an important fungal group, of which most are plant pathogens, it is necessary to organize data and infor...
Source: Database : The Journal of Biological Databases and Curation - October 15, 2021 Category: Databases & Libraries Source Type: research

HBFP: a new repository for human body fluid proteome
In this study, we developed a new database of human body fluid proteome (HBFP) that focuses on experimentally validated proteome in 17 types of human body fluids. The current database archives 11  827 unique proteins reported by 164 scientific publications, with a maximal false discovery rate of 0.01 on both the peptide and protein levels since 2001, and enables users to query, analyze and download protein entries with respect to each body fluid. Three unique features of this new system in clude the following: (i) the protein annotation page includes detailed abundance information based on relative qualitative measures o...
Source: Database : The Journal of Biological Databases and Curation - October 13, 2021 Category: Databases & Libraries Source Type: research

Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market
AbstractFollowing the European Commission No. 1332/2008 regulation and the consequent necessity of a scientific evaluation of food enzymes (FEs) for their approval for sale on the European Union market, many FE dossiers have been submitted to the European Commission and various documents currently co-exist. In order to centralize all relevant information in one structured location that is easily accessible to support enforcement laboratories and the competent authorities, we developed a web application, called Food Enzyme Database (FEDA). FEDA allows searching and collection of information originating from many different s...
Source: Database : The Journal of Biological Databases and Curation - October 9, 2021 Category: Databases & Libraries Source Type: research

Classifying domain-specific text documents containing ambiguous keywords
AbstractA keyword-based search of comprehensive databases such as PubMed may return irrelevant papers, especially if the keywords are used in multiple fields of study. In such cases, domain experts (curators) need to verify the results and remove the irrelevant articles. Automating this filtering process will save time, but it has to be done well enough to ensure few relevant papers are rejected and few irrelevant papers are accepted. A good solution would be fast, work with the limited amount of data freely available (full paper body may be missing), handle ambiguous keywords and be as domain-neutral as possible. In this ...
Source: Database : The Journal of Biological Databases and Curation - September 29, 2021 Category: Databases & Libraries Source Type: research

COVIDium: a COVID-19 resource compendium
AbstractThe severe acute respiratory syndrome coronavirus 2 that causes coronavirus disease 2019 (COVID-19) disrupted the normal functioning throughout the world since early 2020 and it continues to do so. Nonetheless, the global pandemic was taken up as a challenge by researchers across the globe to discover an effective cure, either in the form of a drug or vaccine. This resulted in an unprecedented surge of experimental and computational data and publications, which often translated their findings in the form of databases (DBs) and tools. Over 160 such DBs and more than 80 software tools were developed, which are unchar...
Source: Database : The Journal of Biological Databases and Curation - September 29, 2021 Category: Databases & Libraries Source Type: research

EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species
AbstractEpiSurf is a Web application for selecting viral populations of interest and then analyzing how their amino acid changes are distributed along epitopes. Viral sequences are searched within ViruSurf, which stores curated metadata and amino acid changes imported from the most widely used deposition sources for viral databases (GenBank, COVID-19 Genomics UK (COG-UK) and Global initiative on sharing all influenza data (GISAID)). Epitopes are searched within the open source Immune Epitope Database or directly proposed by users by indicating their start and stop positions in the context of a given viral protein. Amino ac...
Source: Database : The Journal of Biological Databases and Curation - September 29, 2021 Category: Databases & Libraries Source Type: research

QSDB —a graphical Quorum Sensing Database
We present the Quorum Sensing Database (QSDB), a comprehensive database of all published sensing and quenching relations between organisms and signalling molecules of the human microbiome, as well as an interactive web interface that allows browsing the database, provides graphical depictions of sensing mechanisms as Systems Biology Graphical Notation diagrams and links to other databases.Database URL: QSDB (Quorum Sensing DataBase) is freely available via an interactive web interface and as a downloadable csv file athttp://qsdb.org. (Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - September 24, 2021 Category: Databases & Libraries Source Type: research

MODB: a comprehensive mitochondrial genome database for Mollusca
AbstractMollusca is the largest marine phylum, comprising about 23% of all named marine organisms, Mollusca systematics are still in flux, and an increase in human activities has affected Molluscan reproduction and development, strongly impacting diversity and classification. Therefore, it is necessary to explore the mitochondrial genome of Mollusca. The Mollusca mitochondrial database (MODB) was established for the Life and Health Big Data Center of Yantai University. This database is dedicated to collecting, sorting and sharing basic information regarding mollusks, especially their mitochondrial genome information. We al...
Source: Database : The Journal of Biological Databases and Curation - September 12, 2021 Category: Databases & Libraries Source Type: research

Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach
AbstractPeptides have attracted attention during the last decades due to their extraordinary therapeutic properties. Different computational tools have been developed to take advantage of existing information, compiling knowledge and making available the information for common users. Nevertheless, most related tools available are not user-friendly, present redundant information, do not clearly display the data, and usually are specific for particular biological activities, not existing so far, an integrated database with consolidated information to help research peptide sequences. To solve these necessities, we developed P...
Source: Database : The Journal of Biological Databases and Curation - September 3, 2021 Category: Databases & Libraries Source Type: research

lncExplore: a database of pan-cancer analysis and systematic functional annotation for lncRNAs from RNA-sequencing data
In this study, we utilized transcriptomic sequencing data to systematically observe and identify lncRNAs and their potential functions from 5034 The Cancer Genome Atlas RNA-seq datasets covering 24 cancers. Then, we constructed the ‘lncExplore’ database that was developed to comprehensively integrate various types of genomic annotation data for collective interpretation. The distinctive features in our lncExplore database include (i) novel lncRNAs verified by both coding potential and translation efficiency score, (ii) pan -cancer analysis for studying the significantly aberrant expression across 24 human cancers, (iii...
Source: Database : The Journal of Biological Databases and Curation - August 31, 2021 Category: Databases & Libraries Source Type: research

LINPS: a database for cancer-cell-specific perturbations of biological networks
AbstractScreening for potential cancer therapies using existing large datasets of drug perturbations requires expertise and resources not available to all. This is often a barrier for lab scientists to tap into these valuable resources. To address these issues, one can take advantage of prior knowledge especially those coded in standard formats such as causal biological networks (CBN). Large datasets can be converted into appropriate structures, analyzed once and the results made freely available in easy-to-use formats. We used the Library of Integrated Cellular Signatures to model the cell-specific effect of hundreds of d...
Source: Database : The Journal of Biological Databases and Curation - August 20, 2021 Category: Databases & Libraries Source Type: research