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.

NetREx: Network-based Rice Expression Analysis Server for abiotic stress conditions
AbstractRecent focus on transcriptomic studies in food crops like rice, wheat and maize provide new opportunities to address issues related to agriculture and climate change. Re-analysis of such data available in public domain supplemented with annotations across molecular hierarchy can be of immense help to the plant research community, particularly co-expression networks representing transcriptionally coordinated genes that are often part of the same biological process. With this objective, we have developed NetREx, a Network-based Rice Expression Analysis Server, that hosts ranked co-expression networks ofOryza sativa u...
Source: Database : The Journal of Biological Databases and Curation - August 6, 2022 Category: Databases & Libraries Source Type: research

Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues
AbstractStructural features of proteins provide powerful insights into biological function and similarity. Specifically, previous work has demonstrated that structural features of tissue and drug-treated cell line samples can be used to predict tissue type and characterize drug relationships, respectively. We have developed structural signatures, a web server for annotating and analyzing protein features from gene sets that are often found in transcriptomic and proteomic data. This platform provides access to a structural feature database derived from normal and disease human tissue samples. We show how analysis using this...
Source: Database : The Journal of Biological Databases and Curation - July 26, 2022 Category: Databases & Libraries Source Type: research

A sequence labeling framework for extracting drug –protein relations from biomedical literature
AbstractAutomatic extracting interactions between chemical compound/drug and gene/protein are significantly beneficial to drug discovery, drug repurposing, drug design and biomedical knowledge graph construction. To promote the development of the relation extraction between drug and protein, the BioCreative VII challenge organized the DrugProt track. This paper describes the approach we developed for this task. In addition to the conventional text classification framework that has been widely used in relation extraction tasks, we propose a sequence labeling framework to drug –protein relation extraction. We first compreh...
Source: Database : The Journal of Biological Databases and Curation - July 20, 2022 Category: Databases & Libraries Source Type: research

A BERT-based ensemble learning approach for the BioCreative VII challenges: full-text chemical identification and multi-label classification in PubMed articles
AbstractIn this research, we explored various state-of-the-art biomedical-specific pre-trained Bidirectional Encoder Representations from Transformers (BERT) models for the National Library of Medicine - Chemistry (NLM CHEM) and LitCovid tracks in the BioCreative VII Challenge, and propose a BERT-based ensemble learning approach to integrate the advantages of various models to improve the system ’s performance. The experimental results of the NLM-CHEM track demonstrate that our method can achieve remarkable performance, with F1-scores of 85% and 91.8% in strict and approximate evaluations, respectively. Moreover, the pro...
Source: Database : The Journal of Biological Databases and Curation - July 15, 2022 Category: Databases & Libraries Source Type: research

ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics
AbstractThe use of probiotics to improve health via the modulation of gut microbiota has gained wide attention. The growing volume of investigations of probiotic microorganisms and commercialized probiotic products has created the need for a database to organize the health-promoting functions driven by probiotics reported in academic articles, clinical trials and patents. We constructed ProBioQuest to collect up-to-date literature related to probiotics from PubMed.gov, ClinicalTrials.gov and PatentsView. More than 2.8 million articles have been collected. Automated information technology-assisted procedures enabled us to c...
Source: Database : The Journal of Biological Databases and Curation - July 15, 2022 Category: Databases & Libraries Source Type: research

GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics
AbstractIn silico chromosome painting is a technique by which contributions of distinct genetic groups are represented along chromosomes of hybrid individuals. This type of analysis is used to study the mechanisms by which these individuals were formed. Such techniques are well adapted to identify genetic groups contributing to these individuals as well as hybridization events. It can also be used to follow chromosomal recombinations that occurred naturally or were generated by selective breeding. Here, we present GeMo, a novel interactive web-based and user-oriented interface to visualize in a linear-based fashion results...
Source: Database : The Journal of Biological Databases and Curation - July 14, 2022 Category: Databases & Libraries Source Type: research

HumanMine: advanced data searching, analysis and cross-species comparison
AbstractHumanMine (www.humanmine.org) is an integrated database of human genomics and proteomics data that provides a powerful interface to support sophisticated exploration and analysis of data compiled from experimental, computational and curated data sources. Built using the InterMine data integration platform, HumanMine includes genes, proteins, pathways, expression levels, Single nucleotide polymorphism (SNP), diseases and more, integrated into a single searchable database. HumanMine promotes integrative analysis, a powerful approach in modern biology that allows many sources of evidence to be analysed together. The d...
Source: Database : The Journal of Biological Databases and Curation - July 12, 2022 Category: Databases & Libraries Source Type: research

Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins
AbstractDNA metabarcoding is a widespread approach for the molecular identification of organisms. While the associated wet-lab and data processing procedures are well established and highly efficient, the reference databases for taxonomic assignment can be implemented to improve the accuracy of identifications. Insects are among the organisms for which DNA-based identification is most commonly used; yet, a DNA-metabarcoding reference database specifically curated for their species identification using software requiring local databases is lacking. Here, we present COins, a database of 5 ’ regioncytochrome c oxidase subun...
Source: Database : The Journal of Biological Databases and Curation - July 7, 2022 Category: Databases & Libraries Source Type: research

Multi-omics molecular biomarkers and database of osteoarthritis
AbstractOsteoarthritis (OA) is the most common form of arthritis in the adult population and is a leading cause of disability. OA-related genetic loci may play an important role in clinical diagnosis and disease progression. With the rapid development of diverse technologies and omics methods, many OA-related public data sets have been accumulated. Here, we retrieved a diverse set of omics experimental results from 159 publications, including genome-wide association study, differentially expressed genes and differential methylation regions, and 2405 classified OA-related gene markers. Meanwhile, based on recent single-cell...
Source: Database : The Journal of Biological Databases and Curation - July 5, 2022 Category: Databases & Libraries Source Type: research

dbBIP: a comprehensive bipolar disorder database for genetic research
AbstractBipolar disorder (BIP) is one of the most common hereditary psychiatric disorders worldwide. Elucidating the genetic basis of BIP will play a pivotal role in mechanistic delineation. Genome-wide association studies (GWAS) have successfully reported multiple susceptibility loci conferring BIP risk, thus providing insight into the effects of its underlying pathobiology. However, difficulties remain in the extrication of important and biologically relevant data from genetic discoveries related to psychiatric disorders such as BIP. There is an urgent need for an integrated and comprehensive online database with unified...
Source: Database : The Journal of Biological Databases and Curation - July 2, 2022 Category: Databases & Libraries Source Type: research

Continuous development of the semantic search engine preVIEW: from COVID-19 to long COVID
AbstractpreVIEW is a freely available semantic search engine for Coronavirus disease (COVID-19)-related preprint publications. Currently, it contains>43  800 documents indexed with>4000 semantic concepts, annotated automatically. During the last 2 years, the dynamic situation of the corona crisis has demanded dynamic development. Whereas new semantic concepts have been added over time —such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of interest—the service has been also extended with several features improving the usability and user friendliness. Most importantly, the user is n...
Source: Database : The Journal of Biological Databases and Curation - July 1, 2022 Category: Databases & Libraries Source Type: research

Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics
AbstractThe identification of chemicals in articles has attracted a large interest in the biomedical scientific community, given its importance in drug development research. Most of previous research have focused on PubMed abstracts, and further investigation using full-text documents is required because these contain additional valuable information that must be explored. The manual expert task of indexing Medical Subject Headings (MeSH) terms to these articles later helps researchers find the most relevant publications for their ongoing work. The BioCreative  VII NLM-Chem track fostered the development of systems for che...
Source: Database : The Journal of Biological Databases and Curation - July 1, 2022 Category: Databases & Libraries Source Type: research

PHILM2Web: A high-throughput database of macromolecular host –pathogen interactions on the Web
AbstractDuring infection, the pathogen ’s entry into the host organism, breaching the host immune defense, spread and multiplication are frequently mediated by multiple interactions between the host and pathogen proteins. Systematic studying of host–pathogen interactions (HPIs) is a challenging task for both experimental and computat ional approaches and is critically dependent on the previously obtained knowledge about these interactions found in the biomedical literature. While several HPI databases exist that manually filter HPI protein–protein interactions from the generic databases and curated experimental inter...
Source: Database : The Journal of Biological Databases and Curation - June 30, 2022 Category: Databases & Libraries Source Type: research

LBD: a manually curated database of experimentally validated lymphoma biomarkers
AbstractLymphoma is a heterogeneous disease caused by malignant proliferation of lymphocytes, resulting in significant mortality worldwide. While more and more lymphoma biomarkers have been identified with the advent and development of precision medicine, there are currently no databases dedicated to systematically gathering these scattered treasures. Therefore, we developed a lymphoma biomarker database (LBD) to curate experimentally validated lymphoma biomarkers in this study. LBD consists of 793 biomarkers extracted from 978 articles covering diverse subtypes of lymphomas, including 715 single and 78 combined biomarkers...
Source: Database : The Journal of Biological Databases and Curation - June 29, 2022 Category: Databases & Libraries Source Type: research

GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba
AbstractAlthough an increasing number of species-specific databases have been constructed to facilitate the global research community, comprehensive databases remain rare with multidimensional research resources rather than genomic data solely, in particular for non-model species. Here we introduced GinkgoDB, the ecological genome database for the world-renowned living fossil,Ginkgo biloba L., a tree species with extreme longevity, exceptional resistance, global landscape application and dioecy. The present version of GinkgoDB consists of four modules of genome, occurrence, quadrat and gallery. The genome module includes t...
Source: Database : The Journal of Biological Databases and Curation - June 27, 2022 Category: Databases & Libraries Source Type: research